From: Takuo Yasunaga <yasunaga@bio.kyutech.ac.jp>
Date: Sat, 3 Oct 2015 22:03:30 +0000 (+0900)
Subject: Document Added
X-Git-Url: http://git.osdn.net/view?a=commitdiff_plain;h=refs%2Fheads%2Fmaster;p=eos%2Foptional.git

Document Added
---

diff --git a/doc/Objects/.list.html b/doc/Objects/.list.html
index 86676a0..29bb5ca 100755
--- a/doc/Objects/.list.html
+++ b/doc/Objects/.list.html
@@ -1,4 +1,4 @@
-<H4> Update Time 10/12/14---15:03:18 </H4>
+<H4> Update Time 09/22/15---06:39:48 </H4>
 <UL> <H2> Alphabetical List </H2>
 <LI> <A HREF="Cluster.html"> Cluster</A>
 <LI> <A HREF="Contour.html"> Contour</A>
@@ -26,6 +26,7 @@
 <LI> <A HREF="Socket.html"> Socket</A>
 <LI> <A HREF="SpecialNumber.html"> SpecialNumber</A>
 <LI> <A HREF="String.html"> String</A>
+<LI> <A HREF="TclTk.html"> TclTk</A>
 <LI> <A HREF="Vector.html"> Vector</A>
 <LI> <A HREF="Vector.BACKUP.13752.html.html"> Vector.BACKUP.13752.html</A>
 <LI> <A HREF="Vector.BACKUP.13830.html.html"> Vector.BACKUP.13830.html</A>
@@ -51,6 +52,7 @@
 <LI> <A HREF="emData.LOCAL.14307.html.html"> emData.LOCAL.14307.html</A>
 <LI> <A HREF="emData.REMOTE.14307.html.html"> emData.REMOTE.14307.html</A>
 <LI> <A HREF="eosFunc.html"> eosFunc</A>
+<LI> <A HREF="eosOpenGL.html"> eosOpenGL</A>
 <LI> <A HREF="eosPThread.html"> eosPThread</A>
 <LI> <A HREF="eosPoint.html"> eosPoint</A>
 <LI> <A HREF="gifFile.html"> gifFile</A>
diff --git a/doc/Objects/Cluster.html b/doc/Objects/Cluster.html
index 7eec35f..3b9beda 100644
--- a/doc/Objects/Cluster.html
+++ b/doc/Objects/Cluster.html
@@ -50,6 +50,11 @@ struct clusterLogOneRecord {
 		/* Below Layer */
 		clusterLogOneRecord* belowLayerForN;
 		clusterLogOneRecord* belowLayerForM;
+		/* Below Layer Search Flag */
+		clusterTypeInteger alreadySearchedN;
+		clusterTypeInteger alreadySearchedM;
+		clusterTypeReal    posX;
+		clusterTypeReal    posY;
 
 		/* Including the below layer */
 		clusterTypeInteger   clusterSize;	   /* File Number of the cluster */
@@ -134,8 +139,11 @@ extern clusterLog* clusterLogReadAllBinary(clusterLog* cluster, char* basename,
 
 extern clusterLogOneRecord* clusterLogWriteAllBinary(clusterLog* cluster, char* basename, int mode);
 extern clusterLogOneRecord* clusterLogWrite(clusterLog* cluster, FILE* fpt, int mode);
+extern clusterLogOneRecord* clusterLogWriteBinary2(clusterLog* cluster, FILE* fpt, int mode);
 extern clusterLogOneRecord* clusterLogWriteOneRecord(clusterLogOneRecord* cluster, FILE* fpt, int mode);
+extern clusterLogOneRecord* clusterLogWriteOneRecordBinary2(clusterLogOneRecord* cluster, FILE* fpt, int mode);
 extern clusterLogOneRecord* clusterLogWriteAll(clusterLog* cluster, FILE* fpt, int mode);
+extern clusterLogOneRecord* clusterLogWriteAllBinary2(clusterLog* cluster, FILE* fpt, int mode);
 extern clusterLogOneRecord* clusterLogWriteClusterOnly(clusterLog* cluster, FILE* fpt, int mode);
 extern void clusterLogWritePS(clusterLog* cluster, clusterTreeInfo* linfo, FILE* fpt, int mode);
 
diff --git a/doc/Objects/TclTk.html b/doc/Objects/TclTk.html
new file mode 100644
index 0000000..9c3c2f0
--- /dev/null
+++ b/doc/Objects/TclTk.html
@@ -0,0 +1,12 @@
+<HR>
+<A NAME="Information">
+<H2>Information from source codes</H2>
+</A>
+<PRE>
+</PRE>
+<HR>
+<A NAME="include">
+<H2>TclTk.h</H2>
+</A>
+<PRE>
+</PRE>
diff --git a/doc/Objects/ctfInfo.html b/doc/Objects/ctfInfo.html
index eeb9421..979059e 100644
--- a/doc/Objects/ctfInfo.html
+++ b/doc/Objects/ctfInfo.html
@@ -116,7 +116,7 @@ typedef struct ctfInfo {
 	long  flagMolecEnvTable;
 	molecularEnvelope MolecEnvTable;
 	/* For Lorentzian */
-	float flagElastic;
+	long flagElastic;
 	float Elastic;
 	float ElasticShift;
 	float ElasticWidth;
diff --git a/doc/Objects/dmFile.html b/doc/Objects/dmFile.html
index 05cd707..55640e7 100644
--- a/doc/Objects/dmFile.html
+++ b/doc/Objects/dmFile.html
@@ -24,6 +24,7 @@
 #define DMFILE_H 
 
 #include <stdio.h>
+#include "mrcImage.h"
 
 /* constant begin */
 
@@ -37,60 +38,168 @@ typedef __int32_t dmFileInteger4;
 typedef __int16_t dmFileInteger2; 
 typedef __int8_t  dmFileInteger1; 
 
+typedef enum dmFileTagDirType {
+	dmFileTagDirTypeFileEnd = 0x00,
+	dmFileTagDirTypeTagDir  = 0x14, 
+	dmFileTagDirTypeTag     = 0x15
+} dmFileTagDirType;
+
+static char* __dmFileTagDirTypeChar[] = {
+	"FileEnd", "", "", "", "", "", "", "", 
+	"", "", "", "", "", "", "", "",
+	"", "", "", "", "TagDir", "Tag"
+};
+
 typedef enum dmFileTagDataType {
-	dmFileTagDataTypeShort=2,
-	dmFileTagDataTypeLong =3,
-	dmFileTagDataTypeUShort =4,
+	dmFileTagDataTypeInt2   =2,
+	dmFileTagDataTypeInt4   =3,
+	dmFileTagDataTypeUInt2  =4,
+	dmFileTagDataTypeUInt4  =5,
+	dmFileTagDataTypeReal4  =6,
+	dmFileTagDataTypeReal8  =7,
+	dmFileTagDataTypeBool1  =8,
+	dmFileTagDataTypeChar1  =9,
+	dmFileTagDataTypeInt1   =0xa,
+	dmFileTagDataTypeInt8   =0xb,
+	dmFileTagDataTypeUInt8  =0xc,
+	dmFileTagDataTypeStruct =0xf,
+	dmFileTagDataTypeString =0x12,
+	dmFileTagDataTypeArray  =0x14,
+	dmFileTagDataTypeTags   =0x15,
 } dmFileTagDataType;
 
-typedef struct dm3FileHeader {
+typedef enum dmFileImageDataType {
+	dmFileImageDataTypeInt2     = 1, 
+	dmFileImageDataTypeReal4    = 2, 
+	dmFileImageDataTypeComplex8 = 3, 
+	dmFileImageDataTypeUnknown  = 4, 
+	dmFileImageDataTypePackedComplex  = 5, 
+	dmFileImageDataTypeUInt1    = 6, 
+	dmFileImageDataTypeInt4     = 7, 
+	dmFileImageDataTypeRGBInt4  = 8, 
+	dmFileImageDataTypeInt1     = 9, 
+	dmFileImageDataTypeUInt2    = 10, 
+	dmFileImageDataTypeUInt4    = 11, 
+	dmFileImageDataTypeReal8    = 12, 
+	dmFileImageDataTypeComplex16= 13, 
+	dmFileImageDataTypeBool1    = 14,
+	dmFileImageDataTypeIRGInt4Thumnail = 23 
+} dmFileImageDataType;
+
+static size_t __dmFileImageDataTypeSize[] = {
+	0, 2, 3, 8, 0,  4, 1, 4, 
+	4, 1, 2, 4, 6, 16, 1, 0,
+	0, 0, 0, 0, 0,  0, 0, 4 
+};
+
+static size_t __dmFileTagDataTypeSize[] = {
+ 0, 0, 2, 4, 2, 4, 4, 8, 
+ 1, 1, 1, 8, 8, 0, 0, 0, 
+ 0, 0, 0, 0, 0, 0, 0, 0
+}; 
+
+/*
+static char* __dmFileTagDataTypeFormat[] = {
+    0,    0, "%d",   "%d",   "%u", "%u", "%f", "%f", 
+ "%d", "%c", "%d", "%lld", "%llu",     0,   0,	  0, 
+    0,    0,    0,      0,      0,     0,   0,    0
+}; 
+*/
+
+static char* __dmFileTagDataTypeFormat[] = {
+    0,    0,  "%#0x", "%#0x",   "%#0X", "%#0X", "%f", "%f", 
+ "%#0x", "%c", "%#0x", "%#0x", "%#0llX",     0,    0,	 0, 
+    0,    0,      0,     0,       0,     0,    0,    0
+}; 
+
+
+static char* __dmFileTagDataTypeChar[] = {
+     "",      "", "Int2",   "Int4", "UInt2", "UInt4", "Real4",  "Real8", 
+"Bool1", "Char1", "Int1",   "Int8", "UInt8",      "",      "", "Struct", 
+     "",      "", "String",     "", "Array",  "Tags",      "",       ""
+}; 
+
+
+
+// Header
+typedef struct dmFile3Header {
 	dmFileInteger4 version;
 	dmFileInteger4 rootLength;
 	dmFileInteger4 byteOrder;
-} dm3FileHeader;
+} __attribute__((__packed__)) dmFile3Header;
 
-typedef struct dm4FileHeader {
+typedef struct dmFile4Header {
 	dmFileInteger4 version;
 	dmFileInteger8 rootLength;
 	dmFileInteger4 byteOrder;
-} dm4FileHeader;
+} __attribute__((__packed__)) dmFile4Header;
+
+typedef struct dmFile3TagDirectory dmFile3TagDirectory;
+typedef struct dmFile4TagDirectory dmFile4TagDirectory; 
 
-typedef struct dm3FileTagDirectrory {
+// Tag 
+typedef struct dmFile3Tag {
 	dmFileInteger1 tagID;
 	dmFileInteger2 tagNameLength; // Bytes
 	char*          tagName;
-	dmFileInteger8 tagDataSize;   // Bytes
-} dm3FileTagDirectrory;
+	// Tag
+	char           seperator[4];
+	dmFileInteger4 ninfo; 
+	dmFileInteger4* info; 
+	long            pValue; // Offset	
+	void*           value;  // Array or value 
+	void**          value2; // Struct
+	void**          value3; // Array of Struct
+	// TagDirectory 
+	dmFile3TagDirectory* tagDir;
+} dmFile3Tag;
 
-typedef struct dm4FileTagDirectrory {
+typedef struct dmFile4Tag {
 	dmFileInteger1 tagID;
 	dmFileInteger2 tagNameLength; // Bytes
 	char*          tagName;
-	dmFileInteger8 tagDataSize;   // Bytes
-} dm4FileTagDirectrory;
+	dmFileInteger8 tagLength;
+	// Tag
+	char           seperator[4];
+	dmFileInteger8 ninfo; 
+	dmFileInteger8* info; 
+	long            pValue;
+	void*           value;  // Array or value 
+	void**          value2; // Struct
+	void**          value3; // Array of Struct
+	// TagDirectory
+	dmFile4TagDirectory* tagDir;
+} dmFile4Tag;
 
-typedef struct dm3FileRootTagDirectory {
+// Root Tag Directory
+struct dmFile3TagDirectory {
 	dmFileInteger1 sortf;
 	dmFileInteger1 closef;
 	dmFileInteger4 numberOfTags;
-} dm3FileRootTagDirectory;
+	dmFile3Tag* Tags;
+} ;  
 
-typedef struct dm4FileRootTagDirectory {
+struct dmFile4TagDirectory {
 	dmFileInteger1 sortf;
 	dmFileInteger1 closef;
 	dmFileInteger8 numberOfTags;
-} dm4FileRootTagDirectory;
+	dmFile4Tag* Tags;
+} ; 
 
 typedef struct dmFile {
 	// Header
 	dmFileInteger4 version;
-	dm3FileHeader Header3;
-	dm4FileHeader Header4;
+	dmFile3Header Header3;
+	dmFile4Header Header4;
 	// Root Tag
-	dm3FileRootTagDirectory RootTag3;
-	dm4FileRootTagDirectory RootTag4;
-
+	dmFile3TagDirectory RootTag3;
+	dmFile4TagDirectory RootTag4;
+	// Tail
 	dmFileInteger8 Tail;
+
+	// 
+	mrcImage thumnail;
+	mrcImage image;
 } dmFile;
 
 /* struct end */
@@ -103,10 +212,44 @@ extern "C" {
 
 // in dfFileInfo.c
 extern void dmFileInfo(FILE* fpt, dmFile dm, int mode);
+extern void dmFileHeaderInfo(FILE* fpt, dmFile dm, int mode);
+extern void dmFile3TagDirectoryInfo(FILE* fpt, dmFile3TagDirectory tagDir, int layer, int mode);
+extern void dmFile3TagInfo(FILE* fpt, dmFile3Tag tagr, int layer, int mode);
+extern void dmFile4TagDirectoryInfo(FILE* fpt, dmFile4TagDirectory tagDir, int layer, int mode);
+extern void dmFile4TagInfo(FILE* fpt, dmFile4Tag tag, int layer, int mode);
 
 // in dmFileRead.c
 extern void dmFileRead(FILE* fpt, dmFile* dm, char* message, int mode);
+// DM Header and End Read: check file format
+extern void dmFileHeaderTailRead(FILE* fpt, dmFile* dm, char* message, int mode);
+// DM3
+// Header 
+extern void dmFile3HeaderRead(FILE* fpt, dmFile* dm, char* message, int mode);
+//
+extern void dmFile3TagDirectoryHeaderRead(FILE* fpt, dmFile3TagDirectory* dmRoot, char* message, int mode);
+extern void dmFile3TagHeaderRead(FILE* fpt, dmFile3Tag* dmTag, char* message, int mode);
+extern void dmFile3TagRead(FILE* fpt, dmFile3Tag* dmTag, char* message, int mode);
+extern void dmFile3TagDirectoryRead(FILE* fpt, dmFile3TagDirectory* dmTagDir, char* message, int mode);
+
+// DM4
+// Header
+extern void dmFile4HeaderRead(FILE* fpt, dmFile* dm, char* message, int mode);
+//  
+extern void dmFile4TagDirectoryHeaderRead(FILE* fpt, dmFile4TagDirectory* dmRoot, char* message, int mode);
+extern void dmFile4TagHeaderRead(FILE* fpt, dmFile4Tag* dmTag, char* message, int mode);
+extern void dmFile4TagRead(FILE* fpt, dmFile4Tag* dmTag, char* message, int mode);
+extern void dmFile4TagDirectoryRead(FILE* fpt, dmFile4TagDirectory* dmTagDir, char* message, int mode);
+
+// in dmFileUtil.c
+extern void dmFileValuePrint(FILE* fpt, void* value, dmFileTagDataType valueType, int n); 
+
+// in dm2mrc.c 
+extern void ldm2mrc(mrcImage* mrc, dmFile* dm, int mode);
+extern void dmFile3TagDirectory2mrc(dmFile* fpt, dmFile3TagDirectory tagDir, int layer, int mode);
+extern void dmFile4TagDirectory2mrc(dmFile* fpt, dmFile4TagDirectory tagDir, int layer, int mode);
 
+// in dmFileInit.c
+extern void dmFileInit(dmFile* dm, int mode);
 
 /* prototype end */
 
diff --git a/doc/Objects/eosOpenGL.html b/doc/Objects/eosOpenGL.html
new file mode 100644
index 0000000..6b917e2
--- /dev/null
+++ b/doc/Objects/eosOpenGL.html
@@ -0,0 +1,24 @@
+<HR>
+<A NAME="Information">
+<H2>Information from source codes</H2>
+</A>
+<PRE>
+</PRE>
+<HR>
+<A NAME="include">
+<H2>eosOpenGL.h</H2>
+</A>
+<PRE>
+#ifndef EOS_OPENGL
+#define EOS_OPENGL
+
+#ifdef X86MAC64
+#include <GLUT/glut.h>
+#else
+#include <GL/glut.h>
+#endif
+
+extern void __openGLAA(void);
+extern void openGLKeyDefault(char c, int x, int y );
+#endif /* EOS_OPENGL */
+</PRE>
diff --git a/doc/Objects/mrcImage.html b/doc/Objects/mrcImage.html
index 6eed6dd..d7cbb69 100644
--- a/doc/Objects/mrcImage.html
+++ b/doc/Objects/mrcImage.html
@@ -523,6 +523,8 @@ typedef struct mrcImageInformation {
 	long flagrmax;
 	double RMS; /* Root mean square */
 	int mode;
+	mrcImageParaTypeRealCoord sdOfAllAxis;
+	mrcImageParaTypeRealCoord aveOfAllAxis;
 
 	/* For Search Area */
 	int flagXrange;
@@ -552,7 +554,8 @@ typedef enum mrcImageInformationMode {
     meanOfCentre          = 4,
     meanOfSparse          = 5,
 	meanOf2DEdgeY         = 6,
-	RMSofAllPixels       = 7
+	RMSofAllPixels        = 7,
+	sdOfAllAxis           = 8
 } mrcImageInformationMode;
 
 /* 
@@ -862,6 +865,10 @@ extern void lmrcFFTFxG(mrcImage* out, mrcImage* in1, mrcImage* in2);
 extern void lmrcImageCorrelation(mrcImage* out, mrcImage* in, mrcImage* ref, long mode);
 extern void lmrcImageCorrelationModePrint(FILE* fpt);
 
+/* in lMrcImagePattersonFunctionCalc.c */
+extern void lmrcImagePattersonFunctionCalc(mrcImage* out, mrcImage* in);
+extern void lmrcImagePattersonFunctionPrint(FILE* fpt, mrcImage* in, int mode);
+
 #include "ctfInfo.h"
 extern void lmrcImageCorrelationWithCTFCompensation(mrcImage* out, mrcImage* in, ctfInfo* inctf, mrcImage* ref, ctfInfo* refctf, long mode);
 
diff --git a/doc/SmallTools/.smallToolList.html b/doc/SmallTools/.smallToolList.html
index 0ab0a14..2c9ca38 100755
--- a/doc/SmallTools/.smallToolList.html
+++ b/doc/SmallTools/.smallToolList.html
@@ -32,6 +32,7 @@
 <LI> <A HREF="anglediffcalc.html"> anglediffcalc</A>
 <LI> <A HREF="anglediffchk.html"> anglediffchk</A>
 <LI> <A HREF="array2mrc.html"> array2mrc</A>
+<LI> <A HREF="arrayPCA.html"> arrayPCA</A>
 <LI> <A HREF="bin2mrc.html"> bin2mrc</A>
 <LI> <A HREF="bmp2mrc.html"> bmp2mrc</A>
 <LI> <A HREF="bmpFileInfo.html"> bmpFileInfo</A>
@@ -48,6 +49,7 @@
 <LI> <A HREF="ctfDetermine.html"> ctfDetermine</A>
 <LI> <A HREF="ctfDisplay.html"> ctfDisplay</A>
 <LI> <A HREF="ctfEnvelopFunction.html"> ctfEnvelopFunction</A>
+<LI> <A HREF="ctfEnvelopFunctionEstimate.html"> ctfEnvelopFunctionEstimate</A>
 <LI> <A HREF="ctfFunction.html"> ctfFunction</A>
 <LI> <A HREF="ctfFunctionServer.html"> ctfFunctionServer</A>
 <LI> <A HREF="ctfInfoSet.html"> ctfInfoSet</A>
@@ -67,12 +69,14 @@
 <LI> <A HREF="dcdTest.html"> dcdTest</A>
 <LI> <A HREF="dcdTimeSeriesBehavior.html"> dcdTimeSeriesBehavior</A>
 <LI> <A HREF="defocusDeterminationFromThonRing.html"> defocusDeterminationFromThonRing</A>
+<LI> <A HREF="dm2mrc.html"> dm2mrc</A>
 <LI> <A HREF="dmInfo.html"> dmInfo</A>
 <LI> <A HREF="dos2unix.html"> dos2unix</A>
 <LI> <A HREF="electronWaveLength.html"> electronWaveLength</A>
 <LI> <A HREF="emData2mrc.html"> emData2mrc</A>
 <LI> <A HREF="energyTransferModelCheck.html"> energyTransferModelCheck</A>
 <LI> <A HREF="energyTransferModelResultCheck.html"> energyTransferModelResultCheck</A>
+<LI> <A HREF="eosBayesInit.html"> eosBayesInit</A>
 <LI> <A HREF="eosPointProjector.html"> eosPointProjector</A>
 <LI> <A HREF="eosPointRotation.html"> eosPointRotation</A>
 <LI> <A HREF="eosPointTracker.html"> eosPointTracker</A>
@@ -196,6 +200,7 @@
 <LI> <A HREF="mrcImage3DHighResoEmphasis.html"> mrcImage3DHighResoEmphasis</A>
 <LI> <A HREF="mrcImage3DPad.html"> mrcImage3DPad</A>
 <LI> <A HREF="mrcImage3DPad2.html"> mrcImage3DPad2</A>
+<LI> <A HREF="mrcImage3DPeakGet.html"> mrcImage3DPeakGet</A>
 <LI> <A HREF="mrcImage3DSymmetryFind.html"> mrcImage3DSymmetryFind</A>
 <LI> <A HREF="mrcImage3DWindowing.html"> mrcImage3DWindowing</A>
 <LI> <A HREF="mrcImageAbnormalValueRemove.html"> mrcImageAbnormalValueRemove</A>
@@ -213,6 +218,7 @@
 <LI> <A HREF="mrcImageAutoRotationCorrelation.html"> mrcImageAutoRotationCorrelation</A>
 <LI> <A HREF="mrcImageAutoRotationCorrelation3D.html"> mrcImageAutoRotationCorrelation3D</A>
 <LI> <A HREF="mrcImageAutoRotationCorrelationResultPrint.html"> mrcImageAutoRotationCorrelationResultPrint</A>
+<LI> <A HREF="mrcImageAutoTriming.html"> mrcImageAutoTriming</A>
 <LI> <A HREF="mrcImageAverage.html"> mrcImageAverage</A>
 <LI> <A HREF="mrcImageBandPassFilter.html"> mrcImageBandPassFilter</A>
 <LI> <A HREF="mrcImageBilateralFilter.html"> mrcImageBilateralFilter</A>
@@ -231,6 +237,7 @@
 <LI> <A HREF="mrcImageCenterDensityChange.html"> mrcImageCenterDensityChange</A>
 <LI> <A HREF="mrcImageCenterGet.html"> mrcImageCenterGet</A>
 <LI> <A HREF="mrcImageCenterOfMassCalculate.html"> mrcImageCenterOfMassCalculate</A>
+<LI> <A HREF="mrcImageChainCodeCalc.html"> mrcImageChainCodeCalc</A>
 <LI> <A HREF="mrcImageCircumferentialProjection.html"> mrcImageCircumferentialProjection</A>
 <LI> <A HREF="mrcImageClosing.html"> mrcImageClosing</A>
 <LI> <A HREF="mrcImageClusterAnalysis.html"> mrcImageClusterAnalysis</A>
@@ -263,6 +270,7 @@
 <LI> <A HREF="mrcImageDivideInfoForTomography.html"> mrcImageDivideInfoForTomography</A>
 <LI> <A HREF="mrcImageDivideIntoTwoImages.html"> mrcImageDivideIntoTwoImages</A>
 <LI> <A HREF="mrcImageDividedByFile.html"> mrcImageDividedByFile</A>
+<LI> <A HREF="mrcImageEdgeCalc.html"> mrcImageEdgeCalc</A>
 <LI> <A HREF="mrcImageEdgeEnhancement.html"> mrcImageEdgeEnhancement</A>
 <LI> <A HREF="mrcImageEdgeImageGet.html"> mrcImageEdgeImageGet</A>
 <LI> <A HREF="mrcImageEnhancementWithFuzzySets.html"> mrcImageEnhancementWithFuzzySets</A>
@@ -271,8 +279,10 @@
 <LI> <A HREF="mrcImageExpression.html"> mrcImageExpression</A>
 <LI> <A HREF="mrcImageFFT.html"> mrcImageFFT</A>
 <LI> <A HREF="mrcImageFFTLayerLineExtraction.html"> mrcImageFFTLayerLineExtraction</A>
+<LI> <A HREF="mrcImageFFTSetsExtract.html"> mrcImageFFTSetsExtract</A>
 <LI> <A HREF="mrcImageFOMCalc.html"> mrcImageFOMCalc</A>
 <LI> <A HREF="mrcImageFTest.html"> mrcImageFTest</A>
+<LI> <A HREF="mrcImageFeatureCalc.html"> mrcImageFeatureCalc</A>
 <LI> <A HREF="mrcImageFeatureExtraction.html"> mrcImageFeatureExtraction</A>
 <LI> <A HREF="mrcImageFilamentSearch.html"> mrcImageFilamentSearch</A>
 <LI> <A HREF="mrcImageFilterCreate.html"> mrcImageFilterCreate</A>
@@ -295,9 +305,12 @@
 <LI> <A HREF="mrcImageHelicalProjection.html"> mrcImageHelicalProjection</A>
 <LI> <A HREF="mrcImageHighPassFilter.html"> mrcImageHighPassFilter</A>
 <LI> <A HREF="mrcImageHighlighting.html"> mrcImageHighlighting</A>
+<LI> <A HREF="mrcImageHoughTransform.html"> mrcImageHoughTransform</A>
+<LI> <A HREF="mrcImageHoughTransformInverse.html"> mrcImageHoughTransformInverse</A>
 <LI> <A HREF="mrcImageInfo.html"> mrcImageInfo</A>
 <LI> <A HREF="mrcImageInverseRadonTransform.html"> mrcImageInverseRadonTransform</A>
 <LI> <A HREF="mrcImageLabeling.html"> mrcImageLabeling</A>
+<LI> <A HREF="mrcImageLocalMaximumValuesFind.html"> mrcImageLocalMaximumValuesFind</A>
 <LI> <A HREF="mrcImageLogicalOperation.html"> mrcImageLogicalOperation</A>
 <LI> <A HREF="mrcImageLowPassFilter.html"> mrcImageLowPassFilter</A>
 <LI> <A HREF="mrcImageMagnificationChange.html"> mrcImageMagnificationChange</A>
@@ -309,6 +322,7 @@
 <LI> <A HREF="mrcImageMappingtoPdb.html"> mrcImageMappingtoPdb</A>
 <LI> <A HREF="mrcImageMasking.html"> mrcImageMasking</A>
 <LI> <A HREF="mrcImageMaskingByImage.html"> mrcImageMaskingByImage</A>
+<LI> <A HREF="mrcImageMeanFreePathCalc.html"> mrcImageMeanFreePathCalc</A>
 <LI> <A HREF="mrcImageMergebyside.html"> mrcImageMergebyside</A>
 <LI> <A HREF="mrcImageMirroring.html"> mrcImageMirroring</A>
 <LI> <A HREF="mrcImageModeChange.html"> mrcImageModeChange</A>
@@ -344,7 +358,9 @@
 <LI> <A HREF="mrcImagePad.html"> mrcImagePad</A>
 <LI> <A HREF="mrcImagePanoramaCreate.html"> mrcImagePanoramaCreate</A>
 <LI> <A HREF="mrcImageParticleCandidateExtract.html"> mrcImageParticleCandidateExtract</A>
+<LI> <A HREF="mrcImagePattersonFunctionCalc.html"> mrcImagePattersonFunctionCalc</A>
 <LI> <A HREF="mrcImagePeakSearch.html"> mrcImagePeakSearch</A>
+<LI> <A HREF="mrcImagePerimeterCalc.html"> mrcImagePerimeterCalc</A>
 <LI> <A HREF="mrcImagePhaseCTFCompensationFromCTFINFO.html"> mrcImagePhaseCTFCompensationFromCTFINFO</A>
 <LI> <A HREF="mrcImagePixelDataGet.html"> mrcImagePixelDataGet</A>
 <LI> <A HREF="mrcImagePolyROI.html"> mrcImagePolyROI</A>
@@ -372,6 +388,7 @@
 <LI> <A HREF="mrcImageRotation.html"> mrcImageRotation</A>
 <LI> <A HREF="mrcImageRotation3D.html"> mrcImageRotation3D</A>
 <LI> <A HREF="mrcImageSN.html"> mrcImageSN</A>
+<LI> <A HREF="mrcImageSNEstimate.html"> mrcImageSNEstimate</A>
 <LI> <A HREF="mrcImageSamplingUnitChange.html"> mrcImageSamplingUnitChange</A>
 <LI> <A HREF="mrcImageScalarAdd.html"> mrcImageScalarAdd</A>
 <LI> <A HREF="mrcImageSectionGet.html"> mrcImageSectionGet</A>
@@ -379,6 +396,7 @@
 <LI> <A HREF="mrcImageShapeOrientation.html"> mrcImageShapeOrientation</A>
 <LI> <A HREF="mrcImageShapePCA.html"> mrcImageShapePCA</A>
 <LI> <A HREF="mrcImageShapePCAFit.html"> mrcImageShapePCAFit</A>
+<LI> <A HREF="mrcImageShapeSearch.html"> mrcImageShapeSearch</A>
 <LI> <A HREF="mrcImageShift.html"> mrcImageShift</A>
 <LI> <A HREF="mrcImageShiftFollowingGC.html"> mrcImageShiftFollowingGC</A>
 <LI> <A HREF="mrcImageShrink.html"> mrcImageShrink</A>
@@ -400,6 +418,8 @@
 <LI> <A HREF="mrcImageSubstraction.html"> mrcImageSubstraction</A>
 <LI> <A HREF="mrcImageSubtraction.html"> mrcImageSubtraction</A>
 <LI> <A HREF="mrcImageSuperResolution.html"> mrcImageSuperResolution</A>
+<LI> <A HREF="mrcImageSurfaceAreaCalc.html"> mrcImageSurfaceAreaCalc</A>
+<LI> <A HREF="mrcImageSurfaceCalc.html"> mrcImageSurfaceCalc</A>
 <LI> <A HREF="mrcImageSymmetryAverage.html"> mrcImageSymmetryAverage</A>
 <LI> <A HREF="mrcImageSymmetryCentreFind.html"> mrcImageSymmetryCentreFind</A>
 <LI> <A HREF="mrcImageSymmetryFind.html"> mrcImageSymmetryFind</A>
@@ -409,6 +429,7 @@
 <LI> <A HREF="mrcImageTiltAxisSearchHelp.html"> mrcImageTiltAxisSearchHelp</A>
 <LI> <A HREF="mrcImageToNAMDConstantForces.html"> mrcImageToNAMDConstantForces</A>
 <LI> <A HREF="mrcImageToPointsSet.html"> mrcImageToPointsSet</A>
+<LI> <A HREF="mrcImageToneReversal.html"> mrcImageToneReversal</A>
 <LI> <A HREF="mrcImageTopHatTransform.html"> mrcImageTopHatTransform</A>
 <LI> <A HREF="mrcImageTrans.html"> mrcImageTrans</A>
 <LI> <A HREF="mrcImageTransepose.html"> mrcImageTransepose</A>
@@ -418,6 +439,7 @@
 <LI> <A HREF="mrcImageTwoImageTest.html"> mrcImageTwoImageTest</A>
 <LI> <A HREF="mrcImageUnbentROI.html"> mrcImageUnbentROI</A>
 <LI> <A HREF="mrcImageUnexpectedMassFromPDB.html"> mrcImageUnexpectedMassFromPDB</A>
+<LI> <A HREF="mrcImageUnsharpening.html"> mrcImageUnsharpening</A>
 <LI> <A HREF="mrcImageUntwist.html"> mrcImageUntwist</A>
 <LI> <A HREF="mrcImageVarianceAnalysis.html"> mrcImageVarianceAnalysis</A>
 <LI> <A HREF="mrcImageVarianceMap.html"> mrcImageVarianceMap</A>
@@ -520,6 +542,7 @@
 <LI> <A HREF="pgSelect.html"> pgSelect</A>
 <LI> <A HREF="pointAffineTransform.html"> pointAffineTransform</A>
 <LI> <A HREF="pointsSetToPDB.html"> pointsSetToPDB</A>
+<LI> <A HREF="probabilityDensityFunction.html"> probabilityDensityFunction</A>
 <LI> <A HREF="psFileMerge.html"> psFileMerge</A>
 <LI> <A HREF="psFilePageMerge.html"> psFilePageMerge</A>
 <LI> <A HREF="randomNormalGet.html"> randomNormalGet</A>
diff --git a/doc/SmallTools/CheckCommonLineData.html b/doc/SmallTools/CheckCommonLineData.html
index 7a530d8..5974a75 100644
--- a/doc/SmallTools/CheckCommonLineData.html
+++ b/doc/SmallTools/CheckCommonLineData.html
@@ -8,15 +8,15 @@
 <PRE>
 Usage: CheckCommonLineData
 Options:
-    [-I[nput]            In                  (NULL      )] :Essential :InputDataFileList
-    [-o[utput]R[eal]     OutR                (NULL      )] :Essential :OutputDataFile
-    [-o[utput]I[m]       OutI                (NULL      )] :Essential :OutputDataFile
-    [-o[utput]L[ength]   OutL                (NULL      )] :Essential :OutputDataFile
-    [-o[utput]P[hase]    OutP                (NULL      )] :Essential :OutputDataFile
-    [-o[utput]LL         OutLL               (NULL      )] :Essential :OutputDataFile
-    [-Log                Log                 (NULL      )] :Essential :LogFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-I[nput]            In                  (NULL      ).as(inFileListNoOpen    ) ] :Essential :InputDataFileList
+    [-o[utput]R[eal]     OutR                (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-o[utput]I[m]       OutI                (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-o[utput]L[ength]   OutL                (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-o[utput]P[hase]    OutP                (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-o[utput]LL         OutLL               (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-Log                Log                 (NULL      ).as(outFile             ) ] :Essential :LogFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/CheckOfOrientation.html b/doc/SmallTools/CheckOfOrientation.html
index 00a1383..71bf2b1 100644
--- a/doc/SmallTools/CheckOfOrientation.html
+++ b/doc/SmallTools/CheckOfOrientation.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: CheckOfOrientation
 Options:
-    [-I[nputFileList]    InList              (NULL      )] :Essential :InputDataFileList
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-o[utput]v[alue]    OutV                (NULL      )] :Optional  :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-I[nputFileList]    InList              (NULL      ).as(inFileListNoOpen    ) ] :Essential :InputDataFileList
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-o[utput]v[alue]    OutV                (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 
 ----------- Output file  -------------
 -o  : output Matrix data
diff --git a/doc/SmallTools/CommonLineCalculation.html b/doc/SmallTools/CommonLineCalculation.html
index f058ec8..e7f5b07 100644
--- a/doc/SmallTools/CommonLineCalculation.html
+++ b/doc/SmallTools/CommonLineCalculation.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: CommonLineCalculation
 Options:
-    [-i[nput]            In                  (NULL      )] :Optional  :InputDataFile
-    [-I[nputfilelist]    InList              (NULL      )] :Optional  :InputDatalistFile
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (1         )] :Optional  :Mode
-    [-I[nput]m[ode]      Inputmode           (0         )] :Optional  :InputMode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Optional  :InputDataFile
+    [-I[nputfilelist]    InList              (NULL      ).as(inFileListNoOpen    ) ] :Optional  :InputDatalistFile
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (1         ).as(Integer             ) ] :Optional  :Mode
+    [-I[nput]m[ode]      Inputmode           (0         ).as(Integer             ) ] :Optional  :InputMode
 
 ----- mode -----
 -m : 0 : in 2004/07/22 
diff --git a/doc/SmallTools/Descartes2Polar.html b/doc/SmallTools/Descartes2Polar.html
index d749c6f..c2b5cff 100644
--- a/doc/SmallTools/Descartes2Polar.html
+++ b/doc/SmallTools/Descartes2Polar.html
@@ -8,13 +8,21 @@
 <PRE>
 Usage: Descartes2Polar
 Options:
-    [-i                  x                   (0.0       )y                   (1.0       )z                   (0.0       )] :Optional  :input: coord
-    [-o                  Out                 (stdout    )] :Optional  :output: coord
-    [-centre             cx                  (0.0       )cy                  (0.0       )cz                  (0.0       )] :Optional  :Centre
-    [-xaxis              xx                  (1.0       )xy                  (0.0       )xz                  (0.0       )] :Optional  :x-axis
-    [-zaxis              zx                  (0.0       )zy                  (0.0       )zz                  (1.0       )] :Optional  :z-axis
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i                  x                   (0.0       ).as(Real                ) 
+                         y                   (1.0       ).as(Real                ) 
+                         z                   (0.0       ).as(Real                ) ] :Optional  :input: coord
+    [-o                  Out                 (stdout    ).as(outFile             ) ] :Optional  :output: coord
+    [-centre             cx                  (0.0       ).as(Real                ) 
+                         cy                  (0.0       ).as(Real                ) 
+                         cz                  (0.0       ).as(Real                ) ] :Optional  :Centre
+    [-xaxis              xx                  (1.0       ).as(Real                ) 
+                         xy                  (0.0       ).as(Real                ) 
+                         xz                  (0.0       ).as(Real                ) ] :Optional  :x-axis
+    [-zaxis              zx                  (0.0       ).as(Real                ) 
+                         zy                  (0.0       ).as(Real                ) 
+                         zz                  (1.0       ).as(Real                ) ] :Optional  :z-axis
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/Display2.html b/doc/SmallTools/Display2.html
index 8e0568d..8d4e047 100644
--- a/doc/SmallTools/Display2.html
+++ b/doc/SmallTools/Display2.html
@@ -8,17 +8,17 @@
 <PRE>
 Usage: Display2
 Options:
-    [-i[nput]            In                  (NULL      )] :Optional  :InputDataFile
-    [-t[epmlate]         Template            (2056251152.roi    )] :Optional  :Template for InputFile 
-    [-H[ighForThres]     ThresHigh           (0.0       )] :Optional  :Template for InputFile 
-    [-L[owForThres]      ThresLow            (0.0       )] :Optional  :Template for InputFile 
-    [-Zoom               Zoom                (1.0       )] :Optional  :Zoom for InputFile 
-    [-Inverse            ] :Optional  :Inverse (HighValue(dark)<->LowValue(bright)) for InputFile 
-    [-o[utput]           Out                 (.EosLog   )] :Optional  :OutputLogFile
-    [-display            geometry            (:0.0      )] :Optional  :OutputLogFile
-    [-geometry           display             (1024x1024+0+0)] :Optional  :OutputLogFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Optional  :InputDataFile
+    [-t[epmlate]         Template            (%d.roi   ).as(String              ) ] :Optional  :Template for InputFile 
+    [-H[ighForThres]     ThresHigh           (0.0       ).as(Real                ) ] :Optional  :Template for InputFile 
+    [-L[owForThres]      ThresLow            (0.0       ).as(Real                ) ] :Optional  :Template for InputFile 
+    [-Zoom               Zoom                (1.0       ).as(Real                ) ] :Optional  :Zoom for InputFile 
+    [-Inverse                                                                      ] :Optional  :Inverse (HighValue(dark)<->LowValue(bright)) for InputFile 
+    [-o[utput]           Out                 (.EosLog   ).as(String              ) ] :Optional  :OutputLogFile
+    [-display            geometry            (:0.0      ).as(String              ) ] :Optional  :OutputLogFile
+    [-geometry           display             (1024x1024+0+0).as(String              ) ] :Optional  :OutputLogFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 New wish commands of Display2
 mrcInfoSet [z|min|max] value
 mrcInfoSet [log|pow] 
diff --git a/doc/SmallTools/EvaluateCorrelationMapwithCommonLine.html b/doc/SmallTools/EvaluateCorrelationMapwithCommonLine.html
index bba1113..82ea958 100644
--- a/doc/SmallTools/EvaluateCorrelationMapwithCommonLine.html
+++ b/doc/SmallTools/EvaluateCorrelationMapwithCommonLine.html
@@ -8,14 +8,14 @@
 <PRE>
 Usage: EvaluateCorrelationMapwithCommonLine
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputCorrelationMapList
-    [-i[nput]c[ommonLine]InC                 (NULL      )] :Essential :InputCommonLineDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-P[eakArea]M[ode]   Pm                  (0         )] :Optional  :PeakDetectAreaMode
-    [-P[eak]N[umber]     PN                  (10        )] :Optional  :PeakNumber
-    [-PDT[hres]          PDT                 (0.2       )] :Optional  :PeakDetectThreshold_ForMode0
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputCorrelationMapList
+    [-i[nput]c[ommonLine]InC                 (NULL      ).as(inFile              ) ] :Essential :InputCommonLineDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-P[eakArea]M[ode]   Pm                  (0         ).as(Integer             ) ] :Optional  :PeakDetectAreaMode
+    [-P[eak]N[umber]     PN                  (10        ).as(Integer             ) ] :Optional  :PeakNumber
+    [-PDT[hres]          PDT                 (0.2       ).as(Real                ) ] :Optional  :PeakDetectThreshold_ForMode0
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/FETOrientationSearchByAnnealing.html b/doc/SmallTools/FETOrientationSearchByAnnealing.html
index 95be7d2..2d88002 100644
--- a/doc/SmallTools/FETOrientationSearchByAnnealing.html
+++ b/doc/SmallTools/FETOrientationSearchByAnnealing.html
@@ -8,16 +8,16 @@
 <PRE>
 Usage: FETOrientationSearchByAnnealing
 Options:
-    [-i[nputMS]          InMS                (NULL      )] :Essential :InputMapSet
-    [-i[nput]F[ile]      InFL                (NULL      )] :Optional  :InputFETDataFileList
-    [-i[nput]M[aps]      InML                (NULL      )] :Optional  :InputMapDataFileList
-    [-T[emprature]       ITemp               (300.0     )] :Optional  :InitialTemprature
-    [-a[nnealing]s[chedule]1AS1                 (10        )] :Optional  :Repeatas1TimesInSameTemp
-    [-a[nnealing]s[chedule]2AS2                 (0.9       )] :Optional  :TempratureDecreaseConstant
-    [-a[nnealing]s[chedule]3AS3                 (10        )] :Optional  :Repeatas3Times
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nputMS]          InMS                (NULL      ).as(inFile              ) ] :Essential :InputMapSet
+    [-i[nput]F[ile]      InFL                (NULL      ).as(inFile              ) ] :Optional  :InputFETDataFileList
+    [-i[nput]M[aps]      InML                (NULL      ).as(inFile              ) ] :Optional  :InputMapDataFileList
+    [-T[emprature]       ITemp               (300.0     ).as(Real                ) ] :Optional  :InitialTemprature
+    [-a[nnealing]s[chedule]1AS1                 (10        ).as(Integer             ) ] :Optional  :Repeatas1TimesInSameTemp
+    [-a[nnealing]s[chedule]2AS2                 (0.9       ).as(Real                ) ] :Optional  :TempratureDecreaseConstant
+    [-a[nnealing]s[chedule]3AS3                 (10        ).as(Integer             ) ] :Optional  :Repeatas3Times
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 this tool does not work at Oct.31,2007 
 
diff --git a/doc/SmallTools/FETOrientationSearchByFeatureAlignment.html b/doc/SmallTools/FETOrientationSearchByFeatureAlignment.html
index 185afab..3199317 100644
--- a/doc/SmallTools/FETOrientationSearchByFeatureAlignment.html
+++ b/doc/SmallTools/FETOrientationSearchByFeatureAlignment.html
@@ -8,22 +8,22 @@
 <PRE>
 Usage: FETOrientationSearchByFeatureAlignment
 Options:
-    [-i[nput]            InS                 (NULL      )] :Optional  :InputSinogramList
-    [-i[nput]2           InS2                (NULL      )] :Optional  :InputMoreSinogramList
-    [-I[nputFET]         InF                 (NULL      )] :Optional  :InputFETfileList
-    [-i[nput]a[ngle]     InA                 (NULL      )] :Optional  :inputAngleList
-    [-o[utput]           Out                 (NULL      )] :Optional  :OutputDataFile
-    [-o[ut]clog          OutLOG              (NULL      )] :Optional  :OutputCorValueLogFile
-    [-o[ut]a[ngle]       OutA                (NULL      )] :Optional  :OutputAngleList
-    [-o[ut]2d            Out2D               (NULL      )] :Optional  :OutputAngleListFormrc3Dto2D
-    [-itm[ax]            ITMAX               (8         )] :Optional  :iterationMax
-    [-dvm[ax]            DEVMAX              (3         )] :Optional  :sphereDevideMax
-    [-mitm[ax]           MITMAX              (3         )] :Optional  :iterationMax Multiple
-    [-mdvm[ax]           MDEVMAX             (3         )] :Optional  :sphereDevideMax Multiple
-    [-ldn[um]            LDN                 (8         )] :Optional  :LongaxisDevideNum
-    [-srl[imit]          SRL                 (0.0       )] :Optional  :sphereReconstLimit
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (202       )] :Optional  :Mode
+    [-i[nput]            InS                 (NULL      ).as(inFile              ) ] :Optional  :InputSinogramList
+    [-i[nput]2           InS2                (NULL      ).as(inFile              ) ] :Optional  :InputMoreSinogramList
+    [-I[nputFET]         InF                 (NULL      ).as(inFile              ) ] :Optional  :InputFETfileList
+    [-i[nput]a[ngle]     InA                 (NULL      ).as(inFile              ) ] :Optional  :inputAngleList
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-o[ut]clog          OutLOG              (NULL      ).as(outFile             ) ] :Optional  :OutputCorValueLogFile
+    [-o[ut]a[ngle]       OutA                (NULL      ).as(outFile             ) ] :Optional  :OutputAngleList
+    [-o[ut]2d            Out2D               (NULL      ).as(outFile             ) ] :Optional  :OutputAngleListFormrc3Dto2D
+    [-itm[ax]            ITMAX               (8         ).as(Integer             ) ] :Optional  :iterationMax
+    [-dvm[ax]            DEVMAX              (3         ).as(Integer             ) ] :Optional  :sphereDevideMax
+    [-mitm[ax]           MITMAX              (3         ).as(Integer             ) ] :Optional  :iterationMax Multiple
+    [-mdvm[ax]           MDEVMAX             (3         ).as(Integer             ) ] :Optional  :sphereDevideMax Multiple
+    [-ldn[um]            LDN                 (8         ).as(Integer             ) ] :Optional  :LongaxisDevideNum
+    [-srl[imit]          SRL                 (0.0       ).as(Real                ) ] :Optional  :sphereReconstLimit
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (202       ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 Either -i or -I is essential option.
 Input FETimages: smoothed image is recommend.
diff --git a/doc/SmallTools/FETmapOrientationSearchBySimultaneousFitting.html b/doc/SmallTools/FETmapOrientationSearchBySimultaneousFitting.html
index 595abd3..8283e08 100644
--- a/doc/SmallTools/FETmapOrientationSearchBySimultaneousFitting.html
+++ b/doc/SmallTools/FETmapOrientationSearchBySimultaneousFitting.html
@@ -8,15 +8,15 @@
 <PRE>
 Usage: FETmapOrientationSearchBySimultaneousFitting
 Options:
-    [-i[nput]            InML                (NULL      )] :Essential :InputMapList
-    [-i[nput]n[ame]      InNL                (NULL      )] :Essential :InputNameList
-    [-i[nput]C[ore]L[ist]InCL                (NULL      )] :Essential :InputCandidateCoreList
-    [-P[eakArea]M[ode]   PM                  (0         )] :Optional  :PeakDetectAreaMode
-    [-P[eak]N[umber]     PN                  (10        )] :Optional  :PeakNumber
-    [-PDT[hres]          PDT                 (0.2       )] :Optional  :PeakDetectThreshold_ForMode0
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            InML                (NULL      ).as(inFile              ) ] :Essential :InputMapList
+    [-i[nput]n[ame]      InNL                (NULL      ).as(inFile              ) ] :Essential :InputNameList
+    [-i[nput]C[ore]L[ist]InCL                (NULL      ).as(inFile              ) ] :Essential :InputCandidateCoreList
+    [-P[eakArea]M[ode]   PM                  (0         ).as(Integer             ) ] :Optional  :PeakDetectAreaMode
+    [-P[eak]N[umber]     PN                  (10        ).as(Integer             ) ] :Optional  :PeakNumber
+    [-PDT[hres]          PDT                 (0.2       ).as(Real                ) ] :Optional  :PeakDetectThreshold_ForMode0
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 InputMapList: FETcorrelationMapList
 InputNameList: FETfileNameList 
diff --git a/doc/SmallTools/FETsmallMapSetCreate_forSimultaneousMinimization.html b/doc/SmallTools/FETsmallMapSetCreate_forSimultaneousMinimization.html
index a9dfa92..77f6cf8 100644
--- a/doc/SmallTools/FETsmallMapSetCreate_forSimultaneousMinimization.html
+++ b/doc/SmallTools/FETsmallMapSetCreate_forSimultaneousMinimization.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: FETsmallMapSetCreate_forSimultaneousMinimization
 Options:
-    [-i[nput]M[ap]L[ist] InML                (NULL      )] :Essential :InputMapList
-    [-o[utputMapSet]     OutMS               (NULL      )] :Essential :OutputMapSet
-    [-s[tep]s[ize]       InSS                (5         )] :Optional  :StepSize
-    [-s[earch]r[adius]   InSR                (15        )] :Optional  :searchRadius-degree
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]M[ap]L[ist] InML                (NULL      ).as(inFile              ) ] :Essential :InputMapList
+    [-o[utputMapSet]     OutMS               (NULL      ).as(outFile             ) ] :Essential :OutputMapSet
+    [-s[tep]s[ize]       InSS                (5         ).as(Integer             ) ] :Optional  :StepSize
+    [-s[earch]r[adius]   InSR                (15        ).as(Integer             ) ] :Optional  :searchRadius-degree
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 	input MapList must not have empty line.
 	360 % (ss*2) = 0 
diff --git a/doc/SmallTools/LCalculationForOrientationSearch.html b/doc/SmallTools/LCalculationForOrientationSearch.html
index b078c0e..d2937a0 100644
--- a/doc/SmallTools/LCalculationForOrientationSearch.html
+++ b/doc/SmallTools/LCalculationForOrientationSearch.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: LCalculationForOrientationSearch
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/Polar2Descartes.html b/doc/SmallTools/Polar2Descartes.html
index 94f1df2..c908a60 100644
--- a/doc/SmallTools/Polar2Descartes.html
+++ b/doc/SmallTools/Polar2Descartes.html
@@ -8,13 +8,21 @@
 <PRE>
 Usage: Polar2Descartes
 Options:
-    [-i                  r                   (1.0       )phi                 (90.0      )theta               (0.0       )] :Optional  :input: coord
-    [-o                  Out                 (stdout    )] :Optional  :output: coord
-    [-centre             cx                  (0.0       )cy                  (0.0       )cz                  (0.0       )] :Optional  :Centre
-    [-xaxis              xx                  (1.0       )xy                  (0.0       )xz                  (0.0       )] :Optional  :x-axis
-    [-zaxis              zx                  (0.0       )zy                  (0.0       )zz                  (1.0       )] :Optional  :z-axis
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i                  r                   (1.0       ).as(Real                ) 
+                         phi                 (90.0      ).as(Real                ) 
+                         theta               (0.0       ).as(Real                ) ] :Optional  :input: coord
+    [-o                  Out                 (stdout    ).as(outFile             ) ] :Optional  :output: coord
+    [-centre             cx                  (0.0       ).as(Real                ) 
+                         cy                  (0.0       ).as(Real                ) 
+                         cz                  (0.0       ).as(Real                ) ] :Optional  :Centre
+    [-xaxis              xx                  (1.0       ).as(Real                ) 
+                         xy                  (0.0       ).as(Real                ) 
+                         xz                  (0.0       ).as(Real                ) ] :Optional  :x-axis
+    [-zaxis              zx                  (0.0       ).as(Real                ) 
+                         zy                  (0.0       ).as(Real                ) 
+                         zz                  (1.0       ).as(Real                ) ] :Optional  :z-axis
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/ProjectionDirectionMapCreate.html b/doc/SmallTools/ProjectionDirectionMapCreate.html
index feedd1c..19e2b7f 100644
--- a/doc/SmallTools/ProjectionDirectionMapCreate.html
+++ b/doc/SmallTools/ProjectionDirectionMapCreate.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: ProjectionDirectionMapCreate
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Optional  :OutputDataFile
-    [-p[ost]s[cript]     Ps                  (NULL      )] :Optional  :OutputPostScriptFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-R[otation]m[ode]   Rmode               (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-p[ost]s[cript]     Ps                  (NULL      ).as(outFile             ) ] :Optional  :OutputPostScriptFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-R[otation]m[ode]   Rmode               (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Rotational Mode -----
 Final rotation of projection is only Z .
 
diff --git a/doc/SmallTools/WeightCalculationOfCommonLineSearch.html b/doc/SmallTools/WeightCalculationOfCommonLineSearch.html
index 207cedf..03eb6b3 100644
--- a/doc/SmallTools/WeightCalculationOfCommonLineSearch.html
+++ b/doc/SmallTools/WeightCalculationOfCommonLineSearch.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: WeightCalculationOfCommonLineSearch
 Options:
-    [-I[nput]            In                  (NULL      )] :Essential :InputDataFileList
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-L[ength]T[hreshold]M[ode]LengthThresholdMode (0         )] :Essential :Length threshold mode in LengthCorrelation
-    [-L[ength]T[hreshold]R[atio]LengthThresholdRatio(0.25      )] :Optional  :Length threshold ratio in LengthCorrelation : -LTM=0
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-I[nput]            In                  (NULL      ).as(inFileList          ) ] :Essential :InputDataFileList
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-L[ength]T[hreshold]M[ode]LengthThresholdMode (0         ).as(Integer             ) ] :Essential :Length threshold mode in LengthCorrelation
+    [-L[ength]T[hreshold]R[atio]LengthThresholdRatio(0.25      ).as(Real                ) ] :Optional  :Length threshold ratio in LengthCorrelation : -LTM=0
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 
 ----- Mode -----
 -m :
diff --git a/doc/SmallTools/WeightCalculationOfCommonLineSearchByAllSinogram.html b/doc/SmallTools/WeightCalculationOfCommonLineSearchByAllSinogram.html
index 438564c..78ddb41 100644
--- a/doc/SmallTools/WeightCalculationOfCommonLineSearchByAllSinogram.html
+++ b/doc/SmallTools/WeightCalculationOfCommonLineSearchByAllSinogram.html
@@ -8,15 +8,15 @@
 <PRE>
 Usage: WeightCalculationOfCommonLineSearchByAllSinogram
 Options:
-    [-I[nput]1           In1                 (NULL      )] :Optional  :InputDataFileList1 : normal correlation
-    [-I[nput]2           In2                 (NULL      )] :Optional  :InputDataFileList2 : derivation1D correlation
-    [-I[nput]3           In3                 (NULL      )] :Optional  :InputDataFileList3 : derivation2D correlation
-    [-I[nput]4           In4                 (NULL      )] :Optional  :InputDataFileList4 : length correlation
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-M[ode]             Mode                (15        )] :Optional  :Mode : choice of used Correlation
-    [-v[ariance]         variance            (5         )] :Optional  :variance of Gaussian weight function
+    [-I[nput]1           In1                 (NULL      ).as(inFileListNoOpen    ) ] :Optional  :InputDataFileList1 : normal correlation
+    [-I[nput]2           In2                 (NULL      ).as(inFileListNoOpen    ) ] :Optional  :InputDataFileList2 : derivation1D correlation
+    [-I[nput]3           In3                 (NULL      ).as(inFileListNoOpen    ) ] :Optional  :InputDataFileList3 : derivation2D correlation
+    [-I[nput]4           In4                 (NULL      ).as(inFileListNoOpen    ) ] :Optional  :InputDataFileList4 : length correlation
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-M[ode]             Mode                (15        ).as(Integer             ) ] :Optional  :Mode : choice of used Correlation
+    [-v[ariance]         variance            (5         ).as(Real                ) ] :Optional  :variance of Gaussian weight function
 
 ----- Mode -----
 -M : 1 : ued to Normal Correlation
diff --git a/doc/SmallTools/anglediffchk.html b/doc/SmallTools/anglediffchk.html
index e0fdb4f..a2ad992 100644
--- a/doc/SmallTools/anglediffchk.html
+++ b/doc/SmallTools/anglediffchk.html
@@ -1 +1,19 @@
-/bin/bash: anglediffchk: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>anglediffchk</TITLE>
+</HEAD>
+<BODY>
+<H1>anglediffchk</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: anglediffchk
+Options:
+    [-t[estAngle]        Test                (0.0       ).as(Real                ) ] :Essential :test
+    [-r[eferenceAngle]   Reference           (0.0       ).as(Real                ) ] :Essential :reference
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :configFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/array2mrc.html b/doc/SmallTools/array2mrc.html
index c6464e0..0717317 100644
--- a/doc/SmallTools/array2mrc.html
+++ b/doc/SmallTools/array2mrc.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: array2mrc
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-m[ode]m[rcimage]   mm                  (2         )] :Optional  :Mode of mrcImage
-    [-l[ength]m[rcimage] lm                  (0         )] :Optional  :Length of mrcImage
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-m[ode]m[rcimage]   mm                  (2         ).as(Integer             ) ] :Optional  :Mode of mrcImage
+    [-l[ength]m[rcimage] lm                  (0         ).as(Real                ) ] :Optional  :Length of mrcImage
 ----- Additional Usage -----
 -- Attension --
 Array format : left-hand
diff --git a/doc/SmallTools/arrayPCA.html b/doc/SmallTools/arrayPCA.html
new file mode 100644
index 0000000..4096981
--- /dev/null
+++ b/doc/SmallTools/arrayPCA.html
@@ -0,0 +1,19 @@
+<HTML>
+<HEAD>
+<TITLE>arrayPCA</TITLE>
+</HEAD>
+<BODY>
+<H1>arrayPCA</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: arrayPCA
+Options:
+    [-i[nput]            In                  (stdin     ).as(inFile::ASCII       ) ] :Optional  :Input:Array
+    [-o[utput]           Out                 (stdout    ).as(outFile::ASCII      ) ] :Optional  :Output: PCA
+    [-O[utput]           Out2                (stdout    ).as(outFile::ASCII      ) ] :Optional  :Output: Transform
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/bin2mrc.html b/doc/SmallTools/bin2mrc.html
index 922b969..7b64f1e 100644
--- a/doc/SmallTools/bin2mrc.html
+++ b/doc/SmallTools/bin2mrc.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: bin2mrc
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/clusterLog2ToLog.html b/doc/SmallTools/clusterLog2ToLog.html
index cda9680..f30c3ff 100644
--- a/doc/SmallTools/clusterLog2ToLog.html
+++ b/doc/SmallTools/clusterLog2ToLog.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: clusterLog2ToLog
 Options:
-    [-i[nput]            In                  (stdin     )] :Optional  :Input: Log2
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output: Log
-    [-lastNum            lastNum             (1         )] :Optional  :lastClusterNumber
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (stdin     ).as(inFile              ) ] :Optional  :Input: Log2
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output: Log
+    [-lastNum            lastNum             (1         ).as(Integer             ) ] :Optional  :lastClusterNumber
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/clusterLogASCII2Binary.html b/doc/SmallTools/clusterLogASCII2Binary.html
index 81a32ea..9e96d32 100644
--- a/doc/SmallTools/clusterLogASCII2Binary.html
+++ b/doc/SmallTools/clusterLogASCII2Binary.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: clusterLogASCII2Binary
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: ASCII LogFile
+    [-o[utput]           Out                 (log       ).as(String              ) ] :Essential :Output: Binary LogFile BaseName
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/clusterShow.html b/doc/SmallTools/clusterShow.html
index 8d8956e..7c7fc54 100644
--- a/doc/SmallTools/clusterShow.html
+++ b/doc/SmallTools/clusterShow.html
@@ -8,24 +8,28 @@
 <PRE>
 Usage: clusterShow
 Options:
-    [-i[nput]            In                  (NULL      )] :Optional  :InputData: ASCII Log: Need -i, -i2, or -ib
-    [-i[nput]2           In2                 (NULL      )] :Optional  :InputData: ASCII Log2
-    [-i[nput]b[inary]    InB                 (NULL      )] :Optional  :InputData: BinaryLog: basename
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output: All
-    [-O[utput]           Out2                (stdout    )] :Optional  :Output: ClusterOnly
-    [-PS[output]         OutPS               (stdout    )] :Optional  :Output: ClusterForPS: Need -I
-    [-O[utput]L[ist]     OutOL               (stdout    )] :Optional  :Output: ClusterList 
-    [-O[utput]T[reeInfo] TreeInfo            (NULL      )] :Optional  :Output: TreeInfo
-    [-A[verage]L[ist]    OutAL               (stdout    )OutALRange          (0         )OutALSuffix         (avg       )] :Optional  :Output: ClusterList range
-    [-Last[ClusterNumber]LastNum             (1         )] :Optional  :Last: Num
-    [-S[cale]            ShoulderScale       (1         )ArmScale            (1         )] :Optional  :Scale: Shoulder Arm
-    [-P[osition]         PosX                (0         )PosY                (0         )] :Optional  :Position: X Y
-    [-Offset             Offset              (1         )] :Optional  :Offset: Arm
-    [-I[nfileList]       InList              (NULL      )] :Optional  :FileList
-    [-Log                ] :Optional  :Arm: Log Scale
-    [-Scaling            ] :Optional  :with Scaling
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Optional  :InputData: ASCII Log: Need -i, -i2, or -ib
+    [-i[nput]2           In2                 (NULL      ).as(inFile              ) ] :Optional  :InputData: ASCII Log2
+    [-i[nput]b[inary]    InB                 (NULL      ).as(String              ) ] :Optional  :InputData: BinaryLog: basename
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output: All
+    [-O[utput]           Out2                (stdout    ).as(outFile             ) ] :Optional  :Output: ClusterOnly
+    [-PS[output]         OutPS               (stdout    ).as(outFile             ) ] :Optional  :Output: ClusterForPS: Need -I
+    [-O[utput]L[ist]     OutOL               (stdout    ).as(outFile             ) ] :Optional  :Output: ClusterList 
+    [-O[utput]T[reeInfo] TreeInfo            (NULL      ).as(outFile             ) ] :Optional  :Output: TreeInfo
+    [-A[verage]L[ist]    OutAL               (stdout    ).as(outFile             ) 
+                         OutALRange          (0         ).as(Integer             ) 
+                         OutALSuffix         (avg       ).as(String              ) ] :Optional  :Output: ClusterList range
+    [-Last[ClusterNumber]LastNum             (1         ).as(Integer             ) ] :Optional  :Last: Num
+    [-S[cale]            ShoulderScale       (1         ).as(Real                ) 
+                         ArmScale            (1         ).as(Real                ) ] :Optional  :Scale: Shoulder Arm
+    [-P[osition]         PosX                (0         ).as(Real                ) 
+                         PosY                (0         ).as(Real                ) ] :Optional  :Position: X Y
+    [-Offset             Offset              (1         ).as(Real                ) ] :Optional  :Offset: Arm
+    [-I[nfileList]       InList              (NULL      ).as(inFileListNoOpen    ) ] :Optional  :FileList
+    [-Log                                                                          ] :Optional  :Arm: Log Scale
+    [-Scaling                                                                      ] :Optional  :with Scaling
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/coordRotation.html b/doc/SmallTools/coordRotation.html
index bcdace2..26edd00 100644
--- a/doc/SmallTools/coordRotation.html
+++ b/doc/SmallTools/coordRotation.html
@@ -8,11 +8,13 @@
 <PRE>
 Usage: coordRotation
 Options:
-    [-p                  x                   (0         )y                   (0         )z                   (0         )] :Essential :Point:
-    [-mat[rix]           Mat                 (stdin     )] :Essential :Input: matrix
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-p                  x                   (0         ).as(Real                ) 
+                         y                   (0         ).as(Real                ) 
+                         z                   (0         ).as(Real                ) ] :Essential :Point:
+    [-mat[rix]           Mat                 (stdin     ).as(inFile              ) ] :Essential :Input: matrix
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/ctfDeterminationFromMultiImage.html b/doc/SmallTools/ctfDeterminationFromMultiImage.html
index 18ae701..c343c57 100644
--- a/doc/SmallTools/ctfDeterminationFromMultiImage.html
+++ b/doc/SmallTools/ctfDeterminationFromMultiImage.html
@@ -8,13 +8,14 @@
 <PRE>
 Usage: ctfDeterminationFromMultiImage
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: mrcImageList
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output: Result obtained by fitting procedure
-    [-O[utput]           Out2                (.estimate )] :Optional  :Output: Estimated scattering: add this value to input filename
-    [-Molec[ular]Env[elope]MolecEnv            (50        )] :Optional  :Input [A]: Spread : Assign molecular envelope as Gaussian
-    [-Molec[ular]Env[elope]2MolecEnvFile        (NULL      )] :Optional  :Input filename: Scattering Factor suggested by Table
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFileList          ) ] :Optional  :Input: mrcImageList
+    [-i[nput]            In2                 (NULL      ).as(inFileList          ) ] :Optional  :Input: AngularDistributionList
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output: Result obtained by fitting procedure
+    [-O[utput]           Out2                (.estimate ).as(String              ) ] :Optional  :Output: Estimated scattering: add this value to input filename
+    [-Molec[ular]Env[elope]MolecEnv            (50        ).as(Real                ) ] :Optional  :Input [A]: Spread : Assign molecular envelope as Gaussian
+    [-Molec[ular]Env[elope]2MolecEnvFile        (NULL      ).as(String              ) ] :Optional  :Input filename: Scattering Factor suggested by Table
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 ----- InFile format: -i or -i2 
 filename defocus[A] AmpOverPhase kV Cs Cc Ai I SN MTFMode MTF MTF2 MolecEnv Magnification
diff --git a/doc/SmallTools/ctfDeterminationFromThonRing.html b/doc/SmallTools/ctfDeterminationFromThonRing.html
index daa955c..0632791 100644
--- a/doc/SmallTools/ctfDeterminationFromThonRing.html
+++ b/doc/SmallTools/ctfDeterminationFromThonRing.html
@@ -8,16 +8,20 @@
 <PRE>
 Usage: ctfDeterminationFromThonRing
 Options:
-    [-i[nput]            In                  (stdin     )] :Optional  :InputDataFile
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-oP[utput]          Out2                (NULL      )] :Optional  :OutputParameter
-    [-kV                 kV                  (200       )] :Optional  :kV
-    [-Cs                 Cs                  (1.7       )] :Optional  :Cs[mm]
-    [-Def                minDef              (0.0       )maxDef              (200000.0  )delDef              (1000.0    )] :Optional  :Def[A]
-    [-Amp                minAmp              (0.0       )maxAmp              (0.4       )delAmp              (0.005     )] :Optional  :AmpToPhase
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-R[/A]              R                   (NULL      )... ] :Variable  :ThonRing[/A]
+    [-i[nput]            In                  (stdin     ).as(inFile              ) ] :Optional  :InputDataFile
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-oP[utput]          Out2                (NULL      ).as(outFile             ) ] :Optional  :OutputParameter
+    [-kV                 kV                  (200       ).as(Real                ) ] :Optional  :kV
+    [-Cs                 Cs                  (1.7       ).as(Real                ) ] :Optional  :Cs[mm]
+    [-Def                minDef              (0.0       ).as(Real                ) 
+                         maxDef              (200000.0  ).as(Real                ) 
+                         delDef              (1000.0    ).as(Real                ) ] :Optional  :Def[A]
+    [-Amp                minAmp              (0.0       ).as(Real                ) 
+                         maxAmp              (0.4       ).as(Real                ) 
+                         delAmp              (0.005     ).as(Real                ) ] :Optional  :AmpToPhase
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-R[/A]              R                   (NULL      ).as(Real                ) ... ] :Variable  :ThonRing[/A]
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/ctfDetermine.html b/doc/SmallTools/ctfDetermine.html
index 79e0c79..0270cd2 100644
--- a/doc/SmallTools/ctfDetermine.html
+++ b/doc/SmallTools/ctfDetermine.html
@@ -8,32 +8,32 @@
 <PRE>
 Usage: ctfDetermine
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile:  mrcImage
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile: Parameters
-    [-D[efocus]          Defocus             (0.0       )] :Optional  :InitialDefocus[A]
-    [-Cs                 Cs                  (1.7       )] :Optional  :InitialCs[mm]
-    [-Cc                 Cc                  (1.2       )] :Optional  :InitialCs[mm]
-    [-dE                 dE                  (0.2       )] :Optional  :InitialCs[mm]
-    [-Ac[cerratedVoltage]Ac                  (200       )] :Optional  :Ac[kV]
-    [-CutLow             CutLow              (0.05      )] :Optional  :CutOffLowFrequncy[/A]
-    [-CutHigh            CutHigh             (0.5       )] :Optional  :CutOffHighFrequncy[/A]
-    [-I0                 I0                  (1.0       )] :Optional  :I0
-    [-ratio              ratioOfAmpToPhase   (0.1       )] :Optional  :ratioOfAmpToPhase
-    [-Ai                 Ai                  (0.03      )] :Optional  :IlluminationAngle[mrad]
-    [-BofMTF             BofMTF              (15.0      )] :Optional  :B of MTF [A]
-    [-BofV[ibration]     BofVibration        (3.0       )] :Optional  :B of Vibration [A]
-    [-Mag[nification]    Magnification       (1.0       )] :Optional  :Magnification
-    [-[White]Noise       WhiteNoise          (0.0       )] :Optional  :Signal/Noise Ratio
-    [-[White]Noise2      WhiteNoise2         (0.0       )] :Optional  :Signal/Noise Ratio
-    [-MolcEnv            MolcEnv             (0.0       )] :Optional  :Gaussian: Molcular Envelop [A]
-    [-MolcEnv2           MolcEnvTable        (NULL      )] :Optional  :Table: Molcular Envelop
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-min                min                 (-10       )] :Optional  :min of coefficient area
-    [-max                max                 (10        )] :Optional  :max of coefficient area
-    [-s[tep]             step                (0.01      )] :Optional  :step of coefficient
-    [-d[egree]           degree              (6         )] :Optional  :agree of function
-    [-S[ection]          section             (4         )] :Optional  :section number of fft
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile:  mrcImage
+    [-o[utput]           Out                 (NULL      ).as(appendFile          ) ] :Essential :OutputDataFile: Parameters
+    [-D[efocus]          Defocus             (0.0       ).as(Real                ) ] :Optional  :InitialDefocus[A]
+    [-Cs                 Cs                  (1.7       ).as(Real                ) ] :Optional  :InitialCs[mm]
+    [-Cc                 Cc                  (1.2       ).as(Real                ) ] :Optional  :InitialCs[mm]
+    [-dE                 dE                  (0.2       ).as(Real                ) ] :Optional  :InitialCs[mm]
+    [-Ac[cerratedVoltage]Ac                  (200       ).as(Real                ) ] :Optional  :Ac[kV]
+    [-CutLow             CutLow              (0.05      ).as(Real                ) ] :Optional  :CutOffLowFrequncy[/A]
+    [-CutHigh            CutHigh             (0.5       ).as(Real                ) ] :Optional  :CutOffHighFrequncy[/A]
+    [-I0                 I0                  (1.0       ).as(Real                ) ] :Optional  :I0
+    [-ratio              ratioOfAmpToPhase   (0.1       ).as(Real                ) ] :Optional  :ratioOfAmpToPhase
+    [-Ai                 Ai                  (0.03      ).as(Real                ) ] :Optional  :IlluminationAngle[mrad]
+    [-BofMTF             BofMTF              (15.0      ).as(Real                ) ] :Optional  :B of MTF [A]
+    [-BofV[ibration]     BofVibration        (3.0       ).as(Real                ) ] :Optional  :B of Vibration [A]
+    [-Mag[nification]    Magnification       (1.0       ).as(Real                ) ] :Optional  :Magnification
+    [-[White]Noise       WhiteNoise          (0.0       ).as(Real                ) ] :Optional  :Signal/Noise Ratio
+    [-[White]Noise2      WhiteNoise2         (0.0       ).as(Real                ) ] :Optional  :Signal/Noise Ratio
+    [-MolcEnv            MolcEnv             (0.0       ).as(Real                ) ] :Optional  :Gaussian: Molcular Envelop [A]
+    [-MolcEnv2           MolcEnvTable        (NULL      ).as(inFile              ) ] :Optional  :Table: Molcular Envelop
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-min                min                 (-10       ).as(Real                ) ] :Optional  :min of coefficient area
+    [-max                max                 (10        ).as(Real                ) ] :Optional  :max of coefficient area
+    [-s[tep]             step                (0.01      ).as(Real                ) ] :Optional  :step of coefficient
+    [-d[egree]           degree              (6         ).as(Integer             ) ] :Optional  :agree of function
+    [-S[ection]          section             (4         ).as(Integer             ) ] :Optional  :section number of fft
 >>> Mode <<< 
 	  0 : MinMax Methods (Henderson-like CTF determination) 
 	  16: Fitting Methods 
diff --git a/doc/SmallTools/ctfDisplay.html b/doc/SmallTools/ctfDisplay.html
index f1cef89..6b771b9 100644
--- a/doc/SmallTools/ctfDisplay.html
+++ b/doc/SmallTools/ctfDisplay.html
@@ -8,15 +8,15 @@
 <PRE>
 Usage: ctfDisplay
 Options:
-    [-i[nput]            inMRC               (NULL      )] :Optional  :Input:MRC(FFT)
-    [-o[utput]           outCTF              (stdout    )] :Optional  :Input/Output: ctfinfo
-    [-Rmax               Rmax                (0.2       )] :Optional  :Rmax [A-1] 
-    [-Imax               Imax                (0.2       )] :Optional  :Intensity: min-max
-    [-Imin               Imin                (0.02      )] :Optional  :Intensity: min-max
-    [-AutoRange          ] :Optional  :Intensity: min-max
-    [-Log                ] :Optional  :Log of Intensity
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            inMRC               (NULL      ).as(inFile              ) ] :Optional  :Input:MRC(FFT)
+    [-o[utput]           outCTF              (stdout    ).as(appendFile          ) ] :Optional  :Input/Output: ctfinfo
+    [-Rmax               Rmax                (0.2       ).as(Real                ) ] :Optional  :Rmax [A-1] 
+    [-Imax               Imax                (0.2       ).as(Real                ) ] :Optional  :Intensity: min-max
+    [-Imin               Imin                (0.02      ).as(Real                ) ] :Optional  :Intensity: min-max
+    [-AutoRange                                                                    ] :Optional  :Intensity: min-max
+    [-Log                                                                          ] :Optional  :Log of Intensity
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/ctfEnvelopFunction.html b/doc/SmallTools/ctfEnvelopFunction.html
index 239bbdd..ef9912a 100644
--- a/doc/SmallTools/ctfEnvelopFunction.html
+++ b/doc/SmallTools/ctfEnvelopFunction.html
@@ -8,17 +8,17 @@
 <PRE>
 Usage: ctfEnvelopFunction
 Options:
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-Rmax               Rmax                (0.1       )] :Optional  :Rmax[/A]
-    [-dR                 dR                  (0.0001    )] :Optional  :dR[/A]
-    [-kV                 kV                  (200       )] :Optional  :AccVol[kV]
-    [-Cs                 Cs                  (1.7       )] :Optional  :Cs[mm]
-    [-df                 Defocus             (100000    )] :Essential :Defocus[A]:under(+)
-    [-A                  AoverP              (0.0       )] :Optional  :AmplitudeContrast/PhaseContrast
-    [-Ain                Ain                 (0.02      )] :Optional  :IlluminationAperture[mrad]
-    [-ctfMode            ctfMode             (32        )] :Optional  :CTFMode
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-Rmax               Rmax                (0.1       ).as(Real                ) ] :Optional  :Rmax[/A]
+    [-dR                 dR                  (0.0001    ).as(Real                ) ] :Optional  :dR[/A]
+    [-kV                 kV                  (200       ).as(Real                ) ] :Optional  :AccVol[kV]
+    [-Cs                 Cs                  (1.7       ).as(Real                ) ] :Optional  :Cs[mm]
+    [-df                 Defocus             (100000    ).as(Real                ) ] :Essential :Defocus[A]:under(+)
+    [-A                  AoverP              (0.0       ).as(Real                ) ] :Optional  :AmplitudeContrast/PhaseContrast
+    [-Ain                Ain                 (0.02      ).as(Real                ) ] :Optional  :IlluminationAperture[mrad]
+    [-ctfMode            ctfMode             (32        ).as(Integer             ) ] :Optional  :CTFMode
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 >>>> ctfMode <<<< 
 ctfInfoModeWithIlluminationAngle   32 
 ctfInfoModeWithEnergySpread        64 
diff --git a/doc/SmallTools/ctfEnvelopFunctionEstimate.html b/doc/SmallTools/ctfEnvelopFunctionEstimate.html
new file mode 100644
index 0000000..de2bb76
--- /dev/null
+++ b/doc/SmallTools/ctfEnvelopFunctionEstimate.html
@@ -0,0 +1,21 @@
+<HTML>
+<HEAD>
+<TITLE>ctfEnvelopFunctionEstimate</TITLE>
+</HEAD>
+<BODY>
+<H1>ctfEnvelopFunctionEstimate</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: ctfEnvelopFunctionEstimate
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input:
+    [-o[utput]           Out                 (stdout    ).as(outFile::ASCII      ) ] :Optional  :Output:
+    [-degree             degree              (6         ).as(Integer             ) ] :Optional  :[dim]
+    [-Range              CutLow              (0.01      ).as(Real                ) 
+                         CutHigh             (0.2       ).as(Real                ) ] :Optional  :[/A]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/ctfFunction.html b/doc/SmallTools/ctfFunction.html
index 39b31f6..ed5dcc2 100644
--- a/doc/SmallTools/ctfFunction.html
+++ b/doc/SmallTools/ctfFunction.html
@@ -8,19 +8,19 @@
 <PRE>
 Usage: ctfFunction
 Options:
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-Rmax               Rmax                (0.1       )] :Optional  :Rmax[/A]
-    [-dR                 dR                  (0.0001    )] :Optional  :dR[/A]
-    [-kV                 kV                  (200       )] :Optional  :AccVol[kV]
-    [-Cs                 Cs                  (2.1       )] :Optional  :Cs[mm]
-    [-df                 Defocus             (27000     )] :Essential :Defocus[A]:under(+)
-    [-A                  AoverP              (0.0       )] :Optional  :AmplitudeContrast/PhaseContrast
-    [-Ain                Ain                 (0.02      )] :Optional  :IlluminationAperture[mrad]
-    [-ctfMode            ctfMode             (32        )] :Optional  :CTFMode
-    [-pvm                pvm                 (0         )] :Optional  :PVM: MultiProcessor
-    [-pvmList            pvmList             (stdin     )] :Optional  :PVM Host List: MultiProcessor
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-Rmax               Rmax                (0.1       ).as(Real                ) ] :Optional  :Rmax[/A]
+    [-dR                 dR                  (0.0001    ).as(Real                ) ] :Optional  :dR[/A]
+    [-kV                 kV                  (200       ).as(Real                ) ] :Optional  :AccVol[kV]
+    [-Cs                 Cs                  (2.1       ).as(Real                ) ] :Optional  :Cs[mm]
+    [-df                 Defocus             (27000     ).as(Real                ) ] :Essential :Defocus[A]:under(+)
+    [-A                  AoverP              (0.0       ).as(Real                ) ] :Optional  :AmplitudeContrast/PhaseContrast
+    [-Ain                Ain                 (0.02      ).as(Real                ) ] :Optional  :IlluminationAperture[mrad]
+    [-ctfMode            ctfMode             (32        ).as(Integer             ) ] :Optional  :CTFMode
+    [-pvm                pvm                 (0         ).as(Integer             ) ] :Optional  :PVM: MultiProcessor
+    [-pvmList            pvmList             (stdin     ).as(inFile              ) ] :Optional  :PVM Host List: MultiProcessor
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 >>>> ctfMode <<<< 
  0: Phase CTF 
  1: PhaseCTF + ratio*AmpCTF 
diff --git a/doc/SmallTools/ctfInfoSet.html b/doc/SmallTools/ctfInfoSet.html
index e08bac9..070b8d2 100644
--- a/doc/SmallTools/ctfInfoSet.html
+++ b/doc/SmallTools/ctfInfoSet.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: ctfInfoSet
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/ctfMultiFunction.html b/doc/SmallTools/ctfMultiFunction.html
index b3e83fb..d5a740d 100644
--- a/doc/SmallTools/ctfMultiFunction.html
+++ b/doc/SmallTools/ctfMultiFunction.html
@@ -8,14 +8,14 @@
 <PRE>
 Usage: ctfMultiFunction
 Options:
-    [-I[nput array of file]In                  (NULL      )] :Optional  :InputDataFiles
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-Rmax               Rmax                (0.1       )] :Optional  :Rmax[/A]
-    [-dR                 dR                  (0.0001    )] :Optional  :dR[/A]
-    [-Ain                Ain                 (0.02      )] :Optional  :IlluminationAperture[mrad]
-    [-ctfMode            ctfMode             (33        )] :Optional  :CTFMode
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-I[nput array of file]In                  (NULL      ).as(inFileListNoOpen    ) ] :Optional  :InputDataFiles
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-Rmax               Rmax                (0.1       ).as(Real                ) ] :Optional  :Rmax[/A]
+    [-dR                 dR                  (0.0001    ).as(Real                ) ] :Optional  :dR[/A]
+    [-Ain                Ain                 (0.02      ).as(Real                ) ] :Optional  :IlluminationAperture[mrad]
+    [-ctfMode            ctfMode             (33        ).as(Integer             ) ] :Optional  :CTFMode
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 >>>> ctfMode <<<< 
  0: Phase CTF 
diff --git a/doc/SmallTools/ctfWeightMapCreation.html b/doc/SmallTools/ctfWeightMapCreation.html
index 23d3392..eb05774 100644
--- a/doc/SmallTools/ctfWeightMapCreation.html
+++ b/doc/SmallTools/ctfWeightMapCreation.html
@@ -8,18 +8,19 @@
 <PRE>
 Usage: ctfWeightMapCreation
 Options:
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-kV                 kV                  (200       )] :Optional  :AccVol[kV]
-    [-Cs                 Cs                  (1.7       )] :Optional  :Cs[mm]
-    [-df                 Defocus             (2.7       )] :Essential :Defocus[A]:under(+)
-    [-white              WhiteNoise          (1.0       )] :Optional  :WhiteNoise(N/S)
-    [-noise              Noise               (NULL      )] :Optional  :Noise Power Spectrum
-    [-splusn             SplusN              (NULL      )] :Optional  :Signal+Noise Power Spectrum
-    [-dRinv              dRinv               (1024*5/3  )] :Essential :dRinv[A]
-    [-dRmaxInv           dRmaxInv            (10.0      )] :Essential :dRmaxInv[A]
-    [-SinWin             SinWinRminInv       (20.0      )SinWinRmaxInv       (10.0      )] :Optional  :RminInv[A] RmaxInv[A]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-kV                 kV                  (200       ).as(Real                ) ] :Optional  :AccVol[kV]
+    [-Cs                 Cs                  (1.7       ).as(Real                ) ] :Optional  :Cs[mm]
+    [-df                 Defocus             (2.7       ).as(Real                ) ] :Essential :Defocus[A]:under(+)
+    [-white              WhiteNoise          (1.0       ).as(Real                ) ] :Optional  :WhiteNoise(N/S)
+    [-noise              Noise               (NULL      ).as(inFile              ) ] :Optional  :Noise Power Spectrum
+    [-splusn             SplusN              (NULL      ).as(inFile              ) ] :Optional  :Signal+Noise Power Spectrum
+    [-dRinv              dRinv               (1024*5/3  ).as(Real                ) ] :Essential :dRinv[A]
+    [-dRmaxInv           dRmaxInv            (10.0      ).as(Real                ) ] :Essential :dRmaxInv[A]
+    [-SinWin             SinWinRminInv       (20.0      ).as(Real                ) 
+                         SinWinRmaxInv       (10.0      ).as(Real                ) ] :Optional  :RminInv[A] RmaxInv[A]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 Mode:
       0: No correction  : F = G
       1: Phase contrast : F = G*(H/abs(H))(Only 1 or -1)
diff --git a/doc/SmallTools/defocusDeterminationFromThonRing.html b/doc/SmallTools/defocusDeterminationFromThonRing.html
index ae8bf0e..e0a06ae 100644
--- a/doc/SmallTools/defocusDeterminationFromThonRing.html
+++ b/doc/SmallTools/defocusDeterminationFromThonRing.html
@@ -8,23 +8,23 @@
 <PRE>
 Usage: defocusDeterminationFromThonRing
 Options:
-    [-i[nput]            In                  (stdin     )] :Optional  :InputDataFile
-    [-i[nput] N[ame]     InN                 (stdin     )] :Optional  :InputNameInInformationFile
-    [-i[nput] R[eference]InR                 (stdin     )] :Optional  :InputReferenceForLength
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-o[utput] I[nformation]OutI                (stdout    )] :Optional  :OutputInformationFile
-    [-o[utput] I[nformation]OutI2               (stdout    )] :Optional  :OutputInformationFile
-    [-o[utput] I[nformation]OutI3               (stdout    )] :Optional  :OutputInformationFile
-    [-kV                 kV                  (200       )] :Optional  :kV
-    [-Cs                 Cs                  (2.1       )] :Optional  :Cs[mm]
-    [-A[mplitude contrast]AoverP              (0.05      )] :Optional  :The ratio of amplitude contrast to phase contrast
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-ctfMode            ctfMode             (0         )] :Optional  :CTFMode
-    [-truePitch          truePitch           (430       )] :Optional  :True Pitch
-    [-PixelSize          PixelSize           (5         )] :Optional  :Pixel Size [A]
-    [-deltadY            deltadY             (0.5       )] :Optional  :A range of deltadY to determine dY.
-    [-R[/A]              R                   (NULL      )... ] :Variable  :ThonRing[/A]
+    [-i[nput]            In                  (stdin     ).as(inFile              ) ] :Optional  :InputDataFile
+    [-i[nput] N[ame]     InN                 (stdin     ).as(String              ) ] :Optional  :InputNameInInformationFile
+    [-i[nput] R[eference]InR                 (stdin     ).as(String              ) ] :Optional  :InputReferenceForLength
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-o[utput] I[nformation]OutI                (stdout    ).as(outFile             ) ] :Optional  :OutputInformationFile
+    [-o[utput] I[nformation]OutI2               (stdout    ).as(outFile             ) ] :Optional  :OutputInformationFile
+    [-o[utput] I[nformation]OutI3               (stdout    ).as(outFile             ) ] :Optional  :OutputInformationFile
+    [-kV                 kV                  (200       ).as(Real                ) ] :Optional  :kV
+    [-Cs                 Cs                  (2.1       ).as(Real                ) ] :Optional  :Cs[mm]
+    [-A[mplitude contrast]AoverP              (0.05      ).as(Real                ) ] :Optional  :The ratio of amplitude contrast to phase contrast
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-ctfMode            ctfMode             (0         ).as(Integer             ) ] :Optional  :CTFMode
+    [-truePitch          truePitch           (430       ).as(Real                ) ] :Optional  :True Pitch
+    [-PixelSize          PixelSize           (5         ).as(Real                ) ] :Optional  :Pixel Size [A]
+    [-deltadY            deltadY             (0.5       ).as(Real                ) ] :Optional  :A range of deltadY to determine dY.
+    [-R[/A]              R                   (NULL      ).as(Real                ) ... ] :Variable  :ThonRing[/A]
 ----- Additional Usage ----- 
 >>>> o[uput] I[nformation] <<<<
 This file is used for [mrcImageMultiCTFCompensation and mrcImageCTFCompensation] 
diff --git a/doc/SmallTools/dm2mrc.html b/doc/SmallTools/dm2mrc.html
new file mode 100644
index 0000000..240abb8
--- /dev/null
+++ b/doc/SmallTools/dm2mrc.html
@@ -0,0 +1,19 @@
+<HTML>
+<HEAD>
+<TITLE>dm2mrc</TITLE>
+</HEAD>
+<BODY>
+<H1>dm2mrc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: dm2mrc
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile::dmFile      ) ] :Essential :Input:dmFile(dm3|dm4)
+    [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Essential :Output:mrcImage
+    [-t[humnail]         Thumnail            (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Thumnail:mrcImage
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/dmInfo.html b/doc/SmallTools/dmInfo.html
index d8c4247..241c430 100644
--- a/doc/SmallTools/dmInfo.html
+++ b/doc/SmallTools/dmInfo.html
@@ -13,6 +13,8 @@ Options:
     [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
     [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
+ -m 0 ; tagTerm: tagName/tagValue/.. etc 
+ -m 1 ; tagName: tagValue etc
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/dos2unix.html b/doc/SmallTools/dos2unix.html
index d12256b..a0cbc30 100644
--- a/doc/SmallTools/dos2unix.html
+++ b/doc/SmallTools/dos2unix.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: dos2unix
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/electronWaveLength.html b/doc/SmallTools/electronWaveLength.html
index 856eb7d..c7dd491 100644
--- a/doc/SmallTools/electronWaveLength.html
+++ b/doc/SmallTools/electronWaveLength.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: electronWaveLength
 Options:
-    [-kV                 kV                  (200       )] :Optional  :InputDataFile
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-kV                 kV                  (200       ).as(Real                ) ] :Optional  :InputDataFile
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/emData2mrc.html b/doc/SmallTools/emData2mrc.html
index eeeee53..da18d95 100644
--- a/doc/SmallTools/emData2mrc.html
+++ b/doc/SmallTools/emData2mrc.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: emData2mrc
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-m[agCorrection]    magCorrection       (1.0       )] :Optional  :MagCorrection: 
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-m[agCorrection]    magCorrection       (1.0       ).as(Real                ) ] :Optional  :MagCorrection: 
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/energyTransferModelCheck.html b/doc/SmallTools/energyTransferModelCheck.html
index 10b2776..848f159 100644
--- a/doc/SmallTools/energyTransferModelCheck.html
+++ b/doc/SmallTools/energyTransferModelCheck.html
@@ -1 +1,64 @@
-/bin/bash: energyTransferModelCheck: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>energyTransferModelCheck</TITLE>
+</HEAD>
+<BODY>
+<H1>energyTransferModelCheck</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: energyTransferModelCheck
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-p[db]              PDB                 (NULL      ).as(inFile              ) ] :Optional  :Excluded Area by PDB: Input[PDB]
+    [-P[dbs]             PDBs                (NULL      ).as(inFileList          ) ] :Optional  :Excluded Area by PDB: Input[PDBFileList]
+    [-P[DBs]W[ithInfo]                                                             ] :Optional  :PDBFileList With Info: filename sigma[A]
+    [-sigma              sigma               (1.0       ).as(Real                ) ] :Optional  :SigmaOfAtom for All: sigma [pixel]x delta[A/pixel]
+    [-sigmaA             sigmaA              (1.0       ).as(Real                ) ] :Optional  :SigmaOfAtom for All: sigma [A]
+    [-mrc                MRC                 (NULL      ).as(inFile              ) ] :Optional  :Excluded Area by mrc: Input[MRC]
+    [-MRC                MRCs                (NULL      ).as(inFileList          ) ] :Optional  :Excluded Area by MRC: Input[MRCFileList]
+    [-MRCW[ithInfo]                                                                ] :Optional  :MRCFileList with Info: filename contour near[A]
+    [-C[ontour]          EContour            (10.       ).as(Real                ) ] :Optional  :ContourLevel for Exclusion: Density<ContourLevel -> 0
+    [-Near               ENear               (1.        ).as(Real                ) ] :Optional  :Near [pixel]: Exclusion Area: near[pixel] x delta [A/pixel]
+    [-NearA              ENearA              (1.        ).as(Real                ) ] :Optional  :Near [A]: Exclusion Area: near [A]
+    [-r[estrict]         Rest                (NULL      ).as(inFile              ) ] :Optional  :Restricted Area: Input[mrc]
+    [-R[estrict]         Rests               (NULL      ).as(inFileList          ) ] :Optional  :Restricted Area: InputDataFileList[mrcs]
+    [-contour            Contour             (10.       ).as(Real                ) ] :Optional  :ContourLevel for Restriction
+    [-near               Near                (1.        ).as(Real                ) ] :Optional  :Near [pixel]: Restriction Area: near[pixel] x delta [A/pixel]
+    [-nearA              NearA               (1.        ).as(Real                ) ] :Optional  :Near [A]: Restriction Area: near[A] 
+    [-R[estrictWithInfo]                                                           ] :Optional  :WithInfo: filename contour near[A]
+    [-r[estrict]P        RestP               (NULL      ).as(inFile              ) ] :Optional  :Restricted Area: InputDataFile[pdb]
+    [-R[estrict]P        RestsP              (NULL      ).as(inFileList          ) ] :Optional  :Restricted Area: InputDataFileList[pdbs]: format: filename near[pixel]
+    [-sigmaP             SigmaP              (1.        ).as(Real                ) ] :Optional  :Sigma[pixel]: Restriction Area: sigma x delta [A]
+    [-sigmaPA            SigmaPA             (1.        ).as(Real                ) ] :Optional  :Sigma[A]: Restriction Area: sigma [A]
+    [-nearP              NearP               (1.        ).as(Real                ) ] :Optional  :Near [pixel]: Restriction Area: near x delta [A]
+    [-nearPA             NearPA              (1.        ).as(Real                ) ] :Optional  :Near [A]: Restriction Area: near [A]
+    [-R[estrict]PW                                                                 ] :Optional  :WithInfo: filename near[A] sigma[A]
+    [-delta              deltax              (5         ).as(Real                ) 
+                         deltay              (5         ).as(Real                ) 
+                         deltaz              (5         ).as(Real                ) ] :Optional  :delta [A]
+    [-sdelta             sdeltax             (5         ).as(Real                ) 
+                         sdeltay             (5         ).as(Real                ) 
+                         sdeltaz             (5         ).as(Real                ) ] :Optional  :starting delta [A]
+    [-start              startx              (5         ).as(Real                ) 
+                         starty              (5         ).as(Real                ) 
+                         startz              (5         ).as(Real                ) ] :Optional  :start [A]
+    [-end                endx                (5         ).as(Real                ) 
+                         endy                (5         ).as(Real                ) 
+                         endz                (5         ).as(Real                ) ] :Optional  :end [A]
+    [-maxIter            maxIter             (1         ).as(Integer             ) ] :Optional  :Max Iteration 
+    [-startIter          startIter           (0         ).as(Integer             ) ] :Optional  :Start Iteration 
+    [-neglect            neglect             (1e-4      ).as(Real                ) ] :Optional  :neglect: probability for each term: not final probability
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+----- Point Information : Each ID has no space character. -----
+ID fix     x y z rootB radius(noUse)
+......
+ID unfix   x y z rootB radius
+......
+ID connect ID length rootB
+......
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/energyTransferModelResultCheck.html b/doc/SmallTools/energyTransferModelResultCheck.html
index 9b024ef..f7ed933 100644
--- a/doc/SmallTools/energyTransferModelResultCheck.html
+++ b/doc/SmallTools/energyTransferModelResultCheck.html
@@ -8,13 +8,13 @@
 <PRE>
 Usage: energyTransferModelResultCheck
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: 
-    [-I[nput]            InResHead           (test.out  )] :Essential :Input: Result Filename Header
-    [-I[nput]2           InResTail           (0         )] :Optional  :Input: Iteration Number
-    [-neg[lect]          Neg                 (1e-6      )] :Optional  :Input: Neglect
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (1         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: 
+    [-I[nput]            InResHead           (test.out  ).as(String              ) ] :Essential :Input: Result Filename Header
+    [-I[nput]2           InResTail           (0         ).as(Integer             ) ] :Optional  :Input: Iteration Number
+    [-neg[lect]          Neg                 (1e-6      ).as(Real                ) ] :Optional  :Input: Neglect
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (1         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/eosBayesInit.html b/doc/SmallTools/eosBayesInit.html
new file mode 100644
index 0000000..d371cfb
--- /dev/null
+++ b/doc/SmallTools/eosBayesInit.html
@@ -0,0 +1 @@
+/bin/bash: eosBayesInit: No such file or directory
diff --git a/doc/SmallTools/gmolvie.html b/doc/SmallTools/gmolvie.html
index 4a1fdb4..c80fe00 100644
--- a/doc/SmallTools/gmolvie.html
+++ b/doc/SmallTools/gmolvie.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: gmolvie
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/imagesView.html b/doc/SmallTools/imagesView.html
index 29186a7..378721e 100644
--- a/doc/SmallTools/imagesView.html
+++ b/doc/SmallTools/imagesView.html
@@ -1,19 +1 @@
-<HTML>
-<HEAD>
-<TITLE>imagesView</TITLE>
-</HEAD>
-<BODY>
-<H1>imagesView</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: imagesView
-Options:
-    [-i[nput]            In                  (stdin     )] :Optional  :Input: FileList
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output: FileViewCondition
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-Additional Usage
-This command for viewing images with a suffix
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: imagesView: そのようなファイルやディレクトリはありません
diff --git a/doc/SmallTools/imodst2mrc.html b/doc/SmallTools/imodst2mrc.html
index 2e12630..e3e5d00 100644
--- a/doc/SmallTools/imodst2mrc.html
+++ b/doc/SmallTools/imodst2mrc.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: imodst2mrc
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: Imod Store 
-    [-o[utput]           Out                 (NULL      )] :Optional  :Output: MRC 
-    [-O[utput]           ] :Optional  :Output: MRC LIST
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: Imod Store 
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :Output: MRC 
+    [-O[utput]                                                                     ] :Optional  :Output: MRC LIST
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/ip2mrc.html b/doc/SmallTools/ip2mrc.html
index df96cc2..0d68931 100644
--- a/doc/SmallTools/ip2mrc.html
+++ b/doc/SmallTools/ip2mrc.html
@@ -8,16 +8,16 @@
 <PRE>
 Usage: ip2mrc
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile[.img]
-    [-i2[nput]           InTem               (NULL      )] :Optional  :InputDataFile[.tem]
-    [-i3[nput]           InInf               (NULL      )] :Optional  :InputDataFile[.inf]
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-o2[utput]          Out2                (NULL      )] :Optional  :OutputDataFile[1/4]
-    [-Mag                Mag                 (40000     )] :Optional  :Magnification
-    [-SE                 SE                  (200       )] :Optional  :SE
-    [-OutMode            OutMode             (1         )] :Optional  :OutPutMode
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile[.img]
+    [-i2[nput]           InTem               (NULL      ).as(inFile              ) ] :Optional  :InputDataFile[.tem]
+    [-i3[nput]           InInf               (NULL      ).as(inFile              ) ] :Optional  :InputDataFile[.inf]
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-o2[utput]          Out2                (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile[1/4]
+    [-Mag                Mag                 (40000     ).as(Real                ) ] :Optional  :Magnification
+    [-SE                 SE                  (200       ).as(Real                ) ] :Optional  :SE
+    [-OutMode            OutMode             (1         ).as(Integer             ) ] :Optional  :OutPutMode
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 mode: 0: No Skip
 mode: 1: Skip(128 byte)
diff --git a/doc/SmallTools/largeIPInfo.html b/doc/SmallTools/largeIPInfo.html
index 0bc8bf0..9ddc004 100644
--- a/doc/SmallTools/largeIPInfo.html
+++ b/doc/SmallTools/largeIPInfo.html
@@ -8,13 +8,16 @@
 <PRE>
 Usage: largeIPInfo
 Options:
-    [-i[nput]            In                  ] :Essential :InputDataFile
-    [-o[utput]           Out                 ] :Optional  :OutputDataFile
-    [-start              startx              starty              ] :Optional  :StartCoord
-    [-step               stepx               stepy               ] :Optional  :StepCoord
-    [-size               width               height              ] :Optional  :SizeCoord
-    [-c[onfig]           configFile          ] :Optional  :ConfigurationFile
-    [-m[ode]             mode                ] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-start              startx              (0         ).as(Integer             ) 
+                         starty              (0         ).as(Integer             ) ] :Optional  :StartCoord
+    [-step               stepx               (1         ).as(Integer             ) 
+                         stepy               (1         ).as(Integer             ) ] :Optional  :StepCoord
+    [-size               width               (LARGE_IP_IMAGE_WIDTH).as(Integer             ) 
+                         height              (LARGE_IP_IMAGE_HEIGHT).as(Integer             ) ] :Optional  :SizeCoord
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/ll2ltlg.html b/doc/SmallTools/ll2ltlg.html
index e9c1bc3..ea690d7 100644
--- a/doc/SmallTools/ll2ltlg.html
+++ b/doc/SmallTools/ll2ltlg.html
@@ -8,17 +8,17 @@
 <PRE>
 Usage: ll2ltlg
 Options:
-    [-i[nput]            In                  ] :Essential :InputDataFile
-    [-o[utput]           Out                 ] :Essential :OutputDataFile
-    [-c[onfig]           configFile          ] :Optional  :ConfigurationFile
-    [-t[itle]            Title               ] :Optional  :Title
-    [-l[lMax]            llMax               ] :Optional  :llMax
-    [-D[elRInv]          delRInv             ] :Optional  :delRInv[A]
-    [-R[MaxInv]          RMaxInv             ] :Optional  :RMaxInv[A]
-    [-d[elr]             delr                ] :Optional  :delr[A]
-    [-r[Max]             rMax                ] :Optional  :rMax[A]
-    [-f[lagOutputInfo]   flagOutputInfo      ] :Optional  :flagOutputInfo
-    [-m[ode]             mode                ] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-t[itle]            Title               (NULL      ).as(String              ) ] :Optional  :Title
+    [-l[lMax]            llMax               (1         ).as(Integer             ) ] :Optional  :llMax
+    [-D[elRInv]          delRInv             (1.0       ).as(Real                ) ] :Optional  :delRInv[A]
+    [-R[MaxInv]          RMaxInv             (1.0       ).as(Real                ) ] :Optional  :RMaxInv[A]
+    [-d[elr]             delr                (1.0       ).as(Real                ) ] :Optional  :delr[A]
+    [-r[Max]             rMax                (1.0       ).as(Real                ) ] :Optional  :rMax[A]
+    [-f[lagOutputInfo]   flagOutputInfo      (0         ).as(Integer             ) ] :Optional  :flagOutputInfo
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 >> controlFile Format : replaced by other options which are definitely shown.
 
 Title  [char*80]
diff --git a/doc/SmallTools/llDataAverage.html b/doc/SmallTools/llDataAverage.html
index 9079897..52ba2b6 100644
--- a/doc/SmallTools/llDataAverage.html
+++ b/doc/SmallTools/llDataAverage.html
@@ -8,26 +8,32 @@
 <PRE>
 Usage: llDataAverage
 Options:
-    [-M[odel]            Model               (NULL      )] :Essential :Input: ModelFileName(llData)
-    [-i[nput]            In                  (NULL      )] :Essential :Input: InputDataFile
-    [-l[ayer]            llInfo              (NULL      )] :Essential :Input: Layer Line Information
-    [-A[verage]          Ave                 (NULL      )] :Essential :Output: Averaged File Name
-    [-o[utput]           OutParam            (stdout    )] :Optional  :Output: FittedParameter
-    [-o2[utput]          OutParam2           (NULL      )] :Optional  :Output: FittedParameter(phi, z)
-    [-O[utput]           Out                 (NULL      )] :Optional  :Output: FittedData
-    [-P2[plot]           P2                  (NULL      )] :Optional  :Output: P2PlotData
-    [-t[ruePitch]        truePitch           (1.0       )] :Optional  :True Pitch
-    [-d[eltaR]           dR                  (1.0       )] :Optional  :deltaR
-    [-r[adial]           rmin                (1.0       )rmax                (1.0       )dr                  (1.0       )] :Optional  :Radial[Ratio]
-    [-p[hi]              phimin              (0.0       )phimax              (180.0     )dphi                (5.0       )] :Optional  :Phi [degree]
-    [-z[shift]           zmin                (0.0       )zmax                (60.0      )dz                  (5.0       )] :Optional  :z [A]
-    [-withoutAntiPole    ] :Optional  :Not Allow Antipole
-    [-C[utValue]         CutValue            (1.0       )] :Optional  :CutValue
-    [-pvm                pvm                 (0         )] :Optional  :PVM: 
-    [-pvmList            pvmList             (stdin     )] :Optional  :PVM: HostList
-    [-pvmList            Log                 (stdout    )] :Optional  :PVM: HostList
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-M[odel]            Model               (NULL      ).as(inFile              ) ] :Essential :Input: ModelFileName(llData)
+    [-i[nput]            In                  (NULL      ).as(inFileList          ) ] :Essential :Input: InputDataFile
+    [-l[ayer]            llInfo              (NULL      ).as(inFile              ) ] :Essential :Input: Layer Line Information
+    [-A[verage]          Ave                 (NULL      ).as(outFile             ) ] :Essential :Output: Averaged File Name
+    [-o[utput]           OutParam            (stdout    ).as(appendFile          ) ] :Optional  :Output: FittedParameter
+    [-o2[utput]          OutParam2           (NULL      ).as(outFileList         ) ] :Optional  :Output: FittedParameter(phi, z)
+    [-O[utput]           Out                 (NULL      ).as(outFileList         ) ] :Optional  :Output: FittedData
+    [-P2[plot]           P2                  (NULL      ).as(outFile             ) ] :Optional  :Output: P2PlotData
+    [-t[ruePitch]        truePitch           (1.0       ).as(Real                ) ] :Optional  :True Pitch
+    [-d[eltaR]           dR                  (1.0       ).as(Real                ) ] :Optional  :deltaR
+    [-r[adial]           rmin                (1.0       ).as(Real                ) 
+                         rmax                (1.0       ).as(Real                ) 
+                         dr                  (1.0       ).as(Real                ) ] :Optional  :Radial[Ratio]
+    [-p[hi]              phimin              (0.0       ).as(Real                ) 
+                         phimax              (180.0     ).as(Real                ) 
+                         dphi                (5.0       ).as(Real                ) ] :Optional  :Phi [degree]
+    [-z[shift]           zmin                (0.0       ).as(Real                ) 
+                         zmax                (60.0      ).as(Real                ) 
+                         dz                  (5.0       ).as(Real                ) ] :Optional  :z [A]
+    [-withoutAntiPole                                                              ] :Optional  :Not Allow Antipole
+    [-C[utValue]         CutValue            (1.0       ).as(Real                ) ] :Optional  :CutValue
+    [-pvm                pvm                 (0         ).as(Integer             ) ] :Optional  :PVM: 
+    [-pvmList            pvmList             (stdin     ).as(inFile              ) ] :Optional  :PVM: HostList
+    [-pvmList            Log                 (stdout    ).as(appendFile          ) ] :Optional  :PVM: HostList
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/llDataAxisSearch.html b/doc/SmallTools/llDataAxisSearch.html
index 95b12ff..99794ea 100644
--- a/doc/SmallTools/llDataAxisSearch.html
+++ b/doc/SmallTools/llDataAxisSearch.html
@@ -8,20 +8,24 @@
 <PRE>
 Usage: llDataAxisSearch
 Options:
-    [-i1[nput]           In1                 (NULL      )] :Optional  :In: NearSide
-    [-i2[nput]           In2                 (NULL      )] :Optional  :In: FarSide
-    [-o1[utput]          Out1                (NULL      )] :Optional  :Out: NearSide
-    [-o2[utput]          Out2                (NULL      )] :Optional  :Out: FarSide
-    [-a[verage]          Avg                 (NULL      )] :Optional  :Out: Average
-    [-o[utput]           Out                 (NULL      )] :Optional  :Out: FitParam
-    [-op2[utput]         OutP2               (NULL      )] :Optional  :OutParam2: FitParam Distribution [mrcImage]
-    [-t[ruePitch]        truePitch           (0.0       )] :Optional  :TruePitch[A]
-    [-l[ayer]            L                   (NULL      )] :Optional  :LayerInfo
-    [-O[mega]            Omin                (0.0       )Omax                (0.0       )Odelta              (1.0       )] :Optional  :Omega[degree]
-    [-x[shift]           xmin                (-10.0     )xmax                (10.0      )xdelta              (0.1       )] :Optional  :shiftx[A]
-    [-R                  R                   (10.0      )] :Optional  :Resolution[A]
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-i1[nput]           In1                 (NULL      ).as(inFile              ) ] :Optional  :In: NearSide
+    [-i2[nput]           In2                 (NULL      ).as(inFile              ) ] :Optional  :In: FarSide
+    [-o1[utput]          Out1                (NULL      ).as(outFile             ) ] :Optional  :Out: NearSide
+    [-o2[utput]          Out2                (NULL      ).as(outFile             ) ] :Optional  :Out: FarSide
+    [-a[verage]          Avg                 (NULL      ).as(outFile             ) ] :Optional  :Out: Average
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :Out: FitParam
+    [-op2[utput]         OutP2               (NULL      ).as(outFile             ) ] :Optional  :OutParam2: FitParam Distribution [mrcImage]
+    [-t[ruePitch]        truePitch           (0.0       ).as(Real                ) ] :Optional  :TruePitch[A]
+    [-l[ayer]            L                   (NULL      ).as(inFile              ) ] :Optional  :LayerInfo
+    [-O[mega]            Omin                (0.0       ).as(Real                ) 
+                         Omax                (0.0       ).as(Real                ) 
+                         Odelta              (1.0       ).as(Real                ) ] :Optional  :Omega[degree]
+    [-x[shift]           xmin                (-10.0     ).as(Real                ) 
+                         xmax                (10.0      ).as(Real                ) 
+                         xdelta              (0.1       ).as(Real                ) ] :Optional  :shiftx[A]
+    [-R                  R                   (10.0      ).as(Real                ) ] :Optional  :Resolution[A]
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
 ----- Layer Line Information File ----- 
 L N Weight
 ..........
diff --git a/doc/SmallTools/llDataCTFCompensate.html b/doc/SmallTools/llDataCTFCompensate.html
index a09aae2..b8e367c 100644
--- a/doc/SmallTools/llDataCTFCompensate.html
+++ b/doc/SmallTools/llDataCTFCompensate.html
@@ -8,13 +8,13 @@
 <PRE>
 Usage: llDataCTFCompensate
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-I[nput]            In1                 (NULL      )] :Optional  :InputCTFInformation
-    [-I2[nput]           In2                 (NULL      )] :Optional  :InputCTFInformation2
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-t[ruePitch]        truePitch           (430.0     )] :Essential :truePitch[A]
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-I[nput]            In1                 (NULL      ).as(inFile              ) ] :Optional  :InputCTFInformation
+    [-I2[nput]           In2                 (NULL      ).as(inFile              ) ] :Optional  :InputCTFInformation2
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-t[ruePitch]        truePitch           (430.0     ).as(Real                ) ] :Essential :truePitch[A]
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
 ----- CTFInformation file 1 -----
 RR0 F0 PHI0   : If R.lt.RR0, F0=0; If RR0.le.R.lt.RR1, Linear Interpolation F0, F1
 RR1 F1 PHI1   : If RR1.le.R <RR2,
diff --git a/doc/SmallTools/llDataCompare.html b/doc/SmallTools/llDataCompare.html
index dfb3e32..e32b4e8 100644
--- a/doc/SmallTools/llDataCompare.html
+++ b/doc/SmallTools/llDataCompare.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: llDataCompare
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFileList
-    [-r[eference]        Ref                 (NULL      )] :Essential :InputReferenceDataFile
-    [-o[utput]           Out                 (NULL      )] :Optional  :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFileList          ) ] :Essential :InputDataFileList
+    [-r[eference]        Ref                 (NULL      ).as(inFile              ) ] :Essential :InputReferenceDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 Mode
 0: Integral
diff --git a/doc/SmallTools/llDataContributionCalcDifferentN.html b/doc/SmallTools/llDataContributionCalcDifferentN.html
index d8f4066..ba26ea2 100644
--- a/doc/SmallTools/llDataContributionCalcDifferentN.html
+++ b/doc/SmallTools/llDataContributionCalcDifferentN.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: llDataContributionCalcDifferentN
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/llDataDump.html b/doc/SmallTools/llDataDump.html
index 838c859..3118183 100644
--- a/doc/SmallTools/llDataDump.html
+++ b/doc/SmallTools/llDataDump.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: llDataDump
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-R[max]             RMax                (0.1       )] :Optional  :[/A]
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-R[max]             RMax                (0.1       ).as(Real                ) ] :Optional  :[/A]
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/llDataEquatorAdd.html b/doc/SmallTools/llDataEquatorAdd.html
index c694697..7e6ff63 100644
--- a/doc/SmallTools/llDataEquatorAdd.html
+++ b/doc/SmallTools/llDataEquatorAdd.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: llDataEquatorAdd
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/llDataExtract.html b/doc/SmallTools/llDataExtract.html
index d775553..d68e0ca 100644
--- a/doc/SmallTools/llDataExtract.html
+++ b/doc/SmallTools/llDataExtract.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: llDataExtract
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-n                  n                   (0         )] :Optional  :n
-    [-l                  l                   (0         )] :Optional  :l
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-n                  n                   (0         ).as(Real                ) ] :Optional  :n
+    [-l                  l                   (0         ).as(Real                ) ] :Optional  :l
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 input n and l 
 </PRE>
diff --git a/doc/SmallTools/llDataFit.html b/doc/SmallTools/llDataFit.html
index ca95163..d00342e 100644
--- a/doc/SmallTools/llDataFit.html
+++ b/doc/SmallTools/llDataFit.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: llDataFit
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/llDataInfo.html b/doc/SmallTools/llDataInfo.html
index 33d78cf..71b7874 100644
--- a/doc/SmallTools/llDataInfo.html
+++ b/doc/SmallTools/llDataInfo.html
@@ -8,12 +8,13 @@
 <PRE>
 Usage: llDataInfo
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-l[ayer]            layer               (0         )] :Optional  :LayerNumber
-    [-L[ayer]            NN                  (0         )LL                  (0         )] :Optional  :LayerInfo
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-l[ayer]            layer               (0         ).as(Integer             ) ] :Optional  :LayerNumber
+    [-L[ayer]            NN                  (0         ).as(Integer             ) 
+                         LL                  (0         ).as(Integer             ) ] :Optional  :LayerInfo
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
 ----- mode -----
 1	: Total Layer Line Infomation
 2	: Information of Each Layer Line
diff --git a/doc/SmallTools/llDataLowPassFiltering.html b/doc/SmallTools/llDataLowPassFiltering.html
index fb88d8a..8f6ed09 100644
--- a/doc/SmallTools/llDataLowPassFiltering.html
+++ b/doc/SmallTools/llDataLowPassFiltering.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: llDataLowPassFiltering
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-t[ruePitch]        truePitch           (760       )] :Essential :[A]
-    [-R[max]             RMax                (0.1       )] :Optional  :[/A]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-t[ruePitch]        truePitch           (760       ).as(Real                ) ] :Essential :[A]
+    [-R[max]             RMax                (0.1       ).as(Real                ) ] :Optional  :[/A]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 -m 0: SameMemorySize data
 -m 1: SavedMemorySize data
diff --git a/doc/SmallTools/llDataMultiCTFCompensation.html b/doc/SmallTools/llDataMultiCTFCompensation.html
index 68bd2a9..03ec028 100644
--- a/doc/SmallTools/llDataMultiCTFCompensation.html
+++ b/doc/SmallTools/llDataMultiCTFCompensation.html
@@ -8,24 +8,30 @@
 <PRE>
 Usage: llDataMultiCTFCompensation
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: FileList
-    [-M[odel]            Ref                 (NULL      )] :Essential :Input: Model Data
-    [-l[ayerLine]        llInfo              (NULL      )] :Essential :Input: Layer Line Information
-    [-A[verageFile]      Ave                 (NULL      )] :Essential :Output: AverageFile
-    [-o[utput]           OutParam            (NULL      )] :Optional  :Output: FittedParameter
-    [-O[utput]           Out                 (NULL      )] :Optional  :Output: FileList:  PhaseShift of Each Filament
-    [-o2[utput]          OutParam2           (NULL      )] :Optional  :Output: [phi, z] map
-    [-P2[output]         OutParamP2          (NULL      )] :Optional  :Output: For P-P' 
-    [-N[oise]            Noise               (0.0       )] :Optional  :Noise Ratio
-    [-t[ruePitch]        truePitch           (761.4     )] :Essential :truePitch[A]
-    [-d[eltaR]           deltaR              (1.0       )] :Optional  :deltaR[A]
-    [-r[adial]           rmin                (1.0       )rmax                (1.0       )dr                  (1.0       )] :Optional  :Radial[Ratio]
-    [-p[hi]              phimin              (0.0       )phimax              (180.0     )dphi                (1.0       )] :Optional  :Phi [degree]
-    [-z[shift]           zmin                (0.0       )zmax                (180.0     )dz                  (1.0       )] :Optional  :z [A]
-    [-Rmax               Rmax                (0.1       )] :Optional  :Rmax [/A]
-    [-MaxIter[ation]     MaxIter             (1         )] :Optional  :MaxIteration
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFileList          ) ] :Essential :Input: FileList
+    [-M[odel]            Ref                 (NULL      ).as(inFile              ) ] :Essential :Input: Model Data
+    [-l[ayerLine]        llInfo              (NULL      ).as(inFile              ) ] :Essential :Input: Layer Line Information
+    [-A[verageFile]      Ave                 (NULL      ).as(outFile             ) ] :Essential :Output: AverageFile
+    [-o[utput]           OutParam            (NULL      ).as(appendFile          ) ] :Optional  :Output: FittedParameter
+    [-O[utput]           Out                 (NULL      ).as(outFileList         ) ] :Optional  :Output: FileList:  PhaseShift of Each Filament
+    [-o2[utput]          OutParam2           (NULL      ).as(outFileList         ) ] :Optional  :Output: [phi, z] map
+    [-P2[output]         OutParamP2          (NULL      ).as(outFile             ) ] :Optional  :Output: For P-P' 
+    [-N[oise]            Noise               (0.0       ).as(Real                ) ] :Optional  :Noise Ratio
+    [-t[ruePitch]        truePitch           (761.4     ).as(Real                ) ] :Essential :truePitch[A]
+    [-d[eltaR]           deltaR              (1.0       ).as(Real                ) ] :Optional  :deltaR[A]
+    [-r[adial]           rmin                (1.0       ).as(Real                ) 
+                         rmax                (1.0       ).as(Real                ) 
+                         dr                  (1.0       ).as(Real                ) ] :Optional  :Radial[Ratio]
+    [-p[hi]              phimin              (0.0       ).as(Real                ) 
+                         phimax              (180.0     ).as(Real                ) 
+                         dphi                (1.0       ).as(Real                ) ] :Optional  :Phi [degree]
+    [-z[shift]           zmin                (0.0       ).as(Real                ) 
+                         zmax                (180.0     ).as(Real                ) 
+                         dz                  (1.0       ).as(Real                ) ] :Optional  :z [A]
+    [-Rmax               Rmax                (0.1       ).as(Real                ) ] :Optional  :Rmax [/A]
+    [-MaxIter[ation]     MaxIter             (1         ).as(Integer             ) ] :Optional  :MaxIteration
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ---- InputFileFormat ----
 filename weight(NumberOfAveragedFile) deltaF[A] Cs[mm] kV[kV] ratioOfAmpToPhase
 ----- Mode -----
diff --git a/doc/SmallTools/llDataNEstimation.html b/doc/SmallTools/llDataNEstimation.html
index 337e867..d4b3724 100644
--- a/doc/SmallTools/llDataNEstimation.html
+++ b/doc/SmallTools/llDataNEstimation.html
@@ -8,13 +8,13 @@
 <PRE>
 Usage: llDataNEstimation
 Options:
-    [-r[peak]            r                   (220       )] :Essential :Input: rpeak [A]
-    [-R[peak]            R                   (24        )] :Essential :Input: Rpeak [pixel]
-    [-xstep              xstep               (7         )] :Essential :Input: xstep [A]
-    [-W[idth]            Width               (500       )] :Essential :Input: Width [pixel]
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-r[peak]            r                   (220       ).as(Real                ) ] :Essential :Input: rpeak [A]
+    [-R[peak]            R                   (24        ).as(Real                ) ] :Essential :Input: Rpeak [pixel]
+    [-xstep              xstep               (7         ).as(Real                ) ] :Essential :Input: xstep [A]
+    [-W[idth]            Width               (500       ).as(Real                ) ] :Essential :Input: Width [pixel]
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/llDataNormalization.html b/doc/SmallTools/llDataNormalization.html
index ec68433..f0fc8b6 100644
--- a/doc/SmallTools/llDataNormalization.html
+++ b/doc/SmallTools/llDataNormalization.html
@@ -8,13 +8,13 @@
 <PRE>
 Usage: llDataNormalization
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :llData:InputDataFile
-    [-r[eference]        Ref                 (NULL      )] :Essential :llData:Reference
-    [-o[utput]           Out                 (NULL      )] :Optional  :llData(Normalized In):OutputDataFile
-    [-dif[ffence]        Dif                 (NULL      )] :Optional  :llData(Difference):OutputDataFile
-    [-O[utput]           OutParam            (stdout    )] :Optional  :FittedParameter
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :llData:InputDataFile
+    [-r[eference]        Ref                 (NULL      ).as(inFile              ) ] :Essential :llData:Reference
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :llData(Normalized In):OutputDataFile
+    [-dif[ffence]        Dif                 (NULL      ).as(outFile             ) ] :Optional  :llData(Difference):OutputDataFile
+    [-O[utput]           OutParam            (stdout    ).as(outFile             ) ] :Optional  :FittedParameter
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/llDataPrint.html b/doc/SmallTools/llDataPrint.html
index 20d97af..881d1b2 100644
--- a/doc/SmallTools/llDataPrint.html
+++ b/doc/SmallTools/llDataPrint.html
@@ -1,21 +1 @@
-<HTML>
-<HEAD>
-<TITLE>llDataPrint</TITLE>
-</HEAD>
-<BODY>
-<H1>llDataPrint</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: llDataPrint
-Options:
-    [-i[nput]            In                  (NULL      )] :Optional  :InputDataFile
-    [-i[nput]s           Ins                 (NULL      )] :Optional  :InputDataFileList
-    [-i2[nput]           Nea                 (NULL      )Far                 (NULL      )] :Optional  :InputDataFile(nea and far)
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-Rmax               Rmax                (0.1       )] :Optional  :Input: Rmax [/A]
-    [-I[nteractive]      ] :Optional  :Interactive
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: llDataPrint: そのようなファイルやディレクトリはありません
diff --git a/doc/SmallTools/llDataRescaling.html b/doc/SmallTools/llDataRescaling.html
index f6a3565..fdd5752 100644
--- a/doc/SmallTools/llDataRescaling.html
+++ b/doc/SmallTools/llDataRescaling.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: llDataRescaling
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-r[Scale]           rScale              (1.0       )] :Optional  :[]
-    [-dR                 delBR               (0.0 /* No Change */)] :Optional  :[/A]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-r[Scale]           rScale              (1.0       ).as(Real                ) ] :Optional  :[]
+    [-dR                 delBR               (0.0 /* No Change */).as(Real                ) ] :Optional  :[/A]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/llDataResolutionCheck.html b/doc/SmallTools/llDataResolutionCheck.html
index fbe4674..1fb45ce 100644
--- a/doc/SmallTools/llDataResolutionCheck.html
+++ b/doc/SmallTools/llDataResolutionCheck.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: llDataResolutionCheck
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFileList          ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/llDataSelectionEstimation.html b/doc/SmallTools/llDataSelectionEstimation.html
index 704f0b2..daa71d6 100644
--- a/doc/SmallTools/llDataSelectionEstimation.html
+++ b/doc/SmallTools/llDataSelectionEstimation.html
@@ -8,14 +8,16 @@
 <PRE>
 Usage: llDataSelectionEstimation
 Options:
-    [-i1[nput]           N1                  (0         )L1                  (161       )] :Essential :Input: N L
-    [-i2[nput]           N2                  (14        )L2                  (12        )] :Essential :Input: N L
-    [-tmax               tmax                (100       )] :Optional  :Input: tmax
-    [-umax               umax                (200       )] :Optional  :Input: umax
-    [-r[accept]          r                   (0.1       )] :Optional  :Input: acceptable residue
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i1[nput]           N1                  (0         ).as(Real                ) 
+                         L1                  (161       ).as(Real                ) ] :Essential :Input: N L
+    [-i2[nput]           N2                  (14        ).as(Real                ) 
+                         L2                  (12        ).as(Real                ) ] :Essential :Input: N L
+    [-tmax               tmax                (100       ).as(Real                ) ] :Optional  :Input: tmax
+    [-umax               umax                (200       ).as(Real                ) ] :Optional  :Input: umax
+    [-r[accept]          r                   (0.1       ).as(Real                ) ] :Optional  :Input: acceptable residue
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/llDataWeightSet.html b/doc/SmallTools/llDataWeightSet.html
index b0a3c85..c04e96d 100644
--- a/doc/SmallTools/llDataWeightSet.html
+++ b/doc/SmallTools/llDataWeightSet.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: llDataWeightSet
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-l[ayerInfo]        llInfo              (NULL      )] :Optional  :LayerInfomationFile
-    [-w[eight]           weight              (1.0       )] :Optional  :DefaultWeight
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-l[ayerInfo]        llInfo              (NULL      ).as(inFile              ) ] :Optional  :LayerInfomationFile
+    [-w[eight]           weight              (1.0       ).as(Real                ) ] :Optional  :DefaultWeight
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/llDatarMaxLimit.html b/doc/SmallTools/llDatarMaxLimit.html
index c09ffd8..a748c21 100644
--- a/doc/SmallTools/llDatarMaxLimit.html
+++ b/doc/SmallTools/llDatarMaxLimit.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: llDatarMaxLimit
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-r[Max]             rMax                (100.0     )] :Optional  :rMax[A]
-    [-rMin[Max]          rMaxMin             (100.0     )] :Optional  :rMaxMin[A]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-r[Max]             rMax                (100.0     ).as(Real                ) ] :Optional  :rMax[A]
+    [-rMin[Max]          rMaxMin             (100.0     ).as(Real                ) ] :Optional  :rMaxMin[A]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 
 
 ----- rMax Limit Algorithm----- 
diff --git a/doc/SmallTools/llExtractCtfinfFileCreate.html b/doc/SmallTools/llExtractCtfinfFileCreate.html
index d7cfd06..6e1d55e 100644
--- a/doc/SmallTools/llExtractCtfinfFileCreate.html
+++ b/doc/SmallTools/llExtractCtfinfFileCreate.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: llExtractCtfinfFileCreate
 Options:
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-FirstZero          FirstZero           (0.02      )] :Optional  :FirstZeroPoint[1/A]
-    [-df                 Defocus             (27000     )] :Optional  :Defocus[A]:under(+)
-    [-A                  AoverP              (0.05      )] :Optional  :AmplitudeContrast/PhaseContrast
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-FirstZero          FirstZero           (0.02      ).as(Real                ) ] :Optional  :FirstZeroPoint[1/A]
+    [-df                 Defocus             (27000     ).as(Real                ) ] :Optional  :Defocus[A]:under(+)
+    [-A                  AoverP              (0.05      ).as(Real                ) ] :Optional  :AmplitudeContrast/PhaseContrast
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 ----- mode -----
 0: make CTFInformation file 1
diff --git a/doc/SmallTools/llExtractCtrlFileCreate.html b/doc/SmallTools/llExtractCtrlFileCreate.html
index 750d20d..ce0f6f0 100644
--- a/doc/SmallTools/llExtractCtrlFileCreate.html
+++ b/doc/SmallTools/llExtractCtrlFileCreate.html
@@ -8,28 +8,28 @@
 <PRE>
 Usage: llExtractCtrlFileCreate
 Options:
-    [-i[nput]            In                  (NULL      )] :Optional  :InputDataFile
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-t                  turn                (-6        )] :Optional  :Turn
-    [-u                  unit                (13        )] :Optional  :Unit
-    [-N                  nstrand             (1         )] :Optional  :N-strand
-    [-Y1                 Y1                  (36        )] :Optional  :Y1 [pixel]: The Position of LayerLine which l = |t| i.e., |n|=1&&m=0 for the first time
-    [-Y0                 Y0                  (78        )] :Optional  :Y0 [pixel]: The Position of LayerLine which n = 0 , l != 0 for the first time
-    [-rmax               rmax                (250       )] :Optional  :rmax[A]
-    [-Rmax               Rmax                (0.1       )] :Optional  :Rmax[/A]
-    [-lx                 lx                  (5.0       )] :Optional  :Pixel Size
-    [-ly                 ly                  (5.0       )] :Optional  :Pixel Size
-    [-nx                 nx                  (1000.0    )] :Optional  :Image Size[Pixel]
-    [-ny                 ny                  (1000.0    )] :Optional  :Image Size[Pixel]
-    [-center             center              (500.0     )] :Optional  :Center of nx (center of filament)[Pixel]
-    [-layerline          layerline           (21.0      )] :Optional  :Number of Layer Line
-    [-Ax                 Ax                  (5000.0    )] :Optional  :Length of nx (lx * nx)[A]
-    [-dY                 dY                  (12.0      )] :Optional  :Range of Layer Line[pixel]
-    [-truePitch          truePitch           (430       )] :Optional  :True Pitch
-    [-PixelSize          PixelSize           (5         )] :Optional  :Pixel Size [A]
-    [-deltadY            deltadY             (0.5       )] :Optional  :A range of deltadY to determine dY.[pixel]
-    [-m[ode]             mode                (1         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Optional  :InputDataFile
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-t                  turn                (-6        ).as(Integer             ) ] :Optional  :Turn
+    [-u                  unit                (13        ).as(Integer             ) ] :Optional  :Unit
+    [-N                  nstrand             (1         ).as(Integer             ) ] :Optional  :N-strand
+    [-Y1                 Y1                  (36        ).as(Integer             ) ] :Optional  :Y1 [pixel]: The Position of LayerLine which l = |t| i.e., |n|=1&&m=0 for the first time
+    [-Y0                 Y0                  (78        ).as(Integer             ) ] :Optional  :Y0 [pixel]: The Position of LayerLine which n = 0 , l != 0 for the first time
+    [-rmax               rmax                (250       ).as(Real                ) ] :Optional  :rmax[A]
+    [-Rmax               Rmax                (0.1       ).as(Real                ) ] :Optional  :Rmax[/A]
+    [-lx                 lx                  (5.0       ).as(Real                ) ] :Optional  :Pixel Size
+    [-ly                 ly                  (5.0       ).as(Real                ) ] :Optional  :Pixel Size
+    [-nx                 nx                  (1000.0    ).as(Real                ) ] :Optional  :Image Size[Pixel]
+    [-ny                 ny                  (1000.0    ).as(Real                ) ] :Optional  :Image Size[Pixel]
+    [-center             center              (500.0     ).as(Real                ) ] :Optional  :Center of nx (center of filament)[Pixel]
+    [-layerline          layerline           (21.0      ).as(Real                ) ] :Optional  :Number of Layer Line
+    [-Ax                 Ax                  (5000.0    ).as(Real                ) ] :Optional  :Length of nx (lx * nx)[A]
+    [-dY                 dY                  (12.0      ).as(Real                ) ] :Optional  :Range of Layer Line[pixel]
+    [-truePitch          truePitch           (430       ).as(Real                ) ] :Optional  :True Pitch
+    [-PixelSize          PixelSize           (5         ).as(Real                ) ] :Optional  :Pixel Size [A]
+    [-deltadY            deltadY             (0.5       ).as(Real                ) ] :Optional  :A range of deltadY to determine dY.[pixel]
+    [-m[ode]             mode                (1         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 ----- mode -----
     0: for myosin  t=1 u=9
diff --git a/doc/SmallTools/llExtractWithLayerSeparation.html b/doc/SmallTools/llExtractWithLayerSeparation.html
index e05a325..562eb27 100644
--- a/doc/SmallTools/llExtractWithLayerSeparation.html
+++ b/doc/SmallTools/llExtractWithLayerSeparation.html
@@ -8,67 +8,74 @@
 <PRE>
 Usage: llExtractWithLayerSeparation
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile(mrcImage:Fourier Space)
-    [-I[nput]            InLLNea             (NULL      )InLLFar             (NULL      )] :Optional  :InputDataFile(llData:Already separated)
-    [-r[ef]              Ref                 (NULL      )] :Optional  :ReferenceData(llData:Gnl(R) Space)
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile(llData: Average File)
-    [-o2[utput]          Out2                (NULL      )] :Optional  :OutputDataFileList(llData: Each Filament which has the same orientation as average)
-    [-o3[utput]          Out3                (NULL      )] :Optional  :OutputDataFileList(llData: Difference of each filament)
-    [-o4[utput]          Out4                (NULL      )] :Optional  :OutputDataFileList(llData: Each Filament which has the same orientaion as original filament)
-    [-o5[utput]          Out5                (NULL      )] :Optional  :OutputDataFileList(mrcImage: P-Value)
-    [-o6[utput]          Out6                (NULL      )] :Optional  :OutputDataFileList(mrcImage: Q-Value)
-    [-o7[utput]          Out7                (NULL      )] :Optional  :OutputDataFile(Text: Two subsets for resolution estimation)
-    [-o8[utput]          Out8                (NULL      )] :Optional  :OutputDataFile(Text: For Back Projection)
-    [-o9[utput]          Out9                (NULL      )] :Optional  :OutputDataFileList(Text: x shift, z shift and dY information)
-    [-comment            InComment           (NULL      )] :Optional  :Comment
-    [-symmetry           symmetry            (1.0       )] :Optional  :Symmetry for back projection text file
-    [-l[ayerInfo]        llInfo              (NULL      )] :Essential :LayerLineInformation
-    [-l[ayerInfo]final   llInfoFinal         (NULL      )] :Optional  :LayerLineInformation(Final)
-    [-li[ayerInfo]       llInfoImp           (NULL      )] :Optional  :LayerLineInformationImportant
-    [-liw[ayerInfo]      liWeight            (1.0       )] :Optional  :Weight of Important Layer
-    [-liwStart[ayerInfo] liWeightStart       (1.0       )] :Optional  :Weight of Important Layer
-    [-liwStep[ayerInfo]  liWeightStep        (1.0       )] :Optional  :Weight of Important Layer
-    [-la[ayerInfo]       llInfoAxis          (NULL      )] :Optional  :LayerLineInformationForAxisSearch
-    [-law[ayerInfo]      laWeight            (1.0       )] :Optional  :Weight of Important Layer for AS
-    [-lawStart[ayerInfo] laWeightStart       (1.0       )] :Optional  :Weight of Important Layer for AS
-    [-lawStep[ayerInfo]  laWeightStep        (1.0       )] :Optional  :Weight of Important Layer for AS
-    [-truePitch          truePitch           (430.0     )] :Essential :true pitch [A]
-    [-rMax               rMax                (100.0     )] :Essential :rMax [A]
-    [-rMaxMin            rMaxMin             (100.0     )] :Optional  :rMaxMin [A]
-    [-RMax               RMax                (0.1       )] :Optional  :RMax [/A]
-    [-RMaxFirst          RMaxFirst           (0.04      )] :Optional  :RMaxFirst [/A]: Def: RMax
-    [-RMaxStep           RMaxStep            (0.02      )] :Optional  :RMaxStep [/A]
-    [-RRMax              RRMax               (0.1       )] :Optional  :Radial RMax [/A]
-    [-RRMaxFirst         RRMaxFirst          (0.04      )] :Optional  :Radial RMaxFirst [/A]: Def: RMax
-    [-RRMaxStep          RRMaxStep           (0.02      )] :Optional  :Radial RMaxStep [/A]
-    [-delBR              delBR               (0.0002    )] :Optional  :delBR [/A]
-    [-rms                rms                 (1e-6      )] :Optional  :rms:
-    [-narrowSearch       narrowSearch        (1.0       )] :Optional  :narrowSearch[Degree]: P-Value and Q-Value
-    [-nextTimes          nextTimes           (1e-4      )] :Optional  :nextTimes: rms
-    [-maxIter[ation]     MaxIteration        (10        )] :Optional  :max iteration:
-    [-maxIter2[ation]    MaxIter2            (1         )] :Optional  :max iteration on the same RMax and RRMax:
-    [-maxIter3[ation]    MaxIter3            (1         )] :Optional  :max iteration on the same RMax, RRMax, and Weight:
-    [-lambda             lambda              (1.0       )] :Optional  :labda:
-    [-ctf                CTF                 (0         )] :Optional  :CTF Compensation
-    [-WhiteNoise         WhiteNoise          (0.0       )] :Optional  :White Noise
-    [-below              below               (90.0      )] :Optional  :below
-    [-noantipole         ] :Optional  :No Antipole
-    [-magLimit           ] :Optional  :magLimit
-    [-eachTime           ] :Optional  :each time
-    [-continue           Continue            (NULL      )] :Optional  :continue
-    [-forContinue        ForContinue         (NULL      )] :Optional  :For continue
-    [-phi                phimin              (0.0       )phimax              (360.0     )delphi              (10.0      )] :Optional  :phi:[degree]
-    [-z                  zmin                (0.0       )zmax                (30.0      )delz                (5.0       )] :Optional  :z:[A]
-    [-shift              shiftmin            (-10.0     )shiftmax            (10.0      )delshift            (1.0       )] :Optional  :shift:[A]
-    [-log                Log                 (stdout    )] :Optional  :LogFile
-    [-Normalization      ] :Optional  :Normalization
-    [-pvm                pvm                 (0         )] :Optional  :pvmNumber
-    [-pvmList            pvmList             (NULL      )] :Optional  :pvmList
-    [-pvmServer          ] :Optional  :Work as a server !!
-    [-pvmClient          ] :Optional  :Work as a client !!
-    [-wd                 WorkingDir          (./        )] :Optional  :Working Directory !!
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFileListNoOpen    ) ] :Essential :InputDataFile(mrcImage:Fourier Space)
+    [-I[nput]            InLLNea             (NULL      ).as(inFileListNoOpen    ) 
+                         InLLFar             (NULL      ).as(inFileListNoOpen    ) ] :Optional  :InputDataFile(llData:Already separated)
+    [-r[ef]              Ref                 (NULL      ).as(inFile              ) ] :Optional  :ReferenceData(llData:Gnl(R) Space)
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile(llData: Average File)
+    [-o2[utput]          Out2                (NULL      ).as(outFileListNoOpen   ) ] :Optional  :OutputDataFileList(llData: Each Filament which has the same orientation as average)
+    [-o3[utput]          Out3                (NULL      ).as(outFileListNoOpen   ) ] :Optional  :OutputDataFileList(llData: Difference of each filament)
+    [-o4[utput]          Out4                (NULL      ).as(outFileListNoOpen   ) ] :Optional  :OutputDataFileList(llData: Each Filament which has the same orientaion as original filament)
+    [-o5[utput]          Out5                (NULL      ).as(outFileListNoOpen   ) ] :Optional  :OutputDataFileList(mrcImage: P-Value)
+    [-o6[utput]          Out6                (NULL      ).as(outFileListNoOpen   ) ] :Optional  :OutputDataFileList(mrcImage: Q-Value)
+    [-o7[utput]          Out7                (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile(Text: Two subsets for resolution estimation)
+    [-o8[utput]          Out8                (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile(Text: For Back Projection)
+    [-o9[utput]          Out9                (NULL      ).as(outFileListNoOpen   ) ] :Optional  :OutputDataFileList(Text: x shift, z shift and dY information)
+    [-comment            InComment           (NULL      ).as(String              ) ] :Optional  :Comment
+    [-symmetry           symmetry            (1.0       ).as(Real                ) ] :Optional  :Symmetry for back projection text file
+    [-l[ayerInfo]        llInfo              (NULL      ).as(inFileListNoOpen    ) ] :Essential :LayerLineInformation
+    [-l[ayerInfo]final   llInfoFinal         (NULL      ).as(inFile              ) ] :Optional  :LayerLineInformation(Final)
+    [-li[ayerInfo]       llInfoImp           (NULL      ).as(inFileListNoOpen    ) ] :Optional  :LayerLineInformationImportant
+    [-liw[ayerInfo]      liWeight            (1.0       ).as(Real                ) ] :Optional  :Weight of Important Layer
+    [-liwStart[ayerInfo] liWeightStart       (1.0       ).as(Real                ) ] :Optional  :Weight of Important Layer
+    [-liwStep[ayerInfo]  liWeightStep        (1.0       ).as(Real                ) ] :Optional  :Weight of Important Layer
+    [-la[ayerInfo]       llInfoAxis          (NULL      ).as(inFileListNoOpen    ) ] :Optional  :LayerLineInformationForAxisSearch
+    [-law[ayerInfo]      laWeight            (1.0       ).as(Real                ) ] :Optional  :Weight of Important Layer for AS
+    [-lawStart[ayerInfo] laWeightStart       (1.0       ).as(Real                ) ] :Optional  :Weight of Important Layer for AS
+    [-lawStep[ayerInfo]  laWeightStep        (1.0       ).as(Real                ) ] :Optional  :Weight of Important Layer for AS
+    [-truePitch          truePitch           (430.0     ).as(Real                ) ] :Essential :true pitch [A]
+    [-rMax               rMax                (100.0     ).as(Real                ) ] :Essential :rMax [A]
+    [-rMaxMin            rMaxMin             (100.0     ).as(Real                ) ] :Optional  :rMaxMin [A]
+    [-RMax               RMax                (0.1       ).as(Real                ) ] :Optional  :RMax [/A]
+    [-RMaxFirst          RMaxFirst           (0.04      ).as(Real                ) ] :Optional  :RMaxFirst [/A]: Def: RMax
+    [-RMaxStep           RMaxStep            (0.02      ).as(Real                ) ] :Optional  :RMaxStep [/A]
+    [-RRMax              RRMax               (0.1       ).as(Real                ) ] :Optional  :Radial RMax [/A]
+    [-RRMaxFirst         RRMaxFirst          (0.04      ).as(Real                ) ] :Optional  :Radial RMaxFirst [/A]: Def: RMax
+    [-RRMaxStep          RRMaxStep           (0.02      ).as(Real                ) ] :Optional  :Radial RMaxStep [/A]
+    [-delBR              delBR               (0.0002    ).as(Real                ) ] :Optional  :delBR [/A]
+    [-rms                rms                 (1e-6      ).as(Real                ) ] :Optional  :rms:
+    [-narrowSearch       narrowSearch        (1.0       ).as(Real                ) ] :Optional  :narrowSearch[Degree]: P-Value and Q-Value
+    [-nextTimes          nextTimes           (1e-4      ).as(Real                ) ] :Optional  :nextTimes: rms
+    [-maxIter[ation]     MaxIteration        (10        ).as(Integer             ) ] :Optional  :max iteration:
+    [-maxIter2[ation]    MaxIter2            (1         ).as(Integer             ) ] :Optional  :max iteration on the same RMax and RRMax:
+    [-maxIter3[ation]    MaxIter3            (1         ).as(Integer             ) ] :Optional  :max iteration on the same RMax, RRMax, and Weight:
+    [-lambda             lambda              (1.0       ).as(Real                ) ] :Optional  :labda:
+    [-ctf                CTF                 (0         ).as(Integer             ) ] :Optional  :CTF Compensation
+    [-WhiteNoise         WhiteNoise          (0.0       ).as(Real                ) ] :Optional  :White Noise
+    [-below              below               (90.0      ).as(Real                ) ] :Optional  :below
+    [-noantipole                                                                   ] :Optional  :No Antipole
+    [-magLimit                                                                     ] :Optional  :magLimit
+    [-eachTime                                                                     ] :Optional  :each time
+    [-continue           Continue            (NULL      ).as(inFile              ) ] :Optional  :continue
+    [-forContinue        ForContinue         (NULL      ).as(outFile             ) ] :Optional  :For continue
+    [-phi                phimin              (0.0       ).as(Real                ) 
+                         phimax              (360.0     ).as(Real                ) 
+                         delphi              (10.0      ).as(Real                ) ] :Optional  :phi:[degree]
+    [-z                  zmin                (0.0       ).as(Real                ) 
+                         zmax                (30.0      ).as(Real                ) 
+                         delz                (5.0       ).as(Real                ) ] :Optional  :z:[A]
+    [-shift              shiftmin            (-10.0     ).as(Real                ) 
+                         shiftmax            (10.0      ).as(Real                ) 
+                         delshift            (1.0       ).as(Real                ) ] :Optional  :shift:[A]
+    [-log                Log                 (stdout    ).as(outFile             ) ] :Optional  :LogFile
+    [-Normalization                                                                ] :Optional  :Normalization
+    [-pvm                pvm                 (0         ).as(Integer             ) ] :Optional  :pvmNumber
+    [-pvmList            pvmList             (NULL      ).as(inFile              ) ] :Optional  :pvmList
+    [-pvmServer                                                                    ] :Optional  :Work as a server !!
+    [-pvmClient                                                                    ] :Optional  :Work as a client !!
+    [-wd                 WorkingDir          (./        ).as(String              ) ] :Optional  :Working Directory !!
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 -m 0: The 1st version algorism(Sharing)
 -m 1: The 2nd version algorism(Least Square)
diff --git a/doc/SmallTools/llExtractWithLayerSeparationCtrlFileCreate.html b/doc/SmallTools/llExtractWithLayerSeparationCtrlFileCreate.html
index 5678220..556df22 100644
--- a/doc/SmallTools/llExtractWithLayerSeparationCtrlFileCreate.html
+++ b/doc/SmallTools/llExtractWithLayerSeparationCtrlFileCreate.html
@@ -8,18 +8,18 @@
 <PRE>
 Usage: llExtractWithLayerSeparationCtrlFileCreate
 Options:
-    [-i[nput]            In                  (NULL      )] :Optional  :Input DataFile
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-t[urn]             Turn                (-13       )] :Essential :Tern
-    [-u[nit]             Unit                (28        )] :Essential :Unit
-    [-N[-helix]          nHelix              (1         )] :Optional  :Helix
-    [-dY                 dY                  (3         )] :Optional  :Position of the 1st layer line: [pixel]
-    [-truePitch          truePitch           (770       )] :Essential :truePitch [A]
-    [-rMax               rMax                (50        )] :Essential :rMax [A]
-    [-RMax               RMax                (0.1       )] :Optional  :RMax [/A]
-    [-RZMax              RZMax               (0.1       )] :Optional  :RZMax [/A]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Optional  :Input DataFile
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-t[urn]             Turn                (-13       ).as(Integer             ) ] :Essential :Tern
+    [-u[nit]             Unit                (28        ).as(Integer             ) ] :Essential :Unit
+    [-N[-helix]          nHelix              (1         ).as(Integer             ) ] :Optional  :Helix
+    [-dY                 dY                  (3         ).as(Integer             ) ] :Optional  :Position of the 1st layer line: [pixel]
+    [-truePitch          truePitch           (770       ).as(Integer             ) ] :Essential :truePitch [A]
+    [-rMax               rMax                (50        ).as(Real                ) ] :Essential :rMax [A]
+    [-RMax               RMax                (0.1       ).as(Real                ) ] :Optional  :RMax [/A]
+    [-RZMax              RZMax               (0.1       ).as(Real                ) ] :Optional  :RZMax [/A]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/llExtractWithLayerSeparationCtrlFileCreateMyosin.html b/doc/SmallTools/llExtractWithLayerSeparationCtrlFileCreateMyosin.html
index 4b9fe3d..28d463a 100644
--- a/doc/SmallTools/llExtractWithLayerSeparationCtrlFileCreateMyosin.html
+++ b/doc/SmallTools/llExtractWithLayerSeparationCtrlFileCreateMyosin.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: llExtractWithLayerSeparationCtrlFileCreateMyosin
 Options:
-    [-i[nput]            In                  (NULL      )] :Optional  :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-Y                  Y                   (6         )] :Optional  :Range of Layer Line
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Optional  :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-Y                  Y                   (6         ).as(Real                ) ] :Optional  :Range of Layer Line
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/llExtractWithLayerSeparationFilamentInfo.html b/doc/SmallTools/llExtractWithLayerSeparationFilamentInfo.html
index 76ba868..a539c7a 100644
--- a/doc/SmallTools/llExtractWithLayerSeparationFilamentInfo.html
+++ b/doc/SmallTools/llExtractWithLayerSeparationFilamentInfo.html
@@ -8,19 +8,19 @@
 <PRE>
 Usage: llExtractWithLayerSeparationFilamentInfo
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-o[utput] F[ile]    OutF                (NULL      )] :Optional  :OutputDataFile
-    [-o[utput]I[nformation]OutI                (NULL      )] :Optional  :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-truePitch          truePitch           (430       )] :Optional  :True Pitch
-    [-PixelSize          PixelSize           (5         )] :Optional  :Pixel Size [A]
-    [-deltadY            deltadY             (0.5       )] :Optional  :A range of deltadY to determine dY.
-    [-kV                 kV                  (200       )] :Optional  :AccVol[kV]
-    [-Cs                 Cs                  (2.1       )] :Optional  :Cs[mm]
-    [-df                 Defocus             (27000     )] :Optional  :Defocus[A]:under(+)
-    [-A                  AoverP              (0.1       )] :Optional  :AmplitudeContrast/PhaseContrast
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-o[utput] F[ile]    OutF                (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-o[utput]I[nformation]OutI                (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-truePitch          truePitch           (430       ).as(Real                ) ] :Optional  :True Pitch
+    [-PixelSize          PixelSize           (5         ).as(Real                ) ] :Optional  :Pixel Size [A]
+    [-deltadY            deltadY             (0.5       ).as(Real                ) ] :Optional  :A range of deltadY to determine dY.
+    [-kV                 kV                  (200       ).as(Real                ) ] :Optional  :AccVol[kV]
+    [-Cs                 Cs                  (2.1       ).as(Real                ) ] :Optional  :Cs[mm]
+    [-df                 Defocus             (27000     ).as(Real                ) ] :Optional  :Defocus[A]:under(+)
+    [-A                  AoverP              (0.1       ).as(Real                ) ] :Optional  :AmplitudeContrast/PhaseContrast
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/ltlg2mrc.html b/doc/SmallTools/ltlg2mrc.html
index f8d7138..23986c0 100644
--- a/doc/SmallTools/ltlg2mrc.html
+++ b/doc/SmallTools/ltlg2mrc.html
@@ -8,27 +8,27 @@
 <PRE>
 Usage: ltlg2mrc
 Options:
-    [-i[nput]            In                  (NULL      )] :Optional  :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Optional  :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-t[itle]            Title               (NULL      )] :Optional  :Title
-    [-d[elta]            delta               (2.5       )] :Optional  :delta[A]
-    [-C                  RepeatDistance      (2.5       )] :Optional  :RepeatDistance[A]
-    [-r[Max]             rMax                (2.5       )] :Optional  :rMax[A]
-    [-p[hiStart]         phiStart            (0         )] :Optional  :phiStart[degree]
-    [-zmi[n]             zMin                (0.0       )] :Optional  :zMin
-    [-zma[x]             zMax                (55.0      )] :Optional  :zMax
-    [-zde[lta]           deltaz              (2.5       )] :Optional  :deltaz
-    [-w[eight]           WeightOf0thLayer    (0.5       )] :Optional  :WeightOf0thLayer
-    [-l[Weight]          Layer               (NULL      )] :Optional  :Layer WeightOfEachLayer
-    [-f9[9]              ] :Optional  :IF(NN(LL)!=NL(LL)) WT(LL) = 0.0
-    [-O[ffset]           CUT                 (0.5       )] :Optional  :CUT
-    [-a[mean]            Mean                (0.0       )] :Optional  :Mean
-    [-s[igma]            Sigma               (0.0       )] :Optional  :Sigma
-    [-I[nverse]          ] :Optional  :Nega-Posi Reverse
-    [-n[otInteractive]   ] :Optional  :not Intaracitve
-    [-AntiPole           ] :Optional  :Anti Pole: zmax -> zmin:  Else zmin->zmax
-    [-m[ode]             mode                (0         )] :Optional  :
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Optional  :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-t[itle]            Title               (NULL      ).as(String              ) ] :Optional  :Title
+    [-d[elta]            delta               (2.5       ).as(Real                ) ] :Optional  :delta[A]
+    [-C                  RepeatDistance      (2.5       ).as(Real                ) ] :Optional  :RepeatDistance[A]
+    [-r[Max]             rMax                (2.5       ).as(Real                ) ] :Optional  :rMax[A]
+    [-p[hiStart]         phiStart            (0         ).as(Real                ) ] :Optional  :phiStart[degree]
+    [-zmi[n]             zMin                (0.0       ).as(Real                ) ] :Optional  :zMin
+    [-zma[x]             zMax                (55.0      ).as(Real                ) ] :Optional  :zMax
+    [-zde[lta]           deltaz              (2.5       ).as(Real                ) ] :Optional  :deltaz
+    [-w[eight]           WeightOf0thLayer    (0.5       ).as(Real                ) ] :Optional  :WeightOf0thLayer
+    [-l[Weight]          Layer               (NULL      ).as(inFile              ) ] :Optional  :Layer WeightOfEachLayer
+    [-f9[9]                                                                        ] :Optional  :IF(NN(LL)!=NL(LL)) WT(LL) = 0.0
+    [-O[ffset]           CUT                 (0.5       ).as(Real                ) ] :Optional  :CUT
+    [-a[mean]            Mean                (0.0       ).as(Real                ) ] :Optional  :Mean
+    [-s[igma]            Sigma               (0.0       ).as(Real                ) ] :Optional  :Sigma
+    [-I[nverse]                                                                    ] :Optional  :Nega-Posi Reverse
+    [-n[otInteractive]                                                             ] :Optional  :not Intaracitve
+    [-AntiPole                                                                     ] :Optional  :Anti Pole: zmax -> zmin:  Else zmin->zmax
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :
 				0: Normarize
 				1: Not Normarize bu edge average is zero.
 				2: Not Normarize
diff --git a/doc/SmallTools/ltlgDataInfo.html b/doc/SmallTools/ltlgDataInfo.html
index 38af41c..0baecf4 100644
--- a/doc/SmallTools/ltlgDataInfo.html
+++ b/doc/SmallTools/ltlgDataInfo.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: ltlgDataInfo
 Options:
-    [-i[nput]            In                  ] :Essential :InputDataFile
-    [-o[utput]           Out                 ] :Optional  :OutputDataFile
-    [-c[onfig]           configFile          ] :Optional  :ConfigurationFile
-    [-m[ode]             mode                ] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- mode -----
  1: Header Information
  2: (N, L) Information
diff --git a/doc/SmallTools/marker2Dto3DEstimator.html b/doc/SmallTools/marker2Dto3DEstimator.html
index 6ab13bf..83e4804 100644
--- a/doc/SmallTools/marker2Dto3DEstimator.html
+++ b/doc/SmallTools/marker2Dto3DEstimator.html
@@ -13,6 +13,7 @@ Options:
     [-o[utput]           Out                 (NULL      ).as(outFileList::ASCII  ) ] :Essential :Output: 
     [-o[utput]t[ype]     OutType             (2         ).as(Integer             ) ] :Optional  :Input: 
     [-o[utput]EA         OutEA               (NULL      ).as(outFileList::ASCII  ) ] :Essential :Output: 
+    [-zero               ZeroPlane           (0         ).as(Integer             ) ] :Optional  :Zero Plane
     [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
     [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
diff --git a/doc/SmallTools/matrix3DEulerAngleTransform.html b/doc/SmallTools/matrix3DEulerAngleTransform.html
index 7511c18..aaa6103 100644
--- a/doc/SmallTools/matrix3DEulerAngleTransform.html
+++ b/doc/SmallTools/matrix3DEulerAngleTransform.html
@@ -8,12 +8,15 @@
 <PRE>
 Usage: matrix3DEulerAngleTransform
 Options:
-    [-i[nputlist]        In                  (NULL      )] :Essential :InputDataFileList
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-R[otationalMode]   RotationalMode      (ZONS      )] :Optional  :RotationalMode
-    [-M[ultiplyEulerAngle]RotMode             (ZONS      )Rot1                (0.0       )Rot2                (0.0       )Rot3                (0.0       )] :Optional  :M * input
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nputlist]        In                  (NULL      ).as(inFileListNoOpen    ) ] :Essential :InputDataFileList
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-R[otationalMode]   RotationalMode      (ZONS      ).as(String              ) ] :Optional  :RotationalMode
+    [-M[ultiplyEulerAngle]RotMode             (ZONS      ).as(String              ) 
+                         Rot1                (0.0       ).as(Real                ) 
+                         Rot2                (0.0       ).as(Real                ) 
+                         Rot3                (0.0       ).as(Real                ) ] :Optional  :M * input
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 
 ----- input file format -----
  filename rotationalMode phi theta psi
diff --git a/doc/SmallTools/matrix3DFromEulerAngle.html b/doc/SmallTools/matrix3DFromEulerAngle.html
index 9931dae..a03479c 100644
--- a/doc/SmallTools/matrix3DFromEulerAngle.html
+++ b/doc/SmallTools/matrix3DFromEulerAngle.html
@@ -8,11 +8,14 @@
 <PRE>
 Usage: matrix3DFromEulerAngle
 Options:
-    [-i[nput]            In                  (stdin     )] :Optional  :InputDataFile
-    [-R[ot]              EMode               (ZONS      )Rot1                (0.0       )Rot2                (0.0       )Rot3                (0.0       )] :Optional  :Input: RotAngle[degree]
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output: Matrix
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (stdin     ).as(inFile              ) ] :Optional  :InputDataFile
+    [-R[ot]              EMode               (ZONS      ).as(String              ) 
+                         Rot1                (0.0       ).as(Real                ) 
+                         Rot2                (0.0       ).as(Real                ) 
+                         Rot3                (0.0       ).as(Real                ) ] :Optional  :Input: RotAngle[degree]
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output: Matrix
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/matrix3DInverse.html b/doc/SmallTools/matrix3DInverse.html
index 249efeb..17b6c97 100644
--- a/doc/SmallTools/matrix3DInverse.html
+++ b/doc/SmallTools/matrix3DInverse.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: matrix3DInverse
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/matrix3DToEulerAngle.html b/doc/SmallTools/matrix3DToEulerAngle.html
index 0350956..1f6eaf9 100644
--- a/doc/SmallTools/matrix3DToEulerAngle.html
+++ b/doc/SmallTools/matrix3DToEulerAngle.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: matrix3DToEulerAngle
 Options:
-    [-i[nput]            In                  (stdin     )] :Optional  :Input: Matrix3D
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output: File
-    [-E[uler]M[ngle]     EulerMode           (ZONS      )] :Optional  :Input: Mode
-    [-Check              Threshold           (1e-4      )] :Optional  :Input: Check Threshold
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (stdin     ).as(inFile              ) ] :Optional  :Input: Matrix3D
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output: File
+    [-E[uler]M[ngle]     EulerMode           (ZONS      ).as(String              ) ] :Optional  :Input: Mode
+    [-Check              Threshold           (1e-4      ).as(Real                ) ] :Optional  :Input: Check Threshold
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/moi2mrc.html b/doc/SmallTools/moi2mrc.html
index 411b77e..8aa370f 100644
--- a/doc/SmallTools/moi2mrc.html
+++ b/doc/SmallTools/moi2mrc.html
@@ -8,14 +8,14 @@
 <PRE>
 Usage: moi2mrc
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Optional  :OutputDataFile
-    [-Mag[nification]    Mag                 (150       )] :Optional  :Magnification[xk]:
-    [-Mag2[nification]   Mag2                (1.64      )] :Optional  :Magnification[CCD/Film]
-    [-ADUperE            ADUperE             (20        )] :Optional  :[ADU/electron]
-    [-info               Info                (1         )] :Optional  :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (1         )] :Optional  :Mode: 0:char(mean+-3sd) 1:short(direct) 2:float(e-)
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-Mag[nification]    Mag                 (150       ).as(Real                ) ] :Optional  :Magnification[xk]:
+    [-Mag2[nification]   Mag2                (1.64      ).as(Real                ) ] :Optional  :Magnification[CCD/Film]
+    [-ADUperE            ADUperE             (20        ).as(Real                ) ] :Optional  :[ADU/electron]
+    [-info               Info                (1         ).as(Integer             ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (1         ).as(Integer             ) ] :Optional  :Mode: 0:char(mean+-3sd) 1:short(direct) 2:float(e-)
 ----- Additional Usage -----
 >>>> -info Integer
  1: All Header Info List 
diff --git a/doc/SmallTools/molecularEnvelopeResampling.html b/doc/SmallTools/molecularEnvelopeResampling.html
index a03fd7f..3031a29 100644
--- a/doc/SmallTools/molecularEnvelopeResampling.html
+++ b/doc/SmallTools/molecularEnvelopeResampling.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: molecularEnvelopeResampling
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-Rmax               Rmax                (1.0       )] :Optional  :Rmax: [/A]
-    [-dR                 dR                  (0.01      )] :Optional  :dR: [/A]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-Rmax               Rmax                (1.0       ).as(Real                ) ] :Optional  :Rmax: [/A]
+    [-dR                 dR                  (0.01      ).as(Real                ) ] :Optional  :dR: [/A]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/molvie.html b/doc/SmallTools/molvie.html
index 55f8c00..3230d87 100644
--- a/doc/SmallTools/molvie.html
+++ b/doc/SmallTools/molvie.html
@@ -1 +1,18 @@
-/bin/bash: molvie: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>molvie</TITLE>
+</HEAD>
+<BODY>
+<H1>molvie</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: molvie
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/molvieDock.html b/doc/SmallTools/molvieDock.html
index 1efb35b..d3bfe6b 100644
--- a/doc/SmallTools/molvieDock.html
+++ b/doc/SmallTools/molvieDock.html
@@ -1 +1,18 @@
-/bin/bash: molvieDock: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>molvieDock</TITLE>
+</HEAD>
+<BODY>
+<H1>molvieDock</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: molvieDock
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/molvieFlight.html b/doc/SmallTools/molvieFlight.html
index a6fb822..a37d6aa 100644
--- a/doc/SmallTools/molvieFlight.html
+++ b/doc/SmallTools/molvieFlight.html
@@ -1 +1,18 @@
-/bin/bash: molvieFlight: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>molvieFlight</TITLE>
+</HEAD>
+<BODY>
+<H1>molvieFlight</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: molvieFlight
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/molvieMrcViewer.html b/doc/SmallTools/molvieMrcViewer.html
index 2ddb6f3..60aa064 100644
--- a/doc/SmallTools/molvieMrcViewer.html
+++ b/doc/SmallTools/molvieMrcViewer.html
@@ -1 +1,18 @@
-/bin/bash: molvieMrcViewer: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>molvieMrcViewer</TITLE>
+</HEAD>
+<BODY>
+<H1>molvieMrcViewer</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: molvieMrcViewer
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/molvieProjection.html b/doc/SmallTools/molvieProjection.html
index 1794dfd..1e85f32 100644
--- a/doc/SmallTools/molvieProjection.html
+++ b/doc/SmallTools/molvieProjection.html
@@ -1 +1,18 @@
-/bin/bash: molvieProjection: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>molvieProjection</TITLE>
+</HEAD>
+<BODY>
+<H1>molvieProjection</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: molvieProjection
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/molvieViewer.html b/doc/SmallTools/molvieViewer.html
index 0d3fb9f..bca79ac 100644
--- a/doc/SmallTools/molvieViewer.html
+++ b/doc/SmallTools/molvieViewer.html
@@ -1 +1,18 @@
-/bin/bash: molvieViewer: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>molvieViewer</TITLE>
+</HEAD>
+<BODY>
+<H1>molvieViewer</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: molvieViewer
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrc2fld.html b/doc/SmallTools/mrc2fld.html
index 63c8b2d..79c1e9f 100644
--- a/doc/SmallTools/mrc2fld.html
+++ b/doc/SmallTools/mrc2fld.html
@@ -8,16 +8,16 @@
 <PRE>
 Usage: mrc2fld
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-shiftx             shiftx              (0.0       )] :Optional  :shiftx[A]
-    [-shifty             shifty              (0.0       )] :Optional  :shifty[A]
-    [-shiftz             shiftz              (0.0       )] :Optional  :shiftz[A]
-    [-I                  ] :Optional  :Inverse
-    [-R[adius]C[ylindrical]] :Optional  :Radius: Cylindrical
-    [-M[ag]              Mag                 (1.0       )] :Optional  :density x mag
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-shiftx             shiftx              (0.0       ).as(Real                ) ] :Optional  :shiftx[A]
+    [-shifty             shifty              (0.0       ).as(Real                ) ] :Optional  :shifty[A]
+    [-shiftz             shiftz              (0.0       ).as(Real                ) ] :Optional  :shiftz[A]
+    [-I                                                                            ] :Optional  :Inverse
+    [-R[adius]C[ylindrical]                                                          ] :Optional  :Radius: Cylindrical
+    [-M[ag]              Mag                 (1.0       ).as(Real                ) ] :Optional  :density x mag
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 mode 0:Char(Byte) Image 
        If you want to use volume rendering, you must select Char.
 mode 2:Float Image 
diff --git a/doc/SmallTools/mrc2gif.html b/doc/SmallTools/mrc2gif.html
index f4a4e3d..6db92f6 100644
--- a/doc/SmallTools/mrc2gif.html
+++ b/doc/SmallTools/mrc2gif.html
@@ -8,15 +8,20 @@
 <PRE>
 Usage: mrc2gif
 Options:
-    [-i[nput]            inFile              (NULL      )] :Essential :InputDataFile
-    [-o[utput]           outFile             (NULL      )] :Essential :OutputDataFile
-    [-H[igh]             High                (0         )] :Optional  :HighThreshold
-    [-L[ow]              Low                 (0         )] :Optional  :LowThreshold
-    [-I[nverse]          ] :Optional  :Inverse(Black is white)
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode: 
+    [-i[nput]            inFile              (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           outFile             (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-H[igh]             High                (0         ).as(Real                ) ] :Optional  :HighThreshold
+    [-L[ow]              Low                 (0         ).as(Real                ) ] :Optional  :LowThreshold
+    [-I[nverse]                                                                    ] :Optional  :Inverse(Black is white)
+    [-z[Section]         Z                   (0         ).as(Integer             ) ] :Optional  :z-section
+    [-e[xtention]        format              (%s.%04d ).as(String              ) ] :Optional  :SerialSection Format
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode: 
 			0 (8bits), 1(16bits)
 			
+-z
+ -1: Serial Files
+ z(>0): Section at z
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrc2map.html b/doc/SmallTools/mrc2map.html
index 010afb8..75fe170 100644
--- a/doc/SmallTools/mrc2map.html
+++ b/doc/SmallTools/mrc2map.html
@@ -8,15 +8,15 @@
 <PRE>
 Usage: mrc2map
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-noswap             ] :Optional  : NO Byte Swapping 
-    [-shiftx             shiftx              (0.0       )] :Optional  :shiftx
-    [-shifty             shifty              (0.0       )] :Optional  :shifty
-    [-shiftz             shiftz              (0.0       )] :Optional  :shiftz
-    [-mul                mul                 (1.0       )] :Optional  :mrc*mul
-    [-m[ode]             mode                (0         )] :Optional  :Mode: 
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-noswap                                                                       ] :Optional  : NO Byte Swapping 
+    [-shiftx             shiftx              (0.0       ).as(Real                ) ] :Optional  :shiftx
+    [-shifty             shifty              (0.0       ).as(Real                ) ] :Optional  :shifty
+    [-shiftz             shiftz              (0.0       ).as(Real                ) ] :Optional  :shiftz
+    [-mul                mul                 (1.0       ).as(Real                ) ] :Optional  :mrc*mul
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode: 
 		0 : Same as mrc
 		1 : Helix(CentreIsOrigin)
 		2: BottomRight is Origin
diff --git a/doc/SmallTools/mrc2mrc.html b/doc/SmallTools/mrc2mrc.html
index 9b8dfbf..300c88e 100644
--- a/doc/SmallTools/mrc2mrc.html
+++ b/doc/SmallTools/mrc2mrc.html
@@ -8,13 +8,15 @@
 <PRE>
 Usage: mrc2mrc
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: 
-    [-i[nput]t[ype]      InType              (FEIextendedMRC)] :Optional  :InputDataType
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-o[utput]t[ype]     OutType             (Eos       )] :Optional  :OutputDataType
-    [-Length             LenX                (1.0       )LenY                (1.0       )LenZ                (1.0       )] :Optional  :Mode
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: 
+    [-i[nput]t[ype]      InType              (FEIextendedMRC).as(String              ) ] :Optional  :InputDataType
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-o[utput]t[ype]     OutType             (Eos       ).as(String              ) ] :Optional  :OutputDataType
+    [-Length             LenX                (1.0       ).as(Real                ) 
+                         LenY                (1.0       ).as(Real                ) 
+                         LenZ                (1.0       ).as(Real                ) ] :Optional  :Mode
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 >> To be suppoerted (Not all)
 Eos
diff --git a/doc/SmallTools/mrc2tiff.html b/doc/SmallTools/mrc2tiff.html
index fae55b0..660b30d 100644
--- a/doc/SmallTools/mrc2tiff.html
+++ b/doc/SmallTools/mrc2tiff.html
@@ -8,13 +8,15 @@
 <PRE>
 Usage: mrc2tiff
 Options:
-    [-i[nput]            inFile              (NULL      )] :Essential :InputDataFile
-    [-o[utput]           outFile             (NULL      )] :Essential :OutputDataFile
-    [-H[igh]             High                (0         )] :Optional  :HighThreshold
-    [-L[ow]              Low                 (0         )] :Optional  :LowThreshold
-    [-I[nverse]          ] :Optional  :Inverse(Black is white)
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode: 
+    [-i[nput]            inFile              (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           outFile             (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-H[igh]             High                (0         ).as(Real                ) ] :Optional  :HighThreshold
+    [-L[ow]              Low                 (0         ).as(Real                ) ] :Optional  :LowThreshold
+    [-I[nverse]                                                                    ] :Optional  :Inverse(Black is white)
+    [-Z                  Z                   (0         ).as(Integer             ) ] :Optional  :Each: 0<=, SerialSection:-1
+    [-e[xtension]        format              (%s.%04d ).as(String              ) ] :Optional  :SerialSectionFormat
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode: 
 			0 (8bits), 1(16bits)
 			
 --- Attention ---
diff --git a/doc/SmallTools/mrc3DExtractZ.html b/doc/SmallTools/mrc3DExtractZ.html
index 6e6d45a..450ce81 100644
--- a/doc/SmallTools/mrc3DExtractZ.html
+++ b/doc/SmallTools/mrc3DExtractZ.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrc3DExtractZ
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-b[ottom]           ZB                  (0         )] :Optional  :Bottom of output data
-    [-t[op]              ZT                  (-1        )] :Optional  :Top of output data. Default:top of input data
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-b[ottom]           ZB                  (0         ).as(Integer             ) ] :Optional  :Bottom of output data
+    [-t[op]              ZT                  (-1        ).as(Integer             ) ] :Optional  :Top of output data. Default:top of input data
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrc3Dto2D.html b/doc/SmallTools/mrc3Dto2D.html
index 3711c0e..3768e23 100644
--- a/doc/SmallTools/mrc3Dto2D.html
+++ b/doc/SmallTools/mrc3Dto2D.html
@@ -8,18 +8,26 @@
 <PRE>
 Usage: mrc3Dto2D
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: mrcImage[3D]
-    [-o[utput]           Out                 (NULL      )] :Optional  :Output: mrcImage[2D]
-    [-fileList           filenamePrefix      (2D        )filenameSuffix      (2d        )filenameFormat      (%s-%05d.%s)] :Optional  :Output: mrcImage[2D] List 
-    [-Rot1               Rot1Start           (0.0       )Rot1End             (360.0     )Rot1Delta           (10        )] :Optional  :OutputDataFile
-    [-Rot2               Rot2Start           (0.0       )Rot2End             (360.0     )Rot2Delta           (10        )] :Optional  :OutputDataFile
-    [-Rot3               Rot3Start           (0.0       )Rot3End             (360.0     )Rot3Delta           (10        )] :Optional  :OutputDataFile
-    [-EulerMode          EulerMode           (ZOYS      )] :Optional  :OutputDataFile
-    [-InterpolationMode  InterpolationMode   (1         )] :Optional  :OutputDataFile
-    [-AreaMode           AreaMode            (0         )] :Optional  :Cubic: 0, Globular: 1 
-    [-pthread            pthreadMax          (1         )] :Optional  :pthread: max
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: mrcImage[3D]
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :Output: mrcImage[2D]
+    [-fileList           filenamePrefix      (2D        ).as(String              ) 
+                         filenameSuffix      (2d        ).as(String              ) 
+                         filenameFormat      (%s-%05d.%s).as(String              ) ] :Optional  :Output: mrcImage[2D] List 
+    [-Rot1               Rot1Start           (0.0       ).as(Real                ) 
+                         Rot1End             (360.0     ).as(Real                ) 
+                         Rot1Delta           (10        ).as(Real                ) ] :Optional  :OutputDataFile
+    [-Rot2               Rot2Start           (0.0       ).as(Real                ) 
+                         Rot2End             (360.0     ).as(Real                ) 
+                         Rot2Delta           (10        ).as(Real                ) ] :Optional  :OutputDataFile
+    [-Rot3               Rot3Start           (0.0       ).as(Real                ) 
+                         Rot3End             (360.0     ).as(Real                ) 
+                         Rot3Delta           (10        ).as(Real                ) ] :Optional  :OutputDataFile
+    [-EulerMode          EulerMode           (ZOYS      ).as(String              ) ] :Optional  :OutputDataFile
+    [-InterpolationMode  InterpolationMode   (1         ).as(Integer             ) ] :Optional  :OutputDataFile
+    [-AreaMode           AreaMode            (0         ).as(Integer             ) ] :Optional  :Cubic: 0, Globular: 1 
+    [-pthread            pthreadMax          (1         ).as(Integer             ) ] :Optional  :pthread: max
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 ----- Attention !!!!   -----
 -m 0: 
diff --git a/doc/SmallTools/mrcFETnormalizeBySD.html b/doc/SmallTools/mrcFETnormalizeBySD.html
index 69ec4ae..ecfd6f4 100644
--- a/doc/SmallTools/mrcFETnormalizeBySD.html
+++ b/doc/SmallTools/mrcFETnormalizeBySD.html
@@ -8,13 +8,13 @@
 <PRE>
 Usage: mrcFETnormalizeBySD
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputFileList
-    [-i[nput]s[ample]    InSample            (NULL      )] :Optional  :FileListforSDcalc
-    [-r[ead]SD           readSD              (NULL      )] :Optional  :readFETSDfile
-    [-w[rite]SD          writeSD             (NULL      )] :Optional  :writeFETSDfile
-    [-o[utput]           Out                 (NULL      )] :Optional  :OutputASmrcImage
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputFileList
+    [-i[nput]s[ample]    InSample            (NULL      ).as(inFile              ) ] :Optional  :FileListforSDcalc
+    [-r[ead]SD           readSD              (NULL      ).as(inFile              ) ] :Optional  :readFETSDfile
+    [-w[rite]SD          writeSD             (NULL      ).as(outFile             ) ] :Optional  :writeFETSDfile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :OutputASmrcImage
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 
 ----- Additional Usage -----
 -is  :[inputsample] is FileList for SDcalculation.
diff --git a/doc/SmallTools/mrcFFTBandPassFilter.html b/doc/SmallTools/mrcFFTBandPassFilter.html
index 5aea00b..bddb5d9 100644
--- a/doc/SmallTools/mrcFFTBandPassFilter.html
+++ b/doc/SmallTools/mrcFFTBandPassFilter.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: mrcFFTBandPassFilter
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcFFTCTFCompensation.html b/doc/SmallTools/mrcFFTCTFCompensation.html
index 48c2f1e..d038e2e 100644
--- a/doc/SmallTools/mrcFFTCTFCompensation.html
+++ b/doc/SmallTools/mrcFFTCTFCompensation.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcFFTCTFCompensation
 Options:
-    [-i[nput]            In                  ] :Essential :InputDataFile
-    [-o[utput]           Out                 ] :Essential :OutputDataFile
-    [-I[nputWeight]      CTFIn               ] :Essential :InputWeightFile
-    [-c[onfig]           configFile          ] :Optional  :ConfigurationFile
-    [-m[ode]             mode                ] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-I[nputWeight]      CTFIn               (NULL      ).as(inFile              ) ] :Essential :InputWeightFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 >>> CTFWeigting File
 RR0 F0 : If R<RR0, Weight=0. If RR0<=R<RR1,  Weight={(RR1-R)*F0+(R-RR0)*F1}/(RR1-RR0), i.e., Linear Interpolation
 RR1 F1 : 
diff --git a/doc/SmallTools/mrcFFTDigitize.html b/doc/SmallTools/mrcFFTDigitize.html
index 8ee5702..6720067 100644
--- a/doc/SmallTools/mrcFFTDigitize.html
+++ b/doc/SmallTools/mrcFFTDigitize.html
@@ -8,13 +8,13 @@
 <PRE>
 Usage: mrcFFTDigitize
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-l[evel]            Level               (2.0       )] :Optional  :Level
-    [-min[imum]          Min                 (0.0       )] :Essential :Minimum
-    [-max[imum]          Max                 (0.0       )] :Essential :Maximum
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-l[evel]            Level               (2.0       ).as(Real                ) ] :Optional  :Level
+    [-min[imum]          Min                 (0.0       ).as(Real                ) ] :Essential :Minimum
+    [-max[imum]          Max                 (0.0       ).as(Real                ) ] :Essential :Maximum
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcFFTExpression.html b/doc/SmallTools/mrcFFTExpression.html
index a4d5f53..00fe1cf 100644
--- a/doc/SmallTools/mrcFFTExpression.html
+++ b/doc/SmallTools/mrcFFTExpression.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcFFTExpression
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-T[hreshold]        Thres               (1e-16     )] :Optional  :Threshold to calculate.For mode 1 and 3.
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-T[hreshold]        Thres               (1e-16     ).as(Real                ) ] :Optional  :Threshold to calculate.For mode 1 and 3.
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 ----- FFT Expression MOde -----
 0:Amplitude
diff --git a/doc/SmallTools/mrcFFTFibreDiagram.html b/doc/SmallTools/mrcFFTFibreDiagram.html
index b3669ed..07bffd3 100644
--- a/doc/SmallTools/mrcFFTFibreDiagram.html
+++ b/doc/SmallTools/mrcFFTFibreDiagram.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: mrcFFTFibreDiagram
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: HelicalObject/FFT3D or Image3D
-    [-o[utput]           Out                 (NULL      )] :Essential :Output: 2D mrcImage
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: HelicalObject/FFT3D or Image3D
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output: 2D mrcImage
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
   -mode 0 : average PHI-axis to express RZ space
 </PRE>
diff --git a/doc/SmallTools/mrcFFTFiltering.html b/doc/SmallTools/mrcFFTFiltering.html
index 49cc48b..3ad73ef 100644
--- a/doc/SmallTools/mrcFFTFiltering.html
+++ b/doc/SmallTools/mrcFFTFiltering.html
@@ -8,18 +8,20 @@
 <PRE>
 Usage: mrcFFTFiltering
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :Output: Filtered Image
-    [-IQ                 IQ                  (NULL      )] :Optional  :Output: IQ Map
-    [-vx                 vx                  (0         )] :Optional  :Vector(x)
-    [-vy                 vy                  (0         )] :Optional  :Vector(y)
-    [-v1                 v1x                 (0         )v1y                 (0         )] :Optional  :Vector(v1)
-    [-v2                 v2x                 (0         )v2y                 (0         )] :Optional  :Vector(v2)
-    [-sx                 sx                  (1         )] :Optional  :Size(x)
-    [-sy                 sy                  (1         )] :Optional  :Size(y)
-    [-neg[lect]F00       ] :Optional  :Neglect F00
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output: Filtered Image
+    [-IQ                 IQ                  (NULL      ).as(outFile             ) ] :Optional  :Output: IQ Map
+    [-vx                 vx                  (0         ).as(Real                ) ] :Optional  :Vector(x)
+    [-vy                 vy                  (0         ).as(Real                ) ] :Optional  :Vector(y)
+    [-v1                 v1x                 (0         ).as(Real                ) 
+                         v1y                 (0         ).as(Real                ) ] :Optional  :Vector(v1)
+    [-v2                 v2x                 (0         ).as(Real                ) 
+                         v2y                 (0         ).as(Real                ) ] :Optional  :Vector(v2)
+    [-sx                 sx                  (1         ).as(Integer             ) ] :Optional  :Size(x)
+    [-sy                 sy                  (1         ).as(Integer             ) ] :Optional  :Size(y)
+    [-neg[lect]F00                                                                 ] :Optional  :Neglect F00
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcFFTIQEstimation.html b/doc/SmallTools/mrcFFTIQEstimation.html
index baf89ff..9682e90 100644
--- a/doc/SmallTools/mrcFFTIQEstimation.html
+++ b/doc/SmallTools/mrcFFTIQEstimation.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcFFTIQEstimation
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: MRC
-    [-sp[otList]         SpotList            (stdin     )] :Essential :Input: SpotList: X Y Z
-    [-radius             radius              (3         )] :Optional  :Input: [pixel]
-    [-o[utput]           Out                 (NULL      )] :Essential :Output: ASCII
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: MRC
+    [-sp[otList]         SpotList            (stdin     ).as(inFile              ) ] :Essential :Input: SpotList: X Y Z
+    [-radius             radius              (3         ).as(Integer             ) ] :Optional  :Input: [pixel]
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output: ASCII
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcFFTLayerLineCheck.html b/doc/SmallTools/mrcFFTLayerLineCheck.html
index dc76786..933b78f 100644
--- a/doc/SmallTools/mrcFFTLayerLineCheck.html
+++ b/doc/SmallTools/mrcFFTLayerLineCheck.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcFFTLayerLineCheck
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: mrc(FT)
-    [-L[ayer]            L                   (2         )] :Optional  :Input: Layer(pixel)
-    [-NoEq               ] :Optional  :Input: No l=0
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: mrc(FT)
+    [-L[ayer]            L                   (2         ).as(Integer             ) ] :Optional  :Input: Layer(pixel)
+    [-NoEq                                                                         ] :Optional  :Input: No l=0
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcFFTMedianFilter.html b/doc/SmallTools/mrcFFTMedianFilter.html
index 2ac577e..ee16ac1 100644
--- a/doc/SmallTools/mrcFFTMedianFilter.html
+++ b/doc/SmallTools/mrcFFTMedianFilter.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcFFTMedianFilter
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-r                  r                   (1         )] :Optional  :Radius of Kernel Size (Pixel)
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-r                  r                   (1         ).as(Real                ) ] :Optional  :Radius of Kernel Size (Pixel)
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 Calculation is performed on amplitude only.
 Output: Real part is amplitude and imaginary part is zero.
diff --git a/doc/SmallTools/mrcFFTProjection.html b/doc/SmallTools/mrcFFTProjection.html
index 64ffbcc..1805967 100644
--- a/doc/SmallTools/mrcFFTProjection.html
+++ b/doc/SmallTools/mrcFFTProjection.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: mrcFFTProjection
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 The 2D FFT Image projects to Y-axis
 This image is not true.
diff --git a/doc/SmallTools/mrcFFTResampling.html b/doc/SmallTools/mrcFFTResampling.html
index 698f792..1fee44e 100644
--- a/doc/SmallTools/mrcFFTResampling.html
+++ b/doc/SmallTools/mrcFFTResampling.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcFFTResampling
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-nx[umber]          Nx                  (64.0      )] :Optional  :NumberX
-    [-ny[umber]          Ny                  (64.0      )] :Optional  :NumberY
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-nx[umber]          Nx                  (64.0      ).as(Real                ) ] :Optional  :NumberX
+    [-ny[umber]          Ny                  (64.0      ).as(Real                ) ] :Optional  :NumberY
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcFFTShellInfo.html b/doc/SmallTools/mrcFFTShellInfo.html
index a00d2a0..2e91c53 100644
--- a/doc/SmallTools/mrcFFTShellInfo.html
+++ b/doc/SmallTools/mrcFFTShellInfo.html
@@ -8,11 +8,12 @@
 <PRE>
 Usage: mrcFFTShellInfo
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: mrc/FFT
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output: 
-    [-R[angeOfShell]     minR                (0         )maxR                (0.1       )] :Optional  :minR/maxR[/A]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (1         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: mrc/FFT
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output: 
+    [-R[angeOfShell]     minR                (0         ).as(Real                ) 
+                         maxR                (0.1       ).as(Real                ) ] :Optional  :minR/maxR[/A]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (1         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 -mode 1 : AveragedMagnitute
 -mode 2 : AveragedPower
diff --git a/doc/SmallTools/mrcFFTSizeChange.html b/doc/SmallTools/mrcFFTSizeChange.html
index d7e464c..0218faf 100644
--- a/doc/SmallTools/mrcFFTSizeChange.html
+++ b/doc/SmallTools/mrcFFTSizeChange.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcFFTSizeChange
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-x[length]          Nx                  (1.0       )] :Optional  :Pixel size 
-    [-y[length]          Ny                  (1.0       )] :Optional  :Pixel size 
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-x[length]          Nx                  (1.0       ).as(Real                ) ] :Optional  :Pixel size 
+    [-y[length]          Ny                  (1.0       ).as(Real                ) ] :Optional  :Pixel size 
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcFFTSpectrum.html b/doc/SmallTools/mrcFFTSpectrum.html
index 9f9575b..e35a25e 100644
--- a/doc/SmallTools/mrcFFTSpectrum.html
+++ b/doc/SmallTools/mrcFFTSpectrum.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcFFTSpectrum
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input:fft
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output:spectrum
-    [-n                  N                   (1         )] :Optional  :n-division: 2PI/n
-    [-axis               Axis                (0.0       )] :Optional  :axis: 0
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input:fft
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output:spectrum
+    [-n                  N                   (1         ).as(Integer             ) ] :Optional  :n-division: 2PI/n
+    [-axis               Axis                (0.0       ).as(Real                ) ] :Optional  :axis: 0
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcFFTXFiltering.html b/doc/SmallTools/mrcFFTXFiltering.html
index ac6d98a..b439964 100644
--- a/doc/SmallTools/mrcFFTXFiltering.html
+++ b/doc/SmallTools/mrcFFTXFiltering.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcFFTXFiltering
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-RMaxX              RMaxX               (0         )] :Optional  :RMax value of X [1/A]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-RMaxX              RMaxX               (0         ).as(Real                ) ] :Optional  :RMax value of X [1/A]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 This filter cuts high resolution information only X direction.
 RMaxX [1/A] is maximum resolution
diff --git a/doc/SmallTools/mrcFFTplainreduce.html b/doc/SmallTools/mrcFFTplainreduce.html
index a9b9a09..a9225ff 100644
--- a/doc/SmallTools/mrcFFTplainreduce.html
+++ b/doc/SmallTools/mrcFFTplainreduce.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcFFTplainreduce
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-p[osition]         Pos                 (0         )] :Optional  :Position of reduced plain
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-v[alue]            Value               (0         )] :Optional  :Value to multiply
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-p[osition]         Pos                 (0         ).as(Integer             ) ] :Optional  :Position of reduced plain
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-v[alue]            Value               (0         ).as(Real                ) ] :Optional  :Value to multiply
 ----- Additional Usage -----
 mode 0:pos=z.
 mode 1:pos=x.
diff --git a/doc/SmallTools/mrcFTMeridianEquatorRedece.html b/doc/SmallTools/mrcFTMeridianEquatorRedece.html
index fd05de8..2c4b7fe 100644
--- a/doc/SmallTools/mrcFTMeridianEquatorRedece.html
+++ b/doc/SmallTools/mrcFTMeridianEquatorRedece.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcFTMeridianEquatorRedece
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-X                  MaxX                (-1        )] :Optional  :Max X to put zero (pixel).  Default is no operation.
-    [-Y                  MaxY                (-1        )] :Optional  :Max Y to put zero (pixel).  Default is no operation.
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-X                  MaxX                (-1        ).as(Integer             ) ] :Optional  :Max X to put zero (pixel).  Default is no operation.
+    [-Y                  MaxY                (-1        ).as(Integer             ) ] :Optional  :Max Y to put zero (pixel).  Default is no operation.
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImage1DProjectionfrom2D.html b/doc/SmallTools/mrcImage1DProjectionfrom2D.html
index 42d4331..9d05350 100644
--- a/doc/SmallTools/mrcImage1DProjectionfrom2D.html
+++ b/doc/SmallTools/mrcImage1DProjectionfrom2D.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImage1DProjectionfrom2D
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-d[egree]           phi                 (0         )] :Optional  :Degree of the line to project
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-d[egree]           phi                 (0         ).as(Real                ) ] :Optional  :Degree of the line to project
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImage1dAverageByCorrelation.html b/doc/SmallTools/mrcImage1dAverageByCorrelation.html
index 8ecf312..301e5a6 100644
--- a/doc/SmallTools/mrcImage1dAverageByCorrelation.html
+++ b/doc/SmallTools/mrcImage1dAverageByCorrelation.html
@@ -8,11 +8,14 @@
 <PRE>
 Usage: mrcImage1dAverageByCorrelation
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-r[ange]            range               (0         )] :Optional  :Search range of shift.Default:Nx
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-r[eference]        Ref                 (NULL      ).as(inFile              ) ] :Essential :ReferenceDataFile
+    [-range              range               (0         ).as(Integer             ) ] :Optional  :Search range of shift.Default:Nx
+    [-s[ignal position]  Signal              (NULL      ).as(inFile              ) ] :Essential :File to define position of signal
+    [-d[elta]            delta               (1.0       ).as(Real                ) ] :Optional  :Spacing of molecule(Pixel).
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImage1dShiftAverageByAnnealing.html b/doc/SmallTools/mrcImage1dShiftAverageByAnnealing.html
index 2e19fca..4c0299b 100644
--- a/doc/SmallTools/mrcImage1dShiftAverageByAnnealing.html
+++ b/doc/SmallTools/mrcImage1dShiftAverageByAnnealing.html
@@ -8,18 +8,18 @@
 <PRE>
 Usage: mrcImage1dShiftAverageByAnnealing
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-s[ignal position]  Signal              (NULL      )] :Essential :File to define position of signal
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-r[ange]            range               (0         )] :Optional  :Search range of shift.Default:Nx
-    [-d[elta]            delta               (1.0       )] :Optional  :Spacing of molecule(Pixel).
-    [-T[eperature]       temperature         (1.0       )] :Optional  :Initial temperature.
-    [-iter[ation]        iter                (1000      )] :Optional  :Number of iteration before reducing temperature.
-    [-eps[ilon]          eps                 (0.001     )] :Optional  :Temperature(T) reduced to (1-epsilon)T.
-    [-tol                tol                 (1e-2      )] :Optional  :Number to identify convergence
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-M[ode2]            mode2               (0         )] :Optional  :Mode2
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-s[ignal position]  Signal              (NULL      ).as(inFile              ) ] :Essential :File to define position of signal
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-r[ange]            range               (0         ).as(Integer             ) ] :Optional  :Search range of shift.Default:Nx
+    [-d[elta]            delta               (1.0       ).as(Real                ) ] :Optional  :Spacing of molecule(Pixel).
+    [-T[eperature]       temperature         (1.0       ).as(Real                ) ] :Optional  :Initial temperature.
+    [-iter[ation]        iter                (1000      ).as(Integer             ) ] :Optional  :Number of iteration before reducing temperature.
+    [-eps[ilon]          eps                 (0.001     ).as(Real                ) ] :Optional  :Temperature(T) reduced to (1-epsilon)T.
+    [-tol                tol                 (1e-2      ).as(Real                ) ] :Optional  :Number to identify convergence
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-M[ode2]            mode2               (0         ).as(Integer             ) ] :Optional  :Mode2
 ----- mode -----
 0:All search 
 1:annealing method 
diff --git a/doc/SmallTools/mrcImage1dShiftByCorrelation.html b/doc/SmallTools/mrcImage1dShiftByCorrelation.html
index 61b99ab..e11cf06 100644
--- a/doc/SmallTools/mrcImage1dShiftByCorrelation.html
+++ b/doc/SmallTools/mrcImage1dShiftByCorrelation.html
@@ -8,14 +8,14 @@
 <PRE>
 Usage: mrcImage1dShiftByCorrelation
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-r[eference]        Ref                 (NULL      )] :Essential :ReferenceDataFile
-    [-range              range               (0         )] :Optional  :Search range of shift.Default:Nx
-    [-s[ignal position]  Signal              (NULL      )] :Essential :File to define position of signal
-    [-d[elta]            delta               (1.0       )] :Optional  :Spacing of molecule(Pixel).
-    [-norm[alize]        ] :Optional  :Normalize before correlation
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-r[eference]        Ref                 (NULL      ).as(inFile              ) ] :Essential :ReferenceDataFile
+    [-range              range               (0         ).as(Integer             ) ] :Optional  :Search range of shift.Default:Nx
+    [-s[ignal position]  Signal              (NULL      ).as(inFile              ) ] :Essential :File to define position of signal
+    [-d[elta]            delta               (1.0       ).as(Real                ) ] :Optional  :Spacing of molecule(Pixel).
+    [-norm[alize]                                                                  ] :Optional  :Normalize before correlation
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 -----  mode -----
 0:Phase residual
diff --git a/doc/SmallTools/mrcImage2DBackProjection.html b/doc/SmallTools/mrcImage2DBackProjection.html
index bc6e75e..e6dfbf1 100644
--- a/doc/SmallTools/mrcImage2DBackProjection.html
+++ b/doc/SmallTools/mrcImage2DBackProjection.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImage2DBackProjection
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-z                  NumZ                (10        )] :Optional  :Z: pixel  
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-z                  NumZ                (10        ).as(Integer             ) ] :Optional  :Z: pixel  
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImage2DProjection.html b/doc/SmallTools/mrcImage2DProjection.html
index cfe9420..8fbc7da 100644
--- a/doc/SmallTools/mrcImage2DProjection.html
+++ b/doc/SmallTools/mrcImage2DProjection.html
@@ -8,13 +8,13 @@
 <PRE>
 Usage: mrcImage2DProjection
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-w[omega]           Omega               (0         )] :Optional  :Omega
-    [-p[hi]              Phi                 (0         )] :Optional  :Phi
-    [-a[lpha]            Alpha               (0         )] :Optional  :Alpha
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-w[omega]           Omega               (0         ).as(Real                ) ] :Optional  :Omega
+    [-p[hi]              Phi                 (0         ).as(Real                ) ] :Optional  :Phi
+    [-a[lpha]            Alpha               (0         ).as(Real                ) ] :Optional  :Alpha
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImage2pdb.html b/doc/SmallTools/mrcImage2pdb.html
index 173019c..d65a928 100644
--- a/doc/SmallTools/mrcImage2pdb.html
+++ b/doc/SmallTools/mrcImage2pdb.html
@@ -8,16 +8,16 @@
 <PRE>
 Usage: mrcImage2pdb
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (5         )] :Optional  :Mode
-    [-hi[gh]             h                   (0         )] :Optional  :Value of high threshold. Default is the MAX.
-    [-lo[w]              l                   (0         )] :Optional  :Value of low threshold. Default is the MIN.
-    [-L[attice]          ] :Optional  :Atoms are on lattice points
-    [-Skip               Skip                (1         )] :Optional  :Skip atoms.
-    [-R[andom]           Random              (0         )] :Optional  :Random
-    [-d[elta]            delta               (0.1       )] :Optional  :Delta to select atoms to avoid too much concentration. Requiers 0-0.5 value. For mode2-4.
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (5         ).as(Integer             ) ] :Optional  :Mode
+    [-hi[gh]             h                   (0         ).as(Real                ) ] :Optional  :Value of high threshold. Default is the MAX.
+    [-lo[w]              l                   (0         ).as(Real                ) ] :Optional  :Value of low threshold. Default is the MIN.
+    [-L[attice]                                                                    ] :Optional  :Atoms are on lattice points
+    [-Skip               Skip                (1         ).as(Integer             ) ] :Optional  :Skip atoms.
+    [-R[andom]           Random              (0         ).as(Real                ) ] :Optional  :Random
+    [-d[elta]            delta               (0.1       ).as(Real                ) ] :Optional  :Delta to select atoms to avoid too much concentration. Requiers 0-0.5 value. For mode2-4.
 ----- Additional Usage -----
 mode0: One atom for one boxel.
 mode1: Eight atoms for one boxel.
diff --git a/doc/SmallTools/mrcImage3DHighResoEmphasis.html b/doc/SmallTools/mrcImage3DHighResoEmphasis.html
index 697ca6c..ee55614 100644
--- a/doc/SmallTools/mrcImage3DHighResoEmphasis.html
+++ b/doc/SmallTools/mrcImage3DHighResoEmphasis.html
@@ -8,14 +8,14 @@
 <PRE>
 Usage: mrcImage3DHighResoEmphasis
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-L[owThreshold]     L                   (0         )] :Optional  :Low threshold to modify
-    [-H[ighThreshold]    H                   (0         )] :Optional  :High threshold to modify
-    [-A[value]           A                   (0         )] :Optional  :A value
-    [-B[value]           B                   (0         )] :Optional  :B value
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-L[owThreshold]     L                   (0         ).as(Real                ) ] :Optional  :Low threshold to modify
+    [-H[ighThreshold]    H                   (0         ).as(Real                ) ] :Optional  :High threshold to modify
+    [-A[value]           A                   (0         ).as(Real                ) ] :Optional  :A value
+    [-B[value]           B                   (0         ).as(Real                ) ] :Optional  :B value
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- algorithm -----
 R<L data*exp(A*L+B*L*L)
 L<R<H data*exp(A*R+B*R*R) 
diff --git a/doc/SmallTools/mrcImage3DPad.html b/doc/SmallTools/mrcImage3DPad.html
index b9e1455..97e0e62 100644
--- a/doc/SmallTools/mrcImage3DPad.html
+++ b/doc/SmallTools/mrcImage3DPad.html
@@ -8,18 +8,18 @@
 <PRE>
 Usage: mrcImage3DPad
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-r[max]             r                   (0         )] :Optional  :Threshold radius of signal.Default is Nx.
-    [-w[idth]            w                   (1         )] :Optional  :Width of slope. For mode 1.
-    [-v[alue]            v                   (0         )] :Optional  :Value of out of threshold.
-    [-Nx                 Nx                  (0         )] :Optional  :Number of x.Default is inputfile.
-    [-Ny                 Ny                  (0         )] :Optional  :Number of y.Default is inputfile.
-    [-Nz                 Nz                  (0         )] :Optional  :Number of z.Default is inputfile.
-    [-Floating           ] :Optional  :Floating
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-M[ode2]            mode2               (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-r[max]             r                   (0         ).as(Real                ) ] :Optional  :Threshold radius of signal.Default is Nx.
+    [-w[idth]            w                   (1         ).as(Real                ) ] :Optional  :Width of slope. For mode 1.
+    [-v[alue]            v                   (0         ).as(Real                ) ] :Optional  :Value of out of threshold.
+    [-Nx                 Nx                  (0         ).as(Integer             ) ] :Optional  :Number of x.Default is inputfile.
+    [-Ny                 Ny                  (0         ).as(Integer             ) ] :Optional  :Number of y.Default is inputfile.
+    [-Nz                 Nz                  (0         ).as(Integer             ) ] :Optional  :Number of z.Default is inputfile.
+    [-Floating                                                                     ] :Optional  :Floating
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-M[ode2]            mode2               (0         ).as(Integer             ) ] :Optional  :Mode
 ----- mode -----
 0:Default: Out of threshold is avrage of threshold plain.
 1:Mulplying cos function. Default: Out of threshold is avrage of threshold plain.
diff --git a/doc/SmallTools/mrcImage3DPad2.html b/doc/SmallTools/mrcImage3DPad2.html
index a3553eb..09dbeee 100644
--- a/doc/SmallTools/mrcImage3DPad2.html
+++ b/doc/SmallTools/mrcImage3DPad2.html
@@ -8,18 +8,18 @@
 <PRE>
 Usage: mrcImage3DPad2
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-r[max]             r                   (0         )] :Optional  :Threshold radius of signal.Default is Nx.
-    [-w[idth]            w                   (1         )] :Optional  :Width of slope. For mode 1.
-    [-v[alue]            v                   (0         )] :Optional  :Value of out of threshold.
-    [-Nx                 Nx                  (0         )] :Optional  :Number of x.Default is inputfile.
-    [-Ny                 Ny                  (0         )] :Optional  :Number of y.Default is inputfile.
-    [-Nz                 Nz                  (0         )] :Optional  :Number of z.Default is inputfile.
-    [-Floating           ] :Optional  :Floating
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-M[ode2]            mode2               (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-r[max]             r                   (0         ).as(Real                ) ] :Optional  :Threshold radius of signal.Default is Nx.
+    [-w[idth]            w                   (1         ).as(Real                ) ] :Optional  :Width of slope. For mode 1.
+    [-v[alue]            v                   (0         ).as(Real                ) ] :Optional  :Value of out of threshold.
+    [-Nx                 Nx                  (0         ).as(Integer             ) ] :Optional  :Number of x.Default is inputfile.
+    [-Ny                 Ny                  (0         ).as(Integer             ) ] :Optional  :Number of y.Default is inputfile.
+    [-Nz                 Nz                  (0         ).as(Integer             ) ] :Optional  :Number of z.Default is inputfile.
+    [-Floating                                                                     ] :Optional  :Floating
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-M[ode2]            mode2               (0         ).as(Integer             ) ] :Optional  :Mode
 ----- mode -----
 0:Default: Out of threshold is avrage of threshold plain.
 1:Mulplying cos function. Default: Out of threshold is avrage of threshold plain.
diff --git a/doc/SmallTools/mrcImage3DPeakGet.html b/doc/SmallTools/mrcImage3DPeakGet.html
new file mode 100644
index 0000000..f0d15b5
--- /dev/null
+++ b/doc/SmallTools/mrcImage3DPeakGet.html
@@ -0,0 +1 @@
+/bin/bash: mrcImage3DPeakGet: そのようなファイルやディレクトリはありません
diff --git a/doc/SmallTools/mrcImage3DSymmetryFind.html b/doc/SmallTools/mrcImage3DSymmetryFind.html
index eadce7b..c96d47a 100644
--- a/doc/SmallTools/mrcImage3DSymmetryFind.html
+++ b/doc/SmallTools/mrcImage3DSymmetryFind.html
@@ -8,19 +8,23 @@
 <PRE>
 Usage: mrcImage3DSymmetryFind
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: MRC(3D)
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output: SymmetryFindParameters
-    [-a[verage]          Avg                 (NULL      )] :Optional  :Output: SymmetryAverage
-    [-S[paceGroupNumber] ISGN                (0         )] :Optional  :SpaceGroupNumber
-    [-Rot[ation]Mode     RotMode             (XOYS      )] :Optional  :EulerMode
-    [-Rot1               minRot1             (0.        )maxRot1             (360.      )dRot1               (1.0       )] :Optional  :[degree]
-    [-Rot2               minRot2             (-90.      )maxRot2             (90.       )dRot2               (1.0       )] :Optional  :[degree]
-    [-dCos               dCos                (1         )] :Optional  :dCos
-    [-CorMode            corMode             (16        )] :Optional  :CorrelationMode
-    [-OffsetMode         OffsetMode          (0         )] :Optional  :OffsetMode
-    [-InterpolationMode  InterpolationMode   (2         )] :Optional  :InterpolationMode
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: MRC(3D)
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output: SymmetryFindParameters
+    [-a[verage]          Avg                 (NULL      ).as(outFile             ) ] :Optional  :Output: SymmetryAverage
+    [-S[paceGroupNumber] ISGN                (0         ).as(Integer             ) ] :Optional  :SpaceGroupNumber
+    [-Rot[ation]Mode     RotMode             (XOYS      ).as(String              ) ] :Optional  :EulerMode
+    [-Rot1               minRot1             (0.        ).as(Real                ) 
+                         maxRot1             (360.      ).as(Real                ) 
+                         dRot1               (1.0       ).as(Real                ) ] :Optional  :[degree]
+    [-Rot2               minRot2             (-90.      ).as(Real                ) 
+                         maxRot2             (90.       ).as(Real                ) 
+                         dRot2               (1.0       ).as(Real                ) ] :Optional  :[degree]
+    [-dCos               dCos                (1         ).as(Integer             ) ] :Optional  :dCos
+    [-CorMode            corMode             (16        ).as(Integer             ) ] :Optional  :CorrelationMode
+    [-OffsetMode         OffsetMode          (0         ).as(Integer             ) ] :Optional  :OffsetMode
+    [-InterpolationMode  InterpolationMode   (2         ).as(Integer             ) ] :Optional  :InterpolationMode
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImage3DWindowing.html b/doc/SmallTools/mrcImage3DWindowing.html
index 440441f..d0879f2 100644
--- a/doc/SmallTools/mrcImage3DWindowing.html
+++ b/doc/SmallTools/mrcImage3DWindowing.html
@@ -8,15 +8,19 @@
 <PRE>
 Usage: mrcImage3DWindowing
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: mrcImage
-    [-o[utput]           Out                 (NULL      )] :Essential :Output: mrcImage
-    [-center             cx                  (0         )cy                  (0         )cz                  (0         )] :Optional  :Center:
-    [-w[idth]            wx                  (0         )wy                  (0         )wz                  (0         )] :Optional  :Width
-    [-r[dius]            r                   (0         )] :Optional  :Radius
-    [-w[idth]r[dius]     w                   (0         )] :Optional  :Width for R
-    [-w[idth]z           widthz              (0         )] :Optional  :Width for z
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: mrcImage
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output: mrcImage
+    [-center             cx                  (0         ).as(Real                ) 
+                         cy                  (0         ).as(Real                ) 
+                         cz                  (0         ).as(Real                ) ] :Optional  :Center:
+    [-w[idth]            wx                  (0         ).as(Real                ) 
+                         wy                  (0         ).as(Real                ) 
+                         wz                  (0         ).as(Real                ) ] :Optional  :Width
+    [-r[dius]            r                   (0         ).as(Real                ) ] :Optional  :Radius
+    [-w[idth]r[dius]     w                   (0         ).as(Real                ) ] :Optional  :Width for R
+    [-w[idth]z           widthz              (0         ).as(Real                ) ] :Optional  :Width for z
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 0: GaussianRectangularSolid
 1: CosCylindar(+Offset)
diff --git a/doc/SmallTools/mrcImageAbnormalValueRemove.html b/doc/SmallTools/mrcImageAbnormalValueRemove.html
index aa4a52e..12b17c9 100644
--- a/doc/SmallTools/mrcImageAbnormalValueRemove.html
+++ b/doc/SmallTools/mrcImageAbnormalValueRemove.html
@@ -8,12 +8,13 @@
 <PRE>
 Usage: mrcImageAbnormalValueRemove
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: mrc
-    [-o[utput]           Out                 (NULL      )] :Essential :Output: mrc
-    [-v[alueForCut]      cutValue            (3.0       )] :Optional  :CutValue/Sigma
-    [-u[nsigned]         UnsignedMax         (65535     )UnsignedHalf        (16384     )] :Optional  :Unsigned to Signed: Need Max
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: mrc
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output: mrc
+    [-v[alueForCut]      cutValue            (3.0       ).as(Real                ) ] :Optional  :CutValue/Sigma
+    [-u[nsigned]         UnsignedMax         (65535     ).as(Real                ) 
+                         UnsignedHalf        (16384     ).as(Real                ) ] :Optional  :Unsigned to Signed: Need Max
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 ----- Mode: 
     0: Random Value 
diff --git a/doc/SmallTools/mrcImageActinSingleParticleAnalysis.html b/doc/SmallTools/mrcImageActinSingleParticleAnalysis.html
index b8bb06a..14b27f2 100644
--- a/doc/SmallTools/mrcImageActinSingleParticleAnalysis.html
+++ b/doc/SmallTools/mrcImageActinSingleParticleAnalysis.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: mrcImageActinSingleParticleAnalysis
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageAdaptiveBinalization.html b/doc/SmallTools/mrcImageAdaptiveBinalization.html
index ff2a470..aabd6f9 100644
--- a/doc/SmallTools/mrcImageAdaptiveBinalization.html
+++ b/doc/SmallTools/mrcImageAdaptiveBinalization.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageAdaptiveBinalization
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-s[ize]             Size                (10        )] :Optional  :Size of area to average
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-s[ize]             Size                (10        ).as(Integer             ) ] :Optional  :Size of area to average
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageAdd.html b/doc/SmallTools/mrcImageAdd.html
index 2a2c751..e850da9 100644
--- a/doc/SmallTools/mrcImageAdd.html
+++ b/doc/SmallTools/mrcImageAdd.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcImageAdd
 Options:
-    [-i1[input1]         In1                 (NULL      )] :Optional  :InputDataFile1
-    [-i2[input2]         In2                 (NULL      )] :Optional  :InputDataFile2
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-I[nput array of file]In                  (stdin     )] :Optional  :InputDataFiles
+    [-i1[input1]         In1                 (NULL      ).as(inFile              ) ] :Optional  :InputDataFile1
+    [-i2[input2]         In2                 (NULL      ).as(inFile              ) ] :Optional  :InputDataFile2
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-I[nput array of file]In                  (stdin     ).as(inFileListNoOpen    ) ] :Optional  :InputDataFiles
 ----- Additional Usage -----
 mode 0:Add 
 mode 1:Add / (Number of Pictures)
diff --git a/doc/SmallTools/mrcImageAddValue.html b/doc/SmallTools/mrcImageAddValue.html
index 99bfc4e..7e391e6 100644
--- a/doc/SmallTools/mrcImageAddValue.html
+++ b/doc/SmallTools/mrcImageAddValue.html
@@ -8,8 +8,8 @@
 <PRE>
 Usage: mrcImageAddValue
 Options:
-    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: mrc
-    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output: mrc
+    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input: mrc
+    [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Essential :Output: mrc
     [-v[alue]            Value               (0.0       ).as(Real                ) ] :Optional  :Value: o=i+v
     [-cuda               cudaDeviceID        (0         ).as(Integer             ) ] :Optional  :UseCuda
     [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
diff --git a/doc/SmallTools/mrcImageAreaCalc.html b/doc/SmallTools/mrcImageAreaCalc.html
index 33d5adf..7395391 100644
--- a/doc/SmallTools/mrcImageAreaCalc.html
+++ b/doc/SmallTools/mrcImageAreaCalc.html
@@ -8,12 +8,14 @@
 <PRE>
 Usage: mrcImageAreaCalc
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: mrcImage
-    [-o[utput]           Out                 (NULL      )] :Essential :Output: mrcImage:area
-    [-O[utput]           OutInfo             (stdout    )] :Optional  :Output: ASCII: area info
-    [-l[abel]            Label               (NULL      )] :Optional  :Output: mrcImage:labeling
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input: mrcImage
+    [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Essential :Output: mrcImage:area
+    [-O[utput]           OutInfo             (stdout    ).as(outFile::ASCII      ) ] :Optional  :Output: ASCII: area info
+    [-l[abel]            Label               (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output: mrcImage:labeling
+    [-O[utput]H[istgram] OutHist             (NULL      ).as(outFile::ASCII      ) ] :Optional  :Output: ASCII: area info
+    [-H[istgram]         DelHist             (1         ).as(Real                ) ] :Optional  :Delta
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageAssignedToTFofPDB.html b/doc/SmallTools/mrcImageAssignedToTFofPDB.html
index 8b30423..e8d0dba 100644
--- a/doc/SmallTools/mrcImageAssignedToTFofPDB.html
+++ b/doc/SmallTools/mrcImageAssignedToTFofPDB.html
@@ -8,13 +8,13 @@
 <PRE>
 Usage: mrcImageAssignedToTFofPDB
 Options:
-    [-i[nput]            In                  ] :Essential :InputDataFile(mrcImage)
-    [-p[dbFile]          InPDB               ] :Essential :InputDataFile(pdbFile)
-    [-o[utput]           Out                 ] :Essential :OutputDataFile(pdbFile)
-    [-H[igh]             HighLevel           ] :Optional  :HighLevel
-    [-L[ow]              LowLevel            ] :Optional  :LowLevel
-    [-c[onfig]           configFile          ] :Optional  :ConfigurationFile
-    [-m[ode]             mode                ] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile(mrcImage)
+    [-p[dbFile]          InPDB               (NULL      ).as(inFile              ) ] :Essential :InputDataFile(pdbFile)
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile(pdbFile)
+    [-H[igh]             HighLevel           (0.0       ).as(Real                ) ] :Optional  :HighLevel
+    [-L[ow]              LowLevel            (-1.0      ).as(Real                ) ] :Optional  :LowLevel
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 >>> Mode:	
 	0: Default.
 	1 : Origin is Center  (1) or BottomLeft (0).
diff --git a/doc/SmallTools/mrcImageAutoCorrelationWithWindowing.html b/doc/SmallTools/mrcImageAutoCorrelationWithWindowing.html
index d17af3a..e67c823 100644
--- a/doc/SmallTools/mrcImageAutoCorrelationWithWindowing.html
+++ b/doc/SmallTools/mrcImageAutoCorrelationWithWindowing.html
@@ -8,12 +8,13 @@
 <PRE>
 Usage: mrcImageAutoCorrelationWithWindowing
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-O[utput]           OutWin              (NULL      )] :Optional  :Output WindowedFile
-    [-W[indowing]y       Wy                  (6         )] :Optional  :Window Height: N.y * 1/Wy
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input
+    [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Essential :Output
+    [-o[utput]c[entre]   OutCentre           (NULL      ).as(outFile::mrcImage   ) ] :Optional  :OutputDataFile
+    [-O[utput]           OutWin              (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output WindowedFile
+    [-W[indowing]y       Wy                  (6         ).as(Real                ) ] :Optional  :Window Height: N.y * 1/Wy
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageAutoFilamentExtract.html b/doc/SmallTools/mrcImageAutoFilamentExtract.html
index e4525d3..e8160b8 100644
--- a/doc/SmallTools/mrcImageAutoFilamentExtract.html
+++ b/doc/SmallTools/mrcImageAutoFilamentExtract.html
@@ -8,27 +8,34 @@
 <PRE>
 Usage: mrcImageAutoFilamentExtract
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-i[nput]S[ource]fileInS                 (NULL      )] :Essential :InputSourceFile
-    [-o[utput]E[xtract]  OutE                (NULL      )] :Essential :OutputFileForExtraction
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output Log File
-    [-o[utput]F[inal]    OutF                (stdout    )] :Optional  :OutputFinalFile
-    [-r[oi]ROI           blx                 (0.0       )bly                 (0.0       )brx                 (0.0       )bry                 (0.0       )trx                 (0.0       )try                 (0.0       )tlx                 (0.0       )tly                 (0.0       )] :Optional  :Rectangle ROI 
-    [-r[oi]Unbent        roiLine             (0.0       )... ] :Variable  :
-    [-x                  x                   (120       )] :Optional  :x range for ROI or Unbent
-    [-d[elta]dYmax       ddYmax              (0.9       )] :Optional  :delta dY max
-    [-d[elta]dYmin       ddYmin              (0.2       )] :Optional  :delta dY mim
-    [-T[ransepose]       T                   (0         )] :Optional  :corresponding to mrcImageTransepose mode
-    [-maxd[elta]Y        maxdY               (12        )] :Optional  :Maximum number of layer line
-    [-H[eight] R[ange]   HeightRange         (0         )] :Optional  :Height Range [Pixel]
-    [-RMaxX              RMaxX               (0.05      )] :Optional  :RMaxX [1/A] (supported mode 1)
-    [-mag                mag                 (1.1       )] :Optional  :magnification ratio
-    [-truePitch          truePitch           (430       )] :Optional  :True Pitch [A]
-    [-PixelSize          PixelSize           (5         )] :Optional  :Pixel Size [A]
-    [-finaly             finaly              (0         )] :Optional  :final y [pixel] for extraction
-    [-Ignore             Ignore              (0         )] :Optional  :Ignore the final y 
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-i[nput]S[ource]fileInS                 (NULL      ).as(inFile              ) ] :Essential :InputSourceFile
+    [-o[utput]E[xtract]  OutE                (NULL      ).as(inFile              ) ] :Essential :OutputFileForExtraction
+    [-o[utput]           Out                 (stdout    ).as(appendFile          ) ] :Optional  :Output Log File
+    [-o[utput]F[inal]    OutF                (stdout    ).as(outFile             ) ] :Optional  :OutputFinalFile
+    [-r[oi]ROI           blx                 (0.0       ).as(Real                ) 
+                         bly                 (0.0       ).as(Real                ) 
+                         brx                 (0.0       ).as(Real                ) 
+                         bry                 (0.0       ).as(Real                ) 
+                         trx                 (0.0       ).as(Real                ) 
+                         try                 (0.0       ).as(Real                ) 
+                         tlx                 (0.0       ).as(Real                ) 
+                         tly                 (0.0       ).as(Real                ) ] :Optional  :Rectangle ROI 
+    [-r[oi]Unbent        roiLine             (0.0       ).as(Real                ) ... ] :Variable  :
+    [-x                  x                   (120       ).as(Real                ) ] :Optional  :x range for ROI or Unbent
+    [-d[elta]dYmax       ddYmax              (0.9       ).as(Real                ) ] :Optional  :delta dY max
+    [-d[elta]dYmin       ddYmin              (0.2       ).as(Real                ) ] :Optional  :delta dY mim
+    [-T[ransepose]       T                   (0         ).as(Integer             ) ] :Optional  :corresponding to mrcImageTransepose mode
+    [-maxd[elta]Y        maxdY               (12        ).as(Integer             ) ] :Optional  :Maximum number of layer line
+    [-H[eight] R[ange]   HeightRange         (0         ).as(Integer             ) ] :Optional  :Height Range [Pixel]
+    [-RMaxX              RMaxX               (0.05      ).as(Real                ) ] :Optional  :RMaxX [1/A] (supported mode 1)
+    [-mag                mag                 (1.1       ).as(Real                ) ] :Optional  :magnification ratio
+    [-truePitch          truePitch           (430       ).as(Real                ) ] :Optional  :True Pitch [A]
+    [-PixelSize          PixelSize           (5         ).as(Real                ) ] :Optional  :Pixel Size [A]
+    [-finaly             finaly              (0         ).as(Integer             ) ] :Optional  :final y [pixel] for extraction
+    [-Ignore             Ignore              (0         ).as(Integer             ) ] :Optional  :Ignore the final y 
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 ----- mode -----
 0 : Meridian Reflection 
diff --git a/doc/SmallTools/mrcImageAutoFilamentExtractResultAnalysis.html b/doc/SmallTools/mrcImageAutoFilamentExtractResultAnalysis.html
index 89fb6fd..fb22ebc 100644
--- a/doc/SmallTools/mrcImageAutoFilamentExtractResultAnalysis.html
+++ b/doc/SmallTools/mrcImageAutoFilamentExtractResultAnalysis.html
@@ -8,15 +8,15 @@
 <PRE>
 Usage: mrcImageAutoFilamentExtractResultAnalysis
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Optional  :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-truePitch          truePitch           (430       )] :Optional  :True Pitch
-    [-PixelSize          PixelSize           (5         )] :Optional  :Pixel Size [A]
-    [-deltadY            deltadY             (0.5       )] :Optional  :A range of deltadY to determine dY.
-    [-y                  y                   (0         )] :Optional  :y [pixel] for final extraction
-    [-Mag                mag                 (1.1       )] :Optional  :magnification ratio
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-truePitch          truePitch           (430       ).as(Real                ) ] :Optional  :True Pitch
+    [-PixelSize          PixelSize           (5         ).as(Real                ) ] :Optional  :Pixel Size [A]
+    [-deltadY            deltadY             (0.5       ).as(Real                ) ] :Optional  :A range of deltadY to determine dY.
+    [-y                  y                   (0         ).as(Integer             ) ] :Optional  :y [pixel] for final extraction
+    [-Mag                mag                 (1.1       ).as(Real                ) ] :Optional  :magnification ratio
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageAutoRotationCorrelation.html b/doc/SmallTools/mrcImageAutoRotationCorrelation.html
index 592e7cc..383873f 100644
--- a/doc/SmallTools/mrcImageAutoRotationCorrelation.html
+++ b/doc/SmallTools/mrcImageAutoRotationCorrelation.html
@@ -8,49 +8,62 @@
 <PRE>
 Usage: mrcImageAutoRotationCorrelation
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: testImage [mrcImage]
-    [-r[eference]        Ref                 (NULL      )] :Essential :Input: refImage [mrcImage]
-    [-nRot1              nRot1               (1         )] :Optional  :Rotation number of Ref for Rot1: Def 1
-    [-nRot2              nRot2               (1         )] :Optional  :Rotation number of Ref for Rot2: Def 1
-    [-nRot3              nRot3               (1         )] :Optional  :Rotation number of Ref for Rot3: Def 1
-    [-dRot1              dRot1               (1.0       )] :Optional  :Delta Angle [Degree] of Ref for Rot1; Def.: 360/nRot1
-    [-dRot2              dRot2               (1.0       )] :Optional  :Delta Angle [Degree] of Ref for Rot2; Def.: 360/nRot2
-    [-dRot3              dRot3               (1.0       )] :Optional  :Delta Angle [Degree] of Ref for Rot3; Def.: 360/nRot3
-    [-startRot1          startRot1           (0.0       )] :Optional  :Start Angle [Degree] of Ref for Rot1; Def.: 0
-    [-startRot2          startRot2           (0.0       )] :Optional  :Start Angle [Degree] of Ref for Rot2; Def.: 0
-    [-startRot3          startRot3           (0.0       )] :Optional  :Start Angle [Degree] of Ref for Rot3; Def.: 0
-    [-StackOrder         StackOrder          (0         )] :Optional  :Stack Order for Stacked 2D of references, refer to attention
-    [-o[utput]           Out                 (NULL      )] :Optional  :Output: Parameter [mrcImage-format]
-    [-O[utput]           OutASC              (stdout    )] :Optional  :Output: Parameter [ASCII] 
-    [-cor[relation]      corFile             (NULL      )] :Optional  :Correation Map at Maximum (Linear) [mrcImage-format]
-    [-cor[relation]2     corFile2            (NULL      )] :Optional  :Correation Map2 at Maximum (Set Mode Correlation)[mrcImage-format]
-    [-cor[relation]All   corAllFile          (NULL      )] :Optional  :Correation Map with All Rotation [mrcImage-format]
-    [-fit[tedToRef]      fitFile             (NULL      )] :Optional  :Output: rotatedImage at Maximum(Linear Correlation) [mrcImage]
-    [-fit[tedToRef]2     fitFile2            (NULL      )] :Optional  :Output: rotatedImage at Maximum(Set Correlation mode) [mrcImage]
-    [-RefineMode         RefineMode          (0         )] :Optional  :RefinementStep: Linear:0 or SetMode:1
-    [-n[umber]           Rot                 (36        )] :Optional  :Input: Rotation around the vertical axis against image plane: dRot = 360/n [degree]
-    [-range              minAngle            (-5.0      )maxAngle            (5.0       )] :Optional  :Input: SearchRange: Rotation around the vertical axis against image plane 
-    [-refStep1           refStep1            (1         )] :Optional  :SearchStep for Ref: Each Image along Rot1
-    [-refStep2           refStep2            (1         )] :Optional  :SearchStep for Ref: Each Image along Rot2
-    [-refStep3           refStep3            (1         )] :Optional  :SearchStep for Ref: Each Image along Rot3
-    [-nRot1Area          nRot1AreaMin        (-360      )nRot1AreaMax        (360       )nRot1AreaStep       (25        )] :Optional  :number of Ref for Rot1
-    [-nRot2Area          nRot2AreaMin        (-360      )nRot2AreaMax        (360       )nRot2AreaStep       (25        )] :Optional  :number of Ref for Rot2
-    [-nRot3Area          nRot3AreaMin        (-360      )nRot3AreaMax        (360       )nRot3AreaStep       (25        )] :Optional  :number of Ref for Rot3
-    [-Iter[ation]        Iter                (1         )] :Optional  :Iteration for Rotation around the vertical axis against image plane
-    [-Method             Method              (0         )] :Optional  :0: Correlation, 1: SSDA
-    [-s[earchRegion]     sminx               (0         )sminy               (0         )smaxx               (0/*N.x-1*/)smaxy               (0/*N.y-1*/)] :Optional  :SearchRegion [pixel]: used in lmrcImageAutoRotationCorrelation 
-    [-Shift              ] :Optional  :Image Shift, when in > ref
-    [-RepeatX            RepeatX             (27.3      )] :Optional  :RepeatX[A]
-    [-RepeatXDelta       RepeatXDelta        (5         )] :Optional  :RepeatXDelta[A]
-    [-RepeatY            RepeatY             (27.3      )] :Optional  :RepeatY[A]
-    [-RepeatYDelta       RepeatYDelta        (5         )] :Optional  :RepeatYDelta[A]
-    [-Xshift             ] :Optional  :X-Shift Only
-    [-NoShift            ] :Optional  :No-Shift
-    [-Log                Log                 (stdout    )] :Optional  :Output: LogFile
-    [-pvm                pvm                 (1         )] :Optional  :Task Number
-    [-pvmList            pvmList             (NULL      )] :Optional  :ConfigurationFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: testImage [mrcImage]
+    [-r[eference]        Ref                 (NULL      ).as(inFile              ) ] :Essential :Input: refImage [mrcImage]
+    [-nRot1              nRot1               (1         ).as(Integer             ) ] :Optional  :Rotation number of Ref for Rot1: Def 1
+    [-nRot2              nRot2               (1         ).as(Integer             ) ] :Optional  :Rotation number of Ref for Rot2: Def 1
+    [-nRot3              nRot3               (1         ).as(Integer             ) ] :Optional  :Rotation number of Ref for Rot3: Def 1
+    [-dRot1              dRot1               (1.0       ).as(Real                ) ] :Optional  :Delta Angle [Degree] of Ref for Rot1; Def.: 360/nRot1
+    [-dRot2              dRot2               (1.0       ).as(Real                ) ] :Optional  :Delta Angle [Degree] of Ref for Rot2; Def.: 360/nRot2
+    [-dRot3              dRot3               (1.0       ).as(Real                ) ] :Optional  :Delta Angle [Degree] of Ref for Rot3; Def.: 360/nRot3
+    [-startRot1          startRot1           (0.0       ).as(Real                ) ] :Optional  :Start Angle [Degree] of Ref for Rot1; Def.: 0
+    [-startRot2          startRot2           (0.0       ).as(Real                ) ] :Optional  :Start Angle [Degree] of Ref for Rot2; Def.: 0
+    [-startRot3          startRot3           (0.0       ).as(Real                ) ] :Optional  :Start Angle [Degree] of Ref for Rot3; Def.: 0
+    [-StackOrder         StackOrder          (0         ).as(Integer             ) ] :Optional  :Stack Order for Stacked 2D of references, refer to attention
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :Output: Parameter [mrcImage-format]
+    [-O[utput]           OutASC              (stdout    ).as(outFile             ) ] :Optional  :Output: Parameter [ASCII] 
+    [-cor[relation]      corFile             (NULL      ).as(outFile             ) ] :Optional  :Correation Map at Maximum (Linear) [mrcImage-format]
+    [-cor[relation]2     corFile2            (NULL      ).as(outFile             ) ] :Optional  :Correation Map2 at Maximum (Set Mode Correlation)[mrcImage-format]
+    [-cor[relation]All   corAllFile          (NULL      ).as(outFile             ) ] :Optional  :Correation Map with All Rotation [mrcImage-format]
+    [-fit[tedToRef]      fitFile             (NULL      ).as(outFile             ) ] :Optional  :Output: rotatedImage at Maximum(Linear Correlation) [mrcImage]
+    [-fit[tedToRef]2     fitFile2            (NULL      ).as(outFile             ) ] :Optional  :Output: rotatedImage at Maximum(Set Correlation mode) [mrcImage]
+    [-RefineMode         RefineMode          (0         ).as(Integer             ) ] :Optional  :RefinementStep: Linear:0 or SetMode:1
+    [-n[umber]           Rot                 (36        ).as(Real                ) ] :Optional  :Input: Rotation around the vertical axis against image plane: dRot = 360/n [degree]
+    [-range              minAngle            (-5.0      ).as(Real                ) 
+                         maxAngle            (5.0       ).as(Real                ) ] :Optional  :Input: SearchRange: Rotation around the vertical axis against image plane 
+    [-refStep1           refStep1            (1         ).as(Integer             ) ] :Optional  :SearchStep for Ref: Each Image along Rot1
+    [-refStep2           refStep2            (1         ).as(Integer             ) ] :Optional  :SearchStep for Ref: Each Image along Rot2
+    [-refStep3           refStep3            (1         ).as(Integer             ) ] :Optional  :SearchStep for Ref: Each Image along Rot3
+    [-nRot1Area          nRot1AreaMin        (-360      ).as(Real                ) 
+                         nRot1AreaMax        (360       ).as(Real                ) 
+                         nRot1AreaStep       (25        ).as(Real                ) ] :Optional  :number of Ref for Rot1
+    [-nRot2Area          nRot2AreaMin        (-360      ).as(Real                ) 
+                         nRot2AreaMax        (360       ).as(Real                ) 
+                         nRot2AreaStep       (25        ).as(Real                ) ] :Optional  :number of Ref for Rot2
+    [-nRot3Area          nRot3AreaMin        (-360      ).as(Real                ) 
+                         nRot3AreaMax        (360       ).as(Real                ) 
+                         nRot3AreaStep       (25        ).as(Real                ) ] :Optional  :number of Ref for Rot3
+    [-MagRange           MagRangeMin         (1.0       ).as(Real                ) 
+                         MagRangeMax         (1.0       ).as(Real                ) 
+                         MagRangeStep        (0.1       ).as(Real                ) ] :Optional  :Magnification Range
+    [-Iter[ation]        Iter                (1         ).as(Integer             ) ] :Optional  :Iteration for Rotation around the vertical axis against image plane
+    [-Method             Method              (0         ).as(Integer             ) ] :Optional  :0: Correlation, 1: SSDA
+    [-s[earchRegion]     sminx               (0         ).as(Real                ) 
+                         sminy               (0         ).as(Real                ) 
+                         smaxx               (0/*N.x-1*/).as(Real                ) 
+                         smaxy               (0/*N.y-1*/).as(Real                ) ] :Optional  :SearchRegion [pixel]: used in lmrcImageAutoRotationCorrelation 
+    [-Shift                                                                        ] :Optional  :Image Shift, when in > ref
+    [-RepeatX            RepeatX             (27.3      ).as(Real                ) ] :Optional  :RepeatX[A]
+    [-RepeatXDelta       RepeatXDelta        (5         ).as(Real                ) ] :Optional  :RepeatXDelta[A]
+    [-RepeatY            RepeatY             (27.3      ).as(Real                ) ] :Optional  :RepeatY[A]
+    [-RepeatYDelta       RepeatYDelta        (5         ).as(Real                ) ] :Optional  :RepeatYDelta[A]
+    [-Xshift                                                                       ] :Optional  :X-Shift Only
+    [-NoShift                                                                      ] :Optional  :No-Shift
+    [-Log                Log                 (stdout    ).as(outFile             ) ] :Optional  :Output: LogFile
+    [-pvm                pvm                 (1         ).as(Integer             ) ] :Optional  :Task Number
+    [-pvmList            pvmList             (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Mode -----
 When, -Method 0(Default:Correlation)
 0: Normal Correlation FxG*
diff --git a/doc/SmallTools/mrcImageAutoRotationCorrelation3D.html b/doc/SmallTools/mrcImageAutoRotationCorrelation3D.html
index 9d06763..0099cfb 100644
--- a/doc/SmallTools/mrcImageAutoRotationCorrelation3D.html
+++ b/doc/SmallTools/mrcImageAutoRotationCorrelation3D.html
@@ -8,22 +8,31 @@
 <PRE>
 Usage: mrcImageAutoRotationCorrelation3D
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: mrc[test]
-    [-r[ef]              Ref                 (NULL      )] :Essential :Input: mrc[ref]
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output: Parameter
-    [-cor                Cor                 (NULL      )] :Optional  :Output: CorMap
-    [-fit                Fit                 (stdout    )] :Optional  :Output: Best Fit
-    [-E[uler]A[ngle]     EulerAngle          (YOYS      )] :Optional  :Input: EulerAngle
-    [-Rot1               Rot1Min             (0.0       )Rot1Max             (360.0     )Rot1Delta           (5.0       )] :Optional  :Rot1
-    [-Rot2               Rot2Min             (0.0       )Rot2Max             (180.0     )Rot2Delta           (5.0       )] :Optional  :Rot2
-    [-Rot3               Rot3Min             (0.0       )Rot3Max             (360.0     )Rot3Delta           (5.0       )] :Optional  :Rot3
-    [-Xrange             XrangeMin           (0         )XrangeMax           (0         )] :Optional  :Xrange[pixel]: Not set, all space search
-    [-Yrange             YrangeMin           (0         )YrangeMax           (0         )] :Optional  :Yrange[pixel]: Not set, all space search
-    [-Zrange             ZrangeMin           (0         )ZrangeMax           (0         )] :Optional  :Zrange[pixel]: Not set, all space search
-    [-M[ode]             Mode                (0         )] :Optional  :Mode: Correlation Mode
-    [-M[ode]R[otation]   ModeRotation        (0         )] :Optional  :Mode: Rotation3D Mode
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode: InterpolationMode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: mrc[test]
+    [-r[ef]              Ref                 (NULL      ).as(inFile              ) ] :Essential :Input: mrc[ref]
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output: Parameter
+    [-cor                Cor                 (NULL      ).as(outFile             ) ] :Optional  :Output: CorMap
+    [-fit                Fit                 (stdout    ).as(outFile             ) ] :Optional  :Output: Best Fit
+    [-E[uler]A[ngle]     EulerAngle          (YOYS      ).as(String              ) ] :Optional  :Input: EulerAngle
+    [-Rot1               Rot1Min             (0.0       ).as(Real                ) 
+                         Rot1Max             (360.0     ).as(Real                ) 
+                         Rot1Delta           (5.0       ).as(Real                ) ] :Optional  :Rot1
+    [-Rot2               Rot2Min             (0.0       ).as(Real                ) 
+                         Rot2Max             (180.0     ).as(Real                ) 
+                         Rot2Delta           (5.0       ).as(Real                ) ] :Optional  :Rot2
+    [-Rot3               Rot3Min             (0.0       ).as(Real                ) 
+                         Rot3Max             (360.0     ).as(Real                ) 
+                         Rot3Delta           (5.0       ).as(Real                ) ] :Optional  :Rot3
+    [-Xrange             XrangeMin           (0         ).as(Real                ) 
+                         XrangeMax           (0         ).as(Real                ) ] :Optional  :Xrange[pixel]: Not set, all space search
+    [-Yrange             YrangeMin           (0         ).as(Real                ) 
+                         YrangeMax           (0         ).as(Real                ) ] :Optional  :Yrange[pixel]: Not set, all space search
+    [-Zrange             ZrangeMin           (0         ).as(Real                ) 
+                         ZrangeMax           (0         ).as(Real                ) ] :Optional  :Zrange[pixel]: Not set, all space search
+    [-M[ode]             Mode                (0         ).as(Integer             ) ] :Optional  :Mode: Correlation Mode
+    [-M[ode]R[otation]   ModeRotation        (0         ).as(Integer             ) ] :Optional  :Mode: Rotation3D Mode
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode: InterpolationMode
 ----- Additional Usage -----
 ----- -M  CorrelationMode -----
 0: Normal Correlation FxG*
diff --git a/doc/SmallTools/mrcImageAutoTriming.html b/doc/SmallTools/mrcImageAutoTriming.html
new file mode 100644
index 0000000..3edeaff
--- /dev/null
+++ b/doc/SmallTools/mrcImageAutoTriming.html
@@ -0,0 +1,33 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageAutoTriming</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageAutoTriming</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageAutoTriming
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input:mrcImage
+    [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Essential :Output:mrcImage
+    [-O[utput]           OutParam            (stdout    ).as(outFile::YAML       ) ] :Optional  :OutputParams:YAML
+    [-E[uler]A[ngle]Mode EAMode              (ZONS      ).as(String              ) ] :Optional  :EulerAngle
+    [-Rot[ation]1        Rot1Min             (-5        ).as(Real                ) 
+                         Rot1Max             (5         ).as(Real                ) 
+                         Rot1Delta           (1         ).as(Real                ) ] :Optional  :Rot1
+    [-Rot[ation]2        Rot2Min             (-5        ).as(Real                ) 
+                         Rot2Max             (5         ).as(Real                ) 
+                         Rot2Delta           (1         ).as(Real                ) ] :Optional  :Rot2
+    [-Rot[ation]3        Rot3Min             (-5        ).as(Real                ) 
+                         Rot3Max             (5         ).as(Real                ) 
+                         Rot3Delta           (1         ).as(Real                ) ] :Optional  :Rot3
+    [-M[ode]             InterpolationMode   (0         ).as(Integer             ) ] :Optional  :Iterpolation Mode
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+>>> mode
+0: z-layer(minimum of z-axis by min)
+1: z-layer(minimum of z-axis by SD)
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageAverage.html b/doc/SmallTools/mrcImageAverage.html
index a6b858f..f150efb 100644
--- a/doc/SmallTools/mrcImageAverage.html
+++ b/doc/SmallTools/mrcImageAverage.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcImageAverage
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: Image File List
-    [-w[eight]           InWeight            (NULL      )] :Optional  :Input: Weight File List
-    [-o[utput]           Out                 (NULL      )] :Essential :Output: Average
-    [-o[utput]W[eight]   OutWeight           (NULL      )] :Optional  :Output: Weight
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFileList          ) ] :Essential :Input: Image File List
+    [-w[eight]           InWeight            (NULL      ).as(inFileList          ) ] :Optional  :Input: Weight File List
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output: Average
+    [-o[utput]W[eight]   OutWeight           (NULL      ).as(outFile             ) ] :Optional  :Output: Weight
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageBandPassFilter.html b/doc/SmallTools/mrcImageBandPassFilter.html
index c037f8f..b421280 100644
--- a/doc/SmallTools/mrcImageBandPassFilter.html
+++ b/doc/SmallTools/mrcImageBandPassFilter.html
@@ -8,15 +8,15 @@
 <PRE>
 Usage: mrcImageBandPassFilter
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-h[alf]v[aluepoint]l[ow]hvl                 (1.0       )] :Optional  :HalfValuePointLow
-    [-h[alf]v[aluepoint]h[igh]hvh                 (1.0       )] :Optional  :HalfValuePointHigh
-    [-w[idth]l[ow]       wl                  (1.0       )] :Optional  :WidthOfDumpingLow
-    [-w[idth]h[igh]      wh                  (1.0       )] :Optional  :WidthOfDumpingHigh
-    [-lowweight          lowWeight           (0.0       )] :Optional  :Weight of Low Freq.
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-h[alf]v[aluepoint]l[ow]hvl                 (1.0       ).as(Real                ) ] :Optional  :HalfValuePointLow
+    [-h[alf]v[aluepoint]h[igh]hvh                 (1.0       ).as(Real                ) ] :Optional  :HalfValuePointHigh
+    [-w[idth]l[ow]       wl                  (1.0       ).as(Real                ) ] :Optional  :WidthOfDumpingLow
+    [-w[idth]h[igh]      wh                  (1.0       ).as(Real                ) ] :Optional  :WidthOfDumpingHigh
+    [-lowweight          lowWeight           (0.0       ).as(Real                ) ] :Optional  :Weight of Low Freq.
 >>> Mode <<<< 
     1: Step filter : required argumnent: -hvl -hvh
     2: Cos filter  : required argumnent: -hvl -hvh -wl -wh
diff --git a/doc/SmallTools/mrcImageBilateralFilter.html b/doc/SmallTools/mrcImageBilateralFilter.html
index a68e566..a3ad887 100644
--- a/doc/SmallTools/mrcImageBilateralFilter.html
+++ b/doc/SmallTools/mrcImageBilateralFilter.html
@@ -8,17 +8,21 @@
 <PRE>
 Usage: mrcImageBilateralFilter
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-s[igma]D[ensity]   SigmaDensity        (2.0       )] :Optional  :SigmaDensity
-    [-k[ernal]T[type]D[ensity]KernelTypeDensity   (0         )] :Optional  :KernelTypeForDensity
-    [-s[igma]S[pace]     SigmaSpace          (1.0       )] :Optional  :SigmaSpace
-    [-s[igma]S[pace]3    SigmaSpaceX         (1.0       )SigmaSpaceY         (1.0       )SigmaSpaceZ         (1.0       )] :Optional  :SigmaSpace(3D)
-    [-k[ernel]T[ype]S[pace]KernelTypeSpace     (0         )] :Optional  :KernelTypeForSpace
-    [-k[ernel]S[ize]     KernelSize          (5         )] :Optional  :KernelSize
-    [-k[ernel]S[ize]3    KernelSizeX         (5         )KernelSizeY         (5         )KernelSizeZ         (5         )] :Optional  :KernelSize(3D)
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-s[igma]D[ensity]   SigmaDensity        (2.0       ).as(Real                ) ] :Optional  :SigmaDensity
+    [-k[ernal]T[type]D[ensity]KernelTypeDensity   (0         ).as(Integer             ) ] :Optional  :KernelTypeForDensity
+    [-s[igma]S[pace]     SigmaSpace          (1.0       ).as(Real                ) ] :Optional  :SigmaSpace
+    [-s[igma]S[pace]3    SigmaSpaceX         (1.0       ).as(Real                ) 
+                         SigmaSpaceY         (1.0       ).as(Real                ) 
+                         SigmaSpaceZ         (1.0       ).as(Real                ) ] :Optional  :SigmaSpace(3D)
+    [-k[ernel]T[ype]S[pace]KernelTypeSpace     (0         ).as(Integer             ) ] :Optional  :KernelTypeForSpace
+    [-k[ernel]S[ize]     KernelSize          (5         ).as(Integer             ) ] :Optional  :KernelSize
+    [-k[ernel]S[ize]3    KernelSizeX         (5         ).as(Integer             ) 
+                         KernelSizeY         (5         ).as(Integer             ) 
+                         KernelSizeZ         (5         ).as(Real                ) ] :Optional  :KernelSize(3D)
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 Bilateral Filter
     by Tomashi and Manduchi
diff --git a/doc/SmallTools/mrcImageBinalization.html b/doc/SmallTools/mrcImageBinalization.html
index 2aba805..2735fa9 100644
--- a/doc/SmallTools/mrcImageBinalization.html
+++ b/doc/SmallTools/mrcImageBinalization.html
@@ -8,27 +8,34 @@
 <PRE>
 Usage: mrcImageBinalization
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-t[hreshold]        t                   (0         )] :Optional  :Value of threshold
-    [-v[alue]            v                   (0         )] :Optional  :Value
-    [-near               near                (0         )] :Optional  :Near[pixel]: Near-area also binary
-    [-nLevel             nLevel              (256       )] :Optional  :nLevel: For creating histgram by Kittler and Ohtsu 
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-p[tile]            p                   (0.5       )] :Optional  :p
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input:mrcImage
+    [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Essential :Output:mrcImage
+    [-O[utput]           OutParam            (stdout    ).as(outFile::ASCII      ) ] :Optional  :Output:Parameters
+    [-t[hreshold]        t                   (0         ).as(Real                ) ] :Optional  :Value of threshold
+    [-d[elta]t[hreshold] deltaThreshold      (0         ).as(Real                ) ] :Optional  :Difference threshold
+    [-s[igma]t[hreshold] sigmaThreshold      (0.5       ).as(Real                ) ] :Optional  :Sigma threshold(BandPath)
+    [-v[alue]            v                   (0         ).as(Real                ) ] :Optional  :Value
+    [-near               near                (0         ).as(Real                ) ] :Optional  :Near[pixel]: Near-area also binary
+    [-nLevel             nLevel              (256       ).as(Integer             ) ] :Optional  :nLevel: For creating histgram by Kittler and Ohtsu 
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-p[tile]            p                   (0.5       ).as(Real                ) ] :Optional  :p
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 ----- Additional Usage -----
 mode 0: Under thresHold, 0.     Above thresHold, 1.
      1: Above thresHold, 0.     Under thresHold, 1.
      2: Under thresHold, value. Above thresHold, unchanged.
      3: Above thresHold, value. Under thresHold, unchanged.
-     16: Automatically Determine threshold by Kittler Method
-     32: Automatically Determine threshold by Ohtsu Method
-     48: Automatically Determine threshold by p-tile Method
+     4: thresHold +- sigma, 1.     Others 0.
+     5: thresHold +- sigma, 0.     Others 1.
+     6: thresHold +- sigma, unchanged. Others value.
+     7: thresHold +- sigma, value.     Others unchanged.
+     +16: Automatically Determine threshold by Kittler Method
+     +32: Automatically Determine threshold by Ohtsu Method
+     +48: Automatically Determine threshold by p-tile Method
           p range: 0.0 - 1.0
-     64: Automatically Determine threshold by Differential-Histogram Method
-     80: Automatically Determine threshold by Laplacian-Histogram Method
+     +64: Automatically Determine threshold by Differential-Histogram Method
+     +80: Automatically Determine threshold by Laplacian-Histogram Method
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageBlockMerge.html b/doc/SmallTools/mrcImageBlockMerge.html
index bd846ea..31a1b29 100644
--- a/doc/SmallTools/mrcImageBlockMerge.html
+++ b/doc/SmallTools/mrcImageBlockMerge.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: mrcImageBlockMerge
 Options:
-    [-I[nput array of file]In                  (stdin     )] :Essential :InputDataFiles
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-I[nput array of file]In                  (stdin     ).as(inFileListNoOpen    ) ] :Essential :InputDataFiles
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageBoundaryInfo.html b/doc/SmallTools/mrcImageBoundaryInfo.html
index 4de78cc..f087355 100644
--- a/doc/SmallTools/mrcImageBoundaryInfo.html
+++ b/doc/SmallTools/mrcImageBoundaryInfo.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: mrcImageBoundaryInfo
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: mrc-format
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output: ascii
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageCCDNoiseRemove.html b/doc/SmallTools/mrcImageCCDNoiseRemove.html
index 3cf625c..a5b7f79 100644
--- a/doc/SmallTools/mrcImageCCDNoiseRemove.html
+++ b/doc/SmallTools/mrcImageCCDNoiseRemove.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageCCDNoiseRemove
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: mrc
-    [-N[oise]            InNoise             (NULL      )] :Essential :Input: noise information
-    [-o[utput]           Out                 (NULL      )] :Essential :Output: mrc
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: mrc
+    [-N[oise]            InNoise             (NULL      ).as(inFile              ) ] :Essential :Input: noise information
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output: mrc
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 mode: 0   	random values
 mode: 1   	neighbor point's values
diff --git a/doc/SmallTools/mrcImageCTFCompensation.html b/doc/SmallTools/mrcImageCTFCompensation.html
index 3e169c9..5323124 100644
--- a/doc/SmallTools/mrcImageCTFCompensation.html
+++ b/doc/SmallTools/mrcImageCTFCompensation.html
@@ -8,20 +8,23 @@
 <PRE>
 Usage: mrcImageCTFCompensation
 Options:
-    [-i[nput]            In                  (stdin     )] :Essential :InputFile
-    [-o[utput]           Out                 (stdout    )] :Essential :OutputDataFile
-    [-info[mation]       Info                (NULL      )] :Optional  :InformationFile(Essense only)
-    [-info[mation]2      Info2               (NULL      )] :Optional  :InformationFile2(Display2 ctfinfo format)
-    [-kV                 kV                  (200       )] :Optional  :AccVol[kV]
-    [-Cs                 Cs                  (2.1       )] :Optional  :Cs[mm]
-    [-df                 Defocus             (27000     )] :Optional  :Defocus[A]:under(+)
-    [-white              WhiteNoise          (0.1       )] :Optional  :WhiteNoise(N/S)
-    [-SinWin             SinWinRmin          (0.1       )SinWinRmax          (1.0       )] :Optional  :Windowing by sine function from Rmin[/A] to Rmax[/A].Default: No Window.
-    [-A[mplitude contrast]Amp                 (0.1       )] :Optional  :The ratio of amplitude contrast to phase contrast
-    [-Astig[matism]      dfMin               (0         )dfMax               (0         )asAxis              (0         )] :Optional  :With Astigmatism
-    [-NoAstig[matism]    ] :Optional  :Without Astigmatism
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (stdin     ).as(inFile              ) ] :Essential :InputFile
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Essential :OutputDataFile
+    [-info[mation]       Info                (NULL      ).as(inFile              ) ] :Optional  :InformationFile(Essense only)
+    [-info[mation]2      Info2               (NULL      ).as(inFile              ) ] :Optional  :InformationFile2(Display2 ctfinfo format)
+    [-kV                 kV                  (200       ).as(Real                ) ] :Optional  :AccVol[kV]
+    [-Cs                 Cs                  (2.1       ).as(Real                ) ] :Optional  :Cs[mm]
+    [-df                 Defocus             (27000     ).as(Real                ) ] :Optional  :Defocus[A]:under(+)
+    [-white              WhiteNoise          (0.1       ).as(Real                ) ] :Optional  :WhiteNoise(N/S)
+    [-SinWin             SinWinRmin          (0.1       ).as(Real                ) 
+                         SinWinRmax          (1.0       ).as(Real                ) ] :Optional  :Windowing by sine function from Rmin[/A] to Rmax[/A].Default: No Window.
+    [-A[mplitude contrast]Amp                 (0.1       ).as(Real                ) ] :Optional  :The ratio of amplitude contrast to phase contrast
+    [-Astig[matism]      dfMin               (0         ).as(Real                ) 
+                         dfMax               (0         ).as(Real                ) 
+                         asAxis              (0         ).as(Real                ) ] :Optional  :With Astigmatism
+    [-NoAstig[matism]                                                              ] :Optional  :Without Astigmatism
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- mode -----
 mode 0: No Correction
 mode 1: x ctf/|ctf|, phase flipping
diff --git a/doc/SmallTools/mrcImageCTFCompensationForTiltImage.html b/doc/SmallTools/mrcImageCTFCompensationForTiltImage.html
index 760f7ad..4b9e574 100644
--- a/doc/SmallTools/mrcImageCTFCompensationForTiltImage.html
+++ b/doc/SmallTools/mrcImageCTFCompensationForTiltImage.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcImageCTFCompensationForTiltImage
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-I[nformation]      Info                (NULL      )] :Essential :Infomation
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [cut[Back]           cut                 (6         )] :Optional  :Cut
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-I[nformation]      Info                (NULL      ).as(inFile              ) ] :Essential :Infomation
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [cut[Back]           cut                 (6         ).as(Integer             ) ] :Optional  :Cut
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageCTFDetermination.html b/doc/SmallTools/mrcImageCTFDetermination.html
index 3f14adf..9a6d220 100644
--- a/doc/SmallTools/mrcImageCTFDetermination.html
+++ b/doc/SmallTools/mrcImageCTFDetermination.html
@@ -8,33 +8,39 @@
 <PRE>
 Usage: mrcImageCTFDetermination
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-r[eference]        Ref                 (NULL      )] :Essential :ReferenceDataFile
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output Optimum [text]
-    [-oP[utput]          Out2                (NULL      )] :Optional  :Output Distribution [mrc image]
-    [-oC[utput]          OutC                (NULL      )] :Optional  :Output CTF Information file
-    [-oF[utput]          OutF                (NULL      )] :Optional  :Output Result FFT[mrc image]
-    [-kV                 kV                  (200       )] :Optional  :AccVol[kV]
-    [-Cs                 Cs                  (2.1       )] :Optional  :Cs[mm]
-    [-Ain                Ain                 (0.02      )] :Optional  :IlluminationAperture[mrad]
-    [-W[hiteNoise]       WhiteNoise          (1.0       )] :Optional  :
-    [-df                 mindf               (0.0       )maxdf               (200000    )deldf               (1000      )] :Optional  :df[A] for in
-    [-AoverP             minAoverP           (0.0       )maxAoverP           (1.0       )delAoverP           (0.01      )] :Optional  :AoverP[A] for in
-    [-Rmin               Rmin                (0.0       )] :Optional  :Rmin[/A]
-    [-Rmax               Rmax                (0.1       )] :Optional  :Rmax[/A]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]F[ilter type]mF                  (1         )] :Optional  :Filter Type
-    [-m[ode]W[ight type] mW                  (0         )] :Optional  :Wight Type
-    [-m[ode]S[um type]   mS                  (0         )] :Optional  :Sum Type
-    [-m[ode]C[TF Info type]mC                  (0         )] :Optional  :CTF Information Type
-    [-M[ode]             M                   (0         )] :Optional  :ref Type
-    [-PixelSize          PixelSize           (5         )] :Optional  :Pixel Size [A]
-    [-Width              Width               (120       )] :Optional  :Pad Width [pixel]
-    [-truePitch          truePitch           (430       )] :Optional  :True Pitch [A]
-    [-dfRef              firstDf             (70000     )withinDf            (1000      )] :Optional  :dfRef for ref
-    [-AoverPRef          firstAoverP         (0.05      )withinAoverP        (0.01      )] :Optional  :A over P Ref for ref
-    [-MaxIter            maxiter             (10        )] :Optional  :MaxIteration for ref
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-r[eference]        Ref                 (NULL      ).as(inFile              ) ] :Essential :ReferenceDataFile
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output Optimum [text]
+    [-oP[utput]          Out2                (NULL      ).as(outFile             ) ] :Optional  :Output Distribution [mrc image]
+    [-oC[utput]          OutC                (NULL      ).as(outFile             ) ] :Optional  :Output CTF Information file
+    [-oF[utput]          OutF                (NULL      ).as(outFile             ) ] :Optional  :Output Result FFT[mrc image]
+    [-kV                 kV                  (200       ).as(Real                ) ] :Optional  :AccVol[kV]
+    [-Cs                 Cs                  (2.1       ).as(Real                ) ] :Optional  :Cs[mm]
+    [-Ain                Ain                 (0.02      ).as(Real                ) ] :Optional  :IlluminationAperture[mrad]
+    [-W[hiteNoise]       WhiteNoise          (1.0       ).as(Real                ) ] :Optional  :
+    [-df                 mindf               (0.0       ).as(Real                ) 
+                         maxdf               (200000    ).as(Real                ) 
+                         deldf               (1000      ).as(Real                ) ] :Optional  :df[A] for in
+    [-AoverP             minAoverP           (0.0       ).as(Real                ) 
+                         maxAoverP           (1.0       ).as(Real                ) 
+                         delAoverP           (0.01      ).as(Real                ) ] :Optional  :AoverP[A] for in
+    [-Rmin               Rmin                (0.0       ).as(Real                ) ] :Optional  :Rmin[/A]
+    [-Rmax               Rmax                (0.1       ).as(Real                ) ] :Optional  :Rmax[/A]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]F[ilter type]mF                  (1         ).as(Integer             ) ] :Optional  :Filter Type
+    [-m[ode]W[ight type] mW                  (0         ).as(Integer             ) ] :Optional  :Wight Type
+    [-m[ode]S[um type]   mS                  (0         ).as(Integer             ) ] :Optional  :Sum Type
+    [-m[ode]C[TF Info type]mC                  (0         ).as(Integer             ) ] :Optional  :CTF Information Type
+    [-M[ode]             M                   (0         ).as(Integer             ) ] :Optional  :ref Type
+    [-PixelSize          PixelSize           (5         ).as(Integer             ) ] :Optional  :Pixel Size [A]
+    [-Width              Width               (120       ).as(Integer             ) ] :Optional  :Pad Width [pixel]
+    [-truePitch          truePitch           (430       ).as(Real                ) ] :Optional  :True Pitch [A]
+    [-dfRef              firstDf             (70000     ).as(Real                ) 
+                         withinDf            (1000      ).as(Real                ) ] :Optional  :dfRef for ref
+    [-AoverPRef          firstAoverP         (0.05      ).as(Real                ) 
+                         withinAoverP        (0.01      ).as(Real                ) ] :Optional  :A over P Ref for ref
+    [-MaxIter            maxiter             (10        ).as(Integer             ) ] :Optional  :MaxIteration for ref
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 ----- mrcFile -----
 in  <- Original Image 
diff --git a/doc/SmallTools/mrcImageCTFObservation.html b/doc/SmallTools/mrcImageCTFObservation.html
index c7e6184..a4efc23 100644
--- a/doc/SmallTools/mrcImageCTFObservation.html
+++ b/doc/SmallTools/mrcImageCTFObservation.html
@@ -8,19 +8,22 @@
 <PRE>
 Usage: mrcImageCTFObservation
 Options:
-    [-i[nput]            In                  (stdin     )] :Essential :InputFile
-    [-o[utput]           Out                 (stdout    )] :Essential :OutputDataFile
-    [-kV                 kV                  (200       )] :Optional  :AccVol[kV]
-    [-Cs                 Cs                  (2.1       )] :Optional  :Cs[mm]
-    [-df                 Defocus             (27000     )] :Optional  :Defocus [A]:under(+)
-    [-A                  AoverP              (0.0       )] :Optional  :AmplitudeContrast/PhaseContrast
-    [-Ain                Ain                 (0.0       )] :Optional  :IlluminationAperture[mrad]
-    [-white              WhiteNoise          (1.0       )] :Optional  :WhiteNoise(N/S)
-    [-SinWin             SinWinRmin          (0.1       )SinWinRmax          (1.0       )] :Optional  :Windowing by sine function from Rmin[A] to Rmax[A]
-    [-ctfMode            ctfMode             (0         )] :Optional  :CTFMode
-    [-Astig[matism]      dfMin               (0         )dfMax               (0         )asAxis              (0         )] :Optional  :With Atigmatism
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (stdin     ).as(inFile              ) ] :Essential :InputFile
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Essential :OutputDataFile
+    [-kV                 kV                  (200       ).as(Real                ) ] :Optional  :AccVol[kV]
+    [-Cs                 Cs                  (2.1       ).as(Real                ) ] :Optional  :Cs[mm]
+    [-df                 Defocus             (27000     ).as(Real                ) ] :Optional  :Defocus [A]:under(+)
+    [-A                  AoverP              (0.0       ).as(Real                ) ] :Optional  :AmplitudeContrast/PhaseContrast
+    [-Ain                Ain                 (0.0       ).as(Real                ) ] :Optional  :IlluminationAperture[mrad]
+    [-white              WhiteNoise          (1.0       ).as(Real                ) ] :Optional  :WhiteNoise(N/S)
+    [-SinWin             SinWinRmin          (0.1       ).as(Real                ) 
+                         SinWinRmax          (1.0       ).as(Real                ) ] :Optional  :Windowing by sine function from Rmin[A] to Rmax[A]
+    [-ctfMode            ctfMode             (0         ).as(Integer             ) ] :Optional  :CTFMode
+    [-Astig[matism]      dfMin               (0         ).as(Real                ) 
+                         dfMax               (0         ).as(Real                ) 
+                         asAxis              (0         ).as(Real                ) ] :Optional  :With Atigmatism
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- ctfMode -----
 -ctfMode 0  : Phase Only
 -ctfMode 1  : Phase and Amplitude 
diff --git a/doc/SmallTools/mrcImageCTFSN.html b/doc/SmallTools/mrcImageCTFSN.html
index a98b231..36c15b0 100644
--- a/doc/SmallTools/mrcImageCTFSN.html
+++ b/doc/SmallTools/mrcImageCTFSN.html
@@ -8,15 +8,15 @@
 <PRE>
 Usage: mrcImageCTFSN
 Options:
-    [-i[nput]            In                  (stdin     )] :Essential :InputFile
-    [-o[utput]           Out                 (stdout    )] :Essential :OutputDataFile
-    [-kV                 kV                  (200       )] :Optional  :AccVol[kV]
-    [-Cs                 Cs                  (1.7       )] :Optional  :Cs[mm]
-    [-df                 Defocus             (2.7       )] :Essential :Defocus[A]:under(+)
-    [-n1                 deg1                (2         )] :Optional  :Degree of zero point minimum
-    [-n2                 deg2                (4         )] :Optional  :Degree of zero point maximum
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (stdin     ).as(inFile              ) ] :Essential :InputFile
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Essential :OutputDataFile
+    [-kV                 kV                  (200       ).as(Real                ) ] :Optional  :AccVol[kV]
+    [-Cs                 Cs                  (1.7       ).as(Real                ) ] :Optional  :Cs[mm]
+    [-df                 Defocus             (2.7       ).as(Real                ) ] :Essential :Defocus[A]:under(+)
+    [-n1                 deg1                (2         ).as(Integer             ) ] :Optional  :Degree of zero point minimum
+    [-n2                 deg2                (4         ).as(Integer             ) ] :Optional  :Degree of zero point maximum
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageCVE.html b/doc/SmallTools/mrcImageCVE.html
index ed5cd8d..d6962e7 100644
--- a/doc/SmallTools/mrcImageCVE.html
+++ b/doc/SmallTools/mrcImageCVE.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcImageCVE
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-sx                 sx                  (25        )] :Optional  :x of Kernel Size
-    [-sy                 sy                  (25        )] :Optional  :y of Kernel Size
-    [-sz                 sz                  (1         )] :Optional  :z of Kernel Size
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-sx                 sx                  (25        ).as(Integer             ) ] :Optional  :x of Kernel Size
+    [-sy                 sy                  (25        ).as(Integer             ) ] :Optional  :y of Kernel Size
+    [-sz                 sz                  (1         ).as(Integer             ) ] :Optional  :z of Kernel Size
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageCenterDensityChange.html b/doc/SmallTools/mrcImageCenterDensityChange.html
index 65c3b83..159866d 100644
--- a/doc/SmallTools/mrcImageCenterDensityChange.html
+++ b/doc/SmallTools/mrcImageCenterDensityChange.html
@@ -8,14 +8,14 @@
 <PRE>
 Usage: mrcImageCenterDensityChange
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-r[adius]min        rmin                (0         )] :Optional  :min radius[A]
-    [-r[adius]max        rmax                (90        )] :Optional  :max radius[A]
-    [-ratio              ratio               (0         )] :Optional  :ratio
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-M[ode]             radiusMode          (0         )] :Optional  :radiusMode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-r[adius]min        rmin                (0         ).as(Real                ) ] :Optional  :min radius[A]
+    [-r[adius]max        rmax                (90        ).as(Real                ) ] :Optional  :max radius[A]
+    [-ratio              ratio               (0         ).as(Real                ) ] :Optional  :ratio
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-M[ode]             radiusMode          (0         ).as(Integer             ) ] :Optional  :radiusMode
 ----- Additional Usage -----
 ----- radiusMode -----
 0: 
diff --git a/doc/SmallTools/mrcImageCenterGet.html b/doc/SmallTools/mrcImageCenterGet.html
index 6e9e837..3681c9d 100644
--- a/doc/SmallTools/mrcImageCenterGet.html
+++ b/doc/SmallTools/mrcImageCenterGet.html
@@ -8,18 +8,18 @@
 <PRE>
 Usage: mrcImageCenterGet
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-Nx[Number of x]    Nx                  (0         )] :Optional  :Nx:Default Nx of inputfile
-    [-Ny[Number of y]    Ny                  (0         )] :Optional  :Ny:Default Ny of inputfile
-    [-Nz[Number of z]    Nz                  (0         )] :Optional  :Nz:Default Nz of inputfile
-    [-Cx[Center x]       Cx                  (0         )] :Optional  :Cetnter x position of extracted image.Default is center of iuput image.
-    [-Cy[Center y]       Cy                  (0         )] :Optional  :Cetnter y position of extracted image.Default is center of iuput image.
-    [-Cz[Center z]       Cz                  (0         )] :Optional  :Cetnter z position of extracted image.Default is center of iuput image.
-    [-even               ] :Optional  :all dimensions of N are even. 
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-M[ode2]            mode2               (0         )] :Optional  :Mode2
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-Nx[Number of x]    Nx                  (0         ).as(Integer             ) ] :Optional  :Nx:Default Nx of inputfile
+    [-Ny[Number of y]    Ny                  (0         ).as(Integer             ) ] :Optional  :Ny:Default Ny of inputfile
+    [-Nz[Number of z]    Nz                  (0         ).as(Integer             ) ] :Optional  :Nz:Default Nz of inputfile
+    [-Cx[Center x]       Cx                  (0         ).as(Real                ) ] :Optional  :Cetnter x position of extracted image.Default is center of iuput image.
+    [-Cy[Center y]       Cy                  (0         ).as(Real                ) ] :Optional  :Cetnter y position of extracted image.Default is center of iuput image.
+    [-Cz[Center z]       Cz                  (0         ).as(Real                ) ] :Optional  :Cetnter z position of extracted image.Default is center of iuput image.
+    [-even                                                                         ] :Optional  :all dimensions of N are even. 
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-M[ode2]            mode2               (0         ).as(Integer             ) ] :Optional  :Mode2
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageCenterOfMassCalculate.html b/doc/SmallTools/mrcImageCenterOfMassCalculate.html
index 5cb7a1c..66665c4 100644
--- a/doc/SmallTools/mrcImageCenterOfMassCalculate.html
+++ b/doc/SmallTools/mrcImageCenterOfMassCalculate.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: mrcImageCenterOfMassCalculate
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (stdout    )] :Optional  :InputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :InputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageChainCodeCalc.html b/doc/SmallTools/mrcImageChainCodeCalc.html
new file mode 100644
index 0000000..18b099a
--- /dev/null
+++ b/doc/SmallTools/mrcImageChainCodeCalc.html
@@ -0,0 +1,23 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageChainCodeCalc</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageChainCodeCalc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageChainCodeCalc
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+>> mode
+   0: 8-neighbor, chainCode absolute
+   1: 4-neighbor, chainCode absolute
+   2: 8-neighbor, chainCode relative
+   3: 4-neighbor, chainCode relative
+ </PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageCircumferentialProjection.html b/doc/SmallTools/mrcImageCircumferentialProjection.html
index d40f02b..33662da 100644
--- a/doc/SmallTools/mrcImageCircumferentialProjection.html
+++ b/doc/SmallTools/mrcImageCircumferentialProjection.html
@@ -8,18 +8,18 @@
 <PRE>
 Usage: mrcImageCircumferentialProjection
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-dang               dang                (10        )] :Optional  :Delta Angle[degree]
-    [-zmin               zmin                (0         )] :Optional  :Z Minimum[A]
-    [-zmax               zmax                (100       )] :Optional  :Z Maximum[A]
-    [-dz                 dz                  (10        )] :Optional  :Delta Z[A]
-    [-rmin               rmin                (0         )] :Optional  :Radius Minimum[A]
-    [-rmax               rmax                (200       )] :Optional  :Radius Maximum[A]
-    [-threshold          threshold           (0         )] :Optional  :Set threshold value.  Averaged density is more than threshold value
-    [-dr                 dr                  (10        )] :Optional  :Delta Radius[A]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-dang               dang                (10        ).as(Real                ) ] :Optional  :Delta Angle[degree]
+    [-zmin               zmin                (0         ).as(Real                ) ] :Optional  :Z Minimum[A]
+    [-zmax               zmax                (100       ).as(Real                ) ] :Optional  :Z Maximum[A]
+    [-dz                 dz                  (10        ).as(Real                ) ] :Optional  :Delta Z[A]
+    [-rmin               rmin                (0         ).as(Real                ) ] :Optional  :Radius Minimum[A]
+    [-rmax               rmax                (200       ).as(Real                ) ] :Optional  :Radius Maximum[A]
+    [-threshold          threshold           (0         ).as(Real                ) ] :Optional  :Set threshold value.  Averaged density is more than threshold value
+    [-dr                 dr                  (10        ).as(Real                ) ] :Optional  :Delta Radius[A]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 x --> r
 y --> z
diff --git a/doc/SmallTools/mrcImageClosing.html b/doc/SmallTools/mrcImageClosing.html
index 39073ad..438e44f 100644
--- a/doc/SmallTools/mrcImageClosing.html
+++ b/doc/SmallTools/mrcImageClosing.html
@@ -8,23 +8,26 @@
 <PRE>
 Usage: mrcImageClosing
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: MRC
-    [-o[utput]           Out                 (NULL      )] :Essential :Output: MRC
-    [-times              times               (1         )] :Optional  :Times: erosion*times -> dilation*times
-    [-o[utput]SE         OutSE               (NULL      )] :Optional  :Output: MRC(SE)
-    [-S[tructuring]E[lement]SEmode              (0         )] :Optional  :StructuringElement
-    [-r[adius]           radius              (2         )] :Optional  :Radius
-    [-n                  n                   (5         )] :Optional  :size
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: MRC
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output: MRC
+    [-times              times               (1         ).as(Integer             ) ] :Optional  :Times: erosion*times -> dilation*times
+    [-o[utput]SE         OutSE               (NULL      ).as(outFile             ) ] :Optional  :Output: MRC(SE)
+    [-S[tructuring]E[lement]SEmode              (0         ).as(Integer             ) ] :Optional  :StructuringElement
+    [-r[adius]           radius              (2         ).as(Integer             ) ] :Optional  :Radius
+    [-n                  n                   (5         ).as(Integer             ) ] :Optional  :size
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 ----- Structuring Element : Mode 
 0: 2D Cross3x3:  4-neighbour
 1: 2D Square3x3: 8-neighbour
-2: 2D Open Disk , need (radius, n)
+2: 2D Disk , need (radius, n(squre size))
 3: 3D Cross3x3x3:   6-neighbour
 4: 3D Cubic3x3x3: 26-neighbour
-5: 3D Open Disk , need (radius, n)
+5: 3D Sphere, need (radius, n(cubic size))
+6: 2D Rectangle, need nx, ny
+7: 3D Cuboid, need nx, ny, nz
+8: 3D Cylindar, need r, nx, ny, nz
 -----
 Dilation: Max for image : Or  for binary image 
 Erosion:  Min for image : And for binary image 
diff --git a/doc/SmallTools/mrcImageClusterAnalysis.html b/doc/SmallTools/mrcImageClusterAnalysis.html
index 00f921a..c524630 100644
--- a/doc/SmallTools/mrcImageClusterAnalysis.html
+++ b/doc/SmallTools/mrcImageClusterAnalysis.html
@@ -8,25 +8,28 @@
 <PRE>
 Usage: mrcImageClusterAnalysis
 Options:
-    [-I[nput array of file]In                  (NULL      )] :Essential :InputDataFiles
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-O[utput]           ] :Optional  :Output: averaged images: filename is xxxx.avg: xxxx is input filename.
-    [-N[umberOfClusters] N                   (1         )] :Optional  :Number of clusters
-    [-Min[imumCorrelation]Min                 (0.0       )] :Optional  :Minimum: Correlation: Conditions for ending
-    [-Iter[ation]        ] :Optional  :IterationFlag
-    [-A[uto]R[otation]   AutoRotation        (72        )] :Optional  :AutoRotation: rotation divided by this value
-    [-A[utoRot]Range     ARMin               (0         )ARMax               (360       )] :Optional  :AutoRotationRange
-    [-A[uto]R[otation]iter[ation]AutoRotationIteration(2         )] :Optional  :AutoRotationIteration
-    [-A[uto]R[otation]MethodAutoRotationMethod  (0         )] :Optional  :Method for Correlation for Auto Rotation
-    [-M[odeForCorrelation]correlationMode     (19        )] :Optional  :Correlation Mode for AutoRotation
-    [-pvm                ] :Optional  :Parallel Analysis by PVM
-    [-pvmList            pvmList             (NULL      )] :Optional  :pvmList: Input
-    [-Log                Log                 (stdout    )] :Optional  :Log: Output
-    [-Log2               Log2                (NULL      )] :Optional  :Log2: Output: ClusterNode Only
-    [-LogIn              LogIn               (NULL      )] :Optional  :previousLog: Input
-    [-prevF[ileNum]      prevFileNum         (0         )] :Optional  :previousLogFileNum: Input
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (2         )] :Optional  :Mode
+    [-I[nput array of file]In                  (NULL      ).as(inFileListNoOpen    ) ] :Essential :InputDataFiles
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-O[utput]                                                                     ] :Optional  :Output: averaged images: filename is xxxx.avg: xxxx is input filename.
+    [-N[umberOfClusters] N                   (1         ).as(Integer             ) ] :Optional  :Number of clusters
+    [-Min[imumCorrelation]Min                 (0.0       ).as(Real                ) ] :Optional  :Minimum: Correlation: Conditions for ending
+    [-Iter[ation]                                                                  ] :Optional  :IterationFlag
+    [-A[uto]R[otation]   AutoRotation        (72        ).as(Integer             ) ] :Optional  :AutoRotation: rotation divided by this value
+    [-A[utoRot]Range     ARMin               (0         ).as(Real                ) 
+                         ARMax               (360       ).as(Real                ) ] :Optional  :AutoRotationRange
+    [-A[uto]R[otation]iter[ation]AutoRotationIteration(2         ).as(Integer             ) ] :Optional  :AutoRotationIteration
+    [-A[uto]R[otation]MethodAutoRotationMethod  (0         ).as(Integer             ) ] :Optional  :Method for Correlation for Auto Rotation
+    [-M[odeForCorrelation]correlationMode     (19        ).as(Integer             ) ] :Optional  :Correlation Mode for AutoRotation
+    [-Log                Log                 (stdout    ).as(appendFile          ) ] :Optional  :Log: Output
+    [-Log2               Log2                (NULL      ).as(appendFile          ) ] :Optional  :Log2: Output: ClusterNode Only
+    [-LogIn              LogIn               (NULL      ).as(inFile              ) ] :Optional  :previousLog: Input
+    [-prevF[ileNum]      prevFileNum         (0         ).as(Integer             ) ] :Optional  :previousLogFileNum: Input
+    [-pthread            pthread             (0         ).as(Integer             ) ] :Optional  :pthread: Input
+    [-NoRecalc                                                                     ] :Optional  :No recalculation of distances
+    [-pvm                                                                          ] :Optional  :Parallel Analysis by PVM
+    [-pvmList            pvmList             (NULL      ).as(inFile              ) ] :Optional  :pvmList: Input
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (2         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 Distance between clusters: mode
 	mode 0: By Correlation
diff --git a/doc/SmallTools/mrcImageColoring.html b/doc/SmallTools/mrcImageColoring.html
index 647bfea..6f02c7b 100644
--- a/doc/SmallTools/mrcImageColoring.html
+++ b/doc/SmallTools/mrcImageColoring.html
@@ -1,25 +1 @@
-<HTML>
-<HEAD>
-<TITLE>mrcImageColoring</TITLE>
-</HEAD>
-<BODY>
-<H1>mrcImageColoring</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrcImageColoring
-Options:
-    [-r[ed]              rIn                 (NULL      )] :Optional  :Red:InputDataFile
-    [-g[reen]            gIn                 (NULL      )] :Optional  :Green:InputDataFile
-    [-b[lue]             bIn                 (NULL      )] :Optional  :Blue:InputDataFile
-    [-rH[ight]           rHigh               (1         )] :Optional  :Red:HighThres
-    [-rL[ow]             rLow                (0         )] :Optional  :Red:LowThres
-    [-gH[ight]           gHigh               (1         )] :Optional  :Green:HighThres
-    [-gL[ow]             gLow                (0         )] :Optional  :Green:LowThres
-    [-bH[ibht]           bHigh               (1         )] :Optional  :Blue:HibhThres
-    [-bL[ow]             bLow                (0         )] :Optional  :BLue:LowThres
-    [-o[utput]           Out                 (NULL      )] :Optional  :gif:OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrcImageColoring: No such file or directory
diff --git a/doc/SmallTools/mrcImageCommonLineSearch.html b/doc/SmallTools/mrcImageCommonLineSearch.html
index 3ed7a44..f86b096 100644
--- a/doc/SmallTools/mrcImageCommonLineSearch.html
+++ b/doc/SmallTools/mrcImageCommonLineSearch.html
@@ -8,14 +8,14 @@
 <PRE>
 Usage: mrcImageCommonLineSearch
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: mrc
-    [-r[ef]              Ref                 (NULL      )] :Essential :Input: ref
-    [-dtheta             dtheta              (1.0       )] :Optional  :Input: degree
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output: OptimalParameter
-    [-O[utput]           Out2                (NULL      )] :Optional  :Output: ParameterImage
-    [-M[ode]             searchMode          (1         )] :Optional  :SearchMode
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: mrc
+    [-r[ef]              Ref                 (NULL      ).as(inFile              ) ] :Essential :Input: ref
+    [-dtheta             dtheta              (1.0       ).as(Real                ) ] :Optional  :Input: degree
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output: OptimalParameter
+    [-O[utput]           Out2                (NULL      ).as(outFile             ) ] :Optional  :Output: ParameterImage
+    [-M[ode]             searchMode          (1         ).as(Integer             ) ] :Optional  :SearchMode
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 >>>> lmrcImageCommonLineInfo
  ----  mode ----
diff --git a/doc/SmallTools/mrcImageConnection.html b/doc/SmallTools/mrcImageConnection.html
index 784b263..78db4a7 100644
--- a/doc/SmallTools/mrcImageConnection.html
+++ b/doc/SmallTools/mrcImageConnection.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageConnection
 Options:
-    [-i[nput]1           In1                 (NULL      )] :Essential :InputDataFile
-    [-i[nput]2           In2                 (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]1           In1                 (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-i[nput]2           In2                 (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 -m 0: z connection
 </PRE>
diff --git a/doc/SmallTools/mrcImageConnectivityNumberCalc.html b/doc/SmallTools/mrcImageConnectivityNumberCalc.html
index 4808f98..7eec442 100644
--- a/doc/SmallTools/mrcImageConnectivityNumberCalc.html
+++ b/doc/SmallTools/mrcImageConnectivityNumberCalc.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcImageConnectivityNumberCalc
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-f[orm]             form                (0         )] :Optional  :Form
-    [-I[nvers]           invers              (0         )] :Optional  :Invers
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-f[orm]             form                (0         ).as(Integer             ) ] :Optional  :Form
+    [-I[nvers]           invers              (0         ).as(Integer             ) ] :Optional  :Invers
 ----- Additional Usage -----
 mode   0 : Four Neighborhood. [default] : For 2 Dimension. 
        1 : Eight Nieghborhood.          : 
diff --git a/doc/SmallTools/mrcImageContourSurfaceCreate.html b/doc/SmallTools/mrcImageContourSurfaceCreate.html
index 86bc892..f7c1bd0 100644
--- a/doc/SmallTools/mrcImageContourSurfaceCreate.html
+++ b/doc/SmallTools/mrcImageContourSurfaceCreate.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageContourSurfaceCreate
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: mrc
-    [-o[utput]           Out                 (NULL      )] :Essential :Output: mrc
-    [-C[ontour]          Contour             (0.0       )] :Essential :Input: Contour Value
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: mrc
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output: mrc
+    [-C[ontour]          Contour             (0.0       ).as(Real                ) ] :Essential :Input: Contour Value
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
     -m 0 : SimpleMethod
               When a point has contour surfaces between six voxels (Upper-Downward Right-Left For-Back) and the point,
diff --git a/doc/SmallTools/mrcImageConvolution.html b/doc/SmallTools/mrcImageConvolution.html
index 9c890d4..cf28075 100644
--- a/doc/SmallTools/mrcImageConvolution.html
+++ b/doc/SmallTools/mrcImageConvolution.html
@@ -8,13 +8,13 @@
 <PRE>
 Usage: mrcImageConvolution
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: mrcImage
-    [-i[nput]k[ernal]a[rray]InKernelArray       (NULL      )] :Optional  :Input: Array
-    [-i[nput]k[ernal]m[rc]InKernelMRC         (NULL      )] :Optional  :Input: mrcImage
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-times              times               (1         )] :Optional  :Repeat time
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: mrcImage
+    [-i[nput]k[ernal]a[rray]InKernelArray       (NULL      ).as(inFile              ) ] :Optional  :Input: Array
+    [-i[nput]k[ernal]m[rc]InKernelMRC         (NULL      ).as(inFile              ) ] :Optional  :Input: mrcImage
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-times              times               (1         ).as(Integer             ) ] :Optional  :Repeat time
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 >>> Array Format under Eos <<<<
 ndim N0 N1 N2 ...
diff --git a/doc/SmallTools/mrcImageCoordinateChange.html b/doc/SmallTools/mrcImageCoordinateChange.html
index b71fe3e..7c1cfe4 100644
--- a/doc/SmallTools/mrcImageCoordinateChange.html
+++ b/doc/SmallTools/mrcImageCoordinateChange.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: mrcImageCoordinateChange
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageCoreImageCalc.html b/doc/SmallTools/mrcImageCoreImageCalc.html
index a89141f..98c00ae 100644
--- a/doc/SmallTools/mrcImageCoreImageCalc.html
+++ b/doc/SmallTools/mrcImageCoreImageCalc.html
@@ -8,17 +8,20 @@
 <PRE>
 Usage: mrcImageCoreImageCalc
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: Pretreated Core-loss Image
-    [-e[neryg]l[oss]     EL                  (180       )] :Essential :Input: EnergyLoss
-    [-bg[List]           BG                  (NULL      )] :Essential :Input: Bg File List
-    [-o[utput]           Out                 (NULL      )] :Essential :Output: Core-Loss Image
-    [-O[utputBG]         OutBG               (NULL      )] :Optional  :Output: BG-Image
-    [-Chi[sq]            OutChi              (NULL      )] :Optional  :Output: Chi-Image
-    [-initial[Value]     A1                  (5040      )A2                  (500       )A3                  (-12       )] :Optional  :Input: A1 + A2*EELS^A3
-    [-limitA3            LimitA3Min          (-16       )LimitA3Max          (-5        )] :Optional  :Input: limit A3
-    [-baseEELS           BaseEELS            (160.0     )] :Optional  :Input: BaseEELS as 1.0
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: Pretreated Core-loss Image
+    [-e[neryg]l[oss]     EL                  (180       ).as(Real                ) ] :Essential :Input: EnergyLoss
+    [-bg[List]           BG                  (NULL      ).as(inFileList          ) ] :Essential :Input: Bg File List
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output: Core-Loss Image
+    [-O[utputBG]         OutBG               (NULL      ).as(outFile             ) ] :Optional  :Output: BG-Image
+    [-Chi[sq]            OutChi              (NULL      ).as(outFile             ) ] :Optional  :Output: Chi-Image
+    [-initial[Value]     A1                  (5040      ).as(Real                ) 
+                         A2                  (500       ).as(Real                ) 
+                         A3                  (-12       ).as(Real                ) ] :Optional  :Input: A1 + A2*EELS^A3
+    [-limitA3            LimitA3Min          (-16       ).as(Real                ) 
+                         LimitA3Max          (-5        ).as(Real                ) ] :Optional  :Input: limit A3
+    [-baseEELS           BaseEELS            (160.0     ).as(Real                ) ] :Optional  :Input: BaseEELS as 1.0
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 >>> BGFile List 
 FileName1 EEL
diff --git a/doc/SmallTools/mrcImageCorrelation.html b/doc/SmallTools/mrcImageCorrelation.html
index 08eadb2..e6045ac 100644
--- a/doc/SmallTools/mrcImageCorrelation.html
+++ b/doc/SmallTools/mrcImageCorrelation.html
@@ -9,17 +9,19 @@ Init Start
 <PRE>
 Usage: mrcImageCorrelation
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Optional  :OutputDataFile: Correlation Map
-    [-O[utput]           Out2                (NULL      )] :Optional  :OutputDataFile: Correlation Map for Refinement
-    [-r[eference]        Ref                 (NULL      )] :Essential :ReferenceDataFile
-    [-cor[relation]Info  OutCor              (stdout    )] :Optional  :Output: Correlation Info
-    [-a[verage]          Avg                 (NULL      )] :Optional  :OutputDataFile: Averaged File
-    [-s[hit]             Shift               (NULL      )] :Optional  :OutputDataFile: Shifted InputFile
-    [-refine             RefineStep          (0.25      )RefineRange         (3.0       )RefineMode          (2         )] :Optional  :Refinemnet: Step Range[pixelUnit]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-M[ode2]            mode2               (0         )] :Optional  :Mode2
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile: Correlation Map
+    [-O[utput]           Out2                (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile: Correlation Map for Refinement
+    [-r[eference]        Ref                 (NULL      ).as(inFile              ) ] :Essential :ReferenceDataFile
+    [-cor[relation]Info  OutCor              (stdout    ).as(outFile             ) ] :Optional  :Output: Correlation Info
+    [-a[verage]          Avg                 (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile: Averaged File
+    [-s[hit]             Shift               (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile: Shifted InputFile
+    [-refine             RefineStep          (0.25      ).as(Real                ) 
+                         RefineRange         (3.0       ).as(Real                ) 
+                         RefineMode          (2         ).as(Integer             ) ] :Optional  :Refinemnet: Step Range[pixelUnit]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-M[ode2]            mode2               (0         ).as(Integer             ) ] :Optional  :Mode2
 ----- Mode:  -m -----
 0: Normal Correlation FxG*
 1: Phase  Correlation FxG*/     |FxG*|
diff --git a/doc/SmallTools/mrcImageCorrelationInFourierSpace.html b/doc/SmallTools/mrcImageCorrelationInFourierSpace.html
index f5b1e5c..015ec4d 100644
--- a/doc/SmallTools/mrcImageCorrelationInFourierSpace.html
+++ b/doc/SmallTools/mrcImageCorrelationInFourierSpace.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageCorrelationInFourierSpace
 Options:
-    [-i1[input1]         In1                 (NULL      )] :Optional  :InputDataFile
-    [-i2[input2]         In2                 (NULL      )] :Optional  :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i1[input1]         In1                 (NULL      ).as(inFile              ) ] :Optional  :InputDataFile
+    [-i2[input2]         In2                 (NULL      ).as(inFile              ) ] :Optional  :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 Mode 0: (FxG*)/(|FG|) 
 Mode 1: Phase residual 
diff --git a/doc/SmallTools/mrcImageCrystalCreate.html b/doc/SmallTools/mrcImageCrystalCreate.html
index ad07e0f..bee2b9b 100644
--- a/doc/SmallTools/mrcImageCrystalCreate.html
+++ b/doc/SmallTools/mrcImageCrystalCreate.html
@@ -8,13 +8,13 @@
 <PRE>
 Usage: mrcImageCrystalCreate
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-nx                 nx                  (1         )] :Optional  :Number:x-axis
-    [-ny                 ny                  (1         )] :Optional  :Number:y-axis
-    [-nz                 nz                  (1         )] :Optional  :Number:z-axis
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-nx                 nx                  (1         ).as(Integer             ) ] :Optional  :Number:x-axis
+    [-ny                 ny                  (1         ).as(Integer             ) ] :Optional  :Number:y-axis
+    [-nz                 nz                  (1         ).as(Integer             ) ] :Optional  :Number:z-axis
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageCylinderSection.html b/doc/SmallTools/mrcImageCylinderSection.html
index 00f7701..31c2eef 100644
--- a/doc/SmallTools/mrcImageCylinderSection.html
+++ b/doc/SmallTools/mrcImageCylinderSection.html
@@ -8,20 +8,20 @@
 <PRE>
 Usage: mrcImageCylinderSection
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-angmin             angmin              (0         )] :Optional  :Angle Minimum[degree]
-    [-angmax             angmax              (360       )] :Optional  :Angle Maximum[degree]
-    [-dang               dang                (10        )] :Optional  :Delta Angle[degree]
-    [-zmin               zmin                (0         )] :Optional  :Z Minimum[A]
-    [-zmax               zmax                (100       )] :Optional  :Z Maximum[A]
-    [-dz                 dz                  (10        )] :Optional  :Delta Z[A]
-    [-rmin               rmin                (0         )] :Optional  :Radius Minimum[A]
-    [-rmax               rmax                (250       )] :Optional  :Radius Maximum[A]
-    [-dr                 dr                  (10        )] :Optional  :Delta Radius[A]
-    [-W[eight]           ] :Optional  :Data are weithed by r
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-angmin             angmin              (0         ).as(Real                ) ] :Optional  :Angle Minimum[degree]
+    [-angmax             angmax              (360       ).as(Real                ) ] :Optional  :Angle Maximum[degree]
+    [-dang               dang                (10        ).as(Real                ) ] :Optional  :Delta Angle[degree]
+    [-zmin               zmin                (0         ).as(Real                ) ] :Optional  :Z Minimum[A]
+    [-zmax               zmax                (100       ).as(Real                ) ] :Optional  :Z Maximum[A]
+    [-dz                 dz                  (10        ).as(Real                ) ] :Optional  :Delta Z[A]
+    [-rmin               rmin                (0         ).as(Real                ) ] :Optional  :Radius Minimum[A]
+    [-rmax               rmax                (250       ).as(Real                ) ] :Optional  :Radius Maximum[A]
+    [-dr                 dr                  (10        ).as(Real                ) ] :Optional  :Delta Radius[A]
+    [-W[eight]                                                                     ] :Optional  :Data are weithed by r
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 Format Change
 x --> ang
diff --git a/doc/SmallTools/mrcImageDeadPixelCorrection.html b/doc/SmallTools/mrcImageDeadPixelCorrection.html
index 1ba82f0..6b7d33c 100644
--- a/doc/SmallTools/mrcImageDeadPixelCorrection.html
+++ b/doc/SmallTools/mrcImageDeadPixelCorrection.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageDeadPixelCorrection
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-dp[dead point]     Dp                  (NULL      )] :Essential :DeadPointPositionFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-dp[dead point]     Dp                  (NULL      ).as(inFile              ) ] :Essential :DeadPointPositionFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageDensityChangeEstimation.html b/doc/SmallTools/mrcImageDensityChangeEstimation.html
index ffba89c..2c3832a 100644
--- a/doc/SmallTools/mrcImageDensityChangeEstimation.html
+++ b/doc/SmallTools/mrcImageDensityChangeEstimation.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageDensityChangeEstimation
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: mrcImage
-    [-i[nput]2           In2                 (NULL      )] :Essential :Input: mrcImage2
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: mrcImage
+    [-i[nput]2           In2                 (NULL      ).as(inFile              ) ] :Essential :Input: mrcImage2
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 ----- Attention !!!-----
 In Eos system, positive values are regarded as density.
diff --git a/doc/SmallTools/mrcImageDensityInfo.html b/doc/SmallTools/mrcImageDensityInfo.html
index a3a31a4..448885e 100644
--- a/doc/SmallTools/mrcImageDensityInfo.html
+++ b/doc/SmallTools/mrcImageDensityInfo.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcImageDensityInfo
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-C[ontour]          Contour             (10        )] :Optional  :ContourLevel: 10 6.953245e-310ach
-    [-log                Log                 (NULL      )] :Optional  :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-C[ontour]          Contour             (10        ).as(Real                ) ] :Optional  :ContourLevel: 10 5.533535e-322ach
+    [-log                Log                 (NULL      ).as(appendFile          ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Attention !!!-----
 In Eos system, positive values are regarded as density.
 If a pixel has a negative value, the value of the pixel is regarded as zero.lmrcImageDensityInfo Mode: 
diff --git a/doc/SmallTools/mrcImageDensityNormalization.html b/doc/SmallTools/mrcImageDensityNormalization.html
index 2edd6db..ba0d573 100644
--- a/doc/SmallTools/mrcImageDensityNormalization.html
+++ b/doc/SmallTools/mrcImageDensityNormalization.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageDensityNormalization
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: mrc
-    [-o[utput]           Out                 (NULL      )] :Essential :Output: mrc
-    [-V[alue]            Value               (100       )] :Optional  :Output: value
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: mrc
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output: mrc
+    [-V[alue]            Value               (100       ).as(Real                ) ] :Optional  :Output: value
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 Isovolume: 0 : make the sum of pixel values the input value
 </PRE>
diff --git a/doc/SmallTools/mrcImageDensityNormalizationByImage.html b/doc/SmallTools/mrcImageDensityNormalizationByImage.html
index ebb0042..5fe414b 100644
--- a/doc/SmallTools/mrcImageDensityNormalizationByImage.html
+++ b/doc/SmallTools/mrcImageDensityNormalizationByImage.html
@@ -8,16 +8,21 @@
 <PRE>
 Usage: mrcImageDensityNormalizationByImage
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Test: Input
-    [-r[ef]              Ref                 (NULL      )] :Essential :Reference: Input
-    [-o[utput]           Out                 (NULL      )] :Essential :NormalizedImage:  Output
-    [-O[utput]           OutParam            (stdout    )] :Optional  :Parameters:       Output
-    [-D[ataForNormalizing]UsedData            (stdout    )] :Optional  :DataList to be used
-    [-Cylinder           CCenterX            (20        )CCenterY            (20        )CMinR               (10        )CMaxR               (20        )] :Optional  :Cylinder Region
-    [-testBG[Region]     tstBGMin            (-3        )tstBGMax            (3         )tstBGDelta          (0.1       )] :Optional  :SearchRegion
-    [-M[ode]             fitMode             (0         )] :Optional  :DensityFittngMethod: Mode
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Test: Input
+    [-r[ef]              Ref                 (NULL      ).as(inFile              ) ] :Essential :Reference: Input
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :NormalizedImage:  Output
+    [-O[utput]           OutParam            (stdout    ).as(outFile             ) ] :Optional  :Parameters:       Output
+    [-D[ataForNormalizing]UsedData            (stdout    ).as(outFile             ) ] :Optional  :DataList to be used
+    [-Cylinder           CCenterX            (20        ).as(Real                ) 
+                         CCenterY            (20        ).as(Real                ) 
+                         CMinR               (10        ).as(Real                ) 
+                         CMaxR               (20        ).as(Real                ) ] :Optional  :Cylinder Region
+    [-testBG[Region]     tstBGMin            (-3        ).as(Real                ) 
+                         tstBGMax            (3         ).as(Real                ) 
+                         tstBGDelta          (0.1       ).as(Real                ) ] :Optional  :SearchRegion
+    [-M[ode]             fitMode             (0         ).as(Integer             ) ] :Optional  :DensityFittngMethod: Mode
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 ----- Mode -----
   1: Sigma!=1.0 
diff --git a/doc/SmallTools/mrcImageDilation.html b/doc/SmallTools/mrcImageDilation.html
index 70fe244..7b5b124 100644
--- a/doc/SmallTools/mrcImageDilation.html
+++ b/doc/SmallTools/mrcImageDilation.html
@@ -8,22 +8,25 @@
 <PRE>
 Usage: mrcImageDilation
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: MRC
-    [-o[utput]           Out                 (NULL      )] :Essential :Output: MRC
-    [-o[utput]SE         OutSE               (NULL      )] :Optional  :Output: MRC(SE)
-    [-S[tructuring]E[lement]SEmode              (0         )] :Optional  :StructuringElement
-    [-r[adius]           radius              (2         )] :Optional  :Radius
-    [-n                  n                   (5         )] :Optional  :size
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: MRC
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output: MRC
+    [-o[utput]SE         OutSE               (NULL      ).as(outFile             ) ] :Optional  :Output: MRC(SE)
+    [-S[tructuring]E[lement]SEmode              (0         ).as(Integer             ) ] :Optional  :StructuringElement
+    [-r[adius]           radius              (2         ).as(Integer             ) ] :Optional  :Radius
+    [-n                  n                   (5         ).as(Integer             ) ] :Optional  :size
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 ----- Structuring Element : Mode 
 0: 2D Cross3x3:  4-neighbour
 1: 2D Square3x3: 8-neighbour
-2: 2D Open Disk , need (radius, n)
+2: 2D Disk , need (radius, n(squre size))
 3: 3D Cross3x3x3:   6-neighbour
 4: 3D Cubic3x3x3: 26-neighbour
-5: 3D Open Disk , need (radius, n)
+5: 3D Sphere, need (radius, n(cubic size))
+6: 2D Rectangle, need nx, ny
+7: 3D Cuboid, need nx, ny, nz
+8: 3D Cylindar, need r, nx, ny, nz
 -----
 Dilation: Max for image : Or  for binary image 
 Erosion:  Min for image : And for binary image 
diff --git a/doc/SmallTools/mrcImageDisplayDensityAsTempFactor.html b/doc/SmallTools/mrcImageDisplayDensityAsTempFactor.html
index fd317af..fd800c5 100644
--- a/doc/SmallTools/mrcImageDisplayDensityAsTempFactor.html
+++ b/doc/SmallTools/mrcImageDisplayDensityAsTempFactor.html
@@ -8,14 +8,14 @@
 <PRE>
 Usage: mrcImageDisplayDensityAsTempFactor
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-p[dbfile]          Pdb                 (NULL      )] :Essential :InputPdbFile
-    [-v[alue]            Value               (1         )] :Optional  :value to multiply density
-    [-H[ighThreshold]    H                   (0.0       )] :Optional  :High Threshold
-    [-L[owThreshold]     L                   (1.0       )] :Optional  :Low Threshold
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-p[dbfile]          Pdb                 (NULL      ).as(inFile              ) ] :Essential :InputPdbFile
+    [-v[alue]            Value               (1         ).as(Real                ) ] :Optional  :value to multiply density
+    [-H[ighThreshold]    H                   (0.0       ).as(Real                ) ] :Optional  :High Threshold
+    [-L[owThreshold]     L                   (1.0       ).as(Real                ) ] :Optional  :Low Threshold
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageDistanceConversion.html b/doc/SmallTools/mrcImageDistanceConversion.html
index 9172893..0ec3d06 100644
--- a/doc/SmallTools/mrcImageDistanceConversion.html
+++ b/doc/SmallTools/mrcImageDistanceConversion.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageDistanceConversion
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-f[orm]             form                (0         )] :Optional  :Form
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-f[orm]             form                (0         ).as(Integer             ) ] :Optional  :Form
 ----- Additional Usage -----
 mode  0 : 4 Neighborhood. [default]
       1 : 8 Neighborhood.
diff --git a/doc/SmallTools/mrcImageDivideInfoForTomography.html b/doc/SmallTools/mrcImageDivideInfoForTomography.html
index b7775ad..4eaa0fe 100644
--- a/doc/SmallTools/mrcImageDivideInfoForTomography.html
+++ b/doc/SmallTools/mrcImageDivideInfoForTomography.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcImageDivideInfoForTomography
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [cut[Back]           cut                 (6         )] :Optional  :Cut
-    [-d[ivide]           divide              (4         )] :Optional  :Divide
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [cut[Back]           cut                 (6         ).as(Integer             ) ] :Optional  :Cut
+    [-d[ivide]           divide              (4         ).as(Integer             ) ] :Optional  :Divide
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageDivideIntoTwoImages.html b/doc/SmallTools/mrcImageDivideIntoTwoImages.html
index 73811ba..f24b799 100644
--- a/doc/SmallTools/mrcImageDivideIntoTwoImages.html
+++ b/doc/SmallTools/mrcImageDivideIntoTwoImages.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageDivideIntoTwoImages
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]1          Out1                (NULL      )] :Essential :OutputDataFile
-    [-o[utput]2          Out2                (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]1          Out1                (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-o[utput]2          Out2                (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- mode -----
 0:Vertical to the longest axis.
 1:Vertical to x axis
diff --git a/doc/SmallTools/mrcImageEdgeCalc.html b/doc/SmallTools/mrcImageEdgeCalc.html
new file mode 100644
index 0000000..b0579c9
--- /dev/null
+++ b/doc/SmallTools/mrcImageEdgeCalc.html
@@ -0,0 +1,19 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageEdgeCalc</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageEdgeCalc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageEdgeCalc
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-n[eighbor]         Neighbor            (8         ).as(Integer             ) ] :Optional  :Neighbor
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageEdgeImageGet.html b/doc/SmallTools/mrcImageEdgeImageGet.html
index 1b8a530..4af7482 100644
--- a/doc/SmallTools/mrcImageEdgeImageGet.html
+++ b/doc/SmallTools/mrcImageEdgeImageGet.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageEdgeImageGet
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: mrcImage
-    [-o[utput]           Out                 (NULL      )] :Optional  :Output: mrcImage
-    [-s[ize]             Size                (64        )] :Optional  :Size: [pixel]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: mrcImage
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :Output: mrcImage
+    [-s[ize]             Size                (64        ).as(Integer             ) ] :Optional  :Size: [pixel]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 mode: 
        0: 4 Edge (x-y plane) from Image(0-3)
diff --git a/doc/SmallTools/mrcImageErosion.html b/doc/SmallTools/mrcImageErosion.html
index 909d854..f166185 100644
--- a/doc/SmallTools/mrcImageErosion.html
+++ b/doc/SmallTools/mrcImageErosion.html
@@ -8,22 +8,25 @@
 <PRE>
 Usage: mrcImageErosion
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: MRC
-    [-o[utput]           Out                 (NULL      )] :Essential :Output: MRC
-    [-o[utput]SE         OutSE               (NULL      )] :Optional  :Output: MRC(SE)
-    [-S[tructuring]E[lement]SEmode              (0         )] :Optional  :StructuringElement
-    [-r[adius]           radius              (2         )] :Optional  :Radius
-    [-n                  n                   (5         )] :Optional  :size
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input: MRC
+    [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Essential :Output: MRC
+    [-o[utput]SE         OutSE               (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output: MRC(SE)
+    [-S[tructuring]E[lement]SEmode              (0         ).as(Integer             ) ] :Optional  :StructuringElement
+    [-r[adius]           radius              (2         ).as(Integer             ) ] :Optional  :Radius
+    [-n                  n                   (5         ).as(Integer             ) ] :Optional  :size
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 ----- Structuring Element : Mode 
 0: 2D Cross3x3:  4-neighbour
 1: 2D Square3x3: 8-neighbour
-2: 2D Open Disk , need (radius, n)
+2: 2D Disk , need (radius, n(squre size))
 3: 3D Cross3x3x3:   6-neighbour
 4: 3D Cubic3x3x3: 26-neighbour
-5: 3D Open Disk , need (radius, n)
+5: 3D Sphere, need (radius, n(cubic size))
+6: 2D Rectangle, need nx, ny
+7: 3D Cuboid, need nx, ny, nz
+8: 3D Cylindar, need r, nx, ny, nz
 -----
 Dilation: Max for image : Or  for binary image 
 Erosion:  Min for image : And for binary image 
diff --git a/doc/SmallTools/mrcImageEstimateTiltImage.html b/doc/SmallTools/mrcImageEstimateTiltImage.html
index befde18..e4b678b 100644
--- a/doc/SmallTools/mrcImageEstimateTiltImage.html
+++ b/doc/SmallTools/mrcImageEstimateTiltImage.html
@@ -8,13 +8,13 @@
 <PRE>
 Usage: mrcImageEstimateTiltImage
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-tiltAngle          TiltAngle           (0         )] :Optional  :Tilt Angle[degree]
-    [-tiltAxis           TiltAxis            (0         )] :Optional  :Tilt Axis[degree]
-    [-Inverse            ] :Optional  :To Non-tilt
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode: InterpolationMode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-tiltAngle          TiltAngle           (0         ).as(Real                ) ] :Optional  :Tilt Angle[degree]
+    [-tiltAxis           TiltAxis            (0         ).as(Real                ) ] :Optional  :Tilt Axis[degree]
+    [-Inverse                                                                      ] :Optional  :To Non-tilt
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode: InterpolationMode
 ----- Additional Usage -----
 -i in :2D or 3D
 </PRE>
diff --git a/doc/SmallTools/mrcImageExpression.html b/doc/SmallTools/mrcImageExpression.html
index e5cb06c..68ed8e9 100644
--- a/doc/SmallTools/mrcImageExpression.html
+++ b/doc/SmallTools/mrcImageExpression.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageExpression
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-T[hreshold]        Thres               (1e-16     )] :Optional  :Threshold to calculate.For mode 1 and 3.
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-T[hreshold]        Thres               (1e-16     ).as(Real                ) ] :Optional  :Threshold to calculate.For mode 1 and 3.
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 ----- mode -----
 0:Absolute value
diff --git a/doc/SmallTools/mrcImageFFT.html b/doc/SmallTools/mrcImageFFT.html
index f663df1..436c051 100644
--- a/doc/SmallTools/mrcImageFFT.html
+++ b/doc/SmallTools/mrcImageFFT.html
@@ -1 +1,22 @@
-/bin/bash: mrcImageFFT: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>mrcImageFFT</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageFFT</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageFFT
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-cuda               cudaDeviceID        (0         ).as(Integer             ) ] :Optional  :UseCUDA
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+x, y and z must be even pixels.
+Excepts for like that 
+(x, y, z)=(100, 1, 1)
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageFFTLayerLineExtraction.html b/doc/SmallTools/mrcImageFFTLayerLineExtraction.html
index 8961972..79a9c6d 100644
--- a/doc/SmallTools/mrcImageFFTLayerLineExtraction.html
+++ b/doc/SmallTools/mrcImageFFTLayerLineExtraction.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcImageFFTLayerLineExtraction
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-[input] I[nformation]InI                 (NULL      )] :Optional  :InputDataFile
-    [-truePitch          truePitch           (430       )] :Optional  :true Pitch [A]
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-[input] I[nformation]InI                 (NULL      ).as(inFile              ) ] :Optional  :InputDataFile
+    [-truePitch          truePitch           (430       ).as(Real                ) ] :Optional  :true Pitch [A]
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 Input File Format
 FileName  x  z  dY 
diff --git a/doc/SmallTools/mrcImageFFTSetsExtract.html b/doc/SmallTools/mrcImageFFTSetsExtract.html
new file mode 100644
index 0000000..068e23b
--- /dev/null
+++ b/doc/SmallTools/mrcImageFFTSetsExtract.html
@@ -0,0 +1,21 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageFFTSetsExtract</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageFFTSetsExtract</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageFFTSetsExtract
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input:mrcImage
+    [-o[utput]           FTBBase             (out       ).as(String              ) ] :Essential :Output:basename-mrcImage(FT)s
+    [-O[utput]           FTABase             (Out       ).as(String              ) ] :Essential :Output:basename-ascii
+    [-W[idth]            width               (256       ).as(Integer             ) ] :Optional  :Width[pixel]
+    [-H[eight]           height              (256       ).as(Integer             ) ] :Optional  :Height[pixel]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageFOMCalc.html b/doc/SmallTools/mrcImageFOMCalc.html
index b3ec234..15aedda 100644
--- a/doc/SmallTools/mrcImageFOMCalc.html
+++ b/doc/SmallTools/mrcImageFOMCalc.html
@@ -8,21 +8,22 @@
 <PRE>
 Usage: mrcImageFOMCalc
 Options:
-    [-i[nput]            In                  (NULL      )] :Optional  :TestData
-    [-w[eight]           Weight              (1.0       )] :Optional  :Weight
-    [-I[nput]            InList              (NULL      )] :Optional  :TestData Set
-    [-r[ef]              Ref                 (NULL      )] :Essential :Ref, Model Data
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output: 
-    [-RR[ange]           Rmin                (0.0       )Rmax                (0.1       )] :Optional  :Ring Range
-    [-dR[ange]           dR                  (0.0       )] :Optional  :Ring Width
-    [-nS[ector]          nSector             (1         )] :Optional  :Sector Number
-    [-dA[lpha]           dAlpha              (5         )] :Optional  :delta Alpha
-    [-XMax               XMax                (0.0       )] :Optional  :Xmax: If not set, one calc Xmax
-    [-A[uto]S[cale]      ] :Optional  :Auto Scaling
-    [-A[llArea]A[uto]S[cale]AASRMax             (0.05      )] :Optional  :All Area Auto Scaling
-    [-RS[cale]           ] :Optional  :R Scaling
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Optional  :TestData
+    [-w[eight]           Weight              (1.0       ).as(Real                ) ] :Optional  :Weight
+    [-I[nput]            InList              (NULL      ).as(inFileList          ) ] :Optional  :TestData Set
+    [-r[ef]              Ref                 (NULL      ).as(inFile              ) ] :Essential :Ref, Model Data
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output: 
+    [-RR[ange]           Rmin                (0.0       ).as(Real                ) 
+                         Rmax                (0.1       ).as(Real                ) ] :Optional  :Ring Range
+    [-dR[ange]           dR                  (0.0       ).as(Real                ) ] :Optional  :Ring Width
+    [-nS[ector]          nSector             (1         ).as(Integer             ) ] :Optional  :Sector Number
+    [-dA[lpha]           dAlpha              (5         ).as(Real                ) ] :Optional  :delta Alpha
+    [-XMax               XMax                (0.0       ).as(Real                ) ] :Optional  :Xmax: If not set, one calc Xmax
+    [-A[uto]S[cale]                                                                ] :Optional  :Auto Scaling
+    [-A[llArea]A[uto]S[cale]AASRMax             (0.05      ).as(Real                ) ] :Optional  :All Area Auto Scaling
+    [-RS[cale]                                                                     ] :Optional  :R Scaling
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 >> -I FileFormat 
 mrc[0]   weight[0]
diff --git a/doc/SmallTools/mrcImageFeatureCalc.html b/doc/SmallTools/mrcImageFeatureCalc.html
new file mode 100644
index 0000000..07298bb
--- /dev/null
+++ b/doc/SmallTools/mrcImageFeatureCalc.html
@@ -0,0 +1,23 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageFeatureCalc</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageFeatureCalc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageFeatureCalc
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input:binary
+    [-o[utput]           Out                 (stdout    ).as(outFile::ASCII      ) ] :Optional  :Output:
+    [-o[utput]GC         OutGC               (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output:gc
+    [-o[utput]L[abel]    OutLabel            (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output:Label
+    [-o[utput]P[eprimeter]OutPerimeter        (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output:Label
+    [-o[utput]S[urfaceArea]OutSurfaceArea      (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output:SurfaceArea
+    [-n[eighbor]         neighbor            (0         ).as(Integer             ) ] :Optional  :Neighbor: [4(0)|8 or 6(0)|18|26]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageFeatureExtraction.html b/doc/SmallTools/mrcImageFeatureExtraction.html
index 9fd19b6..ebacac1 100644
--- a/doc/SmallTools/mrcImageFeatureExtraction.html
+++ b/doc/SmallTools/mrcImageFeatureExtraction.html
@@ -8,14 +8,14 @@
 <PRE>
 Usage: mrcImageFeatureExtraction
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[oOccurrence]r[adius]co_r                (1         )] :Optional  :Co-Occurrence radius
-    [-c[oOccurrence]t[heta]co_theta            (0         )] :Optional  :Co-Occurrence theta
-    [-r[unLength]t[heta] rl_theta            (0         )] :Optional  :RunLength theta
-    [-r[unLength]d[ev]   rl_dev              (4         )] :Optional  :RunLength devision
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[oOccurrence]r[adius]co_r                (1         ).as(Integer             ) ] :Optional  :Co-Occurrence radius
+    [-c[oOccurrence]t[heta]co_theta            (0         ).as(Integer             ) ] :Optional  :Co-Occurrence theta
+    [-r[unLength]t[heta] rl_theta            (0         ).as(Integer             ) ] :Optional  :RunLength theta
+    [-r[unLength]d[ev]   rl_dev              (4         ).as(Integer             ) ] :Optional  :RunLength devision
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 
 ----- Additional Usage -----
 Feature list
diff --git a/doc/SmallTools/mrcImageFilterCreate.html b/doc/SmallTools/mrcImageFilterCreate.html
index 7d95a4a..765fb6f 100644
--- a/doc/SmallTools/mrcImageFilterCreate.html
+++ b/doc/SmallTools/mrcImageFilterCreate.html
@@ -8,18 +8,18 @@
 <PRE>
 Usage: mrcImageFilterCreate
 Options:
-    [-i[nput]            In                  (stdin     )] :Optional  :Input: ASCII
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output: mrcImage
-    [-nx                 Nx                  (512       )] :Essential :ImageSize: x
-    [-ny                 Ny                  (512       )] :Optional  :ImageSize: y
-    [-nz                 Nz                  (1         )] :Optional  :ImageSize: z
-    [-sx                 Sx                  (3         )] :Essential :FilterSize: x
-    [-sy                 Sy                  (3         )] :Optional  :FilterSize: y
-    [-sz                 Sz                  (1         )] :Optional  :FilterSize: z
-    [-v[erbose]          ] :Optional  :Verbose
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-M[ode]             Mode                (0         )] :Optional  :Mode: Filter shape
-    [-m[ode]             mode                (2         )] :Optional  :mode: output mrc
+    [-i[nput]            In                  (stdin     ).as(inFile              ) ] :Optional  :Input: ASCII
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output: mrcImage
+    [-nx                 Nx                  (512       ).as(Integer             ) ] :Essential :ImageSize: x
+    [-ny                 Ny                  (512       ).as(Integer             ) ] :Optional  :ImageSize: y
+    [-nz                 Nz                  (1         ).as(Integer             ) ] :Optional  :ImageSize: z
+    [-sx                 Sx                  (3         ).as(Integer             ) ] :Essential :FilterSize: x
+    [-sy                 Sy                  (3         ).as(Integer             ) ] :Optional  :FilterSize: y
+    [-sz                 Sz                  (1         ).as(Integer             ) ] :Optional  :FilterSize: z
+    [-v[erbose]                                                                    ] :Optional  :Verbose
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-M[ode]             Mode                (0         ).as(Integer             ) ] :Optional  :Mode: Filter shape
+    [-m[ode]             mode                (2         ).as(Integer             ) ] :Optional  :mode: output mrc
 ----- Additional Usage -----
 >>>> Input file Format nx0 y0 z0 weight0
 x1 y1 z1 weight1
diff --git a/doc/SmallTools/mrcImageFilteringbyFile.html b/doc/SmallTools/mrcImageFilteringbyFile.html
index 4072873..5d6ec44 100644
--- a/doc/SmallTools/mrcImageFilteringbyFile.html
+++ b/doc/SmallTools/mrcImageFilteringbyFile.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageFilteringbyFile
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-f[ilter]           Filter              (NULL      )] :Essential :FilterFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-f[ilter]           Filter              (NULL      ).as(inFile              ) ] :Essential :FilterFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 Mode 0: Filtering input file by filter file.
 Mode 1: Output mrc fourier image of filter file.Size of filter is size of input file.
diff --git a/doc/SmallTools/mrcImageFilteringbyFileForVariance.html b/doc/SmallTools/mrcImageFilteringbyFileForVariance.html
index b14310a..c405289 100644
--- a/doc/SmallTools/mrcImageFilteringbyFileForVariance.html
+++ b/doc/SmallTools/mrcImageFilteringbyFileForVariance.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageFilteringbyFileForVariance
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-f[ilter]           Filter              (NULL      )] :Essential :FilterFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-f[ilter]           Filter              (NULL      ).as(inFile              ) ] :Essential :FilterFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageFourierNeighborCorrelation.html b/doc/SmallTools/mrcImageFourierNeighborCorrelation.html
index 614e811..0da9daf 100644
--- a/doc/SmallTools/mrcImageFourierNeighborCorrelation.html
+++ b/doc/SmallTools/mrcImageFourierNeighborCorrelation.html
@@ -14,11 +14,18 @@ Options:
     [-C[enter]           Centre              (0         ).as(Integer             ) ] :Optional  :CentreMode
     [-M[ode]             GetMode             (0         ).as(Integer             ) ] :Optional  :PixelDataGetHowToGet: InterpolationMode 
     [-FSC                                                                          ] :Optional  :Output:predicted FSC
+    [-Cref                                                                         ] :Optional  :Output:Cref
+    [-FSCfull                                                                      ] :Optional  :Output:FSC full
+    [-NoiseWeighted      Brestore            (0.0       ).as(Real                ) ] :Optional  :NoiseWeighted: Cref*exp(-Brestore/(4*d^2)
     [-mask               InMask              (NULL      ).as(inFile::mrcImage    ) ] :Optional  :Input: Mask for FSC
     [-maskBack           InBackMask          (NULL      ).as(inFile::mrcImage    ) ] :Optional  :Input: Mask for FSC Back
     [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
     [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
+0: Centre is ImageCentre Shift: (Nx/2.0, Ny/2.0, Nz/2.0 ) 
+1: Centre is BottomLeft  Shift: (0,      0,      0      ) 
+2: Use StartN            Shift: (StartNx,StartNy,StartNz) 
+Duncan Sousa, Nikolaus Grigorieff, 2007, JSB 
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageFractalFourierShellCorrelation.html b/doc/SmallTools/mrcImageFractalFourierShellCorrelation.html
index fcd4b18..8bc532f 100644
--- a/doc/SmallTools/mrcImageFractalFourierShellCorrelation.html
+++ b/doc/SmallTools/mrcImageFractalFourierShellCorrelation.html
@@ -8,26 +8,26 @@
 <PRE>
 Usage: mrcImageFractalFourierShellCorrelation
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: mrcImage Input
-    [-r[eference]        Ref                 (NULL      )] :Essential :Input: mrcImage Reference
-    [-o[utput]           Out                 (NULL      )] :Essential :Output: ResolutionMap
-    [-t[hreshold]        Threshold           (0.5       )] :Optional  :Input: Threshold
-    [-s[tep]x            stepx               (1         )] :Optional  :Input: step x
-    [-s[tep]y            stepy               (1         )] :Optional  :Input: step y
-    [-s[tep]z            stepz               (1         )] :Optional  :Input: step z
-    [-maxN               maxN                (32        )] :Optional  :Input: max partIn.HeaderN
-    [-scaling[ up]       scaling             (1.25      )] :Optional  :Input: scaling up
-    [-get[ mode]         getMode             (0         )] :Optional  :Input:mrcPixelDataGetMode
-    [-Log                Log                 (NULL      )] :Optional  :Output: Log File
-    [-xmin               xmin                (0         )] :Optional  :Input: xmin
-    [-ymin               ymin                (0         )] :Optional  :Input: ymin
-    [-zmin               zmin                (0         )] :Optional  :Input: zmin
-    [-xmax               xmax                (0         )] :Optional  :Input: xmax
-    [-ymax               ymax                (0         )] :Optional  :Input: ymax
-    [-zmax               zmax                (0         )] :Optional  :Input: zmax
-    [-d[ensity]          densityThreshold    (0         )] :Optional  :Input: density threshold
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: mrcImage Input
+    [-r[eference]        Ref                 (NULL      ).as(inFile              ) ] :Essential :Input: mrcImage Reference
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output: ResolutionMap
+    [-t[hreshold]        Threshold           (0.5       ).as(Real                ) ] :Optional  :Input: Threshold
+    [-s[tep]x            stepx               (1         ).as(Real                ) ] :Optional  :Input: step x
+    [-s[tep]y            stepy               (1         ).as(Real                ) ] :Optional  :Input: step y
+    [-s[tep]z            stepz               (1         ).as(Real                ) ] :Optional  :Input: step z
+    [-maxN               maxN                (32        ).as(Real                ) ] :Optional  :Input: max partIn.HeaderN
+    [-scaling[ up]       scaling             (1.25      ).as(Real                ) ] :Optional  :Input: scaling up
+    [-get[ mode]         getMode             (0         ).as(Integer             ) ] :Optional  :Input:mrcPixelDataGetMode
+    [-Log                Log                 (NULL      ).as(outFile             ) ] :Optional  :Output: Log File
+    [-xmin               xmin                (0         ).as(Real                ) ] :Optional  :Input: xmin
+    [-ymin               ymin                (0         ).as(Real                ) ] :Optional  :Input: ymin
+    [-zmin               zmin                (0         ).as(Real                ) ] :Optional  :Input: zmin
+    [-xmax               xmax                (0         ).as(Real                ) ] :Optional  :Input: xmax
+    [-ymax               ymax                (0         ).as(Real                ) ] :Optional  :Input: ymax
+    [-zmax               zmax                (0         ).as(Real                ) ] :Optional  :Input: zmax
+    [-d[ensity]          densityThreshold    (0         ).as(Real                ) ] :Optional  :Input: density threshold
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageGaussDisc.html b/doc/SmallTools/mrcImageGaussDisc.html
index 574018e..5b29bfd 100644
--- a/doc/SmallTools/mrcImageGaussDisc.html
+++ b/doc/SmallTools/mrcImageGaussDisc.html
@@ -8,19 +8,19 @@
 <PRE>
 Usage: mrcImageGaussDisc
 Options:
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-sigmax             sigmax              (10        )] :Optional  :sigmax[A]
-    [-sigmay             sigmay              (10        )] :Optional  :sigmay[A]
-    [-sigma_range        sigma_range         (3         )] :Optional  :sigma
-    [-weight             weight              (10        )] :Optional  :weight
-    [-size               size                (5         )] :Optional  :Pixel Size[A]
-    [-W[idth]            Width               (0         )] :Optional  :Image Width[A]
-    [-H[eight]           Height              (0         )] :Optional  :Image Height[A]
-    [-cx                 centrex             (0         )] :Optional  :x: Centre[A]
-    [-cy                 centrey             (0         )] :Optional  :y: Centre[A]
-    [-a[ngle]            Angle               (0         )] :Optional  :Angle: [degree]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (2         )] :Optional  :Mode
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-sigmax             sigmax              (10        ).as(Real                ) ] :Optional  :sigmax[A]
+    [-sigmay             sigmay              (10        ).as(Real                ) ] :Optional  :sigmay[A]
+    [-sigma_range        sigma_range         (3         ).as(Real                ) ] :Optional  :sigma
+    [-weight             weight              (10        ).as(Real                ) ] :Optional  :weight
+    [-size               size                (5         ).as(Real                ) ] :Optional  :Pixel Size[A]
+    [-W[idth]            Width               (0         ).as(Real                ) ] :Optional  :Image Width[A]
+    [-H[eight]           Height              (0         ).as(Real                ) ] :Optional  :Image Height[A]
+    [-cx                 centrex             (0         ).as(Real                ) ] :Optional  :x: Centre[A]
+    [-cy                 centrey             (0         ).as(Real                ) ] :Optional  :y: Centre[A]
+    [-a[ngle]            Angle               (0         ).as(Real                ) ] :Optional  :Angle: [degree]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (2         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 Gauss Disc is cutted at sigma_range*sigma 
 Gauss Disc = weight * exp ( - ((x^2 / sigmax^2)+(y^2 / sigmay^2)) 
diff --git a/doc/SmallTools/mrcImageGaussSphere.html b/doc/SmallTools/mrcImageGaussSphere.html
index d798bc8..3b6f9aa 100644
--- a/doc/SmallTools/mrcImageGaussSphere.html
+++ b/doc/SmallTools/mrcImageGaussSphere.html
@@ -8,20 +8,25 @@
 <PRE>
 Usage: mrcImageGaussSphere
 Options:
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-E[uler]A[ngle]     EA                  (YOYS      )Rot1                (0.0       )Rot2                (0.0       )Rot3                (0.0       )] :Optional  :Input: Gauss Sphere: Rotation
-    [-centre             ShiftX              (0.0       )ShiftY              (0.0       )ShiftZ              (0.0       )] :Optional  :Input: Gauss Sphere: Centre
-    [-sigmax             sigmax              (10        )] :Optional  :sigmax[A]
-    [-sigmay             sigmay              (20        )] :Optional  :sigmay[A]
-    [-sigmaz             sigmaz              (30        )] :Optional  :sigmaz[A]
-    [-sigma_range        sigma_range         (3         )] :Optional  :x times
-    [-weight             weight              (10        )] :Optional  :weight
-    [-size               size                (5         )] :Optional  :Pixel Size[A]
-    [-W[idth]            Width               (0         )] :Optional  :Width[A]
-    [-H[ight]            Height              (0         )] :Optional  :Height[A]
-    [-S[ection]          Section             (0         )] :Optional  :Section[A]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (2         )] :Optional  :Mode
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-E[uler]A[ngle]     EA                  (YOYS      ).as(String              ) 
+                         Rot1                (0.0       ).as(Real                ) 
+                         Rot2                (0.0       ).as(Real                ) 
+                         Rot3                (0.0       ).as(Real                ) ] :Optional  :Input: Gauss Sphere: Rotation
+    [-centre             ShiftX              (0.0       ).as(Real                ) 
+                         ShiftY              (0.0       ).as(Real                ) 
+                         ShiftZ              (0.0       ).as(Real                ) ] :Optional  :Input: Gauss Sphere: Centre
+    [-sigmax             sigmax              (10        ).as(Real                ) ] :Optional  :sigmax[A]
+    [-sigmay             sigmay              (20        ).as(Real                ) ] :Optional  :sigmay[A]
+    [-sigmaz             sigmaz              (30        ).as(Real                ) ] :Optional  :sigmaz[A]
+    [-sigma_range        sigma_range         (3         ).as(Real                ) ] :Optional  :x times
+    [-weight             weight              (10        ).as(Real                ) ] :Optional  :weight
+    [-size               size                (5         ).as(Real                ) ] :Optional  :Pixel Size[A]
+    [-W[idth]            Width               (0         ).as(Real                ) ] :Optional  :Width[A]
+    [-H[ight]            Height              (0         ).as(Real                ) ] :Optional  :Height[A]
+    [-S[ection]          Section             (0         ).as(Real                ) ] :Optional  :Section[A]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (2         ).as(Integer             ) ] :Optional  :Mode
 Gauss Sphere is cutted at sigma_range*sigma 
 Gauss Sphere = weight * exp ( - ((x^2 / sigmax^2)+(y^2 / sigmay^2)+(z^2 / sigmaz^2)) 
 mrcImageFileSize is (sigma_range*sigmax*2) x (sigma_range*sigmay*2) x (sigma_range*sigmaz*2) 
diff --git a/doc/SmallTools/mrcImageHeaderChange.html b/doc/SmallTools/mrcImageHeaderChange.html
index 09a5482..7415d1c 100644
--- a/doc/SmallTools/mrcImageHeaderChange.html
+++ b/doc/SmallTools/mrcImageHeaderChange.html
@@ -8,14 +8,14 @@
 <PRE>
 Usage: mrcImageHeaderChange
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[output]          Out                 (NULL      )] :Essential :OutputDataFile
-    [-r[esolution]       r                   (0.0       )] :Optional  :Pixel size
-    [-x[length]          Lx                  (0.0       )] :Optional  :Pixel size along x axis(A).Default:No change
-    [-y[length]          Ly                  (0.0       )] :Optional  :Pixel size along y axis(A).Default:No change
-    [-z[length]          Lz                  (0.0       )] :Optional  :Pixel size along z axis(A).Default:No change
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[output]          Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-r[esolution]       r                   (0.0       ).as(Real                ) ] :Optional  :Pixel size
+    [-x[length]          Lx                  (0.0       ).as(Real                ) ] :Optional  :Pixel size along x axis(A).Default:No change
+    [-y[length]          Ly                  (0.0       ).as(Real                ) ] :Optional  :Pixel size along y axis(A).Default:No change
+    [-z[length]          Lz                  (0.0       ).as(Real                ) ] :Optional  :Pixel size along z axis(A).Default:No change
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 If r is defined, pixel size is r
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageHelicalAveraging.html b/doc/SmallTools/mrcImageHelicalAveraging.html
index 59b50a1..2d77f76 100644
--- a/doc/SmallTools/mrcImageHelicalAveraging.html
+++ b/doc/SmallTools/mrcImageHelicalAveraging.html
@@ -8,14 +8,14 @@
 <PRE>
 Usage: mrcImageHelicalAveraging
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-dz[deltaz]         dz                  (27.3      )] :Optional  :deltaz(A)
-    [-dp[deltaphi]       dp                  (-167.143  )] :Optional  :deltaphi(degree)
-    [-N[umber]           N                   (1         )] :Optional  :Number of particles to average
-    [-W[indow]           W                   (1         )] :Optional  :Window size to average [pixel].
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-dz[deltaz]         dz                  (27.3      ).as(Real                ) ] :Optional  :deltaz(A)
+    [-dp[deltaphi]       dp                  (-167.143  ).as(Real                ) ] :Optional  :deltaphi(degree)
+    [-N[umber]           N                   (1         ).as(Integer             ) ] :Optional  :Number of particles to average
+    [-W[idth]            W                   (1         ).as(Integer             ) ] :Optional  :Width to average [pixel].
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 0: Discrete.  Parameter N is needed.  
 1: Continuous.  Parameter W is needed.  
diff --git a/doc/SmallTools/mrcImageHelicalMappingFrom2DImage.html b/doc/SmallTools/mrcImageHelicalMappingFrom2DImage.html
index b8fca81..1e1f9e6 100644
--- a/doc/SmallTools/mrcImageHelicalMappingFrom2DImage.html
+++ b/doc/SmallTools/mrcImageHelicalMappingFrom2DImage.html
@@ -8,13 +8,13 @@
 <PRE>
 Usage: mrcImageHelicalMappingFrom2DImage
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-Nz                 Nz                  (1         )] :Essential :Length of output image (pixel).
-    [-dz[deltaz]         dz                  (27.3      )] :Optional  :deltaz(A)
-    [-dp[deltaphi]       dp                  (-167.143  )] :Optional  :deltaphi(degree)
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-Nz                 Nz                  (1         ).as(Integer             ) ] :Essential :Length of output image (pixel).
+    [-dz[deltaz]         dz                  (27.3      ).as(Real                ) ] :Optional  :deltaz(A)
+    [-dp[deltaphi]       dp                  (-167.143  ).as(Real                ) ] :Optional  :deltaphi(degree)
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageHelicalMasking.html b/doc/SmallTools/mrcImageHelicalMasking.html
index e89c1bb..245a024 100644
--- a/doc/SmallTools/mrcImageHelicalMasking.html
+++ b/doc/SmallTools/mrcImageHelicalMasking.html
@@ -8,17 +8,17 @@
 <PRE>
 Usage: mrcImageHelicalMasking
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-dz[deltaz]         dz                  (27.3      )] :Optional  :deltaz(A)
-    [-dp[deltaphi]       dphi                (13.84     )] :Optional  :deltaphi(degree)
-    [-sz[startz]         sz                  (0         )] :Optional  :startz(pixel)
-    [-ez[startz]         ez                  (0         )] :Optional  :endz(pixel)
-    [-sphi[startphi]     sphi                (0         )] :Optional  :startphi(degree) for masking
-    [-ephi[startphi]     ephi                (90        )] :Optional  :endphi(degree) for masking
-    [-v[alue]            value               (0         )] :Optional  :value to pad
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-dz[deltaz]         dz                  (27.3      ).as(Real                ) ] :Optional  :deltaz(A)
+    [-dp[deltaphi]       dphi                (13.84     ).as(Real                ) ] :Optional  :deltaphi(degree)
+    [-sz[startz]         sz                  (0         ).as(Integer             ) ] :Optional  :startz(pixel)
+    [-ez[startz]         ez                  (0         ).as(Integer             ) ] :Optional  :endz(pixel)
+    [-sphi[startphi]     sphi                (0         ).as(Real                ) ] :Optional  :startphi(degree) for masking
+    [-ephi[startphi]     ephi                (90        ).as(Real                ) ] :Optional  :endphi(degree) for masking
+    [-v[alue]            value               (0         ).as(Real                ) ] :Optional  :value to pad
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageHelicalMaskingBy2DImage.html b/doc/SmallTools/mrcImageHelicalMaskingBy2DImage.html
index b0c4894..5f5a39f 100644
--- a/doc/SmallTools/mrcImageHelicalMaskingBy2DImage.html
+++ b/doc/SmallTools/mrcImageHelicalMaskingBy2DImage.html
@@ -8,13 +8,13 @@
 <PRE>
 Usage: mrcImageHelicalMaskingBy2DImage
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-dz[deltaz]         dz                  (27.3      )] :Optional  :deltaz(A)
-    [-dp[deltaphi]       dphi                (13.84     )] :Optional  :deltaphi(degree)
-    [-M[ask]             Mask                (NULL      )] :Essential :2D Image for masking
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-dz[deltaz]         dz                  (27.3      ).as(Real                ) ] :Optional  :deltaz(A)
+    [-dp[deltaphi]       dphi                (13.84     ).as(Real                ) ] :Optional  :deltaphi(degree)
+    [-M[ask]             Mask                (NULL      ).as(inFile              ) ] :Essential :2D Image for masking
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageHelicalProjection.html b/doc/SmallTools/mrcImageHelicalProjection.html
index ac847d9..5026ded 100644
--- a/doc/SmallTools/mrcImageHelicalProjection.html
+++ b/doc/SmallTools/mrcImageHelicalProjection.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcImageHelicalProjection
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-dz[deltaz]         dz                  (27.3      )] :Optional  :deltaz(A)
-    [-dp[deltaphi]       dphi                (13.84     )] :Optional  :deltaphi(degree)
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-dz[deltaz]         dz                  (27.3      ).as(Real                ) ] :Optional  :deltaz(A)
+    [-dp[deltaphi]       dphi                (13.84     ).as(Real                ) ] :Optional  :deltaphi(degree)
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageHighPassFilter.html b/doc/SmallTools/mrcImageHighPassFilter.html
index 6cedd97..dc4051c 100644
--- a/doc/SmallTools/mrcImageHighPassFilter.html
+++ b/doc/SmallTools/mrcImageHighPassFilter.html
@@ -8,13 +8,14 @@
 <PRE>
 Usage: mrcImageHighPassFilter
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-h[alf]v[alue]p[oint]hvp                 (1.0       )] :Optional  :HalfValuePoint
-    [-p[ath]w[indow]     pwLow               (0.0       )pwHigh              (1.0       )] :Optional  :PathWindowWeight: Low <-> High
-    [-w[idth]            width               (1.0       )] :Optional  :WidthOfDumping
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-h[alf]v[alue]p[oint]hvp                 (1.0       ).as(Real                ) ] :Optional  :HalfValuePoint
+    [-p[ath]w[indow]     pwLow               (0.0       ).as(Real                ) 
+                         pwHigh              (1.0       ).as(Real                ) ] :Optional  :PathWindowWeight: Low <-> High
+    [-w[idth]            width               (1.0       ).as(Real                ) ] :Optional  :WidthOfDumping
 >>> Mode <<<< 
     1: Step filter : required argumnent: -hvp
     2: Cos filter  : required argumnent: -hvp -w
diff --git a/doc/SmallTools/mrcImageHighlighting.html b/doc/SmallTools/mrcImageHighlighting.html
index ea7ffa6..d78d6c1 100644
--- a/doc/SmallTools/mrcImageHighlighting.html
+++ b/doc/SmallTools/mrcImageHighlighting.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcImageHighlighting
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-b[ias]             Bias                (0         )] :Optional  :BiasValueFromMean
-    [-g[rad]             Grad                (1         )] :Optional  :GradientOfFunction
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-b[ias]             Bias                (0         ).as(Real                ) ] :Optional  :BiasValueFromMean
+    [-g[rad]             Grad                (1         ).as(Real                ) ] :Optional  :GradientOfFunction
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ---- lmrcImageHighlightInfo ----mode:	0:No Operation 
 	1:ArcTan Filter
 	2:Histgram Equalization
diff --git a/doc/SmallTools/mrcImageHoughTransform.html b/doc/SmallTools/mrcImageHoughTransform.html
new file mode 100644
index 0000000..f073a4b
--- /dev/null
+++ b/doc/SmallTools/mrcImageHoughTransform.html
@@ -0,0 +1,36 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageHoughTransform</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageHoughTransform</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageHoughTransform
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input
+    [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Essential :Output
+    [-d[elta]Theta       DeltaTheta          (1.0       ).as(Real                ) ] :Optional  :DeltaTheta[degree]
+    [-d[elta]Rho         DeltaRho            (1.0       ).as(Real                ) ] :Optional  :DeltaRho[pixel]
+    [-M[ode]             HoughMode           (0         ).as(Integer             ) ] :Optional  :HoughTransformMode
+    [-width              widthMin            (0         ).as(Real                ) 
+                         widthMax            (0         ).as(Integer             ) ] :Optional  :Width[pixel]
+    [-widthOut           widthOut            (0         ).as(Real                ) ] :Optional  :Width[pixel]
+    [-I[nterpolation]M[ode]InterpolationMode   (0         ).as(Integer             ) ] :Optional  :mrcImageMode: HowToGet
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+0: Lines
+    0: Nearest
+    1: Linear
+1: TwoLines
+    0: Nearest(centre) + InterpolationMode
+    1: Linear(centre)  + InterpolationMode
+3: Rectangles (not yet)
+4: FilledRectangles (not yet)
+5: Circles (not yet)
+6: FilledCircles (not yet)
+7: GivenStructure (not yet)
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageHoughTransformInverse.html b/doc/SmallTools/mrcImageHoughTransformInverse.html
new file mode 100644
index 0000000..2403dfe
--- /dev/null
+++ b/doc/SmallTools/mrcImageHoughTransformInverse.html
@@ -0,0 +1,22 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageHoughTransformInverse</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageHoughTransformInverse</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageHoughTransformInverse
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-Nx                 Nx                  (100       ).as(Integer             ) ] :Optional  :Nx[pixel]
+    [-Ny                 Ny                  (100       ).as(Integer             ) ] :Optional  :Ny[pixel]
+    [-d[elta]            delta               (1.0       ).as(Integer             ) ] :Optional  :delta[A]
+    [-M[ode]             HoughSpaceMode      (0         ).as(Integer             ) ] :Optional  :HoughMode
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageInfo.html b/doc/SmallTools/mrcImageInfo.html
index db9a752..4223486 100644
--- a/doc/SmallTools/mrcImageInfo.html
+++ b/doc/SmallTools/mrcImageInfo.html
@@ -36,6 +36,7 @@ The -I option uses -rmax or -m options
    5: mean of Sparse 
    6: mean of 2DEdge
    7: RMS of all pixels 
+   8: sd of all axes
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageInverseRadonTransform.html b/doc/SmallTools/mrcImageInverseRadonTransform.html
index 2e421c4..33adbb8 100644
--- a/doc/SmallTools/mrcImageInverseRadonTransform.html
+++ b/doc/SmallTools/mrcImageInverseRadonTransform.html
@@ -8,14 +8,14 @@
 <PRE>
 Usage: mrcImageInverseRadonTransform
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-Rmax               Rmax                (1.0       )] :Optional  :Input: Rmax
-    [-Rmin               Rmin                (1.0       )] :Optional  :Input: Rmin
-    [-b[ack]p[rojection]m[ode]BackProjectionMode  (1         )] :Optional  :BackProjectionMode
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-T[hreshold]        T                   (1         )] :Optional  :Input: Threshold
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-Rmax               Rmax                (1.0       ).as(Real                ) ] :Optional  :Input: Rmax
+    [-Rmin               Rmin                (1.0       ).as(Real                ) ] :Optional  :Input: Rmin
+    [-b[ack]p[rojection]m[ode]BackProjectionMode  (1         ).as(Integer             ) ] :Optional  :BackProjectionMode
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-T[hreshold]        T                   (1         ).as(Real                ) ] :Optional  :Input: Threshold
 
 ----- BackProjectionMode -----
  1 = SimpleBackProjection
diff --git a/doc/SmallTools/mrcImageLabeling.html b/doc/SmallTools/mrcImageLabeling.html
index 507bb3b..0b7f48b 100644
--- a/doc/SmallTools/mrcImageLabeling.html
+++ b/doc/SmallTools/mrcImageLabeling.html
@@ -8,11 +8,14 @@
 <PRE>
 Usage: mrcImageLabeling
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-n[eighbor]         neighbor            (0         ).as(Integer             ) ] :Optional  :Neighbor[4(0)|8 or 6(0)|18|26]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
+mode: 0 (default: speed)
+      1 (No vacancy)
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageLocalMaximumValuesFind.html b/doc/SmallTools/mrcImageLocalMaximumValuesFind.html
new file mode 100644
index 0000000..98b35ee
--- /dev/null
+++ b/doc/SmallTools/mrcImageLocalMaximumValuesFind.html
@@ -0,0 +1,21 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageLocalMaximumValuesFind</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageLocalMaximumValuesFind</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageLocalMaximumValuesFind
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input:
+    [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Optional  :OutputDataFile
+    [-O[utput]           OutP                (stdout    ).as(outFile::ASCII      ) ] :Optional  :OutputDataFile
+    [-T[hreshold]        Threshold           (0         ).as(Real                ) ] :Optional  :Threshold
+    [-S[ize]             Size                (3         ).as(Integer             ) ] :Optional  :Size
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageLowPassFilter.html b/doc/SmallTools/mrcImageLowPassFilter.html
index b52ff30..e220f57 100644
--- a/doc/SmallTools/mrcImageLowPassFilter.html
+++ b/doc/SmallTools/mrcImageLowPassFilter.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcImageLowPassFilter
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-h[alf]v[alue]p[oint]hvp                 (1.0       )] :Optional  :HalfValuePoint[/A]
-    [-w[idth]            width               (1.0       )] :Optional  :WidthOfDumping
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-h[alf]v[alue]p[oint]hvp                 (1.0       ).as(Real                ) ] :Optional  :HalfValuePoint[/A]
+    [-w[idth]            width               (1.0       ).as(Real                ) ] :Optional  :WidthOfDumping
 >>> Mode <<<< 
     1: Step filter : required argumnent: -hvp
     2: Cos filter  : required argumnent: -hvp -w
diff --git a/doc/SmallTools/mrcImageMagnificationChange.html b/doc/SmallTools/mrcImageMagnificationChange.html
index 05359c6..3fd12b8 100644
--- a/doc/SmallTools/mrcImageMagnificationChange.html
+++ b/doc/SmallTools/mrcImageMagnificationChange.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageMagnificationChange
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-r[atio]            Ratio               (0         )] :Essential :Ratio of new magnification to old magnification
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-r[atio]            Ratio               (0         ).as(Real                ) ] :Essential :Ratio of new magnification to old magnification
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageMake2DArrayImage.html b/doc/SmallTools/mrcImageMake2DArrayImage.html
index d6a86c9..ad939a0 100644
--- a/doc/SmallTools/mrcImageMake2DArrayImage.html
+++ b/doc/SmallTools/mrcImageMake2DArrayImage.html
@@ -8,13 +8,13 @@
 <PRE>
 Usage: mrcImageMake2DArrayImage
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile(Array of input image file)
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-N[umber]           Nx                  (1         )] :Optional  :Number of column
-    [-w[idth]            w                   (0         )] :Optional  :Width of separating line
-    [-v[alue]            v                   (0         )] :Optional  :Value of separating line
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile(Array of input image file)
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-N[umber]           Nx                  (1         ).as(Integer             ) ] :Optional  :Number of column
+    [-w[idth]            w                   (0         ).as(Integer             ) ] :Optional  :Width of separating line
+    [-v[alue]            v                   (0         ).as(Real                ) ] :Optional  :Value of separating line
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 mode 0:Input is data array.
 mode 1:Input is one 3D file. 
diff --git a/doc/SmallTools/mrcImageMakeCylinder.html b/doc/SmallTools/mrcImageMakeCylinder.html
index e1e0c3b..714fac8 100644
--- a/doc/SmallTools/mrcImageMakeCylinder.html
+++ b/doc/SmallTools/mrcImageMakeCylinder.html
@@ -8,13 +8,13 @@
 <PRE>
 Usage: mrcImageMakeCylinder
 Options:
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-i[nput]            In                  (NULL      )] :Optional  :InputDataFile
-    [-r[esolution]       Resolution          (1.666666  )] :Optional  :Size of pixel[A].
-    [-Nx[Number of x]    Nx                  (0         )] :Essential :Number of x
-    [-Ny[Number of y]    Ny                  (0         )] :Essential :Number of y
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Optional  :InputDataFile
+    [-r[esolution]       Resolution          (1.666666  ).as(Real                ) ] :Optional  :Size of pixel[A].
+    [-Nx[Number of x]    Nx                  (0         ).as(Integer             ) ] :Essential :Number of x
+    [-Ny[Number of y]    Ny                  (0         ).as(Integer             ) ] :Essential :Number of y
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageMakeDump.html b/doc/SmallTools/mrcImageMakeDump.html
index 249f8b8..30f8864 100644
--- a/doc/SmallTools/mrcImageMakeDump.html
+++ b/doc/SmallTools/mrcImageMakeDump.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: mrcImageMakeDump
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageMakeFromTextFile.html b/doc/SmallTools/mrcImageMakeFromTextFile.html
index 8e2d4c2..e3275e0 100644
--- a/doc/SmallTools/mrcImageMakeFromTextFile.html
+++ b/doc/SmallTools/mrcImageMakeFromTextFile.html
@@ -8,15 +8,15 @@
 <PRE>
 Usage: mrcImageMakeFromTextFile
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-nx                 nx                  (1         )] :Optional  :Pixel[Def:]
-    [-ny                 ny                  (1         )] :Optional  :Pixel[Def:]
-    [-nz                 nz                  (1         )] :Optional  :Pixel[Def:]
-    [-d                  d                   (2.5       )] :Optional  :d
-    [-v                  v                   (0         )] :Optional  :default value
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-nx                 nx                  (1         ).as(Integer             ) ] :Optional  :Pixel[Def:]
+    [-ny                 ny                  (1         ).as(Integer             ) ] :Optional  :Pixel[Def:]
+    [-nz                 nz                  (1         ).as(Integer             ) ] :Optional  :Pixel[Def:]
+    [-d                  d                   (2.5       ).as(Real                ) ] :Optional  :d
+    [-v                  v                   (0         ).as(Real                ) ] :Optional  :default value
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageMakeSphere.html b/doc/SmallTools/mrcImageMakeSphere.html
index 276dd76..1eff3ac 100644
--- a/doc/SmallTools/mrcImageMakeSphere.html
+++ b/doc/SmallTools/mrcImageMakeSphere.html
@@ -8,16 +8,18 @@
 <PRE>
 Usage: mrcImageMakeSphere
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile (Template file)
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-C[enter]           Cx                  (0         )Cy                  (0         )Cz                  (0         )] :Optional  :Cetnter position of Sphere.
-    [-or[Outer Radius]   or                  (1         )] :Essential :Outer Radius (pixel)
-    [-ir[Inner Radius]   ir                  (0         )] :Optional  :Inner Radius (pixel)
-    [-r[adius]           r                   (0         )] :Optional  :Center Radius (pixel): For mode 1 only.
-    [-v[alue]            Value               (10.0      )] :Optional  :Value of sphere
-    [-Other              Other               (NULL      )] :Optional  :Other acceptors.  For FRET Calculation.
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile (Template file)
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-C[enter]           Cx                  (0         ).as(Real                ) 
+                         Cy                  (0         ).as(Real                ) 
+                         Cz                  (0         ).as(Real                ) ] :Optional  :Cetnter position of Sphere.
+    [-or[Outer Radius]   or                  (1         ).as(Real                ) ] :Essential :Outer Radius (pixel)
+    [-ir[Inner Radius]   ir                  (0         ).as(Real                ) ] :Optional  :Inner Radius (pixel)
+    [-r[adius]           r                   (0         ).as(Real                ) ] :Optional  :Center Radius (pixel): For mode 1 only.
+    [-v[alue]            Value               (10.0      ).as(Real                ) ] :Optional  :Value of sphere
+    [-Other              Other               (NULL      ).as(inFile              ) ] :Optional  :Other acceptors.  For FRET Calculation.
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 mode 0: Constant
 mode 1: Gaussian
diff --git a/doc/SmallTools/mrcImageMappingtoPdb.html b/doc/SmallTools/mrcImageMappingtoPdb.html
index cb0aefb..cac08f6 100644
--- a/doc/SmallTools/mrcImageMappingtoPdb.html
+++ b/doc/SmallTools/mrcImageMappingtoPdb.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageMappingtoPdb
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputPdbFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-ipdb[file]         InPdb               (NULL      )] :Essential :InputPdbFile
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputPdbFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-ipdb[file]         InPdb               (NULL      ).as(inFile              ) ] :Essential :InputPdbFile
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageMasking.html b/doc/SmallTools/mrcImageMasking.html
index 65abb9d..a4d5aaa 100644
--- a/doc/SmallTools/mrcImageMasking.html
+++ b/doc/SmallTools/mrcImageMasking.html
@@ -8,19 +8,22 @@
 <PRE>
 Usage: mrcImageMasking
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-nx                 nx                  (0         )] :Optional  :Default:in.HeaderN.x
-    [-ny                 ny                  (0         )] :Optional  :Default:in.HeaderN.y
-    [-nz                 nz                  (0         )] :Optional  :Default:in.HeaderN.z
-    [-cx                 cx                  (0         )] :Optional  :Default:Center of image
-    [-cy                 cy                  (0         )] :Optional  :Default:Center of image
-    [-cz                 cz                  (0         )] :Optional  :Default:Center of image
-    [-Rot[ation]         Euler               (0         )Rot1                (0         )Rot2                (0         )Rot3                (0         )] :Optional  :Masking Area Rotation Default: ZONS 0 0 0
-    [-Shape              Shape               (0         )] :Optional  :Default:Circle
-    [-Normalize          Normalize           (0         )] :Optional  :Default:No Op
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-nx                 nx                  (0         ).as(Real                ) ] :Optional  :Default:in.HeaderN.x
+    [-ny                 ny                  (0         ).as(Real                ) ] :Optional  :Default:in.HeaderN.y
+    [-nz                 nz                  (0         ).as(Real                ) ] :Optional  :Default:in.HeaderN.z
+    [-cx                 cx                  (0         ).as(Real                ) ] :Optional  :Default:Center of image
+    [-cy                 cy                  (0         ).as(Real                ) ] :Optional  :Default:Center of image
+    [-cz                 cz                  (0         ).as(Real                ) ] :Optional  :Default:Center of image
+    [-Rot[ation]         Euler               (0         ).as(String              ) 
+                         Rot1                (0         ).as(Real                ) 
+                         Rot2                (0         ).as(Real                ) 
+                         Rot3                (0         ).as(Real                ) ] :Optional  :Masking Area Rotation Default: ZONS 0 0 0
+    [-Shape              Shape               (0         ).as(Integer             ) ] :Optional  :Default:Circle
+    [-Normalize          Normalize           (0         ).as(Integer             ) ] :Optional  :Default:No Op
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- -Shape Option ----- 
     -Shape 0 : Circle : radius(nx, ny, nz)
     -Shape 1 : Square : radius(nx, ny, nz)
diff --git a/doc/SmallTools/mrcImageMaskingByImage.html b/doc/SmallTools/mrcImageMaskingByImage.html
index 5026683..d88f3aa 100644
--- a/doc/SmallTools/mrcImageMaskingByImage.html
+++ b/doc/SmallTools/mrcImageMaskingByImage.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcImageMaskingByImage
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-M[askingFile]      MaskFile            (NULL      )] :Essential :FilenameForMasking
-    [-v[alueForCut]      CutValue            (0         )] :Optional  :ValueForCut
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-M[askingFile]      MaskFile            (NULL      ).as(inFile              ) ] :Essential :FilenameForMasking
+    [-v[alueForCut]      CutValue            (0         ).as(Real                ) ] :Optional  :ValueForCut
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 mode = 0  : cut off values larger that CutValue.
 mode = 1  : cut off values smaller that CutValue.
 mode = 2  : multiplying mask image 
diff --git a/doc/SmallTools/mrcImageMeanFreePathCalc.html b/doc/SmallTools/mrcImageMeanFreePathCalc.html
new file mode 100644
index 0000000..25fcbfb
--- /dev/null
+++ b/doc/SmallTools/mrcImageMeanFreePathCalc.html
@@ -0,0 +1,38 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageMeanFreePathCalc</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageMeanFreePathCalc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageMeanFreePathCalc
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input:mrcImage
+    [-o[utput]           Out                 (stdout    ).as(outFile::ASCII      ) ] :Optional  :Output:distribution
+    [-O[utput]w[hite]    OutWhite            (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output: white
+    [-O[utput]b[lack]    OutBlack            (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output: black
+    [-O[utput]w[hite]e[dge]OutWhiteEdge        (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output: whiteEdge
+    [-O[utput]b[lack]e[dge]OutBlackEdge        (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output: blackEdge
+    [-l[ine]t[hickness]  LineThicknessX      (1         ).as(Real                ) 
+                         LineThicknessY      (1         ).as(Real                ) ] :Optional  :[pixel]
+    [-l[ine]m[ode]       LineMode            (0         ).as(Integer             ) ] :Optional  :LineMode
+    [-l[ine]s[hape]      LineShape           (0         ).as(Integer             ) ] :Optional  :LineShape
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+>>>> mode 
+0: AlongZ-axis
+1: AlongX-axis
+2: AlongY-axis
++16: Length is shown in real using HeaderLength 
+>>>> line shape
+0: LineShape-Rectangle
+1: LineShape-Disk
+>>>> line mode
+0: LineMode-And 
+1: LineMode-Or  
+2: LineMode-GE(Greater than or equal to) 
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageMergebyside.html b/doc/SmallTools/mrcImageMergebyside.html
index 1181df6..5bdf3dd 100644
--- a/doc/SmallTools/mrcImageMergebyside.html
+++ b/doc/SmallTools/mrcImageMergebyside.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcImageMergebyside
 Options:
-    [-i1[input1]         In1                 (NULL      )] :Essential :InputDataFile
-    [-i2[input2]         In2                 (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-v[alue]            sep                 (0         )] :Optional  :Value for separation:For mode 1 only
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i1[input1]         In1                 (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-i2[input2]         In2                 (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-v[alue]            sep                 (0         ).as(Real                ) ] :Optional  :Value for separation:For mode 1 only
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageMirroring.html b/doc/SmallTools/mrcImageMirroring.html
index f72c758..ba317b6 100644
--- a/doc/SmallTools/mrcImageMirroring.html
+++ b/doc/SmallTools/mrcImageMirroring.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: mrcImageMirroring
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 lmrcImageMirroring >>>> Usage >>>>
 0: Mirroing against YZ-plane 
diff --git a/doc/SmallTools/mrcImageModeChange.html b/doc/SmallTools/mrcImageModeChange.html
index 338443f..d77903b 100644
--- a/doc/SmallTools/mrcImageModeChange.html
+++ b/doc/SmallTools/mrcImageModeChange.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcImageModeChange
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-Min                Min                 (0.0       )] :Optional  :Min
-    [-Max                Max                 (1.0       )] :Optional  :Max
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-Min                Min                 (0.0       ).as(Real                ) ] :Optional  :Min
+    [-Max                Max                 (1.0       ).as(Real                ) ] :Optional  :Max
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageModelCreate.html b/doc/SmallTools/mrcImageModelCreate.html
index b32cb2b..08b2639 100644
--- a/doc/SmallTools/mrcImageModelCreate.html
+++ b/doc/SmallTools/mrcImageModelCreate.html
@@ -8,29 +8,33 @@
 <PRE>
 Usage: mrcImageModelCreate
 Options:
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-i[nput]            In                  (NULL      )] :Optional  :InputDataFile
-    [-nx                 nx                  (70        )] :Optional  :Real length = nx * lx
-    [-ny                 ny                  (70        )] :Optional  :Real length = ny * ly
-    [-nz                 nz                  (100       )] :Optional  :Real lenght = nz * lz
-    [-r                  r                   (1         )] :Optional  :Radius[pixel]
-    [-lx                 lx                  (5.0       )] :Optional  :Pixel Size[Angstrom]
-    [-ly                 ly                  (5.0       )] :Optional  :Pixel Size[Angstrom]
-    [-lz                 lz                  (5.0       )] :Optional  :Pixel Size[Angstrom]
-    [-radius             radius              (150       )] :Optional  :filament radius [A]
-    [-n                  nHelix              (3         )] :Optional  :n-helix
-    [-dz                 zPitch              (143       )] :Optional  :pitch [A]
-    [-dphi               deltaPhi            (40        )] :Optional  :rotation angle [degree]
-    [-phi                phiAngle            (120       )] :Optional  :rotation angle in the same level [degree]
-    [-sz                 startZ              (0         )] :Optional  :start z [A]
-    [-ez                 endZ                (500       )] :Optional  :end z [A]
-    [-sphi               startPhi            (0         )] :Optional  :start angle [degree]
-    [-sphi2              startPhi2           (40        )] :Optional  :start angle 2 [degree]
-    [-inMode             inMode              (0         )] :Optional  :inMode
-    [-units              units               (9         )] :Optional  :units number
-    [-fm                 fm                  (0         )] :Optional  :formation
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Optional  :InputDataFile
+    [-nx                 nx                  (70        ).as(Integer             ) ] :Optional  :Real length = nx * lx
+    [-ny                 ny                  (70        ).as(Integer             ) ] :Optional  :Real length = ny * ly
+    [-nz                 nz                  (100       ).as(Integer             ) ] :Optional  :Real lenght = nz * lz
+    [-r                  r                   (1         ).as(Integer             ) ] :Optional  :Radius[pixel]
+    [-l                  l                   (1         ).as(Integer             ) ] :Optional  :Length[pixel]
+    [-lx                 lx                  (5.0       ).as(Real                ) ] :Optional  :Pixel Size[Angstrom]
+    [-ly                 ly                  (5.0       ).as(Real                ) ] :Optional  :Pixel Size[Angstrom]
+    [-lz                 lz                  (5.0       ).as(Real                ) ] :Optional  :Pixel Size[Angstrom]
+    [-radius             radius              (150       ).as(Real                ) ] :Optional  :filament radius [A]
+    [-n                  nHelix              (3         ).as(Integer             ) ] :Optional  :n-helix
+    [-dz                 zPitch              (143       ).as(Real                ) ] :Optional  :pitch [A]
+    [-dphi               deltaPhi            (40        ).as(Real                ) ] :Optional  :rotation angle [degree]
+    [-phi                phiAngle            (120       ).as(Real                ) ] :Optional  :rotation angle in the same level [degree]
+    [-sz                 startZ              (0         ).as(Real                ) ] :Optional  :start z [A]
+    [-ez                 endZ                (500       ).as(Real                ) ] :Optional  :end z [A]
+    [-sphi               startPhi            (0         ).as(Real                ) ] :Optional  :start angle [degree]
+    [-sphi2              startPhi2           (40        ).as(Real                ) ] :Optional  :start angle 2 [degree]
+    [-inMode             inMode              (0         ).as(Integer             ) ] :Optional  :inMode
+    [-units              units               (9         ).as(Integer             ) ] :Optional  :units number
+    [-fm                 fm                  (0         ).as(Integer             ) ] :Optional  :formation
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+>>>> 
+-nx -ny -nz : image size[pixel]
+-lx -ly -lz : pixel/voxel size[Angstrom]
 >>>> Mode <<<< (-m)
 0: Circle(a right cylinder:3D) and Triangle(a trigonal prism:3D) 
        Optional argument : -nx -ny -nz -r  
@@ -79,6 +83,8 @@ Options:
        Optional argument : -nx -ny   
 7: SheppLogan 3D 
        Optional argument : -nx -ny -nz  
+8: Cylinder 3D 
+       Optional argument : -nx -ny -nz -r -l 
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageModelSubfilamentsCreate.html b/doc/SmallTools/mrcImageModelSubfilamentsCreate.html
index 042efd7..c65aeed 100644
--- a/doc/SmallTools/mrcImageModelSubfilamentsCreate.html
+++ b/doc/SmallTools/mrcImageModelSubfilamentsCreate.html
@@ -8,20 +8,20 @@
 <PRE>
 Usage: mrcImageModelSubfilamentsCreate
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-nx                 nx                  (71        )] :Optional  :Real length = nx * lx
-    [-ny                 ny                  (71        )] :Optional  :Real length = ny * ly
-    [-nz                 nz                  (100       )] :Optional  :Real lenght = nz * lz
-    [-lx                 lx                  (5.0       )] :Optional  :Pixel Size[Angstrom]
-    [-ly                 ly                  (5.0       )] :Optional  :Pixel Size[Angstrom]
-    [-lz                 lz                  (5.0       )] :Optional  :Pixel Size[Angstrom]
-    [-position           position            (70        )] :Optional  :subfilaments position from center [A]
-    [-n                  nHelix              (3         )] :Optional  :n-helix
-    [-dphi               deltaPhi            (1.395348837)] :Optional  :rotation angle [degree]
-    [-sphi               startPhi            (0         )] :Optional  :start angle [degree]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-nx                 nx                  (71        ).as(Integer             ) ] :Optional  :Real length = nx * lx
+    [-ny                 ny                  (71        ).as(Integer             ) ] :Optional  :Real length = ny * ly
+    [-nz                 nz                  (100       ).as(Integer             ) ] :Optional  :Real lenght = nz * lz
+    [-lx                 lx                  (5.0       ).as(Real                ) ] :Optional  :Pixel Size[Angstrom]
+    [-ly                 ly                  (5.0       ).as(Real                ) ] :Optional  :Pixel Size[Angstrom]
+    [-lz                 lz                  (5.0       ).as(Real                ) ] :Optional  :Pixel Size[Angstrom]
+    [-position           position            (70        ).as(Real                ) ] :Optional  :subfilaments position from center [A]
+    [-n                  nHelix              (3         ).as(Integer             ) ] :Optional  :n-helix
+    [-dphi               deltaPhi            (1.395348837).as(Real                ) ] :Optional  :rotation angle [degree]
+    [-sphi               startPhi            (0         ).as(Real                ) ] :Optional  :start angle [degree]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageMontageCreate.html b/doc/SmallTools/mrcImageMontageCreate.html
index 7c21c5f..917d895 100644
--- a/doc/SmallTools/mrcImageMontageCreate.html
+++ b/doc/SmallTools/mrcImageMontageCreate.html
@@ -8,22 +8,22 @@
 <PRE>
 Usage: mrcImageMontageCreate
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-nx                 Nx                  (10        )] :Optional  :Nx: If this option does not set, the default value will be set
-    [-ny                 Ny                  (10        )] :Optional  :Ny: If this option does not set, the value will be set automatically
-    [-W[idth]            Width               (10        )] :Optional  :Width: If this option does not set, the value will be set automatically
-    [-H[eight]           Height              (10        )] :Optional  :Height: If this option does not set, the value will be set automatically
-    [-AW[indow]          AvgWnd              (2000      )] :Optional  :AverageWindow for Pad
-    [-V[alue]            Value               (0.0       )] :Optional  :
-    [-P[ad]M[ode]        PadMode             (3         )] :Optional  :
-    [-EdgeAverage        ] :Optional  :
-    [-EdgeAverageWindow  EdgeAverageWindow   (4         )] :Optional  :Definition of Edge
-    [-NoAverage          ] :Optional  :
-    [-Max                Max                 (16383     )] :Optional  :MaximumValue: If the pixel value is more than this max, the pixel value is assigned to the Value indicated by -V or -VMax.
-    [-VMax               VMax                (16383     )] :Optional  :Attention: related to -Max 
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFileListNoOpen    ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-nx                 Nx                  (10        ).as(Integer             ) ] :Optional  :Nx: If this option does not set, the default value will be set
+    [-ny                 Ny                  (10        ).as(Integer             ) ] :Optional  :Ny: If this option does not set, the value will be set automatically
+    [-W[idth]            Width               (10        ).as(Integer             ) ] :Optional  :Width: If this option does not set, the value will be set automatically
+    [-H[eight]           Height              (10        ).as(Integer             ) ] :Optional  :Height: If this option does not set, the value will be set automatically
+    [-AW[indow]          AvgWnd              (2000      ).as(Real                ) ] :Optional  :AverageWindow for Pad
+    [-V[alue]            Value               (0.0       ).as(Real                ) ] :Optional  :
+    [-P[ad]M[ode]        PadMode             (3         ).as(Integer             ) ] :Optional  :
+    [-EdgeAverage                                                                  ] :Optional  :
+    [-EdgeAverageWindow  EdgeAverageWindow   (4         ).as(Integer             ) ] :Optional  :Definition of Edge
+    [-NoAverage                                                                    ] :Optional  :
+    [-Max                Max                 (16383     ).as(Real                ) ] :Optional  :MaximumValue: If the pixel value is more than this max, the pixel value is assigned to the Value indicated by -V or -VMax.
+    [-VMax               VMax                (16383     ).as(Real                ) ] :Optional  :Attention: related to -Max 
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 >>> -i inputfile <<<: InputFile Format
 hf0000.roi
diff --git a/doc/SmallTools/mrcImageMove.html b/doc/SmallTools/mrcImageMove.html
index 49c7ee8..0c99646 100644
--- a/doc/SmallTools/mrcImageMove.html
+++ b/doc/SmallTools/mrcImageMove.html
@@ -8,13 +8,13 @@
 <PRE>
 Usage: mrcImageMove
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-x                  x                   (0.0       )] :Optional  :shift:[pixel]
-    [-y                  y                   (0.0       )] :Optional  :shift:[pixel]
-    [-z                  z                   (0.0       )] :Optional  :shift:[pixel]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-x                  x                   (0.0       ).as(Real                ) ] :Optional  :shift:[pixel]
+    [-y                  y                   (0.0       ).as(Real                ) ] :Optional  :shift:[pixel]
+    [-z                  z                   (0.0       ).as(Real                ) ] :Optional  :shift:[pixel]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 Mode for lmrcImageMove
 0: Move following Pixel Unit
diff --git a/doc/SmallTools/mrcImageMultiCTFDetermination.html b/doc/SmallTools/mrcImageMultiCTFDetermination.html
index ddf6063..ce3ec63 100644
--- a/doc/SmallTools/mrcImageMultiCTFDetermination.html
+++ b/doc/SmallTools/mrcImageMultiCTFDetermination.html
@@ -8,15 +8,17 @@
 <PRE>
 Usage: mrcImageMultiCTFDetermination
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output Optimum
-    [-oP[utput]          Out2                (NULL      )] :Optional  :Output Distribution
-    [-kV                 kV                  (200       )] :Optional  :AccVol[kV]
-    [-Cs                 Cs                  (1.7       )] :Optional  :Cs[mm]
-    [-AoverP             minAoverP           (0.0       )maxAoverP           (1.0       )delAoverP           (0.01      )] :Optional  :AoverP[A]
-    [-Rmax               Rmax                (0.1       )] :Optional  :Rmax[/A]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFileList          ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output Optimum
+    [-oP[utput]          Out2                (NULL      ).as(outFile             ) ] :Optional  :Output Distribution
+    [-kV                 kV                  (200       ).as(Real                ) ] :Optional  :AccVol[kV]
+    [-Cs                 Cs                  (1.7       ).as(Real                ) ] :Optional  :Cs[mm]
+    [-AoverP             minAoverP           (0.0       ).as(Real                ) 
+                         maxAoverP           (1.0       ).as(Real                ) 
+                         delAoverP           (0.01      ).as(Real                ) ] :Optional  :AoverP[A]
+    [-Rmax               Rmax                (0.1       ).as(Real                ) ] :Optional  :Rmax[/A]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 >>>> inputfile format <<<<
 filename minDef[A] maxDef[A] deltaDef[A]
diff --git a/doc/SmallTools/mrcImageMultiplying.html b/doc/SmallTools/mrcImageMultiplying.html
index 34260b2..5aae275 100644
--- a/doc/SmallTools/mrcImageMultiplying.html
+++ b/doc/SmallTools/mrcImageMultiplying.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageMultiplying
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-v[alue]            Value               (10.0      )] :Optional  :mrcImage x value
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-v[alue]            Value               (10.0      ).as(Real                ) ] :Optional  :mrcImage x value
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ---- Additional Usage ----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageMultiplyingbyFile.html b/doc/SmallTools/mrcImageMultiplyingbyFile.html
index 30991e5..007649c 100644
--- a/doc/SmallTools/mrcImageMultiplyingbyFile.html
+++ b/doc/SmallTools/mrcImageMultiplyingbyFile.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageMultiplyingbyFile
 Options:
-    [-i1[input1]         In1                 (NULL      )] :Optional  :InputDataFile1
-    [-i2[input2]         In2                 (NULL      )] :Optional  :InputDataFile2
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i1[input1]         In1                 (NULL      ).as(inFile              ) ] :Optional  :InputDataFile1
+    [-i2[input2]         In2                 (NULL      ).as(inFile              ) ] :Optional  :InputDataFile2
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageNLMeansFilter.html b/doc/SmallTools/mrcImageNLMeansFilter.html
index 06c8084..3f989e7 100644
--- a/doc/SmallTools/mrcImageNLMeansFilter.html
+++ b/doc/SmallTools/mrcImageNLMeansFilter.html
@@ -1,20 +1 @@
-<HTML>
-<HEAD>
-<TITLE>mrcImageNLMeansFilter</TITLE>
-</HEAD>
-<BODY>
-<H1>mrcImageNLMeansFilter</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrcImageNLMeansFilter
-Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: MRC
-    [-o[utput]           Out                 (NULL      )] :Essential :Output: MRC
-    [-N[size]            Nsize               (3         )] :Optional  :Input: N-size
-    [-hParam             hParam              (0.5       )] :Optional  :Input: hParam
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrcImageNLMeansFilter: No such file or directory
diff --git a/doc/SmallTools/mrcImageNeuralNetParticleLearning.html b/doc/SmallTools/mrcImageNeuralNetParticleLearning.html
index 9e8b9b9..535261d 100644
--- a/doc/SmallTools/mrcImageNeuralNetParticleLearning.html
+++ b/doc/SmallTools/mrcImageNeuralNetParticleLearning.html
@@ -8,16 +8,16 @@
 <PRE>
 Usage: mrcImageNeuralNetParticleLearning
 Options:
-    [-i[nput]p[ositive]  InPositive          (NULL      )] :Essential :Input: partile image list filename
-    [-i[nput]n[egative]  InNegative          (NULL      )] :Essential :Input: background image list filename
-    [-o[utput]           Out                 (NULL      )] :Essential :Output: Neural Net Parameters after Learning
+    [-i[nput]p[ositive]  InPositive          (NULL      ).as(inFileList          ) ] :Essential :Input: partile image list filename
+    [-i[nput]n[egative]  InNegative          (NULL      ).as(inFileList          ) ] :Essential :Input: background image list filename
+    [-o[utput]           Out                 (NULL      ).as(outFileList         ) ] :Essential :Output: Neural Net Parameters after Learning
  			FileNameOfWeightForTheBelowLayer NumOfCellOfThisLayer BiasOfThisLayer
-    [-B[ias0]            Bias                (1.0       )] :Optional  :Bias: The value of the bias of the input layer
-    [-max[Counter]       MaxCounter          (10        )] :Optional  :MaxCounter
-    [-EPS                EPS                 (0.005     )] :Optional  :Final Error
-    [-lambda             Lambda              (0.1       )] :Optional  :step for backpropagation
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-B[ias0]            Bias                (1.0       ).as(Real                ) ] :Optional  :Bias: The value of the bias of the input layer
+    [-max[Counter]       MaxCounter          (10        ).as(Integer             ) ] :Optional  :MaxCounter
+    [-EPS                EPS                 (0.005     ).as(Real                ) ] :Optional  :Final Error
+    [-lambda             Lambda              (0.1       ).as(Real                ) ] :Optional  :step for backpropagation
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageNfoldAxisSearch.html b/doc/SmallTools/mrcImageNfoldAxisSearch.html
index 52fce80..1a337a7 100644
--- a/doc/SmallTools/mrcImageNfoldAxisSearch.html
+++ b/doc/SmallTools/mrcImageNfoldAxisSearch.html
@@ -8,17 +8,23 @@
 <PRE>
 Usage: mrcImageNfoldAxisSearch
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output: centre
-    [-O[utput]           Out2                (stdout    )] :Optional  :Output: shifted Image
-    [-res[ideu]          Res                 (NULL      )] :Optional  :OutputDataFile
-    [-n[Fold]            nFold               (2         )] :Essential :Input: nFold
-    [-delPHI             delPHI              (1.0       )] :Optional  :Input: delPHI[degree]
-    [-rangex             minx                (-3        )maxx                (3         )delx                (1         )] :Optional  :Input: range [pixel size]
-    [-rangey             miny                (-3        )maxy                (3         )dely                (1         )] :Optional  :Input: range [pixel size]
-    [-rangez             minz                (0         )maxz                (0         )delz                (1         )] :Optional  :Input: range [pixel size]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output: centre
+    [-O[utput]           Out2                (stdout    ).as(outFile             ) ] :Optional  :Output: shifted Image
+    [-res[ideu]          Res                 (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-n[Fold]            nFold               (2         ).as(Integer             ) ] :Essential :Input: nFold
+    [-delPHI             delPHI              (1.0       ).as(Real                ) ] :Optional  :Input: delPHI[degree]
+    [-rangex             minx                (-3        ).as(Real                ) 
+                         maxx                (3         ).as(Real                ) 
+                         delx                (1         ).as(Real                ) ] :Optional  :Input: range [pixel size]
+    [-rangey             miny                (-3        ).as(Real                ) 
+                         maxy                (3         ).as(Real                ) 
+                         dely                (1         ).as(Real                ) ] :Optional  :Input: range [pixel size]
+    [-rangez             minz                (0         ).as(Real                ) 
+                         maxz                (0         ).as(Real                ) 
+                         delz                (1         ).as(Real                ) ] :Optional  :Input: range [pixel size]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageNoiseAdd.html b/doc/SmallTools/mrcImageNoiseAdd.html
index ae2244b..65ae11c 100644
--- a/doc/SmallTools/mrcImageNoiseAdd.html
+++ b/doc/SmallTools/mrcImageNoiseAdd.html
@@ -8,15 +8,15 @@
 <PRE>
 Usage: mrcImageNoiseAdd
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-SD                 SD                  (1.0       )] :Optional  :SD of Image/Signal
-    [-NS                 NS                  (1.0       )] :Optional  :N/S: Attention:Noise to Signal ratio
-    [-SN                 SN                  (1.0       )] :Optional  :S/N: Signal to Noise ratio
-    [-H                  H                   (1.0       )] :Optional  :High threshold of signal
-    [-L                  L                   (1.0       )] :Optional  :Low threshold of signal
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-SD                 SD                  (1.0       ).as(Real                ) ] :Optional  :SD of Image/Signal
+    [-NS                 NS                  (1.0       ).as(Real                ) ] :Optional  :N/S: Attention:Noise to Signal ratio
+    [-SN                 SN                  (1.0       ).as(Real                ) ] :Optional  :S/N: Signal to Noise ratio
+    [-H                  H                   (1.0       ).as(Real                ) ] :Optional  :High threshold of signal
+    [-L                  L                   (1.0       ).as(Real                ) ] :Optional  :Low threshold of signal
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageNoiseCreate.html b/doc/SmallTools/mrcImageNoiseCreate.html
index 6575e96..4621236 100644
--- a/doc/SmallTools/mrcImageNoiseCreate.html
+++ b/doc/SmallTools/mrcImageNoiseCreate.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageNoiseCreate
 Options:
-    [-r[eference]        In                  (NULL      )] :Essential :ReferenceDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-s[tandard deviation]Noise               (1.0       )] :Optional  :Standard deviation of noise
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-r[eference]        In                  (NULL      ).as(inFile              ) ] :Essential :ReferenceDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-s[tandard deviation]Noise               (1.0       ).as(Real                ) ] :Optional  :Standard deviation of noise
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 Output file has the same infomation (Nx Ny Nz Length and so on) as reference file. 
 </PRE>
diff --git a/doc/SmallTools/mrcImageNoiseReductionByRelaxation.html b/doc/SmallTools/mrcImageNoiseReductionByRelaxation.html
index 846d3ca..5e836cc 100644
--- a/doc/SmallTools/mrcImageNoiseReductionByRelaxation.html
+++ b/doc/SmallTools/mrcImageNoiseReductionByRelaxation.html
@@ -8,18 +8,18 @@
 <PRE>
 Usage: mrcImageNoiseReductionByRelaxation
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-n[umber]           Nlab                (8         )] :Optional  :Number of Density Level
-    [-max[imum]          max                 (0         )] :Optional  :Maximum of Density Level
-    [-min[imum]          min                 (0         )] :Optional  :Minimum of Density Level
-    [-m[ode]1            mode1               (1         )] :Optional  :Dij Modeof Personal Style
-    [-m[ode]2            mode2               (1         )] :Optional  :Dij Mode of Figure Style
-    [-m[ode]3            mode3               (1         )] :Optional  :Dij Mode of Dimension Style
-    [-o[ptional]m[ode]   omode               (0         )] :Optional  :Optional Mode of Noise Reduction
-    [-t[imes]            times               (1         )] :Optional  :Times of NoiseReduction
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-n[umber]           Nlab                (8         ).as(Integer             ) ] :Optional  :Number of Density Level
+    [-max[imum]          max                 (0         ).as(Integer             ) ] :Optional  :Maximum of Density Level
+    [-min[imum]          min                 (0         ).as(Integer             ) ] :Optional  :Minimum of Density Level
+    [-m[ode]1            mode1               (1         ).as(Integer             ) ] :Optional  :Dij Modeof Personal Style
+    [-m[ode]2            mode2               (1         ).as(Integer             ) ] :Optional  :Dij Mode of Figure Style
+    [-m[ode]3            mode3               (1         ).as(Integer             ) ] :Optional  :Dij Mode of Dimension Style
+    [-o[ptional]m[ode]   omode               (0         ).as(Integer             ) ] :Optional  :Optional Mode of Noise Reduction
+    [-t[imes]            times               (1         ).as(Integer             ) ] :Optional  :Times of NoiseReduction
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageNormalizedSubtraction.html b/doc/SmallTools/mrcImageNormalizedSubtraction.html
index 31ee249..0e4f5b2 100644
--- a/doc/SmallTools/mrcImageNormalizedSubtraction.html
+++ b/doc/SmallTools/mrcImageNormalizedSubtraction.html
@@ -8,15 +8,15 @@
 <PRE>
 Usage: mrcImageNormalizedSubtraction
 Options:
-    [-i1[nput]           In1                 (NULL      )] :Essential :InputDataFile
-    [-i2[nput]           In2                 (NULL      )] :Essential :InputDataFile
-    [-nori2[nput]        In2_tmp             (NULL      )] :Optional  :OutDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-rmsd               RMSD                (stdout    )] :Optional  :Output: RMSD
-    [-p[rameter]f[ile]   ParamFile           (stdout    )] :Optional  :ParameterOutputFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i1[nput]           In1                 (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-i2[nput]           In2                 (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-nori2[nput]        In2_tmp             (NULL      ).as(outFile             ) ] :Optional  :OutDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-rmsd               RMSD                (stdout    ).as(outFile             ) ] :Optional  :Output: RMSD
+    [-p[rameter]f[ile]   ParamFile           (stdout    ).as(outFile             ) ] :Optional  :ParameterOutputFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 -- Attention ---
-in1(default) -  in2(normalized) : 
+in1(default:ref) -  in2(normalized:tst) : 
 -- Mode ---
   1: Sigma!=1.0 
   2: Stdout     
diff --git a/doc/SmallTools/mrcImageNormalizing.html b/doc/SmallTools/mrcImageNormalizing.html
index 8554985..47ec501 100644
--- a/doc/SmallTools/mrcImageNormalizing.html
+++ b/doc/SmallTools/mrcImageNormalizing.html
@@ -8,15 +8,15 @@
 <PRE>
 Usage: mrcImageNormalizing
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-A                  A                   (1.0       )] :Optional  :A
-    [-B                  B                   (0.0       )] :Optional  :B
-    [-ContourMin         ContourMin          (0.0       )] :Optional  :ContourMin
-    [-ContourMax         ContourMax          (1.0       )] :Optional  :ContourMax
-    [-ContourSolvent     ContourSolvent      (0.0       )] :Optional  :ContourSolvent
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-A                  A                   (1.0       ).as(Real                ) ] :Optional  :A
+    [-B                  B                   (0.0       ).as(Real                ) ] :Optional  :B
+    [-ContourMin         ContourMin          (0.0       ).as(Real                ) ] :Optional  :ContourMin
+    [-ContourMax         ContourMax          (1.0       ).as(Real                ) ] :Optional  :ContourMax
+    [-ContourSolvent     ContourSolvent      (0.0       ).as(Real                ) ] :Optional  :ContourSolvent
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- mode -----
 ----- Mode for lmrcImageNormalizing -----
   0: Double Exponential: Solvent and Object
diff --git a/doc/SmallTools/mrcImageNullImageCreate.html b/doc/SmallTools/mrcImageNullImageCreate.html
index a5242e6..e357bfe 100644
--- a/doc/SmallTools/mrcImageNullImageCreate.html
+++ b/doc/SmallTools/mrcImageNullImageCreate.html
@@ -8,15 +8,20 @@
 <PRE>
 Usage: mrcImageNullImageCreate
 Options:
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-Nx[Number of x]    Nx                  (0         )] :Optional  :Nx:Default Nx of inputfile
-    [-Ny[Number of y]    Ny                  (0         )] :Optional  :Ny:Default Ny of inputfile
-    [-Nz[Number of z]    Nz                  (0         )] :Optional  :Nz:Default Nz of inputfile
-    [-v[alue]            Value               (0.0       )] :Optional  :Value of pixel
-    [-d[elta]            d                   (0.0       )] :Optional  :Pixel size
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Essential :OutputDataFile
+    [-r[eference]        Ref                 (NULL      ).as(inFile::mrcImage    ) ] :Optional  :Input: Reference Header
+    [-Nx[Number of x]    Nx                  (0         ).as(Integer             ) ] :Optional  :Nx:Default Nx of inputfile
+    [-Ny[Number of y]    Ny                  (0         ).as(Integer             ) ] :Optional  :Ny:Default Ny of inputfile
+    [-Nz[Number of z]    Nz                  (0         ).as(Integer             ) ] :Optional  :Nz:Default Nz of inputfile
+    [-v[alue]            Value               (0.0       ).as(Real                ) ] :Optional  :Value of pixel
+    [-d[elta]            d                   (0.0       ).as(Real                ) ] :Optional  :Pixel size
+    [-M[ode]             Mode                (2         ).as(Integer             ) ] :Optional  :ImageMode: 0 char 1 short 2 Float
+    [-Def[ault]                                                                    ] :Optional  :DefaultFixedValueSet
+    [-c[onfig]           configFile          (NULL      ).as(inFile::ASCII       ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
+-r is used to define a reference header.
+-Nx etc. are used preferentially.
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageOddBoxel.html b/doc/SmallTools/mrcImageOddBoxel.html
index f1c31bc..51773de 100644
--- a/doc/SmallTools/mrcImageOddBoxel.html
+++ b/doc/SmallTools/mrcImageOddBoxel.html
@@ -8,17 +8,17 @@
 <PRE>
 Usage: mrcImageOddBoxel
 Options:
-    [-I[nput array of file]In                  (stdin     )] :Essential :InputDataFiles
-    [-Iter[ation]        ] :Optional  :IterationFlag
-    [-M[olecularWeight]  MolecularWeight     (1.0       )] :Optional  :MolecularWeight (for iteration only)
-    [-n[Molecule]        nMolecule           (1.0       )] :Optional  :NumberOfMolecule (for iteration only)
-    [-Boxel              Boxel               (0         )] :Optional  :Final volume for iteration uning boxel unit.
-    [-d[ensty]           Density             (1.35      )] :Optional  :Density (for iteration only)
-    [-I[nverse]          ] :Optional  :Inverse (for iteration only)
-    [-Abs[olute]         ] :Optional  :AbsoluteFlag
-    [-Th[reshold]        Th                  (0.0       )] :Optional  :Threshold for calculation. (for iteration only) 
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-I[nput array of file]In                  (stdin     ).as(inFileListNoOpen    ) ] :Essential :InputDataFiles
+    [-Iter[ation]                                                                  ] :Optional  :IterationFlag
+    [-M[olecularWeight]  MolecularWeight     (1.0       ).as(Real                ) ] :Optional  :MolecularWeight (for iteration only)
+    [-n[Molecule]        nMolecule           (1.0       ).as(Real                ) ] :Optional  :NumberOfMolecule (for iteration only)
+    [-Boxel              Boxel               (0         ).as(Integer             ) ] :Optional  :Final volume for iteration uning boxel unit.
+    [-d[ensty]           Density             (1.35      ).as(Real                ) ] :Optional  :Density (for iteration only)
+    [-I[nverse]                                                                    ] :Optional  :Inverse (for iteration only)
+    [-Abs[olute]                                                                   ] :Optional  :AbsoluteFlag
+    [-Th[reshold]        Th                  (0.0       ).as(Real                ) ] :Optional  :Threshold for calculation. (for iteration only) 
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageOneLineSimilarityCalc.html b/doc/SmallTools/mrcImageOneLineSimilarityCalc.html
index ce6242a..2033cd5 100644
--- a/doc/SmallTools/mrcImageOneLineSimilarityCalc.html
+++ b/doc/SmallTools/mrcImageOneLineSimilarityCalc.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageOneLineSimilarityCalc
 Options:
-    [-i1[nput]           In1                 (NULL      )] :Essential :InputDataFile
-    [-i2[nput]           In2                 (NULL      )] :Essential :InputDataFile
-    [-sm[ode]            shiftflag           (0         )] :Optional  :Shift mode
-    [-v[alue]            value               (0         )] :Optional  :Optional value of shift
-    [-mm[ode]            methodmode          (0         )] :Optional  :Method mode
+    [-i1[nput]           In1                 (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-i2[nput]           In2                 (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-sm[ode]            shiftflag           (0         ).as(Integer             ) ] :Optional  :Shift mode
+    [-v[alue]            value               (0         ).as(Integer             ) ] :Optional  :Optional value of shift
+    [-mm[ode]            methodmode          (0         ).as(Integer             ) ] :Optional  :Method mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageOpening.html b/doc/SmallTools/mrcImageOpening.html
index 0896254..fd53d70 100644
--- a/doc/SmallTools/mrcImageOpening.html
+++ b/doc/SmallTools/mrcImageOpening.html
@@ -8,23 +8,26 @@
 <PRE>
 Usage: mrcImageOpening
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: MRC
-    [-o[utput]           Out                 (NULL      )] :Essential :Output: MRC
-    [-times              times               (1         )] :Optional  :Times: erosion*times -> dilation*times
-    [-o[utput]SE         OutSE               (NULL      )] :Optional  :Output: MRC(SE)
-    [-S[tructuring]E[lement]SEmode              (0         )] :Optional  :StructuringElement
-    [-r[adius]           radius              (2         )] :Optional  :Radius
-    [-n                  n                   (5         )] :Optional  :size
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: MRC
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output: MRC
+    [-times              times               (1         ).as(Integer             ) ] :Optional  :Times: erosion*times -> dilation*times
+    [-o[utput]SE         OutSE               (NULL      ).as(outFile             ) ] :Optional  :Output: MRC(SE)
+    [-S[tructuring]E[lement]SEmode              (0         ).as(Integer             ) ] :Optional  :StructuringElement
+    [-r[adius]           radius              (2         ).as(Integer             ) ] :Optional  :Radius
+    [-n                  n                   (5         ).as(Integer             ) ] :Optional  :size
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 ----- Structuring Element : Mode 
 0: 2D Cross3x3:  4-neighbour
 1: 2D Square3x3: 8-neighbour
-2: 2D Open Disk , need (radius, n)
+2: 2D Disk , need (radius, n(squre size))
 3: 3D Cross3x3x3:   6-neighbour
 4: 3D Cubic3x3x3: 26-neighbour
-5: 3D Open Disk , need (radius, n)
+5: 3D Sphere, need (radius, n(cubic size))
+6: 2D Rectangle, need nx, ny
+7: 3D Cuboid, need nx, ny, nz
+8: 3D Cylindar, need r, nx, ny, nz
 -----
 Dilation: Max for image : Or  for binary image 
 Erosion:  Min for image : And for binary image 
diff --git a/doc/SmallTools/mrcImageOrientationSearchByHigherSelection.html b/doc/SmallTools/mrcImageOrientationSearchByHigherSelection.html
index de9d104..e7c5331 100644
--- a/doc/SmallTools/mrcImageOrientationSearchByHigherSelection.html
+++ b/doc/SmallTools/mrcImageOrientationSearchByHigherSelection.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageOrientationSearchByHigherSelection
 Options:
-    [-I[nputFileList]    In                  (NULL      )] :Essential :InputDataFileList
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-n[umber]           n                   (10        )] :Optional  :Number of selection
+    [-I[nputFileList]    In                  (NULL      ).as(inFileListNoOpen    ) ] :Essential :InputDataFileList
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-n[umber]           n                   (10        ).as(Integer             ) ] :Optional  :Number of selection
 
 ----- Input file format -----
 filename LminAve
diff --git a/doc/SmallTools/mrcImageOrientationSearchByHybridization.html b/doc/SmallTools/mrcImageOrientationSearchByHybridization.html
index 31c01c4..af4719d 100644
--- a/doc/SmallTools/mrcImageOrientationSearchByHybridization.html
+++ b/doc/SmallTools/mrcImageOrientationSearchByHybridization.html
@@ -8,15 +8,15 @@
 <PRE>
 Usage: mrcImageOrientationSearchByHybridization
 Options:
-    [-I[nputFileLiest]   In                  (NULL      )] :Essential :InputDataFileList
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFileHeader
-    [-e[xtension]        extension           (NULL      )] :Essential :OutputDataFileExtension
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-i[ncrease]r[ate]   ir                  (1         )] :Optional  :IncreaseRate
-    [-h[ybridization]p[oint]n[umber]hpn                 (1         )] :Optional  :HybridizationPointNumber
-    [-m[ode]s[election]  ms                  (0         )] :Optional  :ModeOfSelection
-    [-i[nitial]r[andom]d[ata]ird                 (0         )] :Optional  :InitialRandomData
+    [-I[nputFileLiest]   In                  (NULL      ).as(inFileListNoOpen    ) ] :Essential :InputDataFileList
+    [-o[utput]           Out                 (NULL      ).as(String              ) ] :Essential :OutputDataFileHeader
+    [-e[xtension]        extension           (NULL      ).as(String              ) ] :Essential :OutputDataFileExtension
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-i[ncrease]r[ate]   ir                  (1         ).as(Integer             ) ] :Optional  :IncreaseRate
+    [-h[ybridization]p[oint]n[umber]hpn                 (1         ).as(Integer             ) ] :Optional  :HybridizationPointNumber
+    [-m[ode]s[election]  ms                  (0         ).as(Integer             ) ] :Optional  :ModeOfSelection
+    [-i[nitial]r[andom]d[ata]ird                 (0         ).as(Integer             ) ] :Optional  :InitialRandomData
 
 >> This algrithm use results of mrcImageOrientationSearchBySimultaneousMinimization
 
diff --git a/doc/SmallTools/mrcImageOrientationSearchBySimultaneousMinimization.html b/doc/SmallTools/mrcImageOrientationSearchBySimultaneousMinimization.html
index c69489b..37fba60 100644
--- a/doc/SmallTools/mrcImageOrientationSearchBySimultaneousMinimization.html
+++ b/doc/SmallTools/mrcImageOrientationSearchBySimultaneousMinimization.html
@@ -8,27 +8,27 @@
 <PRE>
 Usage: mrcImageOrientationSearchBySimultaneousMinimization
 Options:
-    [-I[nputFileList]    In                  (NULL      )] :Essential :InputDataFileList
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-dt[heta]           dtheta              (1         )] :Optional  :dtheta
-    [-dp[si]             dpsi                (1         )] :Optional  :dpsi
-    [-m[odeof]s[election]ms                  (0         )] :Optional  :modeofselection
-    [-i[nitial]r[andom]d[ata]ird                 (1         )] :Optional  :InitialRandomData
-    [-M[ax]C[ount]       MC                  (100       )] :Optional  :MaxCount
-    [-F[ileName]H[eader] FileNameHeader      (EulerAngle)] :Optional  :FileNameHeader
-    [-m[odeof]i[nitial]d[ada]mid                 (0         )] :Optional  :modeofinitialdata
-    [-i[nputFile]i[nitial]d[ata]InInitial           (NULL      )] :Optional  :InputDataFileOfInitialData
-    [-m[odeof]s[tart]p[oint]msp                 (0         )] :Optional  :mode of start point
-    [-m[odeof]a[ngular]a[rea]maa                 (0         )] :Optional  :mode of angular area
-    [-p[revious]dt[heta] pdtheta             (0         )] :Optional  :previous dtheta
-    [-p[revious]dp[si]   pdpsi               (0         )] :Optional  :previous dpsi
-    [-m[ode]L[calculation]modeL               (0         )] :Optional  :Mode of L calculation
-    [-m[ode]T[hreshold]A[ngularweight]modeTA              (0         )] :Optional  :Mode of Threshold of AngularWeight
-    [-m[ode]c[alculation]a[rea]modeCA              (0         )] :Optional  :mode of Lvalue of calculation area
-    [-t[hreshold]c[alculation]a[rea]TCA                 (0         )] :Optional  :Threshold of Lvalue of calculation area
-    [-m[ode]f[ix]        modeF               (0         )] :Optional  :mode of fix
+    [-I[nputFileList]    In                  (NULL      ).as(inFileListNoOpen    ) ] :Essential :InputDataFileList
+    [-o[utput]           Out                 (NULL      ).as(outFileNoOpen       ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-dt[heta]           dtheta              (1         ).as(Real                ) ] :Optional  :dtheta
+    [-dp[si]             dpsi                (1         ).as(Real                ) ] :Optional  :dpsi
+    [-m[odeof]s[election]ms                  (0         ).as(Integer             ) ] :Optional  :modeofselection
+    [-i[nitial]r[andom]d[ata]ird                 (1         ).as(Integer             ) ] :Optional  :InitialRandomData
+    [-M[ax]C[ount]       MC                  (100       ).as(Integer             ) ] :Optional  :MaxCount
+    [-F[ileName]H[eader] FileNameHeader      (EulerAngle).as(String              ) ] :Optional  :FileNameHeader
+    [-m[odeof]i[nitial]d[ada]mid                 (0         ).as(Integer             ) ] :Optional  :modeofinitialdata
+    [-i[nputFile]i[nitial]d[ata]InInitial           (NULL      ).as(inFile              ) ] :Optional  :InputDataFileOfInitialData
+    [-m[odeof]s[tart]p[oint]msp                 (0         ).as(Integer             ) ] :Optional  :mode of start point
+    [-m[odeof]a[ngular]a[rea]maa                 (0         ).as(Integer             ) ] :Optional  :mode of angular area
+    [-p[revious]dt[heta] pdtheta             (0         ).as(Integer             ) ] :Optional  :previous dtheta
+    [-p[revious]dp[si]   pdpsi               (0         ).as(Integer             ) ] :Optional  :previous dpsi
+    [-m[ode]L[calculation]modeL               (0         ).as(Integer             ) ] :Optional  :Mode of L calculation
+    [-m[ode]T[hreshold]A[ngularweight]modeTA              (0         ).as(Integer             ) ] :Optional  :Mode of Threshold of AngularWeight
+    [-m[ode]c[alculation]a[rea]modeCA              (0         ).as(Integer             ) ] :Optional  :mode of Lvalue of calculation area
+    [-t[hreshold]c[alculation]a[rea]TCA                 (0         ).as(Real                ) ] :Optional  :Threshold of Lvalue of calculation area
+    [-m[ode]f[ix]        modeF               (0         ).as(Integer             ) ] :Optional  :mode of fix
 
 ----- ModeSelection -----
 -ms : 0 : random
diff --git a/doc/SmallTools/mrcImagePCA.html b/doc/SmallTools/mrcImagePCA.html
index fd8625c..6d94db5 100644
--- a/doc/SmallTools/mrcImagePCA.html
+++ b/doc/SmallTools/mrcImagePCA.html
@@ -9,17 +9,17 @@ Program Start
 <PRE>
 Usage: mrcImagePCA
 Options:
-    [-i[nput]            InList              (NULL      )] :Essential :Input: filelist
-    [-o[utput]           OutList             (NULL      )] :Essential :Output: filelist
-    [-EPS                EPS                 (1e2       )] :Optional  :EPS: lambda<EPS, stop calculation. 
-    [-NX                 NX                  (30        )] :Optional  :NX: pixcelNX 
-    [-NY                 NY                  (30        )] :Optional  :NY: pixcelNX 
-    [-O[utput]           Outvector           (NULL      )] :Optional  :Output: vectorfile
-    [-EPSO[utput]        EPSOutcaletime      (NULL      )] :Optional  :EPSOutput: caletimefile
-    [-E[igenImage]       EigenImage          (eigen     )] :Optional  :Output: eigenImage
-    [-numE[igenImage]    numOfEigenImage     (10        )] :Optional  :Number of eigenImages
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            InList              (NULL      ).as(inFileListNoOpen    ) ] :Essential :Input: filelist
+    [-o[utput]           OutList             (NULL      ).as(outFileListNoOpen   ) ] :Essential :Output: filelist
+    [-EPS                EPS                 (1e2       ).as(Real                ) ] :Optional  :EPS: lambda<EPS, stop calculation. 
+    [-NX                 NX                  (30        ).as(Integer             ) ] :Optional  :NX: pixcelNX 
+    [-NY                 NY                  (30        ).as(Integer             ) ] :Optional  :NY: pixcelNX 
+    [-O[utput]           Outvector           (NULL      ).as(outFile             ) ] :Optional  :Output: vectorfile
+    [-EPSO[utput]        EPSOutcaletime      (NULL      ).as(outFile             ) ] :Optional  :EPSOutput: caletimefile
+    [-E[igenImage]       EigenImage          (eigen     ).as(String              ) ] :Optional  :Output: eigenImage
+    [-numE[igenImage]    numOfEigenImage     (10        ).as(Integer             ) ] :Optional  :Number of eigenImages
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImagePad.html b/doc/SmallTools/mrcImagePad.html
index cfe4a65..d1bebeb 100644
--- a/doc/SmallTools/mrcImagePad.html
+++ b/doc/SmallTools/mrcImagePad.html
@@ -8,18 +8,19 @@
 <PRE>
 Usage: mrcImagePad
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input DataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :Output DataFile
-    [-W[idth]            Width               (0         )] :Optional  :Width[pixel]
-    [-H[eight]           Height              (0         )] :Optional  :Height[pixel]
-    [-V[alue]            Value               (0.0       )] :Optional  :Padding Value(float on avgrage density)
-    [-E[xpected]V[alue]  ExpectedValue       (0.0       )] :Optional  :Expected Value for Background
-    [-AW                 AvgWnd              (2000.0    )] :Optional  :Averaging Window Size [A]
-    [-AWMin              AWMin               (20        )] :Optional  :Averaging Window Size[pixel]
-    [-AWMax              AWMax               (22        )] :Optional  :Averaging Window Size[pixel]
-    [-Tilt               TiltAxisAngle       (0         )TiltAngle           (0         )] :Optional  :TiltImage: TiltAxisAngle TiltAngle
-    [-c[onfig]           configFile          (NULL      )] :Optional  :Configuration File
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input DataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output DataFile
+    [-W[idth]            Width               (0         ).as(Integer             ) ] :Optional  :Width[pixel]
+    [-H[eight]           Height              (0         ).as(Integer             ) ] :Optional  :Height[pixel]
+    [-V[alue]            Value               (0.0       ).as(Real                ) ] :Optional  :Padding Value(float on avgrage density)
+    [-E[xpected]V[alue]  ExpectedValue       (0.0       ).as(Real                ) ] :Optional  :Expected Value for Background
+    [-AW                 AvgWnd              (2000.0    ).as(Real                ) ] :Optional  :Averaging Window Size [A]
+    [-AWMin              AWMin               (20        ).as(Real                ) ] :Optional  :Averaging Window Size[pixel]
+    [-AWMax              AWMax               (22        ).as(Real                ) ] :Optional  :Averaging Window Size[pixel]
+    [-Tilt               TiltAxisAngle       (0         ).as(Real                ) 
+                         TiltAngle           (0         ).as(Real                ) ] :Optional  :TiltImage: TiltAxisAngle TiltAngle
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :Configuration File
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Mode -----
 0: Pad average density(Image Center)
 1: Pad average density of x=0 and x=MAX(x)(Image Center)
diff --git a/doc/SmallTools/mrcImagePanoramaCreate.html b/doc/SmallTools/mrcImagePanoramaCreate.html
index 9f62bb4..411b5a3 100644
--- a/doc/SmallTools/mrcImagePanoramaCreate.html
+++ b/doc/SmallTools/mrcImagePanoramaCreate.html
@@ -8,13 +8,15 @@
 <PRE>
 Usage: mrcImagePanoramaCreate
 Options:
-    [-I[nput]            In                  (stdin     )] :Essential :Input:FileList[mrcImage x y z]
-    [-o[utput]           Out                 (NULL      )] :Essential :Output:mrcImage
-    [-o[utput]C[ount]    Count               (NULL      )] :Optional  :Output(Count):mrcImage
-    [-N                  Nx                  (0         )Ny                  (0         )Nz                  (0         )] :Optional  :Input:OutImageSize
-    [-M[ode]             InterpolationMode   (0         )] :Optional  :InterpolationMode
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-I[nput]            In                  (stdin     ).as(inFileList          ) ] :Essential :Input:FileList[mrcImage x y z]
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output:mrcImage
+    [-o[utput]C[ount]    Count               (NULL      ).as(outFile             ) ] :Optional  :Output(Count):mrcImage
+    [-N                  Nx                  (0         ).as(Integer             ) 
+                         Ny                  (0         ).as(Integer             ) 
+                         Nz                  (0         ).as(Integer             ) ] :Optional  :Input:OutImageSize
+    [-M[ode]             InterpolationMode   (0         ).as(Integer             ) ] :Optional  :InterpolationMode
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 >>>InputFileList Format
 FileName OffsetX OffsetY OffsetZ
diff --git a/doc/SmallTools/mrcImageParticleCandidateExtract.html b/doc/SmallTools/mrcImageParticleCandidateExtract.html
index 9f32485..0ccee30 100644
--- a/doc/SmallTools/mrcImageParticleCandidateExtract.html
+++ b/doc/SmallTools/mrcImageParticleCandidateExtract.html
@@ -8,14 +8,14 @@
 <PRE>
 Usage: mrcImageParticleCandidateExtract
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: MRC
-    [-o[utput]           Out                 (NULL      )] :Essential :Output: MRC
-    [-R[ing]R[adius]     RingRadius          (100.0     )] :Optional  :Input: [A]
-    [-R[ing]W[idth]      RingWidth           (10.0      )] :Optional  :Input: [A]
-    [-thres[hold]        Threshold           (3.0       )] :Optional  :Input: threshold of IQ
-    [-out[Threshold]     outFileThres        (stdout    )] :Optional  :Output: Output
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: MRC
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output: MRC
+    [-R[ing]R[adius]     RingRadius          (100.0     ).as(Real                ) ] :Optional  :Input: [A]
+    [-R[ing]W[idth]      RingWidth           (10.0      ).as(Real                ) ] :Optional  :Input: [A]
+    [-thres[hold]        Threshold           (3.0       ).as(Real                ) ] :Optional  :Input: threshold of IQ
+    [-out[Threshold]     outFileThres        (stdout    ).as(outFile             ) ] :Optional  :Output: Output
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImagePattersonFunctionCalc.html b/doc/SmallTools/mrcImagePattersonFunctionCalc.html
new file mode 100644
index 0000000..c1561be
--- /dev/null
+++ b/doc/SmallTools/mrcImagePattersonFunctionCalc.html
@@ -0,0 +1,19 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImagePattersonFunctionCalc</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImagePattersonFunctionCalc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImagePattersonFunctionCalc
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input:mrcImage
+    [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Essential :Output:mrcImage
+    [-O[utput]           OutPat              (stdout    ).as(outFile::ASCII      ) ] :Optional  :Output:ASCII
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImagePeakSearch.html b/doc/SmallTools/mrcImagePeakSearch.html
index ae27edd..5e96776 100644
--- a/doc/SmallTools/mrcImagePeakSearch.html
+++ b/doc/SmallTools/mrcImagePeakSearch.html
@@ -8,18 +8,18 @@
 <PRE>
 Usage: mrcImagePeakSearch
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: mrcImage
-    [-o[utput]           Out                 (NULL      )] :Optional  :Output: mrcImage
-    [-o[utput]B          OutB                (NULL      )] :Optional  :Output: mrcImage:Binary
-    [-o[utput]L          OutL                (NULL      )] :Optional  :Output: mrcImage:Label
-    [-o[utput]A          OutA                (NULL      )] :Optional  :Output: mrcImage:Aarea
-    [-O[utputPeakStatics]OutStatics          (stdout    )] :Optional  :Output as ASCII: Peak statics
-    [-t[hreshold]        Sigma               (3.0       )] :Optional  :Input: Peak's values are more than t*sigma.
-    [-T[hreshold]        Threshold           (0.0       )] :Optional  :Input: Peak's values are more than T.
-    [-a[rea]             Area                (6.0       )] :Optional  :Input[A^2]: Peak's area are more than a.
-    [-A[rea]             AreaPixel           (9         )] :Optional  :Input[pixel^2]: Peak's area are more than A.
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: mrcImage
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :Output: mrcImage
+    [-o[utput]B          OutB                (NULL      ).as(outFile             ) ] :Optional  :Output: mrcImage:Binary
+    [-o[utput]L          OutL                (NULL      ).as(outFile             ) ] :Optional  :Output: mrcImage:Label
+    [-o[utput]A          OutA                (NULL      ).as(outFile             ) ] :Optional  :Output: mrcImage:Aarea
+    [-O[utputPeakStatics]OutStatics          (stdout    ).as(outFile             ) ] :Optional  :Output as ASCII: Peak statics
+    [-t[hreshold]        Sigma               (3.0       ).as(Real                ) ] :Optional  :Input: Peak's values are more than t*sigma.
+    [-T[hreshold]        Threshold           (0.0       ).as(Real                ) ] :Optional  :Input: Peak's values are more than T.
+    [-a[rea]             Area                (6.0       ).as(Real                ) ] :Optional  :Input[A^2]: Peak's area are more than a.
+    [-A[rea]             AreaPixel           (9         ).as(Real                ) ] :Optional  :Input[pixel^2]: Peak's area are more than A.
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImagePerimeterCalc.html b/doc/SmallTools/mrcImagePerimeterCalc.html
new file mode 100644
index 0000000..cf5cbed
--- /dev/null
+++ b/doc/SmallTools/mrcImagePerimeterCalc.html
@@ -0,0 +1,26 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImagePerimeterCalc</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImagePerimeterCalc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImagePerimeterCalc
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input(Binary)
+    [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Essential :Output
+    [-o[utput]A[rea]     OutArea             (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output
+    [-o[utput]C[hainCode]OutChainCode        (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output
+    [-o[utput]L[abel]    OutLabel            (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+>> mode
+   0: 8-neighbor, chainCode absolute
+   1: 4-neighbor, chainCode absolute
+   2: 8-neighbor, chainCode relative
+   3: 4-neighbor, chainCode relative
+ </PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImagePhaseCTFCompensationFromCTFINFO.html b/doc/SmallTools/mrcImagePhaseCTFCompensationFromCTFINFO.html
index b303b9c..1e54179 100644
--- a/doc/SmallTools/mrcImagePhaseCTFCompensationFromCTFINFO.html
+++ b/doc/SmallTools/mrcImagePhaseCTFCompensationFromCTFINFO.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: mrcImagePhaseCTFCompensationFromCTFINFO
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImagePolyROI.html b/doc/SmallTools/mrcImagePolyROI.html
index df377c4..21caf47 100644
--- a/doc/SmallTools/mrcImagePolyROI.html
+++ b/doc/SmallTools/mrcImagePolyROI.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: mrcImagePolyROI
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImagePosterization.html b/doc/SmallTools/mrcImagePosterization.html
index c94b404..adb0331 100644
--- a/doc/SmallTools/mrcImagePosterization.html
+++ b/doc/SmallTools/mrcImagePosterization.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImagePosterization
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-g[radation]        Grad                (16        )] :Optional  :gradation level
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-g[radation]        Grad                (16        ).as(Integer             ) ] :Optional  :gradation level
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImagePrint.html b/doc/SmallTools/mrcImagePrint.html
index 7d1db30..3820190 100644
--- a/doc/SmallTools/mrcImagePrint.html
+++ b/doc/SmallTools/mrcImagePrint.html
@@ -8,42 +8,74 @@
 <PRE>
 Usage: mrcImagePrint
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputImageFile
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputImageFile
-    [-H[ighThreshold]    thresHigh           (0.0       )] :Optional  :High Threshold
-    [-L[owThreshold]     thresLow            (1.0       )] :Optional  :Low Threshold
-    [-Section            section             (z         )] :Optional  :[z|x|y]Section: Def: z-section
-    [-x[Section]         xMin                (0         )xMax                (0         )] :Optional  :x section
-    [-y[Section]         yMin                (0         )yMax                (0         )] :Optional  :y section
-    [-z[Section]         zMin                (0         )zMax                (0         )] :Optional  :z section
-    [-S[cale]            Scale               (1.0       )] :Optional  :Scale(Centre is Bottom Left): -S 1 := 1 mm/pixel
-    [-A[bsolute]S[cale]  AbScale             (1.0       )] :Optional  :Scale(Centre is Bottom Left): -AS 1 := 1 mm/A (Real) or 1 mm/A-1 (Fourier Space)
-    [-E[nlarge]          Enlarge             (1.0       )] :Optional  :Enlargement(image center is center)
-    [-center             cx                  (0.0/* in case of FT or N.x/2.0 in case of Image*/)cy                  (0.0/* in case of FT or N.y/2.0 in case of Image */)] :Optional  :Center of a printed image
-    [-C[ontour]          contourLevel        (1.0       )... ] :Variable  :ContourLevel
-    [-I[nverse]          ] :Optional  :Black is High Density.
-    [-A[uto]             ] :Optional  :HighThres=Mean-SD, LowThres=Mean+SD
-    [-AC[ontour]         AutoContour         (10        )] :Optional  :Auto Contour(thresHigh <-> mean)
-    [-PC[ontour]         PeakContour         (10        )] :Optional  :Peak Contour(thresHigh <-> (mean+thresHigh)/2
-    [-AC[ontour]2        AutoContour2        (10        )] :Optional  :Auto Contour2(thresHigh <-> thresLow)
-    [-Y[expand]          Yexpand             (1         )] :Optional  :Y-axis expanding
-    [-RGB                Red                 (0         )Green               (0         )Blue                (0         )] :Optional  :Contour Color Mode: RGB
-    [-RGBGradient        RedFirst            (0         )GreenFirst          (0         )BlueFirst           (0         )RedLast             (0         )GreenLast           (0         )BlueLast            (0         )] :Optional  :Contour Color GradientMode: RGB
-    [-HSB                Hue                 (0         )Saturation          (0         )Brightness          (0         )] :Optional  :Contour Color Mode: HSB
-    [-HSBGradient        HueFirst            (0         )SaturationFirst     (0         )BrightnessFirst     (0         )HueLast             (0         )SaturationLast      (0         )BrightnessLast      (0         )] :Optional  :Contour Color GradientMode: HSB
-    [-LineColourRGB      LineRed             (0         )LineGreen           (0         )LineBlue            (0         )] :Optional  :Contour Color Mode: RGB
-    [-LineColourRGBGradientLineRedFirst        (0         )LineGreenFirst      (0         )LineBlueFirst       (0         )LineRedLast         (0         )LineGreenLast       (0         )LineBlueLast        (0         )] :Optional  :Contour Color GradientMode: RGB
-    [-LineColourHSB      LineHue             (0         )LineSaturation      (0         )LineBrightness      (0         )] :Optional  :Contour Color Mode: HSB
-    [-LineColourHSBGradientLineHueFirst        (0         )LineSaturationFirst (0         )LineBrightnessFirst (0         )LineHueLast         (0         )LineSaturationLast  (0         )LineBrightnessLast  (0         )] :Optional  :Contour Color GradientMode: HSB
-    [-LineChange         LineColorChange     (0.1       )] :Optional  :Contour Color Change
-    [-LineWidthStart     LineWidthStart      (0.1       )] :Optional  :Contour Line Width Step
-    [-LineWidthStep      LineWidthStep       (0.05      )] :Optional  :Contour Line Width Step
-    [-ReverseOrder       ] :Optional  :Reverse Print Order
-    [-Untwist            untwist             (0.0       )] :Optional  :Untwist Angle [degree/A], example: (-13,28) = 0.4709576
-    [-UpsideDown         ] :Optional  :Upside Down
-    [-Centre             ] :Optional  :Image Centre is at the centre of paper.
-    [-CircleRadius       CircleRadius        (0.5       )] :Optional  :Radius of circles in the case of imageCircles
-    [-m[ode]             mode                (49        )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputImageFile
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputImageFile
+    [-H[ighThreshold]    thresHigh           (0.0       ).as(Real                ) ] :Optional  :High Threshold
+    [-L[owThreshold]     thresLow            (1.0       ).as(Real                ) ] :Optional  :Low Threshold
+    [-Section            section             (z         ).as(Character           ) ] :Optional  :[z|x|y]Section: Def: z-section
+    [-x[Section]         xMin                (0         ).as(Integer             ) 
+                         xMax                (0         ).as(Integer             ) ] :Optional  :x section
+    [-y[Section]         yMin                (0         ).as(Integer             ) 
+                         yMax                (0         ).as(Integer             ) ] :Optional  :y section
+    [-z[Section]         zMin                (0         ).as(Integer             ) 
+                         zMax                (0         ).as(Integer             ) ] :Optional  :z section
+    [-S[cale]            Scale               (1.0       ).as(Real                ) ] :Optional  :Scale(Centre is Bottom Left): -S 1 := 1 mm/pixel
+    [-A[bsolute]S[cale]  AbScale             (1.0       ).as(Real                ) ] :Optional  :Scale(Centre is Bottom Left): -AS 1 := 1 mm/A (Real) or 1 mm/A-1 (Fourier Space)
+    [-E[nlarge]          Enlarge             (1.0       ).as(Real                ) ] :Optional  :Enlargement(image center is center)
+    [-center             cx                  (0.0/* in case of FT or N.x/2.0 in case of Image*/).as(Real                ) 
+                         cy                  (0.0/* in case of FT or N.y/2.0 in case of Image */).as(Real                ) ] :Optional  :Center of a printed image
+    [-C[ontour]          contourLevel        (1.0       ).as(Real                ) ... ] :Variable  :ContourLevel
+    [-I[nverse]                                                                    ] :Optional  :Black is High Density.
+    [-A[uto]                                                                       ] :Optional  :HighThres=Mean-SD, LowThres=Mean+SD
+    [-AC[ontour]         AutoContour         (10        ).as(Integer             ) ] :Optional  :Auto Contour(thresHigh <-> mean)
+    [-PC[ontour]         PeakContour         (10        ).as(Integer             ) ] :Optional  :Peak Contour(thresHigh <-> (mean+thresHigh)/2
+    [-AC[ontour]2        AutoContour2        (10        ).as(Integer             ) ] :Optional  :Auto Contour2(thresHigh <-> thresLow)
+    [-Y[expand]          Yexpand             (1         ).as(Real                ) ] :Optional  :Y-axis expanding
+    [-RGB                Red                 (0         ).as(Real                ) 
+                         Green               (0         ).as(Real                ) 
+                         Blue                (0         ).as(Real                ) ] :Optional  :Contour Color Mode: RGB
+    [-RGBGradient        RedFirst            (0         ).as(Real                ) 
+                         GreenFirst          (0         ).as(Real                ) 
+                         BlueFirst           (0         ).as(Real                ) 
+                         RedLast             (0         ).as(Real                ) 
+                         GreenLast           (0         ).as(Real                ) 
+                         BlueLast            (0         ).as(Real                ) ] :Optional  :Contour Color GradientMode: RGB
+    [-HSB                Hue                 (0         ).as(Real                ) 
+                         Saturation          (0         ).as(Real                ) 
+                         Brightness          (0         ).as(Real                ) ] :Optional  :Contour Color Mode: HSB
+    [-HSBGradient        HueFirst            (0         ).as(Real                ) 
+                         SaturationFirst     (0         ).as(Real                ) 
+                         BrightnessFirst     (0         ).as(Real                ) 
+                         HueLast             (0         ).as(Real                ) 
+                         SaturationLast      (0         ).as(Real                ) 
+                         BrightnessLast      (0         ).as(Real                ) ] :Optional  :Contour Color GradientMode: HSB
+    [-LineColourRGB      LineRed             (0         ).as(Real                ) 
+                         LineGreen           (0         ).as(Real                ) 
+                         LineBlue            (0         ).as(Real                ) ] :Optional  :Contour Color Mode: RGB
+    [-LineColourRGBGradientLineRedFirst        (0         ).as(Real                ) 
+                         LineGreenFirst      (0         ).as(Real                ) 
+                         LineBlueFirst       (0         ).as(Real                ) 
+                         LineRedLast         (0         ).as(Real                ) 
+                         LineGreenLast       (0         ).as(Real                ) 
+                         LineBlueLast        (0         ).as(Real                ) ] :Optional  :Contour Color GradientMode: RGB
+    [-LineColourHSB      LineHue             (0         ).as(Real                ) 
+                         LineSaturation      (0         ).as(Real                ) 
+                         LineBrightness      (0         ).as(Real                ) ] :Optional  :Contour Color Mode: HSB
+    [-LineColourHSBGradientLineHueFirst        (0         ).as(Real                ) 
+                         LineSaturationFirst (0         ).as(Real                ) 
+                         LineBrightnessFirst (0         ).as(Real                ) 
+                         LineHueLast         (0         ).as(Real                ) 
+                         LineSaturationLast  (0         ).as(Real                ) 
+                         LineBrightnessLast  (0         ).as(Real                ) ] :Optional  :Contour Color GradientMode: HSB
+    [-LineChange         LineColorChange     (0.1       ).as(Real                ) ] :Optional  :Contour Color Change
+    [-LineWidthStart     LineWidthStart      (0.1       ).as(Real                ) ] :Optional  :Contour Line Width Step
+    [-LineWidthStep      LineWidthStep       (0.05      ).as(Real                ) ] :Optional  :Contour Line Width Step
+    [-ReverseOrder                                                                 ] :Optional  :Reverse Print Order
+    [-Untwist            untwist             (0.0       ).as(Real                ) ] :Optional  :Untwist Angle [degree/A], example: (-13,28) = 0.4709576
+    [-UpsideDown                                                                   ] :Optional  :Upside Down
+    [-Centre                                                                       ] :Optional  :Image Centre is at the centre of paper.
+    [-CircleRadius       CircleRadius        (0.5       ).as(Real                ) ] :Optional  :Radius of circles in the case of imageCircles
+    [-m[ode]             mode                (49        ).as(Integer             ) ] :Optional  :Mode
 ----- mode -----
 		     1: ImageDensity
 		     2: Contour(DiffrentLineWidth)
diff --git a/doc/SmallTools/mrcImagePrint3D.html b/doc/SmallTools/mrcImagePrint3D.html
index ce59981..30c4d52 100644
--- a/doc/SmallTools/mrcImagePrint3D.html
+++ b/doc/SmallTools/mrcImagePrint3D.html
@@ -8,13 +8,20 @@
 <PRE>
 Usage: mrcImagePrint3D
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-eye[Position]      eyeX                (100.0     )eyeY                (0.0       )eyeZ                (0.0       )] :Optional  :Eye Position
-    [-plane[Position]    planeX              (0.0       )planeY              (0.0       )planeZ              (0.0       )] :Optional  :Plane Position
-    [-C[ontour]          contourLevel        (0.0       )... ] :Variable  :Contour Level ...
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-stereo             Stereo              (6.0       ).as(Real                ) ] :Optional  :Stereo View [degree] around z-axis
+    [-rotation           nRotation           (60        ).as(Integer             ) 
+                         RotationAngle       (6.0       ).as(Real                ) ] :Optional  :(Number, angle) : Rotation View around z-axis
+    [-eye[Position]      eyeX                (100.0     ).as(Real                ) 
+                         eyeY                (0.0       ).as(Real                ) 
+                         eyeZ                (0.0       ).as(Real                ) ] :Optional  :Eye Position
+    [-plane[Position]    planeX              (0.0       ).as(Real                ) 
+                         planeY              (0.0       ).as(Real                ) 
+                         planeZ              (0.0       ).as(Real                ) ] :Optional  :Plane Position
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-C[ontour]          contourLevel        (0.0       ).as(Real                ) ... ] :Variable  :Contour Level ...
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageProjection.html b/doc/SmallTools/mrcImageProjection.html
index 367d6d2..6010163 100644
--- a/doc/SmallTools/mrcImageProjection.html
+++ b/doc/SmallTools/mrcImageProjection.html
@@ -8,16 +8,16 @@
 <PRE>
 Usage: mrcImageProjection
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Mode -----
 0: x-y sufacae along z-axis [3D to 2D]
 1: y-z sufacae along x-axis [3D to 2D]
-2: x-z sufacae along y-axis [3D to 2D]
-3: x-y sufacae to y-axis [2D/3D to 1D]
-4: x-y sufacae to x-axis [2D/3D to 1D]
+2: z-x sufacae along y-axis [3D to 2D]
+3: z-x sufacae to y-axis [2D/3D to 1D]
+4: y-z sufacae to x-axis [2D/3D to 1D]
 5: x-y sufacae to z-axis [2D/3D to 1D]
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageROI3D.html b/doc/SmallTools/mrcImageROI3D.html
index c29c53f..2fbbf68 100644
--- a/doc/SmallTools/mrcImageROI3D.html
+++ b/doc/SmallTools/mrcImageROI3D.html
@@ -8,13 +8,16 @@
 <PRE>
 Usage: mrcImageROI3D
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-x                  x1                  (0.0       )x2                  (0.0       )] :Optional  :from x1[pixel] to x2[pixel]
-    [-y                  y1                  (0.0       )y2                  (0.0       )] :Optional  :from y1[pixel] to y2[pixel]
-    [-z                  z1                  (0.0       )z2                  (0.0       )] :Optional  :from z1[pixel] to z2[pixel]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-x                  x1                  (0.0       ).as(Real                ) 
+                         x2                  (0.0       ).as(Real                ) ] :Optional  :from x1[pixel] to x2[pixel]
+    [-y                  y1                  (0.0       ).as(Real                ) 
+                         y2                  (0.0       ).as(Real                ) ] :Optional  :from y1[pixel] to y2[pixel]
+    [-z                  z1                  (0.0       ).as(Real                ) 
+                         z2                  (0.0       ).as(Real                ) ] :Optional  :from z1[pixel] to z2[pixel]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 from z1 to z2
 </PRE>
diff --git a/doc/SmallTools/mrcImageROIs.html b/doc/SmallTools/mrcImageROIs.html
index 35fb82d..ed362aa 100644
--- a/doc/SmallTools/mrcImageROIs.html
+++ b/doc/SmallTools/mrcImageROIs.html
@@ -8,16 +8,16 @@
 <PRE>
 Usage: mrcImageROIs
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-I[nformation]      Info                (NULL      )] :Essential :Information
-    [-o[utput]           Out                 (NULL      )] :Optional  :MontageFile
-    [-S[hrink]           Shrink              (NULL      )] :Optional  :When inputimage was shrunk
-    [-width              Width               (0.0       )] :Optional  :Width
-    [-height             Height              (0.0       )] :Optional  :Height
-    [-NonPeriodic        ] :Optional  :Zero Outof Range
-    [-M[ode]             Mode                (2         )] :Optional  :ImageType:0 byte 1 short 2 float
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-I[nformation]      Info                (NULL      ).as(inFile              ) ] :Essential :Information
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :MontageFile
+    [-S[hrink]           Shrink              (NULL      ).as(Integer             ) ] :Optional  :When inputimage was shrunk
+    [-width              Width               (0.0       ).as(Real                ) ] :Optional  :Width
+    [-height             Height              (0.0       ).as(Real                ) ] :Optional  :Height
+    [-NonPeriodic                                                                  ] :Optional  :Zero Outof Range
+    [-M[ode]             Mode                (2         ).as(Integer             ) ] :Optional  :ImageType:0 byte 1 short 2 float
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 ----- Mode -----
 0: Nearest 
diff --git a/doc/SmallTools/mrcImageROItoPCAoutputImage.html b/doc/SmallTools/mrcImageROItoPCAoutputImage.html
index 6e3a028..ca53a7b 100644
--- a/doc/SmallTools/mrcImageROItoPCAoutputImage.html
+++ b/doc/SmallTools/mrcImageROItoPCAoutputImage.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: mrcImageROItoPCAoutputImage
 Options:
-    [-i[nput]            InList              (NULL      )] :Essential :Input: filelist
-    [-o[utput]           OutList             (NULL      )] :Essential :Output: filelist
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            InList              (NULL      ).as(inFileListNoOpen    ) ] :Essential :Input: filelist
+    [-o[utput]           OutList             (NULL      ).as(outFileListNoOpen   ) ] :Essential :Output: filelist
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageRadialDistribution.html b/doc/SmallTools/mrcImageRadialDistribution.html
index d4916b8..71af78f 100644
--- a/doc/SmallTools/mrcImageRadialDistribution.html
+++ b/doc/SmallTools/mrcImageRadialDistribution.html
@@ -8,14 +8,15 @@
 <PRE>
 Usage: mrcImageRadialDistribution
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output: ASCII
-    [-O[utputMRC]        Out2                (NULL      )] :Optional  :Output: MRC
-    [-centre             Cx                  (0.0       )Cy                  (0.0       )] :Optional  :[pixel]
-    [-Avg                ] :Optional  :flagAvg: Averaged Intensity
-    [-Inv                ] :Optional  :flagInv: Inversed Intensity
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output: ASCII
+    [-O[utputMRC]        Out2                (NULL      ).as(outFile             ) ] :Optional  :Output: MRC
+    [-centre             Cx                  (0.0       ).as(Real                ) 
+                         Cy                  (0.0       ).as(Real                ) ] :Optional  :[pixel]
+    [-Avg                                                                          ] :Optional  :flagAvg: Averaged Intensity
+    [-Inv                                                                          ] :Optional  :flagInv: Inversed Intensity
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageRadonTransform.html b/doc/SmallTools/mrcImageRadonTransform.html
index 8ed3d2f..3d55198 100644
--- a/doc/SmallTools/mrcImageRadonTransform.html
+++ b/doc/SmallTools/mrcImageRadonTransform.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageRadonTransform
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-dtheta             dtheta              (1.0       )] :Optional  :Input: detaTheta
-    [-dphi               dphi                (1.0       )] :Optional  :Input: detaPhi
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-dtheta             dtheta              (1.0       ).as(Real                ) ] :Optional  :Input: detaTheta
+    [-dphi               dphi                (1.0       ).as(Real                ) ] :Optional  :Input: detaPhi
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageRandomParticlesImageCreate.html b/doc/SmallTools/mrcImageRandomParticlesImageCreate.html
index fa38638..a9d4328 100644
--- a/doc/SmallTools/mrcImageRandomParticlesImageCreate.html
+++ b/doc/SmallTools/mrcImageRandomParticlesImageCreate.html
@@ -8,13 +8,14 @@
 <PRE>
 Usage: mrcImageRandomParticlesImageCreate
 Options:
-    [-i[nput]            In                  (stdin     )] :Essential :Input: ParticlesList[mrcImage]
-    [-o[utput]           Out                 (stdout    )] :Essential :Output: Image[mrcImage]
-    [-N                  Nx                  (1024      )Ny                  (1024      )] :Optional  :Input: ImageSize
-    [-seed               Seed                (0         )] :Optional  :Input: Seed[]
-    [-InterpolationMode  InterpolationMode   (2         )] :Optional  :Input: InterpolationMode
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (stdin     ).as(inFileList          ) ] :Essential :Input: ParticlesList[mrcImage]
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Essential :Output: Image[mrcImage]
+    [-N                  Nx                  (1024      ).as(Integer             ) 
+                         Ny                  (1024      ).as(Integer             ) ] :Optional  :Input: ImageSize
+    [-seed               Seed                (0         ).as(Integer             ) ] :Optional  :Input: Seed[]
+    [-InterpolationMode  InterpolationMode   (2         ).as(Integer             ) ] :Optional  :Input: InterpolationMode
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageRealValueAdd.html b/doc/SmallTools/mrcImageRealValueAdd.html
index a27acca..050f8f2 100644
--- a/doc/SmallTools/mrcImageRealValueAdd.html
+++ b/doc/SmallTools/mrcImageRealValueAdd.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageRealValueAdd
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-v[alue]            Value               (0         )] :Essential :Input: Value
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-v[alue]            Value               (0         ).as(Real                ) ] :Essential :Input: Value
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageRectangleGet.html b/doc/SmallTools/mrcImageRectangleGet.html
index a3b8393..fdbac7d 100644
--- a/doc/SmallTools/mrcImageRectangleGet.html
+++ b/doc/SmallTools/mrcImageRectangleGet.html
@@ -8,11 +8,14 @@
 <PRE>
 Usage: mrcImageRectangleGet
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-r[oi]              blx                 (0         )bly                 (0         )trx                 (0         )try                 (0         )] :Optional  :Rectangle ROI 
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-r[oi]              blx                 (0         ).as(Integer             ) 
+                         bly                 (0         ).as(Integer             ) 
+                         trx                 (0         ).as(Integer             ) 
+                         try                 (0         ).as(Integer             ) ] :Optional  :Rectangle ROI 
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageRectangleGetByCorrelation.html b/doc/SmallTools/mrcImageRectangleGetByCorrelation.html
index 539b790..805177b 100644
--- a/doc/SmallTools/mrcImageRectangleGetByCorrelation.html
+++ b/doc/SmallTools/mrcImageRectangleGetByCorrelation.html
@@ -8,13 +8,13 @@
 <PRE>
 Usage: mrcImageRectangleGetByCorrelation
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-r[eference]        Ref                 (NULL      )] :Optional  :ReferenceFile
-    [-Nx[Number of x]    Nx                  (0         )] :Optional  :Nx:Default If Nx of inputfile is even Nx ,else Nx-1
-    [-Ny[Number of y]    Ny                  (0         )] :Optional  :Ny:Default If Ny of inputfile is even Ny ,else Ny-1
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-r[eference]        Ref                 (NULL      ).as(inFile              ) ] :Optional  :ReferenceFile
+    [-Nx[Number of x]    Nx                  (0         ).as(Integer             ) ] :Optional  :Nx:Default If Nx of inputfile is even Nx ,else Nx-1
+    [-Ny[Number of y]    Ny                  (0         ).as(Integer             ) ] :Optional  :Ny:Default If Ny of inputfile is even Ny ,else Ny-1
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageRefConv2D.html b/doc/SmallTools/mrcImageRefConv2D.html
index 3f3a531..675ca00 100644
--- a/doc/SmallTools/mrcImageRefConv2D.html
+++ b/doc/SmallTools/mrcImageRefConv2D.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: mrcImageRefConv2D
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode(For fourier space) 0:Absolute Value  1:Phase
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode(For fourier space) 0:Absolute Value  1:Phase
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageRefCreate.html b/doc/SmallTools/mrcImageRefCreate.html
index a258376..1d89a3d 100644
--- a/doc/SmallTools/mrcImageRefCreate.html
+++ b/doc/SmallTools/mrcImageRefCreate.html
@@ -8,15 +8,21 @@
 <PRE>
 Usage: mrcImageRefCreate
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-p[osition]         iP                  (0         )iW                  (0         )iA                  (0         )] :Optional  :Position of Center of model creation. Phi(degree) ,Omega(degree) ,Alpha(degree) 
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-p[osition]         iP                  (0         ).as(Real                ) 
+                         iW                  (0         ).as(Real                ) 
+                         iA                  (0         ).as(Real                ) ] :Optional  :Position of Center of model creation. Phi(degree) ,Omega(degree) ,Alpha(degree) 
 :Omega and Alpha range must be around 0 or 180. 
-    [-w[idth]            Wp                  (360       )Ww                  (10        )Wa                  (10        )] :Optional  :Width of Phi(degree,plus minus) ,Omega(degree,plus minus) ,Alpha(degree,plus minus) 
-    [-d[elta]            Dp                  (5         )Dw                  (5         )Da                  (5         )] :Optional  :Interval of model creation(degree) Phi(around Z axis),Omega(Y axis),Alpha(X axis)
-    [-x                  Wx                  (NULL      )] :Optional  :Data length of x in the outputfile.Default:Data length of x in the inputfile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-w[idth]            Wp                  (360       ).as(Real                ) 
+                         Ww                  (10        ).as(Real                ) 
+                         Wa                  (10        ).as(Real                ) ] :Optional  :Width of Phi(degree,plus minus) ,Omega(degree,plus minus) ,Alpha(degree,plus minus) 
+    [-d[elta]            Dp                  (5         ).as(Real                ) 
+                         Dw                  (5         ).as(Real                ) 
+                         Da                  (5         ).as(Real                ) ] :Optional  :Interval of model creation(degree) Phi(around Z axis),Omega(Y axis),Alpha(X axis)
+    [-x                  Wx                  (NULL      ).as(Integer             ) ] :Optional  :Data length of x in the outputfile.Default:Data length of x in the inputfile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageRefFFTConv2D.html b/doc/SmallTools/mrcImageRefFFTConv2D.html
index d004478..fc31780 100644
--- a/doc/SmallTools/mrcImageRefFFTConv2D.html
+++ b/doc/SmallTools/mrcImageRefFFTConv2D.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: mrcImageRefFFTConv2D
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageRefScaleChangeWithPad.html b/doc/SmallTools/mrcImageRefScaleChangeWithPad.html
index 7349ac3..3df0039 100644
--- a/doc/SmallTools/mrcImageRefScaleChangeWithPad.html
+++ b/doc/SmallTools/mrcImageRefScaleChangeWithPad.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcImageRefScaleChangeWithPad
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Optional  :OutputDataFile
-    [-r[eference]        Ref                 (NULL      )] :Optional  :ReferenceDataFile
-    [-width              width               (140       )] :Optional  :width [Pixel]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-r[eference]        Ref                 (NULL      ).as(inFile              ) ] :Optional  :ReferenceDataFile
+    [-width              width               (140       ).as(Real                ) ] :Optional  :width [Pixel]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageResolutionEstimateForFilaments.html b/doc/SmallTools/mrcImageResolutionEstimateForFilaments.html
index bb5f6b9..ee69d48 100644
--- a/doc/SmallTools/mrcImageResolutionEstimateForFilaments.html
+++ b/doc/SmallTools/mrcImageResolutionEstimateForFilaments.html
@@ -8,13 +8,13 @@
 <PRE>
 Usage: mrcImageResolutionEstimateForFilaments
 Options:
-    [-i1[input1]         In1                 (NULL      )] :Optional  :InputDataFile
-    [-i2[input2]         In2                 (NULL      )] :Optional  :InputDataFile
-    [-d[elta]            delta               (0         )] :Optional  :Interval of output data(1/A). Default 1/(Nx*size of pixel)
-    [-H[ighThreshold]    H                   (0         )] :Optional  :High threshold.
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-M[ode2]            mode2               (0         )] :Optional  :Mode
+    [-i1[input1]         In1                 (NULL      ).as(inFile              ) ] :Optional  :InputDataFile
+    [-i2[input2]         In2                 (NULL      ).as(inFile              ) ] :Optional  :InputDataFile
+    [-d[elta]            delta               (0         ).as(Real                ) ] :Optional  :Interval of output data(1/A). Default 1/(Nx*size of pixel)
+    [-H[ighThreshold]    H                   (0         ).as(Real                ) ] :Optional  :High threshold.
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-M[ode2]            mode2               (0         ).as(Integer             ) ] :Optional  :Mode
 ----- mode -----
 0: Fourier shell correlation.
 1: Fourier shell phase residual.
diff --git a/doc/SmallTools/mrcImageReverse.html b/doc/SmallTools/mrcImageReverse.html
index d7e8a5d..cbc498b 100644
--- a/doc/SmallTools/mrcImageReverse.html
+++ b/doc/SmallTools/mrcImageReverse.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: mrcImageReverse
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 y values keep the same.
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageRotation.html b/doc/SmallTools/mrcImageRotation.html
index 08c212a..9c8a082 100644
--- a/doc/SmallTools/mrcImageRotation.html
+++ b/doc/SmallTools/mrcImageRotation.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcImageRotation
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-a[ngle]            Angle               (90.0      )] :Optional  :Angle[degree]
-    [-Periodic           ] :Optional  :Periodic
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode: HowToGet 
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-a[ngle]            Angle               (90.0      ).as(Real                ) ] :Optional  :Angle[degree]
+    [-Periodic                                                                     ] :Optional  :Periodic
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode: HowToGet 
 ----- Mode -----
 0:Nearest 
 1:Bi-linear Interpolation
diff --git a/doc/SmallTools/mrcImageRotation3D.html b/doc/SmallTools/mrcImageRotation3D.html
index 387c18a..660ee0a 100644
--- a/doc/SmallTools/mrcImageRotation3D.html
+++ b/doc/SmallTools/mrcImageRotation3D.html
@@ -8,12 +8,15 @@
 <PRE>
 Usage: mrcImageRotation3D
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: mrc
-    [-o[utput]           Out                 (NULL      )] :Essential :Output: mrc
-    [-E[uler]A[ngle]     EulerAngle          (YOYS      )Rot1                (0.0       )Rot2                (0.0       )Rot3                (0.0       )] :Optional  :Input: Euler Angle
-    [-M[ode]             Mode                (2         )] :Optional  :InterpolationMode
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: mrc
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output: mrc
+    [-E[uler]A[ngle]     EulerAngle          (YOYS      ).as(String              ) 
+                         Rot1                (0.0       ).as(Real                ) 
+                         Rot2                (0.0       ).as(Real                ) 
+                         Rot3                (0.0       ).as(Real                ) ] :Optional  :Input: Euler Angle
+    [-M[ode]             Mode                (2         ).as(Integer             ) ] :Optional  :InterpolationMode
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 -m 
  0: padding 0 
diff --git a/doc/SmallTools/mrcImageSN.html b/doc/SmallTools/mrcImageSN.html
index 51e5035..752f000 100644
--- a/doc/SmallTools/mrcImageSN.html
+++ b/doc/SmallTools/mrcImageSN.html
@@ -8,15 +8,15 @@
 <PRE>
 Usage: mrcImageSN
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputList
-    [-A[verage]          Avg                 (NULL      )] :Optional  :Output: Average
-    [-SN                 SN                  (NULL      )] :Optional  :Output: SN:=Average/SD
-    [-t                  t                   (NULL      )] :Optional  :Output: t=:Average/SD/sqrt(n-2)
-    [-SE                 SE                  (NULL      )] :Optional  :Output: Standard Error
-    [-SD                 SD                  (NULL      )] :Optional  :Output: Standard Deviation
-    [-Var                Var                 (NULL      )] :Optional  :Output: Variance
-    [-c[onfigFile]       configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFileList          ) ] :Essential :InputList
+    [-A[verage]          Avg                 (NULL      ).as(outFile             ) ] :Optional  :Output: Average
+    [-SN                 SN                  (NULL      ).as(outFile             ) ] :Optional  :Output: SN:=Average/SD
+    [-t                  t                   (NULL      ).as(outFile             ) ] :Optional  :Output: t=:Average/SD/sqrt(n-2)
+    [-SE                 SE                  (NULL      ).as(outFile             ) ] :Optional  :Output: Standard Error
+    [-SD                 SD                  (NULL      ).as(outFile             ) ] :Optional  :Output: Standard Deviation
+    [-Var                Var                 (NULL      ).as(outFile             ) ] :Optional  :Output: Variance
+    [-c[onfigFile]       configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageSNEstimate.html b/doc/SmallTools/mrcImageSNEstimate.html
new file mode 100644
index 0000000..d96efba
--- /dev/null
+++ b/doc/SmallTools/mrcImageSNEstimate.html
@@ -0,0 +1 @@
+/bin/bash: mrcImageSNEstimate: No such file or directory
diff --git a/doc/SmallTools/mrcImageSamplingUnitChange.html b/doc/SmallTools/mrcImageSamplingUnitChange.html
index 6452739..5261325 100644
--- a/doc/SmallTools/mrcImageSamplingUnitChange.html
+++ b/doc/SmallTools/mrcImageSamplingUnitChange.html
@@ -8,12 +8,16 @@
 <PRE>
 Usage: mrcImageSamplingUnitChange
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-S[amplingUnit]     Sx                  (0.0       )Sy                  (0.0       )Sz                  (0.0       )] :Optional  :SamplingUnit[A]
-    [-N                  Nx                  (0.0       )Ny                  (0.0       )Nz                  (0.0       )] :Optional  :N[Integer]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-S[amplingUnit]     Sx                  (0.0       ).as(Real                ) 
+                         Sy                  (0.0       ).as(Real                ) 
+                         Sz                  (0.0       ).as(Real                ) ] :Optional  :SamplingUnit[A]
+    [-N                  Nx                  (0.0       ).as(Integer             ) 
+                         Ny                  (0.0       ).as(Integer             ) 
+                         Nz                  (0.0       ).as(Real                ) ] :Optional  :N[Integer]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ---- Mode ---- 
 0: Nearest
 1: Linear 
diff --git a/doc/SmallTools/mrcImageScalarAdd.html b/doc/SmallTools/mrcImageScalarAdd.html
index 9dc4a02..137a22e 100644
--- a/doc/SmallTools/mrcImageScalarAdd.html
+++ b/doc/SmallTools/mrcImageScalarAdd.html
@@ -8,14 +8,14 @@
 <PRE>
 Usage: mrcImageScalarAdd
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-x[position]        x                   (0         )] :Optional  :x position to add value
-    [-y[position]        y                   (0         )] :Optional  :y position to add value
-    [-z[position]        z                   (0         )] :Optional  :z position to add value
-    [-v[alue]            Value               (0.0       )] :Optional  :mrcImage + value
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-x[position]        x                   (0         ).as(Real                ) ] :Optional  :x position to add value
+    [-y[position]        y                   (0         ).as(Real                ) ] :Optional  :y position to add value
+    [-z[position]        z                   (0         ).as(Real                ) ] :Optional  :z position to add value
+    [-v[alue]            Value               (0.0       ).as(Real                ) ] :Optional  :mrcImage + value
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 mode 0:Scalar value is added to each pixel.
 mode 1:Scalar value is added to one pixel.
diff --git a/doc/SmallTools/mrcImageSectionGet.html b/doc/SmallTools/mrcImageSectionGet.html
index 9d279fc..1c20583 100644
--- a/doc/SmallTools/mrcImageSectionGet.html
+++ b/doc/SmallTools/mrcImageSectionGet.html
@@ -8,11 +8,12 @@
 <PRE>
 Usage: mrcImageSectionGet
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-z                  z                   (0         )] :Optional  :z-Section number
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFileNoOpen       ) ] :Essential :OutputDataFile
+    [-z                  z                   (0         ).as(Integer             ) ] :Optional  :z-Section number: -1 Serial section
+    [-e[xtention]        format              (%s.%04d ).as(String              ) ] :Optional  :Serial section format
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 mode 0: Copy the selected section into a new area indicated by dst
 mode 1: Share the selected section between dst and src: replacement of pointers
diff --git a/doc/SmallTools/mrcImageSetFunction.html b/doc/SmallTools/mrcImageSetFunction.html
index 46c9dde..122bd39 100644
--- a/doc/SmallTools/mrcImageSetFunction.html
+++ b/doc/SmallTools/mrcImageSetFunction.html
@@ -8,9 +8,9 @@
 <PRE>
 Usage: mrcImageSetFunction
 Options:
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageShapeOrientation.html b/doc/SmallTools/mrcImageShapeOrientation.html
index 0606b4b..00d09bc 100644
--- a/doc/SmallTools/mrcImageShapeOrientation.html
+++ b/doc/SmallTools/mrcImageShapeOrientation.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageShapeOrientation
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: mrcImage
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output: ASCII
-    [-thres[hold]        threshold           (0         )] :Optional  :Threshold: if dens<thres, pixel is ignored.
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: mrcImage
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output: ASCII
+    [-thres[hold]        threshold           (0         ).as(Real                ) ] :Optional  :Threshold: if dens<thres, pixel is ignored.
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageShapePCA.html b/doc/SmallTools/mrcImageShapePCA.html
index 3bd6a0e..2384338 100644
--- a/doc/SmallTools/mrcImageShapePCA.html
+++ b/doc/SmallTools/mrcImageShapePCA.html
@@ -11,7 +11,7 @@ Options:
     [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input: mrcImage
     [-o[utput]           Out                 (stdout    ).as(outFile::ASCII      ) ] :Optional  :Output: ASCII
     [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-m[ode]             mode                (1         ).as(Integer             ) ] :Optional  :Mode
     [-C[ontour]          Contour             (1.0       ).as(Real                ) ... ] :Variable  :Contour
 ----- Additional Usage -----
 -C : ContourLevels
@@ -19,7 +19,11 @@ Options:
            100% 60% 40%
 ----- Objectives -----
 Determine the orientations/molecular axis by PCA alogrism
-  $ mrcImagePCA -i mrc -o parameter -C C1 C2 C3 ...
+  $ mrcImageShapePCA -i mrc -o parameter -C C1 C2 C3 ...
+-m 
+  +1: Sphere (default)
+  +2: Disk
+  +4: Cylinder
 
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageShapePCAFit.html b/doc/SmallTools/mrcImageShapePCAFit.html
index f85451a..7613ea3 100644
--- a/doc/SmallTools/mrcImageShapePCAFit.html
+++ b/doc/SmallTools/mrcImageShapePCAFit.html
@@ -8,15 +8,15 @@
 <PRE>
 Usage: mrcImageShapePCAFit
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: test(mrcImage)
-    [-r[eference]        Ref                 (NULL      )] :Essential :Input: ref(mrcImage)
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output: Parameters
-    [-fit                Fit                 (NULL      )] :Optional  :Output: fit(mrcImage) <- test 
-    [-fitMat             FitMat              (NULL      )] :Optional  :Output: Matrix3D for fit(mrcImage) <- test 
-    [-iMode              IMode               (2         )] :Optional  :InterpolationMode
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-C[ontour]          Contour             (1.0       )... ] :Variable  :Contour(test/ref)
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: test(mrcImage)
+    [-r[eference]        Ref                 (NULL      ).as(inFile              ) ] :Essential :Input: ref(mrcImage)
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output: Parameters
+    [-fit                Fit                 (NULL      ).as(outFile             ) ] :Optional  :Output: fit(mrcImage) <- test 
+    [-fitMat             FitMat              (NULL      ).as(outFile             ) ] :Optional  :Output: Matrix3D for fit(mrcImage) <- test 
+    [-iMode              IMode               (2         ).as(Integer             ) ] :Optional  :InterpolationMode
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-C[ontour]          Contour             (1.0       ).as(Real                ) ... ] :Variable  :Contour(test/ref)
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageShapeSearch.html b/doc/SmallTools/mrcImageShapeSearch.html
new file mode 100644
index 0000000..2b807e8
--- /dev/null
+++ b/doc/SmallTools/mrcImageShapeSearch.html
@@ -0,0 +1,41 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageShapeSearch</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageShapeSearch</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageShapeSearch
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input
+    [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Essential :Output
+    [-Shape              Shape               (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output
+    [-n[Cube]            nCube               (0         ).as(Integer             ) ] :Optional  :Mode
+    [-r[adius]           minR                (3         ).as(Integer             ) 
+                         maxR                (5         ).as(Integer             ) 
+                         delR                (1         ).as(Integer             ) ] :Optional  :Radius[pixel]
+    [-l[ength]           minL                (3         ).as(Integer             ) 
+                         maxL                (5         ).as(Integer             ) 
+                         delL                (1         ).as(Integer             ) ] :Optional  :Length[pixel]
+    [-O[utput]V[ector]BILDOutVectorBILD       (NULL      ).as(outFile::BILD       ) ] :Optional  :Output:BILD-vector
+    [-Phi                minPhi              (0.0       ).as(Real                ) 
+                         maxPhi              (359.0     ).as(Real                ) 
+                         delPhi              (45.0      ).as(Real                ) ] :Optional  :around z-axis[degree]
+    [-Theta              minTheta            (0.0       ).as(Real                ) 
+                         maxTheta            (359.0     ).as(Real                ) 
+                         delTheta            (45.0      ).as(Real                ) ] :Optional  :around x-axis[degree]
+    [-Psi                minPsi              (0.0       ).as(Real                ) 
+                         maxPsi              (350.0     ).as(Real                ) 
+                         delPsi              (45.0      ).as(Real                ) ] :Optional  :around x-axis[degree]
+    [-thres[Zscore]      thresZscore         (1.0       ).as(Real                ) ] :Optional  :Zscore
+    [-interp[olationMode]interpMode          (0         ).as(Integer             ) ] :Optional  :interpMode
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+0: Cylinder with radius and length
+1: Disk with radius and length(thickness)
+2: Sphere with radius 
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageShift.html b/doc/SmallTools/mrcImageShift.html
index c0faf9d..d61e3e4 100644
--- a/doc/SmallTools/mrcImageShift.html
+++ b/doc/SmallTools/mrcImageShift.html
@@ -8,13 +8,13 @@
 <PRE>
 Usage: mrcImageShift
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-x[shift]           xshift              (0.0       )] :Optional  :x-shift[pixel]
-    [-y[shift]           yshift              (0.0       )] :Optional  :y-shift[pixel]
-    [-z[shift]           zshift              (0.0       )] :Optional  :z-shift[pixel]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-x[shift]           xshift              (0.0       ).as(Real                ) ] :Optional  :x-shift[pixel]
+    [-y[shift]           yshift              (0.0       ).as(Real                ) ] :Optional  :y-shift[pixel]
+    [-z[shift]           zshift              (0.0       ).as(Real                ) ] :Optional  :z-shift[pixel]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageShiftFollowingGC.html b/doc/SmallTools/mrcImageShiftFollowingGC.html
index 0385b1a..488286c 100644
--- a/doc/SmallTools/mrcImageShiftFollowingGC.html
+++ b/doc/SmallTools/mrcImageShiftFollowingGC.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageShiftFollowingGC
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-I[nverse]          ] :Optional  :DensityInverse
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-I[nverse]                                                                    ] :Optional  :DensityInverse
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageShrink.html b/doc/SmallTools/mrcImageShrink.html
index 05b3444..0f5c406 100644
--- a/doc/SmallTools/mrcImageShrink.html
+++ b/doc/SmallTools/mrcImageShrink.html
@@ -8,14 +8,14 @@
 <PRE>
 Usage: mrcImageShrink
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-S[hrink]           S                   (2         )] :Optional  :Shrink(1/S)
-    [-S[hrink]x          Sx                  (2         )] :Optional  :Shrink(1/S) for x axis.
-    [-S[hrink]y          Sy                  (2         )] :Optional  :Shrink(1/S) for y axis.
-    [-S[hrink]z          Sz                  (2         )] :Optional  :Shrink(1/S) for z axis.
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-S[hrink]           S                   (2         ).as(Integer             ) ] :Optional  :Shrink(1/S)
+    [-S[hrink]x          Sx                  (2         ).as(Integer             ) ] :Optional  :Shrink(1/S) for x axis.
+    [-S[hrink]y          Sy                  (2         ).as(Integer             ) ] :Optional  :Shrink(1/S) for y axis.
+    [-S[hrink]z          Sz                  (2         ).as(Integer             ) ] :Optional  :Shrink(1/S) for z axis.
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ---- Note -----
 If S = 2, N.x -> N.x/2 and Length.x -> 2*Length.x.
 Image 0 0 1 1 -> Image 0   1 
diff --git a/doc/SmallTools/mrcImageSimilarImageSearch.html b/doc/SmallTools/mrcImageSimilarImageSearch.html
index c118b0a..a0c4f91 100644
--- a/doc/SmallTools/mrcImageSimilarImageSearch.html
+++ b/doc/SmallTools/mrcImageSimilarImageSearch.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: mrcImageSimilarImageSearch
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFileList          ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageSimilarityEstimate.html b/doc/SmallTools/mrcImageSimilarityEstimate.html
index 851f942..6b7d69c 100644
--- a/doc/SmallTools/mrcImageSimilarityEstimate.html
+++ b/doc/SmallTools/mrcImageSimilarityEstimate.html
@@ -8,15 +8,15 @@
 <PRE>
 Usage: mrcImageSimilarityEstimate
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput] information fileOut                 (NULL      )] :Optional  :OutputDataFile
-    [-o[utput] Cor[relation]OutCor              (NULL      )] :Optional  :OutputDataFile
-    [-ref[erence array of file]ref                 (stdin     )] :Essential :InputDataFiles
-    [-cor[relation] file namecorfilename         (stdin     )] :Optional  :InputDataFiles
-    [-cormode            cormode             (0         )] :Optional  :Mode
-    [-ctfinfo            ctfinfo             (NULL      )] :Optional  :InputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput] information fileOut                 (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-o[utput] Cor[relation]OutCor              (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-ref[erence array of file]ref                 (stdin     ).as(inFileListNoOpen    ) ] :Essential :InputDataFiles
+    [-cor[relation] file namecorfilename         (stdin     ).as(inFileListNoOpen    ) ] :Optional  :InputDataFiles
+    [-cormode            cormode             (0         ).as(Integer             ) ] :Optional  :Mode
+    [-ctfinfo            ctfinfo             (NULL      ).as(inFile              ) ] :Optional  :InputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 cormode:(lmrcImageCorrelation)
 0: Normal Correlation FxG*
diff --git a/doc/SmallTools/mrcImageSinogramCorrelation.html b/doc/SmallTools/mrcImageSinogramCorrelation.html
index 83834e7..70e3065 100644
--- a/doc/SmallTools/mrcImageSinogramCorrelation.html
+++ b/doc/SmallTools/mrcImageSinogramCorrelation.html
@@ -8,20 +8,22 @@
 <PRE>
 Usage: mrcImageSinogramCorrelation
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: in[sinogram: mrc]
-    [-r[ef]              Ref                 (NULL      )] :Essential :Input: ref[sinogram: mrc]
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-w[eigth]           w0th                (1.0       )w1st                (0.0       )w2nd                (0.0       )] :Optional  :Weigth for Mode: 1
-    [-T[hreshold]        threshold           (0.0       )] :Optional  :threshold for Mode: 2
-    [-M[odeforCorrelation]corMode             (0         )] :Optional  :Mode: for Correlation
-    [-L[ength]M[ode]     LengthMode          (0         )] :Optional  :Length Mode: for LengthCorrelation
-    [-L[ength]T[hreshold]M[ode]LengthThresholdMode (0         )] :Optional  :Length Threshold Mode: for LengthCorrelation
-    [-L[ength]T[hreshold]R[atio]LengthThresholdRatio(1.0       )] :Optional  :ratio of threshold for LenthMode: 1
-    [-L[ength]C[orrelation]M[ode]LCMode              (0         )] :Optional  :Mode: for LengthCorrelationMode
-    [-L[ength]C[orrelation]T[hreshold]LengthCorrelationThreshold(0.0       )] :Optional  :threshold for LengthCorrelation
-    [-w[eight]L[ength]   weightLength        (1.0       )] :Optional  :Weight for LengthCorrelation
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: in[sinogram: mrc]
+    [-r[ef]              Ref                 (NULL      ).as(inFile              ) ] :Essential :Input: ref[sinogram: mrc]
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-w[eigth]           w0th                (1.0       ).as(Real                ) 
+                         w1st                (0.0       ).as(Real                ) 
+                         w2nd                (0.0       ).as(Real                ) ] :Optional  :Weigth for Mode: 1
+    [-T[hreshold]        threshold           (0.0       ).as(Real                ) ] :Optional  :threshold for Mode: 2
+    [-M[odeforCorrelation]corMode             (0         ).as(Integer             ) ] :Optional  :Mode: for Correlation
+    [-L[ength]M[ode]     LengthMode          (0         ).as(Integer             ) ] :Optional  :Length Mode: for LengthCorrelation
+    [-L[ength]T[hreshold]M[ode]LengthThresholdMode (0         ).as(Integer             ) ] :Optional  :Length Threshold Mode: for LengthCorrelation
+    [-L[ength]T[hreshold]R[atio]LengthThresholdRatio(1.0       ).as(Real                ) ] :Optional  :ratio of threshold for LenthMode: 1
+    [-L[ength]C[orrelation]M[ode]LCMode              (0         ).as(Integer             ) ] :Optional  :Mode: for LengthCorrelationMode
+    [-L[ength]C[orrelation]T[hreshold]LengthCorrelationThreshold(0.0       ).as(Real                ) ] :Optional  :threshold for LengthCorrelation
+    [-w[eight]L[ength]   weightLength        (1.0       ).as(Real                ) ] :Optional  :Weight for LengthCorrelation
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 
 ----- LengthMode -----
 -LM = 0 : without Length Correlation
diff --git a/doc/SmallTools/mrcImageSinogramCreate.html b/doc/SmallTools/mrcImageSinogramCreate.html
index 057b46a..ff3efa3 100644
--- a/doc/SmallTools/mrcImageSinogramCreate.html
+++ b/doc/SmallTools/mrcImageSinogramCreate.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcImageSinogramCreate
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-dphi               dphi                (1.0       )] :Optional  :Input: dphi[degree] in mode=0 and 1
-    [-S[mall]dphi        Smalldphi           (1.0       )] :Optional  :Input: Smalldphi[degree] in mode=1
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-dphi               dphi                (1.0       ).as(Real                ) ] :Optional  :Input: dphi[degree] in mode=0 and 1
+    [-S[mall]dphi        Smalldphi           (1.0       ).as(Real                ) ] :Optional  :Input: Smalldphi[degree] in mode=1
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageSinogramFFT.html b/doc/SmallTools/mrcImageSinogramFFT.html
index 8b27f20..60df86e 100644
--- a/doc/SmallTools/mrcImageSinogramFFT.html
+++ b/doc/SmallTools/mrcImageSinogramFFT.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: mrcImageSinogramFFT
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageSmoothing.html b/doc/SmallTools/mrcImageSmoothing.html
index 886a7ec..5c71573 100644
--- a/doc/SmallTools/mrcImageSmoothing.html
+++ b/doc/SmallTools/mrcImageSmoothing.html
@@ -8,17 +8,17 @@
 <PRE>
 Usage: mrcImageSmoothing
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-sx                 sx                  (3         )] :Optional  :x of Kernel Size
-    [-sy                 sy                  (3         )] :Optional  :y of Kernel Size
-    [-sz                 sz                  (3         )] :Optional  :z of Kernel Size
-    [-r                  r                   (1         )] :Optional  :Radius of Kernel Size
-    [-sigma              sigma               (2.0       )] :Optional  :Sigma for Lee-Sigma
-    [-times              times               (1         )] :Optional  :Repeat time
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-M[ode2]            mode2               (0         )] :Optional  :Mode
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-sx                 sx                  (3         ).as(Real                ) ] :Optional  :x of Kernel Size
+    [-sy                 sy                  (3         ).as(Real                ) ] :Optional  :y of Kernel Size
+    [-sz                 sz                  (3         ).as(Real                ) ] :Optional  :z of Kernel Size
+    [-r                  r                   (1         ).as(Real                ) ] :Optional  :Radius of Kernel Size
+    [-sigma              sigma               (2.0       ).as(Real                ) ] :Optional  :Sigma for Lee-Sigma
+    [-times              times               (1         ).as(Integer             ) ] :Optional  :Repeat time
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-M[ode2]            mode2               (0         ).as(Integer             ) ] :Optional  :Mode
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
 >>> Mode <<<< 
     1: Median filter
     2: Mean filter 
diff --git a/doc/SmallTools/mrcImageSolventFlattening.html b/doc/SmallTools/mrcImageSolventFlattening.html
index b04a342..7fdb7b8 100644
--- a/doc/SmallTools/mrcImageSolventFlattening.html
+++ b/doc/SmallTools/mrcImageSolventFlattening.html
@@ -8,15 +8,15 @@
 <PRE>
 Usage: mrcImageSolventFlattening
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-rmax               rmax                (190       )] :Optional  :rmax [A]
-    [-sd                 Range               (0         )] :Optional  :Assign voxels below MeanOfSolvent+Range*SDofSolvent as Solvent
-    [-density            density             (0         )] :Optional  :embed mean lower than density value
-    [-Floating           ] :Optional  :data minus mean of Solvent
-    [-oparam[eter]       OutParam            (stdout    )] :Optional  :Output: Parameters
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-rmax               rmax                (190       ).as(Real                ) ] :Optional  :rmax [A]
+    [-sd                 Range               (0         ).as(Real                ) ] :Optional  :Assign voxels below MeanOfSolvent+Range*SDofSolvent as Solvent
+    [-density            density             (0         ).as(Real                ) ] :Optional  :embed mean lower than density value
+    [-Floating                                                                     ] :Optional  :data minus mean of Solvent
+    [-oparam[eter]       OutParam            (stdout    ).as(outFile             ) ] :Optional  :Output: Parameters
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 -m 0: mean of all density
    1: mean of sphere surface density at rmax
diff --git a/doc/SmallTools/mrcImageSpatialFrequencyFilter.html b/doc/SmallTools/mrcImageSpatialFrequencyFilter.html
index 4658ea6..0291b3e 100644
--- a/doc/SmallTools/mrcImageSpatialFrequencyFilter.html
+++ b/doc/SmallTools/mrcImageSpatialFrequencyFilter.html
@@ -12,7 +12,7 @@ Options:
     [-filter             filterIn            (NULL      ).as(inFile::ASCII       ) ] :Essential :Input: filterFile
     [-filterCol[lumn]    colR                (1         ).as(Integer             ) 
                          colW                (2         ).as(Integer             ) ] :Optional  :R W
-    [-o[utput]           Out                 (NULL      ).as(outFile::ASCII      ) ] :Essential :Output: mrcImage
+    [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Essential :Output: mrcImage
     [-L[owCut]           Low                 (-0.1      ).as(Real                ) ] :Optional  :LowCut: [/A]
     [-H[ighCut]          High                (1.0       ).as(Real                ) ] :Optional  :HighCut: [/A]
     [-c[onfig]           configFile          (NULL      ).as(inFile::ASCII       ) ] :Optional  :ConfigurationFile
diff --git a/doc/SmallTools/mrcImageSphere.html b/doc/SmallTools/mrcImageSphere.html
index ecdec6a..0ce7c63 100644
--- a/doc/SmallTools/mrcImageSphere.html
+++ b/doc/SmallTools/mrcImageSphere.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcImageSphere
 Options:
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-size               size                (5         )] :Optional  :Pixel Size[A]
-    [-r[adius]           r                   (5         )] :Optional  :radius[Pixel]
-    [-w[eight]           w                   (100       )] :Optional  :Weight
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-size               size                (5         ).as(Real                ) ] :Optional  :Pixel Size[A]
+    [-r[adius]           r                   (5         ).as(Real                ) ] :Optional  :radius[Pixel]
+    [-w[eight]           w                   (100       ).as(Real                ) ] :Optional  :Weight
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 mode 0 char 
 mode 2 float 
diff --git a/doc/SmallTools/mrcImageSplit.html b/doc/SmallTools/mrcImageSplit.html
index ffbffea..8f782fa 100644
--- a/doc/SmallTools/mrcImageSplit.html
+++ b/doc/SmallTools/mrcImageSplit.html
@@ -9,17 +9,17 @@
 <PRE>
 Usage: mrcImageSplit
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: mrcImage
-    [-o[utput]           Out                 (          )] :Optional  :Output: Basename
-    [-s[uffix]           Suffix              (205625115200000064.splt)] :Optional  :Output: Suffix
-    [-H[eight]           Height              (0         )] :Optional  :Input: Height[y]: SplitSize [pixel]
-    [-W[idth]            Width               (0         )] :Optional  :Input: Width[x]: SplitSize [pixel]
-    [-S[ection]          Section             (0         )] :Optional  :Input: Section[z]: SplitSize [pixel]
-    [-H[eight]A[ngstrom] HeightA             (0         )] :Optional  :Input: Height: SplitSize [A]
-    [-W[idth]A[ngstrom]  WidthA              (0         )] :Optional  :Input: Width: SplitSize [A]
-    [-S[ection]A[ngstrom]SectionA            (0         )] :Optional  :Input: Section: SplitSize [A]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: mrcImage
+    [-o[utput]           Out                 (          ).as(String              ) ] :Optional  :Output: Basename
+    [-s[uffix]           Suffix              (%04d%04d%04d.splt).as(String              ) ] :Optional  :Output: Suffix
+    [-H[eight]           Height              (0         ).as(Integer             ) ] :Optional  :Input: Height[y]: SplitSize [pixel]
+    [-W[idth]            Width               (0         ).as(Integer             ) ] :Optional  :Input: Width[x]: SplitSize [pixel]
+    [-S[ection]          Section             (0         ).as(Integer             ) ] :Optional  :Input: Section[z]: SplitSize [pixel]
+    [-H[eight]A[ngstrom] HeightA             (0         ).as(Integer             ) ] :Optional  :Input: Height: SplitSize [A]
+    [-W[idth]A[ngstrom]  WidthA              (0         ).as(Integer             ) ] :Optional  :Input: Width: SplitSize [A]
+    [-S[ection]A[ngstrom]SectionA            (0         ).as(Integer             ) ] :Optional  :Input: Section: SplitSize [A]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageSquare.html b/doc/SmallTools/mrcImageSquare.html
index 7105069..6e57422 100644
--- a/doc/SmallTools/mrcImageSquare.html
+++ b/doc/SmallTools/mrcImageSquare.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageSquare
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-eps                eps                 (1e-15     )] :Optional  :Epsilon to consider zero. For mode 1 only
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-eps                eps                 (1e-15     ).as(Real                ) ] :Optional  :Epsilon to consider zero. For mode 1 only
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 mode 0: Square 
 mode 1: Square Root
diff --git a/doc/SmallTools/mrcImageStandardDeviation.html b/doc/SmallTools/mrcImageStandardDeviation.html
index cf5778a..1832ffe 100644
--- a/doc/SmallTools/mrcImageStandardDeviation.html
+++ b/doc/SmallTools/mrcImageStandardDeviation.html
@@ -8,13 +8,13 @@
 <PRE>
 Usage: mrcImageStandardDeviation
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Optional  :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-h[ighThreshold]    Hth                 (0         )] :Optional  :High threshold. Mode2=0 only.
-    [-l[ow threshold]    Lth                 (0         )] :Optional  :Low threshold. Mode2=0 only.
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-M[ode2]            mode2               (0         )] :Optional  :Mode2
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-h[ighThreshold]    Hth                 (0         ).as(Real                ) ] :Optional  :High threshold. Mode2=0 only.
+    [-l[ow threshold]    Lth                 (0         ).as(Real                ) ] :Optional  :Low threshold. Mode2=0 only.
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-M[ode2]            mode2               (0         ).as(Integer             ) ] :Optional  :Mode2
 ----- Additional Usage -----
 Input file is a list of mrc files.
 mode 0: Standard deviation
diff --git a/doc/SmallTools/mrcImageSubtraction.html b/doc/SmallTools/mrcImageSubtraction.html
index 0b513e8..b4ea373 100644
--- a/doc/SmallTools/mrcImageSubtraction.html
+++ b/doc/SmallTools/mrcImageSubtraction.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcImageSubtraction
 Options:
-    [-i1[input1]         In1                 (NULL      )] :Essential :InputDataFile1
-    [-i2[input2]         In2                 (NULL      )] :Essential :InputDataFile2
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-rmsd               RMSD                (stdout    )] :Optional  :Output:
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i1[input1]         In1                 (NULL      ).as(inFile              ) ] :Essential :InputDataFile1
+    [-i2[input2]         In2                 (NULL      ).as(inFile              ) ] :Essential :InputDataFile2
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-rmsd               RMSD                (stdout    ).as(outFile             ) ] :Optional  :Output:
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 mode 0:out = in1 - in2 
      1:out = abs (in1 - in2) 
diff --git a/doc/SmallTools/mrcImageSuperResolution.html b/doc/SmallTools/mrcImageSuperResolution.html
index 8fe5a02..38617b2 100644
--- a/doc/SmallTools/mrcImageSuperResolution.html
+++ b/doc/SmallTools/mrcImageSuperResolution.html
@@ -8,35 +8,43 @@
 <PRE>
 Usage: mrcImageSuperResolution
 Options:
-    [-I[nput]            InOriginal          (NULL      )] :Essential :Input: Original 
-    [-i[nput]            InPrevious          (NULL      )] :Essential :Input: Previous 
-    [-i[nput]c[ounter]   FFTInCount          (NULL      )] :Optional  :Input: CounterforWeight FourierSpace 
-    [-o[utput]           Out                 (NULL      )] :Essential :Output: Next    
-    [-t[ime]             t                   (1         )] :Optional  :Number of time: Iteration(Real Space)
-    [-fromp[oint]1       x00                 (0         )y00                 (0         )z00                 (0         )] :Optional  :First value near origin of coordinates: x00[pixel] y00[pixel] z00[pixel] 
-    [-top[oint]1         x01                 (2         )y01                 (2         )z01                 (2         )] :Optional  :target value: x01[pixel] y01[pixel] z01[pixel] 
-    [-fromp[oint]2       x10                 (0         )y10                 (0         )z10                 (0         )] :Optional  :First value far from origin of coordinates: x10[pixel] y10[pixel] z10[pixel] 
-    [-top[oint]2         x11                 (0         )y11                 (0         )z11                 (0         )] :Optional  :target value: x11[pixel] y11[pixel] z11[pixel] 
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Essential :RealSpaceCalculating
-    [-LabelingMode       labelingmode        (0         )] :Optional  :LabelingMode
-    [-max[value]         max                 (800       )] :Optional  :Density Max value:Support Constraint() 
-    [-min[value]         min                 (200       )] :Optional  :Density Min value:Support Constraint() 
-    [-sh[ape]            shape               (0         )] :Optional  :Shape:0(Rectangule),1(Globe)
-    [-h[alf]v[alue]p[oint]hvp                 (0.0       )] :Optional  :Half value point(/[A])
-    [-Inverse            ] :Optional  :Inverse
-    [-nM[olecule]        nMolecule           (1         )] :Optional  :Number of Molecule
-    [-M[olecularWeight]  MolecularWeight     (80000     )] :Optional  :MolecularWeight
-    [-D[ensity]          Density             (1.35      )] :Optional  :Density(g/cm3)
-    [-counter            incounter           (3.0       )] :Optional  :Counter(Fourier Space)
-    [-d[elta]Density     deltaDens           (100.0     )] :Optional  :Delta (Convergence)
-    [-d[elta]Area        deltaArea           (100.0     )] :Optional  :Area (Convergence)
-    [-sub[traction]      sub                 (0.2       )] :Optional  :Subtraction(Convergence)
-    [-ratio              ratio               (0.3       )] :Optional  :Ratio(Convergence)
-    [-t[ime]max          tmax                (1000      )] :Optional  :Time Max(Convergence)
-    [-w[eight]d[elta]    WeightDelta         (0.1       )] :Optional  :WeightDelta(Fourier Space)
-    [-w[eight]m[ax]      WeightMax           (2         )] :Optional  :WeightMax(Fourier Space)
-    [-Subtraction        ] :Optional  :Subtraction(Real Space)
+    [-I[nput]            InOriginal          (NULL      ).as(inFile              ) ] :Essential :Input: Original 
+    [-i[nput]            InPrevious          (NULL      ).as(inFile              ) ] :Essential :Input: Previous 
+    [-i[nput]c[ounter]   FFTInCount          (NULL      ).as(inFile              ) ] :Optional  :Input: CounterforWeight FourierSpace 
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output: Next    
+    [-t[ime]             t                   (1         ).as(Integer             ) ] :Optional  :Number of time: Iteration(Real Space)
+    [-fromp[oint]1       x00                 (0         ).as(Integer             ) 
+                         y00                 (0         ).as(Integer             ) 
+                         z00                 (0         ).as(Integer             ) ] :Optional  :First value near origin of coordinates: x00[pixel] y00[pixel] z00[pixel] 
+    [-top[oint]1         x01                 (2         ).as(Integer             ) 
+                         y01                 (2         ).as(Integer             ) 
+                         z01                 (2         ).as(Integer             ) ] :Optional  :target value: x01[pixel] y01[pixel] z01[pixel] 
+    [-fromp[oint]2       x10                 (0         ).as(Integer             ) 
+                         y10                 (0         ).as(Integer             ) 
+                         z10                 (0         ).as(Integer             ) ] :Optional  :First value far from origin of coordinates: x10[pixel] y10[pixel] z10[pixel] 
+    [-top[oint]2         x11                 (0         ).as(Integer             ) 
+                         y11                 (0         ).as(Integer             ) 
+                         z11                 (0         ).as(Integer             ) ] :Optional  :target value: x11[pixel] y11[pixel] z11[pixel] 
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Essential :RealSpaceCalculating
+    [-LabelingMode       labelingmode        (0         ).as(Integer             ) ] :Optional  :LabelingMode
+    [-max[value]         max                 (800       ).as(Integer             ) ] :Optional  :Density Max value:Support Constraint() 
+    [-min[value]         min                 (200       ).as(Integer             ) ] :Optional  :Density Min value:Support Constraint() 
+    [-sh[ape]            shape               (0         ).as(Integer             ) ] :Optional  :Shape:0(Rectangule),1(Globe)
+    [-h[alf]v[alue]p[oint]hvp                 (0.0       ).as(Real                ) ] :Optional  :Half value point(/[A])
+    [-Inverse                                                                      ] :Optional  :Inverse
+    [-nM[olecule]        nMolecule           (1         ).as(Integer             ) ] :Optional  :Number of Molecule
+    [-M[olecularWeight]  MolecularWeight     (80000     ).as(Integer             ) ] :Optional  :MolecularWeight
+    [-D[ensity]          Density             (1.35      ).as(Real                ) ] :Optional  :Density(g/cm3)
+    [-counter            incounter           (3.0       ).as(Real                ) ] :Optional  :Counter(Fourier Space)
+    [-d[elta]Density     deltaDens           (100.0     ).as(Real                ) ] :Optional  :Delta (Convergence)
+    [-d[elta]Area        deltaArea           (100.0     ).as(Real                ) ] :Optional  :Area (Convergence)
+    [-sub[traction]      sub                 (0.2       ).as(Real                ) ] :Optional  :Subtraction(Convergence)
+    [-ratio              ratio               (0.3       ).as(Real                ) ] :Optional  :Ratio(Convergence)
+    [-t[ime]max          tmax                (1000      ).as(Integer             ) ] :Optional  :Time Max(Convergence)
+    [-w[eight]d[elta]    WeightDelta         (0.1       ).as(Real                ) ] :Optional  :WeightDelta(Fourier Space)
+    [-w[eight]m[ax]      WeightMax           (2         ).as(Integer             ) ] :Optional  :WeightMax(Fourier Space)
+    [-Subtraction                                                                  ] :Optional  :Subtraction(Real Space)
 ----- Additional Usage -----
 -m Option
      1 : AreaAndLocation
diff --git a/doc/SmallTools/mrcImageSurfaceAreaCalc.html b/doc/SmallTools/mrcImageSurfaceAreaCalc.html
new file mode 100644
index 0000000..fc3ff27
--- /dev/null
+++ b/doc/SmallTools/mrcImageSurfaceAreaCalc.html
@@ -0,0 +1,21 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageSurfaceAreaCalc</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageSurfaceAreaCalc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageSurfaceAreaCalc
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Essential :OutputDataFile
+    [-o[utput]S[urface]  OutSurface          (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output:Surface
+    [-o[utput]S[urface]A[rea]OutSurfaceArea      (stdout    ).as(outFile::ASCII      ) ] :Optional  :Output:Surface
+    [-n[eighbor]         Neighbor            (0         ).as(Integer             ) ] :Optional  :Neighbor: 6(0)|18|26
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageSurfaceCalc.html b/doc/SmallTools/mrcImageSurfaceCalc.html
new file mode 100644
index 0000000..c940e0c
--- /dev/null
+++ b/doc/SmallTools/mrcImageSurfaceCalc.html
@@ -0,0 +1,19 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageSurfaceCalc</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageSurfaceCalc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageSurfaceCalc
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-n[eighbor]         neighbor            (26        ).as(Integer             ) ] :Optional  :Neighbor[6|18|26]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageSymmetryAverage.html b/doc/SmallTools/mrcImageSymmetryAverage.html
index fd5ccc8..ca995e1 100644
--- a/doc/SmallTools/mrcImageSymmetryAverage.html
+++ b/doc/SmallTools/mrcImageSymmetryAverage.html
@@ -8,12 +8,14 @@
 <PRE>
 Usage: mrcImageSymmetryAverage
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-n[sym]             NSym                (8         )] :Optional  :nsym
-    [-centre             cx                  (0         )cy                  (0         )cz                  (0         )] :Optional  :Centre:
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-n[sym]             NSym                (8         ).as(Real                ) ] :Optional  :nsym
+    [-centre             cx                  (0         ).as(Real                ) 
+                         cy                  (0         ).as(Real                ) 
+                         cz                  (0         ).as(Real                ) ] :Optional  :Centre:
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageSymmetryCentreFind.html b/doc/SmallTools/mrcImageSymmetryCentreFind.html
index ec7a929..bea6c09 100644
--- a/doc/SmallTools/mrcImageSymmetryCentreFind.html
+++ b/doc/SmallTools/mrcImageSymmetryCentreFind.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageSymmetryCentreFind
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: mrcImage
-    [-o[utput]           Out                 (NULL      )] :Optional  :Output: mrcImage
-    [-O[utput]           Out2                (stdout    )] :Optional  :Output: ASCII
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: mrcImage
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :Output: mrcImage
+    [-O[utput]           Out2                (stdout    ).as(outFile             ) ] :Optional  :Output: ASCII
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageSymmetryFind.html b/doc/SmallTools/mrcImageSymmetryFind.html
index e256054..3ebe2dc 100644
--- a/doc/SmallTools/mrcImageSymmetryFind.html
+++ b/doc/SmallTools/mrcImageSymmetryFind.html
@@ -8,24 +8,32 @@
 <PRE>
 Usage: mrcImageSymmetryFind
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Optional  :Output: correlation
-    [-O[utput]           Out2                (stdout    )] :Optional  :Output: SymmetryInformation 
-    [-A[verage]          Avg                 (NULL      )] :Optional  :Output: Average
-    [-centreMode         centreMode          (1         )] :Optional  :Input: 0 : Gravity of Centre; 1 : Search n-fold
-    [-t1[threshold1]     threshold1          (1.8       )] :Optional  :Threshold of CheckByAdd
-    [-t2[threshold2]     threshold2          (0.9       )] :Optional  :Threshold in deciding the symmetry number
-    [-m1[mode1]          mode1               (3         )] :Optional  :Mode of Check
-    [-m2[mode2]          mode2               (2         )] :Optional  :Mode of Substruction
-    [-dr[delta r]        dr                  (1         )] :Optional  :Delta r of outputfile.
-    [-dtheta[delta theta]dtheta              (1         )] :Optional  :Delta theta of outputfile.[DEGREE]
-    [-n[umber]           n                   (10        )] :Optional  :Check to the number.
-    [-n[umber]Range      nmin                (2         )nmax                (10        )] :Optional  :Check to the number.
-    [-In                 Image               (NULL      )Back                (NULL      )] :Optional  :InputDataFile: Image and Back
-    [-rangex             minx                (-3        )maxx                (3         )delx                (1         )] :Optional  :Input: 
-    [-rangey             miny                (-3        )maxy                (3         )dely                (1         )] :Optional  :Input: 
-    [-rangez             minz                (0         )maxz                (0         )delz                (1         )] :Optional  :Input: 
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :Output: correlation
+    [-O[utput]           Out2                (stdout    ).as(outFile             ) ] :Optional  :Output: SymmetryInformation 
+    [-A[verage]          Avg                 (NULL      ).as(outFile             ) ] :Optional  :Output: Average
+    [-centreMode         centreMode          (1         ).as(Integer             ) ] :Optional  :Input: 0 : Gravity of Centre; 1 : Search n-fold
+    [-t1[threshold1]     threshold1          (1.8       ).as(Real                ) ] :Optional  :Threshold of CheckByAdd
+    [-t2[threshold2]     threshold2          (0.9       ).as(Real                ) ] :Optional  :Threshold in deciding the symmetry number
+    [-m1[mode1]          mode1               (3         ).as(Integer             ) ] :Optional  :Mode of Check
+    [-m2[mode2]          mode2               (2         ).as(Integer             ) ] :Optional  :Mode of Substruction
+    [-dr[delta r]        dr                  (1         ).as(Real                ) ] :Optional  :Delta r of outputfile.
+    [-dtheta[delta theta]dtheta              (1         ).as(Real                ) ] :Optional  :Delta theta of outputfile.[DEGREE]
+    [-n[umber]           n                   (10        ).as(Integer             ) ] :Optional  :Check to the number.
+    [-n[umber]Range      nmin                (2         ).as(Integer             ) 
+                         nmax                (10        ).as(Integer             ) ] :Optional  :Check to the number.
+    [-In                 Image               (NULL      ).as(inFileList          ) 
+                         Back                (NULL      ).as(inFileList          ) ] :Optional  :InputDataFile: Image and Back
+    [-rangex             minx                (-3        ).as(Real                ) 
+                         maxx                (3         ).as(Real                ) 
+                         delx                (1         ).as(Real                ) ] :Optional  :Input: 
+    [-rangey             miny                (-3        ).as(Real                ) 
+                         maxy                (3         ).as(Real                ) 
+                         dely                (1         ).as(Real                ) ] :Optional  :Input: 
+    [-rangez             minz                (0         ).as(Real                ) 
+                         maxz                (0         ).as(Real                ) 
+                         delz                (1         ).as(Real                ) ] :Optional  :Input: 
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
 ----- Additional Usage -----
 >>>> check type mode
     1 : Check by Add 
diff --git a/doc/SmallTools/mrcImageTfunction.html b/doc/SmallTools/mrcImageTfunction.html
index 456b50c..b922673 100644
--- a/doc/SmallTools/mrcImageTfunction.html
+++ b/doc/SmallTools/mrcImageTfunction.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcImageTfunction
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-sx                 sx                  (25        )] :Optional  :x of Kernel Size
-    [-sy                 sy                  (25        )] :Optional  :y of Kernel Size
-    [-sz                 sz                  (1         )] :Optional  :z of Kernel Size
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-sx                 sx                  (25        ).as(Integer             ) ] :Optional  :x of Kernel Size
+    [-sy                 sy                  (25        ).as(Integer             ) ] :Optional  :y of Kernel Size
+    [-sz                 sz                  (1         ).as(Integer             ) ] :Optional  :z of Kernel Size
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageTiltAxisSearch.html b/doc/SmallTools/mrcImageTiltAxisSearch.html
index 3ea5b5a..0f9c6ea 100644
--- a/doc/SmallTools/mrcImageTiltAxisSearch.html
+++ b/doc/SmallTools/mrcImageTiltAxisSearch.html
@@ -8,17 +8,19 @@
 <PRE>
 Usage: mrcImageTiltAxisSearch
 Options:
-    [-i[nput]            In                  (NULL      )] :Optional  :In: MRC
-    [-I[nput]            InList              (NULL      )] :Optional  :In: MRC
-    [-r[ef]              Ref                 (NULL      )] :Essential :Ref: MRC
-    [-o[utput]           Out                 (NULL      )] :Essential :Output: Correlation
-    [-O[utput]           Out2                (stdout    )] :Optional  :Output: Estimated
-    [-range              thetaMin            (-90       )thetaMax            (+90       )thetaDelta          (1         )] :Optional  :Search Range [degree]
-    [-w[idth]            Width               (0.5       )] :Optional  :Projection Range[MIn(Nx,Ny)*Width] around centre
-    [-M[ode]             Mode                (2         )] :Optional  :Interpolation Mode
-    [-C[orrelation]M[ode]CorrelationMode     (17        )] :Optional  :Correlation Mode
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Optional  :In: MRC
+    [-I[nput]            InList              (NULL      ).as(inFileList          ) ] :Optional  :In: MRC
+    [-r[ef]              Ref                 (NULL      ).as(inFile              ) ] :Essential :Ref: MRC
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output: Correlation
+    [-O[utput]           Out2                (stdout    ).as(outFile             ) ] :Optional  :Output: Estimated
+    [-range              thetaMin            (-90       ).as(Real                ) 
+                         thetaMax            (+90       ).as(Real                ) 
+                         thetaDelta          (1         ).as(Real                ) ] :Optional  :Search Range [degree]
+    [-w[idth]            Width               (0.5       ).as(Real                ) ] :Optional  :Projection Range[MIn(Nx,Ny)*Width] around centre
+    [-M[ode]             Mode                (2         ).as(Integer             ) ] :Optional  :Interpolation Mode
+    [-C[orrelation]M[ode]CorrelationMode     (17        ).as(Integer             ) ] :Optional  :Correlation Mode
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageTiltAxisSearchHelp.html b/doc/SmallTools/mrcImageTiltAxisSearchHelp.html
index cbfb476..57db32d 100644
--- a/doc/SmallTools/mrcImageTiltAxisSearchHelp.html
+++ b/doc/SmallTools/mrcImageTiltAxisSearchHelp.html
@@ -8,16 +8,20 @@
 <PRE>
 Usage: mrcImageTiltAxisSearchHelp
 Options:
-    [-I[nput]            InList              (NULL      )] :Essential :Input:ImageFileList
-    [-o[utput]1d         Out1D               (NULL      )] :Optional  :Output:
-    [-o[utput]1de[nlarged]Out1DEnlarged       (NULL      )] :Optional  :Output:
-    [-o[utput]2d         Out2D               (NULL      )] :Optional  :Output:
-    [-a[xis]P[osition]   OriginX             (0.0       )OriginY             (0.0       )OriginZ             (0.0       )] :Optional  :Input: AxisPosition
-    [-a[xisAngle]        AxisAngleYaw        (0.0       )AxisAnglePitch      (0.0       )] :Optional  :Input: AxisAngleYaw/Pitch[degree]
-    [-R                  Rmin                (0.05      )Rmax                (0.1       )] :Optional  :Input: LowPathFiltering
-    [-Interp[olationMode]InterpolationMode   (2         )] :Optional  :Input: InterpolationMode
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-I[nput]            InList              (NULL      ).as(inFileList          ) ] :Essential :Input:ImageFileList
+    [-o[utput]1d         Out1D               (NULL      ).as(outFile             ) ] :Optional  :Output:
+    [-o[utput]1de[nlarged]Out1DEnlarged       (NULL      ).as(outFile             ) ] :Optional  :Output:
+    [-o[utput]2d         Out2D               (NULL      ).as(outFile             ) ] :Optional  :Output:
+    [-a[xis]P[osition]   OriginX             (0.0       ).as(Real                ) 
+                         OriginY             (0.0       ).as(Real                ) 
+                         OriginZ             (0.0       ).as(Real                ) ] :Optional  :Input: AxisPosition
+    [-a[xisAngle]        AxisAngleYaw        (0.0       ).as(Real                ) 
+                         AxisAnglePitch      (0.0       ).as(Real                ) ] :Optional  :Input: AxisAngleYaw/Pitch[degree]
+    [-R                  Rmin                (0.05      ).as(Real                ) 
+                         Rmax                (0.1       ).as(Real                ) ] :Optional  :Input: LowPathFiltering
+    [-Interp[olationMode]InterpolationMode   (2         ).as(Integer             ) ] :Optional  :Input: InterpolationMode
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 -I fileList format
 filename tiltAngle[degree] relativeTiltAxisYaw[degree] relativeTiltAxisPitch[degree] relativePosX[pixel] relativePosY[pixel] relativePosZ[pixel]
diff --git a/doc/SmallTools/mrcImageToNAMDConstantForces.html b/doc/SmallTools/mrcImageToNAMDConstantForces.html
index d16e704..166add5 100644
--- a/doc/SmallTools/mrcImageToNAMDConstantForces.html
+++ b/doc/SmallTools/mrcImageToNAMDConstantForces.html
@@ -8,18 +8,18 @@
 <PRE>
 Usage: mrcImageToNAMDConstantForces
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input:MRC
-    [-ip[db]             InPDB               (NULL      )] :Essential :Input:PDB
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output: PDB with Constant Force
-    [-w[eight]           Weight              (1.0       )] :Optional  :Input: Weight for Constant Force
-    [-s[calingFactor]    ScalingFactor       (1.0       )] :Optional  :Input: Scaling Factor for Constant Force
-    [-C[ontour]          Contour             (0.0       )] :Optional  :Input: Contour[if density>Contour, force=0]
-    [-R[otatemode]       Rotate              (0         )] :Optional  :Input: RotateMode
-    [-RW[eight]          RWeight             (0.1       )] :Optional  :Input: RotateWeight
-    [-S[eed]             Seed                (0.0       )] :Optional  :Input: Seed
-    [-nowat[er]          ] :Optional  :No force for WAT (water residue) 
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input:MRC
+    [-ip[db]             InPDB               (NULL      ).as(inFile              ) ] :Essential :Input:PDB
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output: PDB with Constant Force
+    [-w[eight]           Weight              (1.0       ).as(Real                ) ] :Optional  :Input: Weight for Constant Force
+    [-s[calingFactor]    ScalingFactor       (1.0       ).as(Real                ) ] :Optional  :Input: Scaling Factor for Constant Force
+    [-C[ontour]          Contour             (0.0       ).as(Real                ) ] :Optional  :Input: Contour[if density>Contour, force=0]
+    [-R[otatemode]       Rotate              (0         ).as(Integer             ) ] :Optional  :Input: RotateMode
+    [-RW[eight]          RWeight             (0.1       ).as(Real                ) ] :Optional  :Input: RotateWeight
+    [-S[eed]             Seed                (0.0       ).as(Real                ) ] :Optional  :Input: Seed
+    [-nowat[er]                                                                    ] :Optional  :No force for WAT (water residue) 
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 More Density is lower potential.
 </PRE>
diff --git a/doc/SmallTools/mrcImageToPointsSet.html b/doc/SmallTools/mrcImageToPointsSet.html
index 184e149..aa4e91e 100644
--- a/doc/SmallTools/mrcImageToPointsSet.html
+++ b/doc/SmallTools/mrcImageToPointsSet.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageToPointsSet
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: mrc
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output: Coord Set
-    [-t[hreshold]        Threshold           (0.0       )] :Optional  :Input: threshold
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: mrc
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output: Coord Set
+    [-t[hreshold]        Threshold           (0.0       ).as(Real                ) ] :Optional  :Input: threshold
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageToneReversal.html b/doc/SmallTools/mrcImageToneReversal.html
new file mode 100644
index 0000000..633fa54
--- /dev/null
+++ b/doc/SmallTools/mrcImageToneReversal.html
@@ -0,0 +1,18 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageToneReversal</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageToneReversal</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageToneReversal
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input
+    [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Essential :Output
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageTrans.html b/doc/SmallTools/mrcImageTrans.html
index 701ca7e..47cdb59 100644
--- a/doc/SmallTools/mrcImageTrans.html
+++ b/doc/SmallTools/mrcImageTrans.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageTrans
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: mrc3D
-    [-o[utput]           Out                 (NULL      )] :Essential :Output: mrc3D
-    [-M[atrix]           InMatrix            (NULL      )] :Essential :Input: Matrix3D
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: mrc3D
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output: mrc3D
+    [-M[atrix]           InMatrix            (NULL      ).as(inFile              ) ] :Essential :Input: Matrix3D
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 mode: Interpolation mode
 </PRE>
diff --git a/doc/SmallTools/mrcImageTransformDescartesIntoPolar.html b/doc/SmallTools/mrcImageTransformDescartesIntoPolar.html
index da478c3..6a5f5e9 100644
--- a/doc/SmallTools/mrcImageTransformDescartesIntoPolar.html
+++ b/doc/SmallTools/mrcImageTransformDescartesIntoPolar.html
@@ -8,17 +8,23 @@
 <PRE>
 Usage: mrcImageTransformDescartesIntoPolar
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-dr                 dr                  (1         )] :Optional  :Delta r of outputfile[A].
-    [-dtheta             dtheta              (1         )] :Optional  :Delta theta of outputfile.[degree]
-    [-dphi               dphi                (1         )] :Optional  :Delta phi of outputfile.[degree]
-    [-zaxis              zx                  (0         )zy                  (0         )zz                  (1         )] :Optional  :vector of z-axis
-    [-xaxis              xx                  (1         )xy                  (0         )xz                  (0         )] :Optional  :vector of x-axis
-    [-centre             cx                  (0         )cy                  (0         )cz                  (0         )] :Optional  :centre of image
-    [-rweight            ] :Optional  :r-weighted
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-dr                 dr                  (1         ).as(Real                ) ] :Optional  :Delta r of outputfile[A].
+    [-dtheta             dtheta              (1         ).as(Real                ) ] :Optional  :Delta theta of outputfile.[degree]
+    [-dphi               dphi                (1         ).as(Real                ) ] :Optional  :Delta phi of outputfile.[degree]
+    [-zaxis              zx                  (0         ).as(Real                ) 
+                         zy                  (0         ).as(Real                ) 
+                         zz                  (1         ).as(Real                ) ] :Optional  :vector of z-axis
+    [-xaxis              xx                  (1         ).as(Real                ) 
+                         xy                  (0         ).as(Real                ) 
+                         xz                  (0         ).as(Real                ) ] :Optional  :vector of x-axis
+    [-centre             cx                  (0         ).as(Real                ) 
+                         cy                  (0         ).as(Real                ) 
+                         cz                  (0         ).as(Real                ) ] :Optional  :centre of image
+    [-rweight                                                                      ] :Optional  :r-weighted
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 >>>>> -m 
          0 : Image centre is gravity of centre of image.
diff --git a/doc/SmallTools/mrcImageTransformSign.html b/doc/SmallTools/mrcImageTransformSign.html
index 043c21c..58b5859 100644
--- a/doc/SmallTools/mrcImageTransformSign.html
+++ b/doc/SmallTools/mrcImageTransformSign.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcImageTransformSign
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: MRC
-    [-o[utput]           Out                 (NULL      )] :Essential :Output: MRC[default: ToSigned]
-    [-toU[nsigned]       ] :Optional  :Flag: To Unsigned
-    [-Offset             Offset              (0         )] :Optional  :Input: Offset
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: MRC
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output: MRC[default: ToSigned]
+    [-toU[nsigned]                                                                 ] :Optional  :Flag: To Unsigned
+    [-Offset             Offset              (0         ).as(Integer             ) ] :Optional  :Input: Offset
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageTranspose.html b/doc/SmallTools/mrcImageTranspose.html
index 4e2bac9..c72238f 100644
--- a/doc/SmallTools/mrcImageTranspose.html
+++ b/doc/SmallTools/mrcImageTranspose.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcImageTranspose
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-M[ode2]            Mode                (0         )] :Optional  :Mode2
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-M[ode2]            Mode                (0         ).as(Integer             ) ] :Optional  :Mode2
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageUnbentROI.html b/doc/SmallTools/mrcImageUnbentROI.html
index c1bfbbf..d043c58 100644
--- a/doc/SmallTools/mrcImageUnbentROI.html
+++ b/doc/SmallTools/mrcImageUnbentROI.html
@@ -8,17 +8,17 @@
 <PRE>
 Usage: mrcImageUnbentROI
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-r[oi]              roiLine             (NULL      )... ] :Variable  :
-    [-x                  x                   (1.0       )] :Essential :Width :Source 
-    [-y                  y                   (1.0       )] :Optional  :Height:Source
-    [-W                  Width               (1.0       )] :Optional  :Width :Dst 
-    [-H                  Height              (1.0       )] :Optional  :Height:Dst 
-    [-cor                Cor                 (360.0     )] :Optional  :Correlation Window along Y-axis [A]
-    [-S[hrink]           Shrink              (1         )] :Optional  :When inputfile is shrinked:
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-r[oi]              roiLine             (NULL      ).as(Real                ) ... ] :Variable  :
+    [-x                  x                   (1.0       ).as(Real                ) ] :Essential :Width :Source 
+    [-y                  y                   (1.0       ).as(Real                ) ] :Optional  :Height:Source
+    [-W                  Width               (1.0       ).as(Real                ) ] :Optional  :Width :Dst 
+    [-H                  Height              (1.0       ).as(Real                ) ] :Optional  :Height:Dst 
+    [-cor                Cor                 (360.0     ).as(Real                ) ] :Optional  :Correlation Window along Y-axis [A]
+    [-S[hrink]           Shrink              (1         ).as(Integer             ) ] :Optional  :When inputfile is shrinked:
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageUnexpectedMassFromPDB.html b/doc/SmallTools/mrcImageUnexpectedMassFromPDB.html
index 6f2cb31..ef79f48 100644
--- a/doc/SmallTools/mrcImageUnexpectedMassFromPDB.html
+++ b/doc/SmallTools/mrcImageUnexpectedMassFromPDB.html
@@ -8,15 +8,15 @@
 <PRE>
 Usage: mrcImageUnexpectedMassFromPDB
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-p[dbFile]          InPDB               (NULL      )] :Essential :InputPDBDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-T[hres]            Thres               (0.0       )] :Essential :ThresHold
-    [-D[ata]             Data                (0.0       )] :Essential :AssinedData
-    [-M[ode]             AtomMode            (1         )] :Optional  :AtomMode
-    [-r[adius]           radius              (3.4       )] :Optional  :Radius
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-p[dbFile]          InPDB               (NULL      ).as(inFile              ) ] :Essential :InputPDBDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-T[hres]            Thres               (0.0       ).as(Real                ) ] :Essential :ThresHold
+    [-D[ata]             Data                (0.0       ).as(Real                ) ] :Essential :AssinedData
+    [-M[ode]             AtomMode            (1         ).as(Integer             ) ] :Optional  :AtomMode
+    [-r[adius]           radius              (3.4       ).as(Real                ) ] :Optional  :Radius
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 >>> Mode:	
 	0: Origin is BottomLeft.
 	1: Origin is Center.(Helix)
diff --git a/doc/SmallTools/mrcImageUnsharpening.html b/doc/SmallTools/mrcImageUnsharpening.html
new file mode 100644
index 0000000..144ed0c
--- /dev/null
+++ b/doc/SmallTools/mrcImageUnsharpening.html
@@ -0,0 +1,28 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageUnsharpening</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageUnsharpening</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageUnsharpening
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input: mrcImage
+    [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Essential :Output: mrcImage
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+--UnsharpeningMode--
+0: 0 -1  0 
+  -1  5 -1 
+   0 -1  0 
+1:-1 -1 -1 
+  -1  9 -1 
+  -1 -1 -1 
+2: 1 -2  1 
+  -2  5 -2 
+   1 -2  1 
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageUntwist.html b/doc/SmallTools/mrcImageUntwist.html
index 3206a47..ddcd542 100644
--- a/doc/SmallTools/mrcImageUntwist.html
+++ b/doc/SmallTools/mrcImageUntwist.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcImageUntwist
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-dz[deltaz]         dz                  (27.3      )] :Optional  :deltaz(A)
-    [-dp[deltaphi]       dphi                (13.84     )] :Optional  :deltaphi(degree)
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-dz[deltaz]         dz                  (27.3      ).as(Real                ) ] :Optional  :deltaz(A)
+    [-dp[deltaphi]       dphi                (13.84     ).as(Real                ) ] :Optional  :deltaphi(degree)
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageVarianceAnalysis.html b/doc/SmallTools/mrcImageVarianceAnalysis.html
index 97dfdaa..fc09dcb 100644
--- a/doc/SmallTools/mrcImageVarianceAnalysis.html
+++ b/doc/SmallTools/mrcImageVarianceAnalysis.html
@@ -8,12 +8,11 @@
 <PRE>
 Usage: mrcImageVarianceAnalysis
 Options:
-    [-i[nput]            In                  (NULL      )] :Optional  :In: InputList
-    [-r[ef]              Ref                 (NULL      )] :Optional  :Ref: InputList
-    [-o[utput]           Out                 (NULL      )] :Optional  :Output: Variance Probability
-    [-v[arianceAnalysis] OutV                (NULL      )] :Optional  :Output: Variance Analysis
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFileList          ) ] :Optional  :In: InputList
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :Output: Variance Probability
+    [-v[arianceAnalysis] OutV                (NULL      ).as(outFile             ) ] :Optional  :Output: Variance Analysis
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 -i inFileList
 >>>>> Within inFileList
diff --git a/doc/SmallTools/mrcImageVarianceMap.html b/doc/SmallTools/mrcImageVarianceMap.html
index 536942d..e019480 100644
--- a/doc/SmallTools/mrcImageVarianceMap.html
+++ b/doc/SmallTools/mrcImageVarianceMap.html
@@ -8,17 +8,25 @@
 <PRE>
 Usage: mrcImageVarianceMap
 Options:
-    [-i[nput]            In                  (NULL      )] :Optional  :In: InputList
-    [-I[nput]            In2                 (NULL      )In2Var              (NULL      )In2N                (0         )] :Optional  :In: Input
-    [-Nor[malizingParameter]NorA                (0.0       )NorB                (1.0       )] :Optional  :In: A + B*x: NormalizingParameter
-    [-r[ef]              Ref                 (NULL      )] :Optional  :Ref: InputList
-    [-R[ef]              Ref2                (NULL      )Ref2Var             (NULL      )Ref2N               (0         )] :Optional  :Ref: Input
-    [-Nor[malizingParameter]RNorARef             (0.0       )NorBRef             (1.0       )] :Optional  :In: A + B*x: NormalizingParameter for Ref
-    [-I[and]R            InAndRef2           (NULL      )InAndRef2Var        (NULL      )InAndRef2N          (0         )] :Optional  :In and Ref: Input
-    [-o[utput]           Out                 (NULL      )] :Optional  :Output: Variance Probability
-    [-v[arianceMap]      OutV                (NULL      )] :Optional  :Output: Variance Map
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFileList          ) ] :Optional  :In: InputList
+    [-I[nput]            In2                 (NULL      ).as(inFile              ) 
+                         In2Var              (NULL      ).as(inFile              ) 
+                         In2N                (0         ).as(Integer             ) ] :Optional  :In: Input
+    [-Nor[malizingParameter]NorA                (0.0       ).as(Real                ) 
+                         NorB                (1.0       ).as(Real                ) ] :Optional  :In: A + B*x: NormalizingParameter
+    [-r[ef]              Ref                 (NULL      ).as(inFileList          ) ] :Optional  :Ref: InputList
+    [-R[ef]              Ref2                (NULL      ).as(inFile              ) 
+                         Ref2Var             (NULL      ).as(inFile              ) 
+                         Ref2N               (0         ).as(Integer             ) ] :Optional  :Ref: Input
+    [-Nor[malizingParameter]RNorARef             (0.0       ).as(Real                ) 
+                         NorBRef             (1.0       ).as(Real                ) ] :Optional  :In: A + B*x: NormalizingParameter for Ref
+    [-I[and]R            InAndRef2           (NULL      ).as(inFile              ) 
+                         InAndRef2Var        (NULL      ).as(inFile              ) 
+                         InAndRef2N          (0         ).as(Integer             ) ] :Optional  :In and Ref: Input
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :Output: Variance Probability
+    [-v[arianceMap]      OutV                (NULL      ).as(outFile             ) ] :Optional  :Output: Variance Map
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 ---- Variance Map -----
 -- Algorithm
diff --git a/doc/SmallTools/mrcImageVolumeCalc.html b/doc/SmallTools/mrcImageVolumeCalc.html
index 3410319..ff087d1 100644
--- a/doc/SmallTools/mrcImageVolumeCalc.html
+++ b/doc/SmallTools/mrcImageVolumeCalc.html
@@ -8,17 +8,19 @@
 <PRE>
 Usage: mrcImageVolumeCalc
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-n[Molecule]        nMolecule           (1.0       )] :Optional  :NumberOfMolecule
-    [-M[olecularWeight]  MolecularWeight     (1.0       )] :Optional  :MolecularWeight
-    [-d[ensty]           Density             (1.35      )] :Optional  :Density
-    [-D[elta]            Delta               (5.0       )] :Optional  :Delta[A]
-    [-R[ange]            MinVol              (0.0       )MaxVol              (200.0     )DeltaVol            (10.0      )] :Optional  :vol
-    [-I[nverse]          ] :Optional  :Inverse
-    [-format             Format              (ContourLevel(%3g): %g %lu)] :Optional  :Format
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-n[Molecule]        nMolecule           (1.0       ).as(Real                ) ] :Optional  :NumberOfMolecule
+    [-M[olecularWeight]  MolecularWeight     (1.0       ).as(Real                ) ] :Optional  :MolecularWeight
+    [-d[ensty]           Density             (1.35      ).as(Real                ) ] :Optional  :Density
+    [-D[elta]            Delta               (5.0       ).as(Real                ) ] :Optional  :Delta[A]
+    [-R[ange]            MinVol              (0.0       ).as(Real                ) 
+                         MaxVol              (200.0     ).as(Real                ) 
+                         DeltaVol            (10.0      ).as(Real                ) ] :Optional  :vol
+    [-I[nverse]                                                                    ] :Optional  :Inverse
+    [-format             Format              (ContourLevel(%3g): %g %lu).as(StringAll           ) ] :Optional  :Format
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 -format 
  1st double  # ContourLevel[%] 
diff --git a/doc/SmallTools/mrcImageWindowing.html b/doc/SmallTools/mrcImageWindowing.html
index a1afdf4..9dbb1c9 100644
--- a/doc/SmallTools/mrcImageWindowing.html
+++ b/doc/SmallTools/mrcImageWindowing.html
@@ -31,11 +31,17 @@ Options:
    WxMax < x/Nx < Wx      or    1-Wx    < x/Nx < 1-WxMax : cos window  
                   Wx   < x/Nx < 1-Wx                     : 1
    Wy and WyMax are also used for windowing in the similar manner.
-+0 : To Zero.  
+    In general, this is called Tukey window.
 3: Rectangle Window
 4: Hanning Window
 5: Hamming Window
 6: Blackman Window
+7: Dolph-Chebyshev Window
+8: Kaiser Window
+      Wx, Wy corresponding to alpha. As alpha increases, window becomes narrower.
+9: Gauss Window
+10: Exponentail Window
+>> Boundary  
 +0 : To Zero.  
 +16: Contrast down around mean.
 </PRE>
diff --git a/doc/SmallTools/mrcImageZPad.html b/doc/SmallTools/mrcImageZPad.html
index 60c4d20..d2d6e5f 100644
--- a/doc/SmallTools/mrcImageZPad.html
+++ b/doc/SmallTools/mrcImageZPad.html
@@ -8,17 +8,17 @@
 <PRE>
 Usage: mrcImageZPad
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-r[max]             r                   (0         )] :Optional  :rmax = height of z window * 0.5 .
-    [-w[idth]            w                   (1         )] :Optional  :Width of slope. For mode 1. Usually w>=3 is good enough. 
-    [-v[alue]            v                   (0         )] :Optional  :Value of out of threshold.
-    [-Nx                 Nx                  (0         )] :Optional  :Number of x.Default is inputfile.
-    [-Ny                 Ny                  (0         )] :Optional  :Number of y.Default is inputfile.
-    [-Nz                 Nz                  (0         )] :Optional  :Number of z.Default is inputfile.
-    [-Floating           ] :Optional  :Floating
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-r[max]             r                   (0         ).as(Real                ) ] :Optional  :rmax = height of z window * 0.5 .
+    [-w[idth]            w                   (1         ).as(Real                ) ] :Optional  :Width of slope. For mode 1. Usually w>=3 is good enough. 
+    [-v[alue]            v                   (0         ).as(Real                ) ] :Optional  :Value of out of threshold.
+    [-Nx                 Nx                  (0         ).as(Integer             ) ] :Optional  :Number of x.Default is inputfile.
+    [-Ny                 Ny                  (0         ).as(Integer             ) ] :Optional  :Number of y.Default is inputfile.
+    [-Nz                 Nz                  (0         ).as(Integer             ) ] :Optional  :Number of z.Default is inputfile.
+    [-Floating                                                                     ] :Optional  :Floating
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- mode -----
 0:Default: Out of threshold is avrage of threshold plain.
 1:Mulplying cos function. Default: Out of threshold is avrage of threshold plain.
diff --git a/doc/SmallTools/mrcImagepdbFileReduce.html b/doc/SmallTools/mrcImagepdbFileReduce.html
index a324083..84e2e0d 100644
--- a/doc/SmallTools/mrcImagepdbFileReduce.html
+++ b/doc/SmallTools/mrcImagepdbFileReduce.html
@@ -8,15 +8,15 @@
 <PRE>
 Usage: mrcImagepdbFileReduce
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-p[dbfile]          Pdb                 (NULL      )] :Essential :InputPdbFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-t[hreshold]        Th                  (0         )] :Essential :Threshold
-    [-r[adius]           R                   (1         )] :Optional  :Radius of Atom
-    [-v[alue]            Value               (0         )] :Optional  :Value for pixels in pdbFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-IT[interfacethreshold]ITh                 (0         )] :Optional  :Threshold for interface recognition.
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-p[dbfile]          Pdb                 (NULL      ).as(inFile              ) ] :Essential :InputPdbFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-t[hreshold]        Th                  (0         ).as(Real                ) ] :Essential :Threshold
+    [-r[adius]           R                   (1         ).as(Real                ) ] :Optional  :Radius of Atom
+    [-v[alue]            Value               (0         ).as(Real                ) ] :Optional  :Value for pixels in pdbFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-IT[interfacethreshold]ITh                 (0         ).as(Real                ) ] :Optional  :Threshold for interface recognition.
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImagesSinogramCorrelation.html b/doc/SmallTools/mrcImagesSinogramCorrelation.html
index 73128b1..c092ac4 100644
--- a/doc/SmallTools/mrcImagesSinogramCorrelation.html
+++ b/doc/SmallTools/mrcImagesSinogramCorrelation.html
@@ -8,24 +8,24 @@
 <PRE>
 Usage: mrcImagesSinogramCorrelation
 Options:
-    [-I[nputList]        In                  (NULL      )] :Essential :InputDataFileList
-    [-o[utput]H[eader]   OutHeader           (test      )] :Optional  :OutputDataFileHeader
-    [-R[sults]d[irectoryname]Rd                  (Result    )] :Optional  :output results directory name
-    [-N[ormalCorrelation]d[irectoryname]Nd                  (Normal    )] :Optional  :directory name of output normalcorrelation in results directory
-    [-D[erivation]1[DCorrelation]d[irectoryname]D1d                 (Derivation1D)] :Optional  :directory name of output derivation1Dcorrelation in results directory
-    [-D[erivation]2[DCorrelation]d[irectoryname]D2d                 (Derivation2D)] :Optional  :directory name of output derivation2Dcorrelation in results directory
-    [-L[engthCorrelation]d[irectoryname]Ld                  (Length    )] :Optional  :directory name of output lengthcorrelation in results directory
-    [-C[orrelation]E[xtension]CorrelationExtension(cor       )] :Optional  :output correlation file extension
-    [-L[ist]E[xtension]  ListExtension       (list      )] :Optional  :output file list extension
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-N[ormalCorrelation]m[ode]Nmode               (0         )] :Optional  :
-    [-D[erivation]1[DCorrelation]m[ode]D1mode              (0         )] :Optional  :
-    [-D[erivation]2[DCorrelation]m[ode]D2mode              (0         )] :Optional  :
-    [-L[engthCorrelation]m[ode]Lmode               (0         )] :Optional  :
-    [-L[ength]T[hreshold]M[ode]LengthThresholdMode (0         )] :Optional  :LengthThresholdMode
-    [-L[ength]T[hreshold]M[ode]LengthThresholdRatio(0.25      )] :Optional  :LengthThresholdRatio
-    [-C[reate]M[ode]     CM                  (0         )] :Optional  :CreateMode
+    [-I[nputList]        In                  (NULL      ).as(inFileList          ) ] :Essential :InputDataFileList
+    [-o[utput]H[eader]   OutHeader           (test      ).as(String              ) ] :Optional  :OutputDataFileHeader
+    [-R[sults]d[irectoryname]Rd                  (Result    ).as(String              ) ] :Optional  :output results directory name
+    [-N[ormalCorrelation]d[irectoryname]Nd                  (Normal    ).as(String              ) ] :Optional  :directory name of output normalcorrelation in results directory
+    [-D[erivation]1[DCorrelation]d[irectoryname]D1d                 (Derivation1D).as(String              ) ] :Optional  :directory name of output derivation1Dcorrelation in results directory
+    [-D[erivation]2[DCorrelation]d[irectoryname]D2d                 (Derivation2D).as(String              ) ] :Optional  :directory name of output derivation2Dcorrelation in results directory
+    [-L[engthCorrelation]d[irectoryname]Ld                  (Length    ).as(String              ) ] :Optional  :directory name of output lengthcorrelation in results directory
+    [-C[orrelation]E[xtension]CorrelationExtension(cor       ).as(String              ) ] :Optional  :output correlation file extension
+    [-L[ist]E[xtension]  ListExtension       (list      ).as(String              ) ] :Optional  :output file list extension
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-N[ormalCorrelation]m[ode]Nmode               (0         ).as(Integer             ) ] :Optional  :
+    [-D[erivation]1[DCorrelation]m[ode]D1mode              (0         ).as(Integer             ) ] :Optional  :
+    [-D[erivation]2[DCorrelation]m[ode]D2mode              (0         ).as(Integer             ) ] :Optional  :
+    [-L[engthCorrelation]m[ode]Lmode               (0         ).as(Integer             ) ] :Optional  :
+    [-L[ength]T[hreshold]M[ode]LengthThresholdMode (0         ).as(Integer             ) ] :Optional  :LengthThresholdMode
+    [-L[ength]T[hreshold]M[ode]LengthThresholdRatio(0.25      ).as(Real                ) ] :Optional  :LengthThresholdRatio
+    [-C[reate]M[ode]     CM                  (0         ).as(Integer             ) ] :Optional  :CreateMode
 
 ----- create mode -----
 -CM : 0 : image of correlation and list
diff --git a/doc/SmallTools/mrcImagestoRef.html b/doc/SmallTools/mrcImagestoRef.html
index 718dc4c..0fd18af 100644
--- a/doc/SmallTools/mrcImagestoRef.html
+++ b/doc/SmallTools/mrcImagestoRef.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: mrcImagestoRef
 Options:
-    [-I[nput array of file]In                  (stdin     )] :Optional  :InputDataFiles
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-I[nput array of file]In                  (stdin     ).as(inFileListNoOpen    ) ] :Optional  :InputDataFiles
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 This program packs same size images to no header reference file.</PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImateToPointsSet.html b/doc/SmallTools/mrcImateToPointsSet.html
index 8802288..f3dc2d3 100644
--- a/doc/SmallTools/mrcImateToPointsSet.html
+++ b/doc/SmallTools/mrcImateToPointsSet.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: mrcImateToPointsSet
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcInfoSet.html b/doc/SmallTools/mrcInfoSet.html
index ddd0886..dcd3e54 100644
--- a/doc/SmallTools/mrcInfoSet.html
+++ b/doc/SmallTools/mrcInfoSet.html
@@ -8,12 +8,14 @@
 <PRE>
 Usage: mrcInfoSet
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputMrcFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-Length             Lengthx             (2.5       )Lengthy             (2.5       )Lengthz             (2.5       )] :Optional  :Length[A]
-    [-Fixed              ] :Optional  :Fixed Values in mrcImageHeader are fixed.
-    [-Interactive        ] :Optional  :Interactive(CUI) 
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputMrcFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-Length             Lengthx             (2.5       ).as(Real                ) 
+                         Lengthy             (2.5       ).as(Real                ) 
+                         Lengthz             (2.5       ).as(Real                ) ] :Optional  :Length[A]
+    [-Fixed                                                                        ] :Optional  :Fixed Values in mrcImageHeader are fixed.
+    [-Interactive                                                                  ] :Optional  :Interactive(CUI) 
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcMask.html b/doc/SmallTools/mrcMask.html
index d0b9c37..75847f1 100644
--- a/doc/SmallTools/mrcMask.html
+++ b/doc/SmallTools/mrcMask.html
@@ -8,16 +8,19 @@
 <PRE>
 Usage: mrcMask
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-s[ize]             sizeX               (1         )sizeY               (1         )] :Optional  :Mask Size (Odd Only) /pixel
-    [-v[ector]1          v1x                 (1         )v1y                 (0         )] :Essential :Vector1(/A):x y
-    [-v[ector]2          v2x                 (0         )v2y                 (1         )] :Optional  :Vector2(/A):x y
-    [-in[initial number] inum                (1         )] :Optional  :Initialn number of data to cut out.For 1D only.
-    [-fn[final number]   num                 (0         )] :Optional  :Final number of data to cut out.For 1D only.Default:All.
-    [-en[extra number]   exnum               (0         )] :Optional  :Extra number of data to cut out.For mode 2 only
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-s[ize]             sizeX               (1         ).as(Integer             ) 
+                         sizeY               (1         ).as(Integer             ) ] :Optional  :Mask Size (Odd Only) /pixel
+    [-v[ector]1          v1x                 (1         ).as(Real                ) 
+                         v1y                 (0         ).as(Real                ) ] :Essential :Vector1(/A):x y
+    [-v[ector]2          v2x                 (0         ).as(Real                ) 
+                         v2y                 (1         ).as(Real                ) ] :Optional  :Vector2(/A):x y
+    [-in[initial number] inum                (1         ).as(Integer             ) ] :Optional  :Initialn number of data to cut out.For 1D only.
+    [-fn[final number]   num                 (0         ).as(Integer             ) ] :Optional  :Final number of data to cut out.For 1D only.Default:All.
+    [-en[extra number]   exnum               (0         ).as(Integer             ) ] :Optional  :Extra number of data to cut out.For mode 2 only
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcMeanYlinePos.html b/doc/SmallTools/mrcMeanYlinePos.html
index 208ce05..fd78a53 100644
--- a/doc/SmallTools/mrcMeanYlinePos.html
+++ b/doc/SmallTools/mrcMeanYlinePos.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcMeanYlinePos
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-w[idth]            width               (-1        )] :Optional  :GetMeanWidth
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-w[idth]            width               (-1        ).as(Integer             ) ] :Optional  :GetMeanWidth
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcMirrorImageCreate.html b/doc/SmallTools/mrcMirrorImageCreate.html
index b4ca2e5..d2e437b 100644
--- a/doc/SmallTools/mrcMirrorImageCreate.html
+++ b/doc/SmallTools/mrcMirrorImageCreate.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: mrcMirrorImageCreate
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcRadon2Dto3D.html b/doc/SmallTools/mrcRadon2Dto3D.html
index 489cbd7..bc7179c 100644
--- a/doc/SmallTools/mrcRadon2Dto3D.html
+++ b/doc/SmallTools/mrcRadon2Dto3D.html
@@ -8,18 +8,18 @@
 <PRE>
 Usage: mrcRadon2Dto3D
 Options:
-    [-I[nput]            In2                 (NULL      )] :Essential :InputDataFileList
-    [-I[nput]b[efore]    InBefore            (NULL      )] :Optional  :InputDataFileListBefore
-    [-i[nput]b[efore]    inbefore            (NULL      )] :Optional  :InputDataFileBeforeData: mrcImageRadon3D
-    [-i[nput]w[eight]b[efore]inWbefore           (NULL      )] :Optional  :InputWeightDataFileBeforeData: mrcImageRadon3D
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile: radon3D
-    [-o[utput]w[eight]   OutW                (NULL      )] :Essential :OutputDataFile: weight
-    [-dp                 dp                  (2.0       )] :Essential :Input: deltaP
-    [-dtheta             dtheta              (1         )] :Essential :Input: deltaTheta
-    [-dphi               dphi                (1         )] :Essential :Input: deltaPhi
-    [-T[hreshold]        T                   (1.0       )] :Optional  :Threshold
-    [-InterpolationMode  InterpolationMode   (0         )] :Optional  :InterpolationMode
-    [-m[ode]             mode                (0         )] :Optional  :Radon2Dto3D Intepolation Mode
+    [-I[nput]            In2                 (NULL      ).as(inFileList          ) ] :Essential :InputDataFileList
+    [-I[nput]b[efore]    InBefore            (NULL      ).as(inFileList          ) ] :Optional  :InputDataFileListBefore
+    [-i[nput]b[efore]    inbefore            (NULL      ).as(inFile              ) ] :Optional  :InputDataFileBeforeData: mrcImageRadon3D
+    [-i[nput]w[eight]b[efore]inWbefore           (NULL      ).as(inFile              ) ] :Optional  :InputWeightDataFileBeforeData: mrcImageRadon3D
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile: radon3D
+    [-o[utput]w[eight]   OutW                (NULL      ).as(outFile             ) ] :Essential :OutputDataFile: weight
+    [-dp                 dp                  (2.0       ).as(Real                ) ] :Essential :Input: deltaP
+    [-dtheta             dtheta              (1         ).as(Real                ) ] :Essential :Input: deltaTheta
+    [-dphi               dphi                (1         ).as(Real                ) ] :Essential :Input: deltaPhi
+    [-T[hreshold]        T                   (1.0       ).as(Real                ) ] :Optional  :Threshold
+    [-InterpolationMode  InterpolationMode   (0         ).as(Integer             ) ] :Optional  :InterpolationMode
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Radon2Dto3D Intepolation Mode
 
 ----- mode -----
  0 = NearestNeighbor
diff --git a/doc/SmallTools/mrcRefCorEstimate.html b/doc/SmallTools/mrcRefCorEstimate.html
index 7b837aa..ad634fc 100644
--- a/doc/SmallTools/mrcRefCorEstimate.html
+++ b/doc/SmallTools/mrcRefCorEstimate.html
@@ -8,9 +8,9 @@
 <PRE>
 Usage: mrcRefCorEstimate
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode 0:Alignment is just. 1:Alignment is just.To display distance of max.2:No alignment 3:No alignment and alpha of reference is 180.
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode 0:Alignment is just. 1:Alignment is just.To display distance of max.2:No alignment 3:No alignment and alpha of reference is 180.
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcRefCorModify.html b/doc/SmallTools/mrcRefCorModify.html
index 1277ef8..bb845a3 100644
--- a/doc/SmallTools/mrcRefCorModify.html
+++ b/doc/SmallTools/mrcRefCorModify.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: mrcRefCorModify
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode:0 Absolute Value 1: The max of y line is normalize to 1.(Absolute Value)
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode:0 Absolute Value 1: The max of y line is normalize to 1.(Absolute Value)
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcRefCoreGet.html b/doc/SmallTools/mrcRefCoreGet.html
index 782acde..88b7033 100644
--- a/doc/SmallTools/mrcRefCoreGet.html
+++ b/doc/SmallTools/mrcRefCoreGet.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcRefCoreGet
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-C[utoff]           Cutoff              (0         )] :Optional  :Cutoff
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode:0 If |Pixel of Image| < Cutoff ,|Pixel of Image|=0 ,1:If |Pixel of Image| < Cutoff*SqrAvr ,|Pixel of Image|=0
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-C[utoff]           Cutoff              (0         ).as(Real                ) ] :Optional  :Cutoff
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode:0 If |Pixel of Image| < Cutoff ,|Pixel of Image|=0 ,1:If |Pixel of Image| < Cutoff*SqrAvr ,|Pixel of Image|=0
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcRefCorrelation.html b/doc/SmallTools/mrcRefCorrelation.html
index b637cfb..e12e9c8 100644
--- a/doc/SmallTools/mrcRefCorrelation.html
+++ b/doc/SmallTools/mrcRefCorrelation.html
@@ -8,18 +8,18 @@
 <PRE>
 Usage: mrcRefCorrelation
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-r[eference]        In2                 (NULL      )] :Optional  :For Mode1=1 only:ReferenceDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-r[eference]        In2                 (NULL      ).as(inFile              ) ] :Optional  :For Mode1=1 only:ReferenceDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :
  Mode1 	 0:AutoCorrelation 
 	 1:CrossCorrelation
-    [-M[ode]             mode2               (0         )] :Optional  :
+    [-M[ode]             mode2               (0         ).as(Integer             ) ] :Optional  :
  Mode2 	 0:All is to be calculated.
 	 1:Pick up at random 
 	 2:Calculate only Omega=0,Alpha=0 
-    [-n[umber]           number              (NULL      )] :Optional  :For mode 1 only. Number of points to pick up at random. Defalt:Data size along z axis of inputfile / 10 
+    [-n[umber]           number              (NULL      ).as(Integer             ) ] :Optional  :For mode 1 only. Number of points to pick up at random. Defalt:Data size along z axis of inputfile / 10 
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcRefCorrelationConv.html b/doc/SmallTools/mrcRefCorrelationConv.html
index c9d0899..272f6e3 100644
--- a/doc/SmallTools/mrcRefCorrelationConv.html
+++ b/doc/SmallTools/mrcRefCorrelationConv.html
@@ -8,10 +8,13 @@
 <PRE>
 Usage: mrcRefCorrelationConv
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode 0:phi,omega 1:phi,alpha 2:omega,alpha
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode 0:phi,omega 1:phi,alpha 2:omega,alpha 3:For one point
+    [p[oint]             Phi                 (0         ).as(Integer             ) 
+                         Omega               (0         ).as(Integer             ) 
+                         Alpha               (0         ).as(Integer             ) ] :Optional  :For mode 3 only:Central point of Correlatin.(Phi,Omega,Alpha)
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcRefEstimate.html b/doc/SmallTools/mrcRefEstimate.html
index 680b08e..f9994a2 100644
--- a/doc/SmallTools/mrcRefEstimate.html
+++ b/doc/SmallTools/mrcRefEstimate.html
@@ -8,8 +8,8 @@
 <PRE>
 Usage: mrcRefEstimate
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcRefFFTConvert.html b/doc/SmallTools/mrcRefFFTConvert.html
index 3f1da5f..3f3ba27 100644
--- a/doc/SmallTools/mrcRefFFTConvert.html
+++ b/doc/SmallTools/mrcRefFFTConvert.html
@@ -8,10 +8,11 @@
 <PRE>
 Usage: mrcRefFFTConvert
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode 0:Fourier translation  1:Create Fourier phase image
+    [-p[ower]            Power               (1         ).as(Real                ) ] :Optional  :For mode 1 only: Use F/( |F|^p ) to create fourier phase image
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcRefHeaderCreate.html b/doc/SmallTools/mrcRefHeaderCreate.html
index 1cdedf0..942f265 100644
--- a/doc/SmallTools/mrcRefHeaderCreate.html
+++ b/doc/SmallTools/mrcRefHeaderCreate.html
@@ -8,17 +8,23 @@
 <PRE>
 Usage: mrcRefHeaderCreate
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-p[osition]         iP                  (0         )iW                  (0         )iA                  (0         )] :Optional  :Position of Center of model creation. Phi(degree) ,Omega(degree) ,Alpha(degree) 
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-p[osition]         iP                  (0         ).as(Real                ) 
+                         iW                  (0         ).as(Real                ) 
+                         iA                  (0         ).as(Real                ) ] :Optional  :Position of Center of model creation. Phi(degree) ,Omega(degree) ,Alpha(degree) 
 :Omega and Alpha range must be around 0 or 180. 
-    [-w[idth]            Wp                  (360       )Ww                  (10        )Wa                  (10        )] :Optional  :Width of Phi(degree,plus minus) ,Omega(degree,plus minus) ,Alpha(degree,plus minus) 
-    [-d[elta]            Dp                  (5         )Dw                  (5         )Da                  (5         )] :Optional  :Interval of model creation(degree) Phi(around Z axis),Omega(Y axis),Alpha(X axis)
-    [-s[tart]y           Sy                  (0         )] :Optional  :Start y: For mode 1 only
-    [-e[end]y            Ey                  (0         )] :Optional  :End y: For mode 1 only. Default is Ny-1
-    [-refsize            Refsize             (0         )] :Optional  :Size of reference data.
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-w[idth]            Wp                  (360       ).as(Real                ) 
+                         Ww                  (10        ).as(Real                ) 
+                         Wa                  (10        ).as(Real                ) ] :Optional  :Width of Phi(degree,plus minus) ,Omega(degree,plus minus) ,Alpha(degree,plus minus) 
+    [-d[elta]            Dp                  (5         ).as(Real                ) 
+                         Dw                  (5         ).as(Real                ) 
+                         Da                  (5         ).as(Real                ) ] :Optional  :Interval of model creation(degree) Phi(around Z axis),Omega(Y axis),Alpha(X axis)
+    [-s[tart]y           Sy                  (0         ).as(Integer             ) ] :Optional  :Start y: For mode 1 only
+    [-e[end]y            Ey                  (0         ).as(Integer             ) ] :Optional  :End y: For mode 1 only. Default is Ny-1
+    [-refsize            Refsize             (0         ).as(Integer             ) ] :Optional  :Size of reference data.
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcRefHighPassFilter.html b/doc/SmallTools/mrcRefHighPassFilter.html
index 817cef7..99f9839 100644
--- a/doc/SmallTools/mrcRefHighPassFilter.html
+++ b/doc/SmallTools/mrcRefHighPassFilter.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcRefHighPassFilter
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-h[alf]v[alue]p[oint]hvp                 (1.0       )] :Optional  :HalfValuePoint
-    [-w[idth]            width               (1.0       )] :Optional  :WidthOfDumping
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-h[alf]v[alue]p[oint]hvp                 (1.0       ).as(Real                ) ] :Optional  :HalfValuePoint
+    [-w[idth]            width               (1.0       ).as(Real                ) ] :Optional  :WidthOfDumping
 >>> Mode <<<< 
     1: Step filter : required argumnent: -hvp
     2: Cos filter  : required argumnent: -hvp -w
diff --git a/doc/SmallTools/mrcRefImageCorrelation.html b/doc/SmallTools/mrcRefImageCorrelation.html
index 31d9557..72d47bc 100644
--- a/doc/SmallTools/mrcRefImageCorrelation.html
+++ b/doc/SmallTools/mrcRefImageCorrelation.html
@@ -8,11 +8,12 @@
 <PRE>
 Usage: mrcRefImageCorrelation
 Options:
-    [-i[nput]            In                  (NULL      )] :Optional  :InputDataFile
-    [-r[eference]        Ref                 (NULL      )] :Essential :ReferenceDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-I[nput array of file]InArray             (stdin     )] :Optional  :InputDataFiles
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Optional  :InputDataFile
+    [-r[eference]        Ref                 (NULL      ).as(inFile              ) ] :Essential :ReferenceDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-I[nput array of file]InArray             (stdin     ).as(inFileList          ) ] :Optional  :InputDataFiles
+    [-z[position]        z                   (0         ).as(Integer             ) ] :Optional  :z position of reference file to correlate.For mode 1 only
 ----- Additional Usage -----
 mode 0: To find the images in the reference file of min and max correlation.  Correlation is calclated in the real space.
 mode 1: To calculate the correlation between one image of the reference file and input file.  The calculation is performed in the fourier space and the output is a mrc image file.  option z is needed.
diff --git a/doc/SmallTools/mrcRefImageOmegaCorrelation.html b/doc/SmallTools/mrcRefImageOmegaCorrelation.html
index 5a2c73d..bec47f4 100644
--- a/doc/SmallTools/mrcRefImageOmegaCorrelation.html
+++ b/doc/SmallTools/mrcRefImageOmegaCorrelation.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: mrcRefImageOmegaCorrelation
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcRefImagepwzCorEstimate.html b/doc/SmallTools/mrcRefImagepwzCorEstimate.html
index 6840546..520c707 100644
--- a/doc/SmallTools/mrcRefImagepwzCorEstimate.html
+++ b/doc/SmallTools/mrcRefImagepwzCorEstimate.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: mrcRefImagepwzCorEstimate
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Optional  :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcRefImagepwzCorModify.html b/doc/SmallTools/mrcRefImagepwzCorModify.html
index 079075e..3e5c252 100644
--- a/doc/SmallTools/mrcRefImagepwzCorModify.html
+++ b/doc/SmallTools/mrcRefImagepwzCorModify.html
@@ -8,14 +8,14 @@
 <PRE>
 Usage: mrcRefImagepwzCorModify
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-nr[Ny of reference file]Nry                 (0         )] :Optional  :Needed only for old format
-    [-mag[nification]    mag                 (1         )] :Optional  :Ratio of new magnification to old magnification
-    [-s[hift]            shift               (0.0       )] :Optional  :y-shift[pixel]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-M[ode2]            mode2               (0         )] :Optional  :Mode2
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-nr[Ny of reference file]Nry                 (0         ).as(Integer             ) ] :Optional  :Needed only for old format
+    [-mag[nification]    mag                 (1         ).as(Real                ) ] :Optional  :Ratio of new magnification to old magnification
+    [-s[hift]            shift               (0.0       ).as(Real                ) ] :Optional  :y-shift[pixel]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-M[ode2]            mode2               (0         ).as(Integer             ) ] :Optional  :Mode2
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcRefImagepwzCorPeakFind.html b/doc/SmallTools/mrcRefImagepwzCorPeakFind.html
index 96bfe0d..2d13e00 100644
--- a/doc/SmallTools/mrcRefImagepwzCorPeakFind.html
+++ b/doc/SmallTools/mrcRefImagepwzCorPeakFind.html
@@ -8,17 +8,17 @@
 <PRE>
 Usage: mrcRefImagepwzCorPeakFind
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-N[unber]           N                   (20        )] :Optional  :Number of peaks
-    [-dN[delta number]   dN                  (5         )] :Optional  :Number of template shift
-    [-d[elta]p[hi]       dp                  (166.1538462)] :Optional  :Delta phi(Degree)
-    [-d[elta]z           dz                  (27.3      )] :Optional  :Delta z(A)
-    [-l[ength]           length              (1000      )] :Optional  :Length to extract.:mode 2 only
-    [-div[ision]         div                 (1         )] :Optional  :Number to division.:mode 2 only
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-M[ode2]            mode2               (0         )] :Optional  :Mode2
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-N[unber]           N                   (20        ).as(Integer             ) ] :Optional  :Number of peaks
+    [-dN[delta number]   dN                  (5         ).as(Integer             ) ] :Optional  :Number of template shift
+    [-d[elta]p[hi]       dp                  (166.1538462).as(Real                ) ] :Optional  :Delta phi(Degree)
+    [-d[elta]z           dz                  (27.3      ).as(Real                ) ] :Optional  :Delta z(A)
+    [-l[ength]           length              (1000      ).as(Integer             ) ] :Optional  :Length to extract.:mode 2 only
+    [-div[ision]         div                 (1         ).as(Integer             ) ] :Optional  :Number to division.:mode 2 only
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-M[ode2]            mode2               (0         ).as(Integer             ) ] :Optional  :Mode2
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcRefImagepwzCorSmoothing.html b/doc/SmallTools/mrcRefImagepwzCorSmoothing.html
index ea8a563..09d9ba6 100644
--- a/doc/SmallTools/mrcRefImagepwzCorSmoothing.html
+++ b/doc/SmallTools/mrcRefImagepwzCorSmoothing.html
@@ -8,13 +8,13 @@
 <PRE>
 Usage: mrcRefImagepwzCorSmoothing
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-N[unber]           N                   (20        )] :Optional  :Number of peaks
-    [-d[elta]p[hi]       dp                  (166.1538462)] :Optional  :Delta phi(Degree)
-    [-d[elta]z           dz                  (27.3      )] :Optional  :Delta z(A)
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-N[unber]           N                   (20        ).as(Integer             ) ] :Optional  :Number of peaks
+    [-d[elta]p[hi]       dp                  (166.1538462).as(Real                ) ] :Optional  :Delta phi(Degree)
+    [-d[elta]z           dz                  (27.3      ).as(Real                ) ] :Optional  :Delta z(A)
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcRefImagepwzCorrelation.html b/doc/SmallTools/mrcRefImagepwzCorrelation.html
index eb009dd..799f16d 100644
--- a/doc/SmallTools/mrcRefImagepwzCorrelation.html
+++ b/doc/SmallTools/mrcRefImagepwzCorrelation.html
@@ -8,13 +8,13 @@
 <PRE>
 Usage: mrcRefImagepwzCorrelation
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-r[eference]        Ref                 (NULL      )] :Optional  :ReferenceFile
-    [-dy[deltay]         dy                  (1         )] :Optional  :Deltay
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-M[ode2]            mode2               (0         )] :Optional  :Mode2
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-r[eference]        Ref                 (NULL      ).as(inFile              ) ] :Optional  :ReferenceFile
+    [-dy[deltay]         dy                  (1         ).as(Integer             ) ] :Optional  :Deltay
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-M[ode2]            mode2               (0         ).as(Integer             ) ] :Optional  :Mode2
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcRefImagepwzCorrelationByFFT.html b/doc/SmallTools/mrcRefImagepwzCorrelationByFFT.html
index 2a01ab0..6db699a 100644
--- a/doc/SmallTools/mrcRefImagepwzCorrelationByFFT.html
+++ b/doc/SmallTools/mrcRefImagepwzCorrelationByFFT.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: mrcRefImagepwzCorrelationByFFT
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcRefImagexaFit.html b/doc/SmallTools/mrcRefImagexaFit.html
index 9eef166..e6d42b2 100644
--- a/doc/SmallTools/mrcRefImagexaFit.html
+++ b/doc/SmallTools/mrcRefImagexaFit.html
@@ -8,18 +8,18 @@
 <PRE>
 Usage: mrcRefImagexaFit
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-ix[initial x]      ix                  (NULL      )] :Optional  :Initial x(pixel)
-    [-ia[initial alpha]  ia                  (0         )] :Optional  :Initial alpha(degree)
-    [-r[eference]        Ref                 (NULL      )] :Optional  :ReferenceFile
-    [-dy[deltay]         Dy                  (10        )] :Optional  :Deltay
-    [-xrange             xrange              (3         )] :Optional  :x range to search (pixel)
-    [-arange             arange              (2         )] :Optional  :alpha range to search (degree)
-    [-v[alue]            Value               (1         )] :Optional  :Value of Peak Pixel :for mode2
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-M[ode2]            mode2               (0         )] :Optional  :Mode2
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-ix[initial x]      ix                  (NULL      ).as(Integer             ) ] :Optional  :Initial x(pixel)
+    [-ia[initial alpha]  ia                  (0         ).as(Real                ) ] :Optional  :Initial alpha(degree)
+    [-r[eference]        Ref                 (NULL      ).as(inFile              ) ] :Optional  :ReferenceFile
+    [-dy[deltay]         Dy                  (10        ).as(Integer             ) ] :Optional  :Deltay
+    [-xrange             xrange              (3         ).as(Integer             ) ] :Optional  :x range to search (pixel)
+    [-arange             arange              (2         ).as(Integer             ) ] :Optional  :alpha range to search (degree)
+    [-v[alue]            Value               (1         ).as(Real                ) ] :Optional  :Value of Peak Pixel :for mode2
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-M[ode2]            mode2               (0         ).as(Integer             ) ] :Optional  :Mode2
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcRefLowPassFilter.html b/doc/SmallTools/mrcRefLowPassFilter.html
index 520bad5..3e92b7c 100644
--- a/doc/SmallTools/mrcRefLowPassFilter.html
+++ b/doc/SmallTools/mrcRefLowPassFilter.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcRefLowPassFilter
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-h[alf]v[alue]p[oint]hvp                 (1.0       )] :Optional  :HalfValuePoint
-    [-w[idth]            width               (1.0       )] :Optional  :WidthOfDumping
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-h[alf]v[alue]p[oint]hvp                 (1.0       ).as(Real                ) ] :Optional  :HalfValuePoint
+    [-w[idth]            width               (1.0       ).as(Real                ) ] :Optional  :WidthOfDumping
 >>> Mode <<<< 
     1: Step filter : required argumnent: -hvp
     2: Cos filter  : required argumnent: -hvp -w
diff --git a/doc/SmallTools/mrcRefNoiseAdd.html b/doc/SmallTools/mrcRefNoiseAdd.html
index 8ea2e34..06a90cb 100644
--- a/doc/SmallTools/mrcRefNoiseAdd.html
+++ b/doc/SmallTools/mrcRefNoiseAdd.html
@@ -8,13 +8,13 @@
 <PRE>
 Usage: mrcRefNoiseAdd
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-s[trength]         Noise               (1.0       )] :Optional  :Strength of Noise.Unit is standard deviation of input reference.
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-h[igh]             H                   (0         )] :Optional  :High threshold to calclate S.D.  Default is max of input file.
-    [-l[ow]              L                   (0         )] :Optional  :Low threshold to calclate S.D.  Default is min of input file.
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-s[trength]         Noise               (1.0       ).as(Real                ) ] :Optional  :Strength of Noise.Unit is standard deviation of input reference.
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-h[igh]             H                   (0         ).as(Real                ) ] :Optional  :High threshold to calclate S.D.  Default is max of input file.
+    [-l[ow]              L                   (0         ).as(Real                ) ] :Optional  :Low threshold to calclate S.D.  Default is min of input file.
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcRefNormalizing.html b/doc/SmallTools/mrcRefNormalizing.html
index a454a84..3f68883 100644
--- a/doc/SmallTools/mrcRefNormalizing.html
+++ b/doc/SmallTools/mrcRefNormalizing.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: mrcRefNormalizing
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcRefPhaseImageCreate.html b/doc/SmallTools/mrcRefPhaseImageCreate.html
index 87d0b64..896f05b 100644
--- a/doc/SmallTools/mrcRefPhaseImageCreate.html
+++ b/doc/SmallTools/mrcRefPhaseImageCreate.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcRefPhaseImageCreate
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-p[ower]            Power               (1         )] :Optional  :Use (|F|^p ) to create fourier phase image
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-C[utoff]           Cutoff              (-1.0      )] :Optional  :Mode 0:If |F|<Cutoff ,this pixel is not used.Default:Mean/10 
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-p[ower]            Power               (1         ).as(Real                ) ] :Optional  :Use (|F|^p ) to create fourier phase image
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-C[utoff]           Cutoff              (-1.0      ).as(Real                ) ] :Optional  :Mode 0:If |F|<Cutoff ,this pixel is not used.Default:Mean/10 
  Mode 1:|F|<Cutoff*Mean is used to cut.Default:0.1
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcRefSmoothing.html b/doc/SmallTools/mrcRefSmoothing.html
index c7c7d14..d0d5f1d 100644
--- a/doc/SmallTools/mrcRefSmoothing.html
+++ b/doc/SmallTools/mrcRefSmoothing.html
@@ -8,13 +8,13 @@
 <PRE>
 Usage: mrcRefSmoothing
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-sx                 sx                  (3         )] :Optional  :x of Kernel Size
-    [-sy                 sy                  (3         )] :Optional  :y of Kernel Size
-    [-sz                 sz                  (3         )] :Optional  :z of Kernel Size
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-sx                 sx                  (3         ).as(Integer             ) ] :Optional  :x of Kernel Size
+    [-sy                 sy                  (3         ).as(Integer             ) ] :Optional  :y of Kernel Size
+    [-sz                 sz                  (3         ).as(Integer             ) ] :Optional  :z of Kernel Size
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcRefz1ImageCorrelation.html b/doc/SmallTools/mrcRefz1ImageCorrelation.html
index 80bb4e2..c1d6662 100644
--- a/doc/SmallTools/mrcRefz1ImageCorrelation.html
+++ b/doc/SmallTools/mrcRefz1ImageCorrelation.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcRefz1ImageCorrelation
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-r[eference]        Ref                 (NULL      )] :Optional  :ReferenceFile
-    [-z[position]        z                   (0         )] :Optional  :z position of reference file to correlate
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-r[eference]        Ref                 (NULL      ).as(inFile              ) ] :Optional  :ReferenceFile
+    [-z[position]        z                   (0         ).as(Integer             ) ] :Optional  :z position of reference file to correlate
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcSinogramFET.html b/doc/SmallTools/mrcSinogramFET.html
index c6b0e22..7b87637 100644
--- a/doc/SmallTools/mrcSinogramFET.html
+++ b/doc/SmallTools/mrcSinogramFET.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: mrcSinogramFET
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-ch[eck]            OutC                (NULL      )] :Optional  :OutputDataForCheckByEye
-    [-sm[ooth]           sm                  (1         )] :Optional  :SmoothingFilter
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-ch[eck]            OutC                (NULL      ).as(outFile             ) ] :Optional  :OutputDataForCheckByEye
+    [-sm[ooth]           sm                  (1         ).as(Integer             ) ] :Optional  :SmoothingFilter
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 -sm : move range of column smoothing by moving-average
 </PRE>
diff --git a/doc/SmallTools/mrcSinogramFETcalcSDforNormalize.html b/doc/SmallTools/mrcSinogramFETcalcSDforNormalize.html
index 8134926..b7f35ea 100644
--- a/doc/SmallTools/mrcSinogramFETcalcSDforNormalize.html
+++ b/doc/SmallTools/mrcSinogramFETcalcSDforNormalize.html
@@ -8,13 +8,13 @@
 <PRE>
 Usage: mrcSinogramFETcalcSDforNormalize
 Options:
-    [-i[nput]            In                  (NULL      )] :Optional  :InputFETDataFile
-    [-s[elect]           Sm                  (1         )] :Optional  :selectFETfile
-    [-l[ibrary]          Libl                (NULL      )] :Essential :SDlibraryFile
-    [-o[utput]           Out                 (NULL      )] :Optional  :OutputSDdataFile
-    [-o[ut]w[eight]      OW                  (NULL      )] :Optional  :OutputWeightdataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Optional  :InputFETDataFile
+    [-s[elect]           Sm                  (1         ).as(Integer             ) ] :Optional  :selectFETfile
+    [-l[ibrary]          Libl                (NULL      ).as(inFile              ) ] :Essential :SDlibraryFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :OutputSDdataFile
+    [-o[ut]w[eight]      OW                  (NULL      ).as(outFile             ) ] :Optional  :OutputWeightdataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 mode 0: SDfile writeout from liblary file
         Library(option -l) is Essential
diff --git a/doc/SmallTools/mrcSinogramFETcalcWeight.html b/doc/SmallTools/mrcSinogramFETcalcWeight.html
index e34e90d..4cac7d8 100644
--- a/doc/SmallTools/mrcSinogramFETcalcWeight.html
+++ b/doc/SmallTools/mrcSinogramFETcalcWeight.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcSinogramFETcalcWeight
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-c[ommon]l[ine]     InC                 (NULL      )] :Essential :inputCommonLineFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-c[ommon]l[ine]     InC                 (NULL      ).as(inFile              ) ] :Essential :inputCommonLineFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcSinogramFETcorrelationMap.html b/doc/SmallTools/mrcSinogramFETcorrelationMap.html
index e2e0ba3..a5e125a 100644
--- a/doc/SmallTools/mrcSinogramFETcorrelationMap.html
+++ b/doc/SmallTools/mrcSinogramFETcorrelationMap.html
@@ -8,15 +8,15 @@
 <PRE>
 Usage: mrcSinogramFETcorrelationMap
 Options:
-    [-i[nput]1           In1                 (NULL      )] :Essential :InputSinogramFETFile1
-    [-i[nput]2           In2                 (NULL      )] :Essential :InputSinogramFETFile2
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-w[eight]           Weight              (NULL      )] :Optional  :WeightDataFile mrcFormat
-    [-s[tandard]d[eviation]SD                  (NULL      )] :Optional  :readSDfileForNormalize
-    [-n[orm]m[ode]       NM                  (0         )] :Optional  :normalizemode
-    [-c[alc]mode         CMode               (0         )] :Optional  :calculateMode
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]1           In1                 (NULL      ).as(inFile              ) ] :Essential :InputSinogramFETFile1
+    [-i[nput]2           In2                 (NULL      ).as(inFile              ) ] :Essential :InputSinogramFETFile2
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-w[eight]           Weight              (NULL      ).as(inFile              ) ] :Optional  :WeightDataFile mrcFormat
+    [-s[tandard]d[eviation]SD                  (NULL      ).as(inFile              ) ] :Optional  :readSDfileForNormalize
+    [-n[orm]m[ode]       NM                  (0         ).as(Integer             ) ] :Optional  :normalizemode
+    [-c[alc]mode         CMode               (0         ).as(Integer             ) ] :Optional  :calculateMode
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 mode 0 : default, normal distance correlation
 mode 1 : average of counter pixel presents same line
diff --git a/doc/SmallTools/mrcSinogramFETnormalizedMap.html b/doc/SmallTools/mrcSinogramFETnormalizedMap.html
index e187853..647aa2d 100644
--- a/doc/SmallTools/mrcSinogramFETnormalizedMap.html
+++ b/doc/SmallTools/mrcSinogramFETnormalizedMap.html
@@ -8,14 +8,14 @@
 <PRE>
 Usage: mrcSinogramFETnormalizedMap
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputFETlistFile
-    [-o[utput]           OutFET              (NULL      )] :Essential :OutputFETmrcformat
-    [-cl[ine]List        comList             (NULL      )] :Optional  :commonlineList
-    [-O[utput]           OutMAP              (NULL      )] :Optional  :OutputMAPmrcformat
-    [-w[eight]           Weight              (NULL      )] :Optional  :WeightForDistanceCalc
-    [-atm[ode]           AAtm                (1         )] :Optional  :AAtestmode
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputFETlistFile
+    [-o[utput]           OutFET              (NULL      ).as(outFile             ) ] :Essential :OutputFETmrcformat
+    [-cl[ine]List        comList             (NULL      ).as(inFile              ) ] :Optional  :commonlineList
+    [-O[utput]           OutMAP              (NULL      ).as(outFile             ) ] :Optional  :OutputMAPmrcformat
+    [-w[eight]           Weight              (NULL      ).as(inFile              ) ] :Optional  :WeightForDistanceCalc
+    [-atm[ode]           AAtm                (1         ).as(Integer             ) ] :Optional  :AAtestmode
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
  "-O" option do not work at Oct.24,2007
  aatestmode 0: default, check whole distance
diff --git a/doc/SmallTools/mrcSinogramFETreferredCorrelation.html b/doc/SmallTools/mrcSinogramFETreferredCorrelation.html
index 8049db9..2cc5e3c 100644
--- a/doc/SmallTools/mrcSinogramFETreferredCorrelation.html
+++ b/doc/SmallTools/mrcSinogramFETreferredCorrelation.html
@@ -8,17 +8,17 @@
 <PRE>
 Usage: mrcSinogramFETreferredCorrelation
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputFETDataFileList
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputEulerAngleDataFileList
-    [-i[nput]Ref         InR                 (NULL      )] :Essential :InputReferenceFETDataFileList
-    [-i[nput]Euler       InE                 (NULL      )] :Essential :InputEulerAngleDataFile
-    [-n[ormalize]m[ode]  NM                  (0         )] :Optional  :normalizeMode
-    [-o[utputList]m[ode] OM                  (2         )] :Optional  :outputListMode
-    [-t[op]n[um]         TN                  (10        )] :Optional  :top number
-    [-refR[ange]         RR                  (15        )] :Optional  :reference select Range
-    [-w[eight]           WEIGHT              (NULL      )] :Optional  :CorrelationCalcWeight
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputFETDataFileList
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputEulerAngleDataFileList
+    [-i[nput]Ref         InR                 (NULL      ).as(inFile              ) ] :Essential :InputReferenceFETDataFileList
+    [-i[nput]Euler       InE                 (NULL      ).as(inFile              ) ] :Essential :InputEulerAngleDataFile
+    [-n[ormalize]m[ode]  NM                  (0         ).as(Integer             ) ] :Optional  :normalizeMode
+    [-o[utputList]m[ode] OM                  (2         ).as(Integer             ) ] :Optional  :outputListMode
+    [-t[op]n[um]         TN                  (10        ).as(Integer             ) ] :Optional  :top number
+    [-refR[ange]         RR                  (15        ).as(Integer             ) ] :Optional  :reference select Range
+    [-w[eight]           WEIGHT              (NULL      ).as(inFile              ) ] :Optional  :CorrelationCalcWeight
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 
 Input EulerAngleDataFile example
diff --git a/doc/SmallTools/mrcSinogramFETsmoothParameterMatching.html b/doc/SmallTools/mrcSinogramFETsmoothParameterMatching.html
index fef41d7..f947b3f 100644
--- a/doc/SmallTools/mrcSinogramFETsmoothParameterMatching.html
+++ b/doc/SmallTools/mrcSinogramFETsmoothParameterMatching.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: mrcSinogramFETsmoothParameterMatching
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputFileList
-    [-i[nput]s[tandard]  InSTD               (NULL      )] :Essential :StandardSinogramFile
-    [-o[utput]           Out                 (NULL      )] :Optional  :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputFileList
+    [-i[nput]s[tandard]  InSTD               (NULL      ).as(inFile              ) ] :Essential :StandardSinogramFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/pdb2SketchMacro.html b/doc/SmallTools/pdb2SketchMacro.html
index 994f83d..2828251 100644
--- a/doc/SmallTools/pdb2SketchMacro.html
+++ b/doc/SmallTools/pdb2SketchMacro.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: pdb2SketchMacro
 Options:
-    [-i[nput]            In                  (stdin     )] :Optional  :InputDataFile
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-MolName            MolName             (TS        )] :Optional  :MolecularName[prefer to <=2]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (15        )] :Optional  :Mode
+    [-i[nput]            In                  (stdin     ).as(inFile              ) ] :Optional  :InputDataFile
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-MolName            MolName             (TS        ).as(String              ) ] :Optional  :MolecularName[prefer to <=2]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (15        ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 >>>> -m 
   1 : Helix sketched with spirals 
diff --git a/doc/SmallTools/pdb2bender.html b/doc/SmallTools/pdb2bender.html
index 06e63e8..49f187c 100644
--- a/doc/SmallTools/pdb2bender.html
+++ b/doc/SmallTools/pdb2bender.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: pdb2bender
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/pdb2mrc.html b/doc/SmallTools/pdb2mrc.html
index 6e486ff..d6991cb 100644
--- a/doc/SmallTools/pdb2mrc.html
+++ b/doc/SmallTools/pdb2mrc.html
@@ -8,21 +8,21 @@
 <PRE>
 Usage: pdb2mrc
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Optional  :OutputDataFile(3D)
-    [-nx                 nx                  (1         )] :Optional  :Pixel[Def:]
-    [-ny                 ny                  (1         )] :Optional  :Pixel[Def:]
-    [-nz                 nz                  (1         )] :Optional  :Pixel[Def:]
-    [-Sx[tart]           Startx              (0.0       )] :Optional  :Startx[A]
-    [-Sy[tart]           Starty              (0.0       )] :Optional  :Starty[A]
-    [-Sz[tart]           Startz              (0.0       )] :Optional  :Startz[A]
-    [-dx                 dx                  (2.5       )] :Optional  :dx
-    [-dy                 dy                  (2.5       )] :Optional  :dy
-    [-dz                 dz                  (2.5       )] :Optional  :dz
-    [-w[eight]           Weight              (1.0       )] :Optional  :Weight
-    [-sig[ma]            Sigma               (0.0       )] :Optional  :Sigma[A]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile(3D)
+    [-nx                 nx                  (1         ).as(Integer             ) ] :Optional  :Pixel[Def:]
+    [-ny                 ny                  (1         ).as(Integer             ) ] :Optional  :Pixel[Def:]
+    [-nz                 nz                  (1         ).as(Integer             ) ] :Optional  :Pixel[Def:]
+    [-Sx[tart]           Startx              (0.0       ).as(Real                ) ] :Optional  :Startx[A]
+    [-Sy[tart]           Starty              (0.0       ).as(Real                ) ] :Optional  :Starty[A]
+    [-Sz[tart]           Startz              (0.0       ).as(Real                ) ] :Optional  :Startz[A]
+    [-dx                 dx                  (2.5       ).as(Real                ) ] :Optional  :dx
+    [-dy                 dy                  (2.5       ).as(Real                ) ] :Optional  :dy
+    [-dz                 dz                  (2.5       ).as(Real                ) ] :Optional  :dz
+    [-w[eight]           Weight              (1.0       ).as(Real                ) ] :Optional  :Weight
+    [-sig[ma]            Sigma               (0.0       ).as(Real                ) ] :Optional  :Sigma[A]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 >>> mode 
 mode: DensityMode
 0: Same Gaussian 
diff --git a/doc/SmallTools/pdb2mrc2d.html b/doc/SmallTools/pdb2mrc2d.html
index f600fec..0a6bc3e 100644
--- a/doc/SmallTools/pdb2mrc2d.html
+++ b/doc/SmallTools/pdb2mrc2d.html
@@ -1 +1,50 @@
-/bin/bash: pdb2mrc2d: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdb2mrc2d</TITLE>
+</HEAD>
+<BODY>
+<H1>pdb2mrc2d</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdb2mrc2d
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile(2D)
+    [-O[utput]           Out3D               (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile(3D)
+    [-d[elta]            dx                  (5.0       ).as(Real                ) 
+                         dy                  (5.0       ).as(Real                ) ] :Essential :delta: dx[A] dy[A]
+    [-s[tart]            sx                  (0.0       ).as(Real                ) 
+                         sy                  (0.0       ).as(Real                ) ] :Optional  :start: startx[A] starty[A]: When -s was not set, image centre is the origin(0,0,0)
+    [-n[umber]           nx                  (0         ).as(Integer             ) 
+                         ny                  (0         ).as(Integer             ) ] :Essential :N:     nx ny (image size)
+    [-Rot[ation]         rotnx               (1         ).as(Integer             ) 
+                         rotny               (1         ).as(Integer             ) ] :Optional  :rotnx rotny
+    [-S[tart]            srotx               (0.0       ).as(Real                ) 
+                         sroty               (0.0       ).as(Real                ) 
+                         srotz               (0.0       ).as(Real                ) ] :Optional  :start(rotx roty rotz):ZXY
+    [-startE[uler]A[ngle]sRotMode            (YOYS      ).as(String              ) 
+                         sRot1               (0.0       ).as(Real                ) 
+                         sRot2               (0.0       ).as(Real                ) 
+                         sRot3               (0.0       ).as(Real                ) ] :Optional  :EulerAngle: Start Angle
+    [-E[uler]A[ngle]Mode RotMode             (YOYS      ).as(String              ) ] :Optional  :RotationMode
+    [-E[uler]A[ngle]Rot1 dRot1               (5.0       ).as(Real                ) 
+                         minRot1             (0.0       ).as(Real                ) 
+                         maxRot1             (180.0     ).as(Real                ) ] :Optional  :FirstRotation
+    [-E[uler]A[ngle]Rot2 dRot2               (5.0       ).as(Real                ) 
+                         minRot2             (0.0       ).as(Real                ) 
+                         maxRot2             (180.0     ).as(Real                ) ] :Optional  :SecondRotation
+    [-w[eight]           Weight              (1.0       ).as(Real                ) ] :Optional  :weight
+    [-sig[ma]            Sigma               (0.0       ).as(Real                ) ] :Optional  :Sigma[A]:Atom radius
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-cuda               cudaDeviceID        (0         ).as(Integer             ) ] :Optional  :UseCuda
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode: 0 Merc; 1: Earth
+----- Attention1 -----
+If both of -s and -startEA, first -s and second -startEA will be performed
+----- Attention2 -----
+Bug fixed: rotation around x-axis. + is changed to - 
+----- Mode -----
+1: 0: equal angle 1: equal area
+2: 0: Mercatol    1: Morwide 
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/pdb2mrc2dWithCTF.html b/doc/SmallTools/pdb2mrc2dWithCTF.html
index d900bbd..a5c6d70 100644
--- a/doc/SmallTools/pdb2mrc2dWithCTF.html
+++ b/doc/SmallTools/pdb2mrc2dWithCTF.html
@@ -1 +1,37 @@
-/bin/bash: pdb2mrc2dWithCTF: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdb2mrc2dWithCTF</TITLE>
+</HEAD>
+<BODY>
+<H1>pdb2mrc2dWithCTF</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdb2mrc2dWithCTF
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: PDB
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output: MRC
+    [-N                  Nx                  (2048      ).as(Integer             ) 
+                         Ny                  (2048      ).as(Integer             ) ] :Optional  :Input: Nx Ny [pixel]
+    [-d                  dx                  (1.72      ).as(Real                ) 
+                         dy                  (1.72      ).as(Real                ) ] :Optional  :Input: dx dy [A]
+    [-Centre             cx                  (0         ).as(Real                ) 
+                         cy                  (0         ).as(Real                ) 
+                         cz                  (0         ).as(Real                ) ] :Optional  :Input: CentreX CentreY [A]
+    [-n                  nx                  (64        ).as(Integer             ) 
+                         ny                  (64        ).as(Integer             ) ] :Optional  :Input: nx ny for subimage [pixel]
+    [-kV                 kV                  (200.      ).as(Real                ) ] :Optional  :kV 
+    [-Cs                 Cs                  (1.7       ).as(Real                ) ] :Optional  :Cs 
+    [-d[e]f[ocus]        Defocus             (10000     ).as(Real                ) ] :Optional  :Defocus [A] at z = 0
+    [-A[overP]           AoverP              (0.07      ).as(Real                ) ] :Optional  :AoverP
+    [-Ain                Ain                 (0.2       ).as(Real                ) ] :Optional  :Beta: IlluminationAngle [mrad]
+    [-ctfMode            ctfMode             (33        ).as(Integer             ) ] :Optional  :ctfMode
+    [-E[uler]A[ngle]     EulerAngle          (XEYS      ).as(String              ) 
+                         Rot1                (0         ).as(Real                ) 
+                         Rot2                (0         ).as(Real                ) 
+                         Rot3                (0         ).as(Real                ) ] :Optional  :EulerAngle: [degree]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/pdb2ucd.html b/doc/SmallTools/pdb2ucd.html
index d0d5da9..739559f 100644
--- a/doc/SmallTools/pdb2ucd.html
+++ b/doc/SmallTools/pdb2ucd.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: pdb2ucd
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/pdbAtomSection.html b/doc/SmallTools/pdbAtomSection.html
index c616ca9..72689ca 100644
--- a/doc/SmallTools/pdbAtomSection.html
+++ b/doc/SmallTools/pdbAtomSection.html
@@ -8,23 +8,23 @@
 <PRE>
 Usage: pdbAtomSection
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-i[nput of ]f[lags] InFlags             (NULL      )] :Optional  :InputFlagsFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-dist[ance]         distance            (2.5       )] :Optional  :DistanceOfSections
-    [-zmin[imum]         zmin                (0.0       )] :Optional  :Minimum of Z
-    [-zmax[imum]         zmax                (90.0      )] :Optional  :Maximum of Z
-    [-f[lag]m[ode]       flagMode            (13        )] :Optional  :flag mode
-    [-r[adius]           radius              (1.0       )] :Optional  :radius of the circle
-    [-c[ircle]l[ine]w[idth]clinewidth          (0.1       )] :Optional  :circle line width
-    [-p[eptide bond]l[ine]w[idth]plinewidth          (0.1       )] :Optional  :peptide bond line width
-    [-fontsize           fontsize            (2.0       )] :Optional  :font size
-    [-A[bsolute]S[caleofPSFile]scale               (1.0       )] :Optional  :absolute scale of PS file (-AS 1 := 1 mm/A)
-    [-shiftx             shiftx              (0.0       )] :Optional  :pdb Shift x [A]
-    [-shifty             shifty              (0.0       )] :Optional  :pdb Shift y [A]
-    [-shiftz             shiftz              (0.0       )] :Optional  :pdb Shift z [A]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-i[nput of ]f[lags] InFlags             (NULL      ).as(inFile              ) ] :Optional  :InputFlagsFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-dist[ance]         distance            (2.5       ).as(Real                ) ] :Optional  :DistanceOfSections
+    [-zmin[imum]         zmin                (0.0       ).as(Real                ) ] :Optional  :Minimum of Z
+    [-zmax[imum]         zmax                (90.0      ).as(Real                ) ] :Optional  :Maximum of Z
+    [-f[lag]m[ode]       flagMode            (13        ).as(Integer             ) ] :Optional  :flag mode
+    [-r[adius]           radius              (1.0       ).as(Real                ) ] :Optional  :radius of the circle
+    [-c[ircle]l[ine]w[idth]clinewidth          (0.1       ).as(Real                ) ] :Optional  :circle line width
+    [-p[eptide bond]l[ine]w[idth]plinewidth          (0.1       ).as(Real                ) ] :Optional  :peptide bond line width
+    [-fontsize           fontsize            (2.0       ).as(Real                ) ] :Optional  :font size
+    [-A[bsolute]S[caleofPSFile]scale               (1.0       ).as(Real                ) ] :Optional  :absolute scale of PS file (-AS 1 := 1 mm/A)
+    [-shiftx             shiftx              (0.0       ).as(Real                ) ] :Optional  :pdb Shift x [A]
+    [-shifty             shifty              (0.0       ).as(Real                ) ] :Optional  :pdb Shift y [A]
+    [-shiftz             shiftz              (0.0       ).as(Real                ) ] :Optional  :pdb Shift z [A]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 
 
 
diff --git a/doc/SmallTools/pdbCAOnly.html b/doc/SmallTools/pdbCAOnly.html
index 779a034..8074ff2 100644
--- a/doc/SmallTools/pdbCAOnly.html
+++ b/doc/SmallTools/pdbCAOnly.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: pdbCAOnly
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: pdb
-    [-o[utput]           Out                 (NULL      )] :Optional  :Output: pdb
-    [-o[utput]Coord      OutCoord            (NULL      )] :Optional  :Output: x,y,z
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: pdb
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :Output: pdb
+    [-o[utput]Coord      OutCoord            (NULL      ).as(outFile             ) ] :Optional  :Output: x,y,z
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/pdbChargeFit.html b/doc/SmallTools/pdbChargeFit.html
index 2622898..a429b73 100644
--- a/doc/SmallTools/pdbChargeFit.html
+++ b/doc/SmallTools/pdbChargeFit.html
@@ -1 +1,29 @@
-/bin/bash: pdbChargeFit: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbChargeFit</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbChargeFit</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbChargeFit
+Options:
+    [-i[nput]f[ixed pdb] InFix               (NULL      ).as(inFile              ) ] :Essential :InputFixedPdbFile
+    [-i[nput]m[oved pdb] InMove              (NULL      ).as(inFile              ) ] :Essential :InputMovedPdbFile
+    [-o[utput]           OutTxt              (NULL      ).as(outFile             ) ] :Essential :OutputTextFile
+    [-s[ymmetry of helix(degree/A)]symmetry            (0.47096   ).as(Real                ) ] :Optional  :default: 13/28
+    [-zmin               zmin                (-28       ).as(Real                ) ] :Optional  :minimum z
+    [-zmax               zmax                (28        ).as(Real                ) ] :Optional  :maximum z
+    [-zDel[ta]           zDel                (1         ).as(Real                ) ] :Optional  :delta z
+    [-mind[istance]      mind                (1         ).as(Real                ) ] :Optional  :set atoms distance to mind
+    [-maxd[istance]      maxd                (5         ).as(Real                ) ] :Optional  :ignore atoms distance
+    [-a[xis coordinate]  axisX               (70        ).as(Real                ) 
+                         axisY               (70        ).as(Real                ) ] :Optional  :(x, y)
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Algorythm -----
+score = Sum(1/SQR(length))
+, where length is the set of length between charged atoms
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/pdbCoordAdd.html b/doc/SmallTools/pdbCoordAdd.html
index 95daf98..fb5af08 100644
--- a/doc/SmallTools/pdbCoordAdd.html
+++ b/doc/SmallTools/pdbCoordAdd.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: pdbCoordAdd
 Options:
-    [-i[nput]1           In1                 (NULL      )] :Essential :Input:PDB
-    [-i[nput]2           In2                 (NULL      )] :Essential :Input:PDB
-    [-o[utput]           Out                 (NULL      )] :Essential :Output:PDB
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]1           In1                 (NULL      ).as(inFile              ) ] :Essential :Input:PDB
+    [-i[nput]2           In2                 (NULL      ).as(inFile              ) ] :Essential :Input:PDB
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output:PDB
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 In2 is a subgroup of In1. 
 </PRE>
diff --git a/doc/SmallTools/pdbCrystalCreate.html b/doc/SmallTools/pdbCrystalCreate.html
index 076ce13..24999d3 100644
--- a/doc/SmallTools/pdbCrystalCreate.html
+++ b/doc/SmallTools/pdbCrystalCreate.html
@@ -1 +1,36 @@
-/bin/bash: pdbCrystalCreate: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbCrystalCreate</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbCrystalCreate</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbCrystalCreate
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input:PDB
+    [-I[nfo]             Info                (NULL      ).as(inFile              ) ] :Essential :Input:Crystal Information
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output:PDB
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+----- CrystalInfo -----
+aAxis       %15.6g %15.6g %15.6g
+bAxis       %15.6g %15.6g %15.6g
+cAxis       %15.6g %15.6g %15.6g
+CellLength  %15.6g %15.6g %15.6g
+Origin      %15.6g %15.6g %15.6g
+N           %15d %15d %15d
+StartN      %15d %15d %15d
+SpaceGroup  %15d
+HelixInfo   %10d %10d %10d
+### Attention ###
+Parameter Order is important: Dependent between CellLength and a|b|cAxis.
+                              Because each of aAxis, bAxis, cAxis must be a unit vector.
+HelixInfo   t  u  n
+----- CrystalSpaceGroup -----
+    0 P1
+    1 HelicalSymmmetry
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/pdbDisplay.html b/doc/SmallTools/pdbDisplay.html
index 3ac59d9..2387820 100644
--- a/doc/SmallTools/pdbDisplay.html
+++ b/doc/SmallTools/pdbDisplay.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: pdbDisplay
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/pdbFileMerge.html b/doc/SmallTools/pdbFileMerge.html
index cb61ebc..6e18f71 100644
--- a/doc/SmallTools/pdbFileMerge.html
+++ b/doc/SmallTools/pdbFileMerge.html
@@ -8,12 +8,13 @@
 <PRE>
 Usage: pdbFileMerge
 Options:
-    [-i[nput]1           In1                 (NULL      )] :Essential :InputDataFile
-    [-i[nput]2           In2                 (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-startC             startID             (A         )] :Optional  :start chain ID
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]1           In1                 (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-i[nput]2           In2                 (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-startC             startID             (A         ).as(Character           ) ] :Optional  :start chain ID
+    [-NCC[NotChangingChainID]                                                          ] :Optional  :NotChangingChainID
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/pdbHelix.html b/doc/SmallTools/pdbHelix.html
index 0ec5a3f..5da8fe6 100644
--- a/doc/SmallTools/pdbHelix.html
+++ b/doc/SmallTools/pdbHelix.html
@@ -1 +1,37 @@
-/bin/bash: pdbHelix: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbHelix</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbHelix</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbHelix
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-3[D]               Out3D               (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile(3D-mrc)
+    [-2[D]               Out2D               (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile(2D-mrc projection(y-z))
+    [-d[elta]            delta               (5         ).as(Real                ) ] :Optional  :delta[A](mrc-file)
+    [-p[delphi]          delphi              (165       ).as(Real                ) ] :Essential :deltaPhi
+    [-dp[delphi]         deldelphi           (5         ).as(Real                ) ] :Optional  :deltaDeltaPhi
+    [-z[deltaz]          delz                (5         ).as(Real                ) ] :Essential :deltaz
+    [-n[Molecule]        nMolecule           (1         ).as(Integer             ) ] :Essential :NumberOfMolecules
+    [-nx                 nx                  (1         ).as(Integer             ) ] :Optional  :Pixel[Def:]
+    [-ny                 ny                  (1         ).as(Integer             ) ] :Optional  :Pixel[Def:]
+    [-nz                 nz                  (1         ).as(Integer             ) ] :Optional  :Pixel[Def:]
+    [-Sx[tart]           Startx              (0.0       ).as(Real                ) ] :Optional  :Startx[A]
+    [-Sy[tart]           Starty              (0.0       ).as(Real                ) ] :Optional  :Starty[A]
+    [-Sz[tart]           Startz              (0.0       ).as(Real                ) ] :Optional  :Startz[A]
+    [-w[eight]           Weight              (1.0       ).as(Real                ) ] :Optional  :Weight
+    [-dx                 dx                  (2.5       ).as(Real                ) ] :Optional  :dx
+    [-dy                 dy                  (2.5       ).as(Real                ) ] :Optional  :dy
+    [-dz                 dz                  (2.5       ).as(Real                ) ] :Optional  :dz
+    [-startn             startn              (0         ).as(Integer             ) ] :Optional  :start molecule's index
+    [-startC             startID             (A         ).as(Character           ) ] :Optional  :start chain ID
+    [-deltaSeq           deltaSeq            (1000      ).as(Integer             ) ] :Optional  :start chain ID
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/pdbInfo.html b/doc/SmallTools/pdbInfo.html
index 27761c0..9deb3ee 100644
--- a/doc/SmallTools/pdbInfo.html
+++ b/doc/SmallTools/pdbInfo.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: pdbInfo
 Options:
-    [-i[nput]            In                  (stdin     )] :Essential :InputDataFile
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-o[utputWith]a[ppend]OutAppend           (stdout    )] :Optional  :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (stdin     ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-o[utputWith]a[ppend]OutAppend           (stdout    ).as(appendFile          ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/pdbListRMSDCalc.html b/doc/SmallTools/pdbListRMSDCalc.html
index de6bc0c..0d77f77 100644
--- a/doc/SmallTools/pdbListRMSDCalc.html
+++ b/doc/SmallTools/pdbListRMSDCalc.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: pdbListRMSDCalc
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-r[ef]              Ref                 (NULL      )] :Optional  :ReferenceDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFileList          ) ] :Essential :InputDataFile
+    [-r[ef]              Ref                 (NULL      ).as(inFile              ) ] :Optional  :ReferenceDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 >> -m  
  0: -i only   : against average 
diff --git a/doc/SmallTools/pdbListVectorCalc.html b/doc/SmallTools/pdbListVectorCalc.html
index c54464c..c65cb2b 100644
--- a/doc/SmallTools/pdbListVectorCalc.html
+++ b/doc/SmallTools/pdbListVectorCalc.html
@@ -1 +1,18 @@
-/bin/bash: pdbListVectorCalc: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbListVectorCalc</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbListVectorCalc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbListVectorCalc
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/pdbMolecularInterfaceFind.html b/doc/SmallTools/pdbMolecularInterfaceFind.html
index c88e0f5..d27cd37 100644
--- a/doc/SmallTools/pdbMolecularInterfaceFind.html
+++ b/doc/SmallTools/pdbMolecularInterfaceFind.html
@@ -8,13 +8,13 @@
 <PRE>
 Usage: pdbMolecularInterfaceFind
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Optional  :OutputDataFile
-    [-id1[]              ID1                 (A         )] :Optional  :ChainId1
-    [-id2[]              ID2                 (B         )] :Optional  :ChainId2
-    [-d[istance]         d                   (1         )] :Optional  :Threshold distance
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-id1[]              ID1                 (A         ).as(Character           ) ] :Optional  :ChainId1
+    [-id2[]              ID2                 (B         ).as(Character           ) ] :Optional  :ChainId2
+    [-d[istance]         d                   (1         ).as(Real                ) ] :Optional  :Threshold distance
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/pdbMove.html b/doc/SmallTools/pdbMove.html
index 9a2b54e..4b6f1f1 100644
--- a/doc/SmallTools/pdbMove.html
+++ b/doc/SmallTools/pdbMove.html
@@ -1 +1,28 @@
-/bin/bash: pdbMove: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbMove</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbMove</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbMove
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-x                  X                   (0.0       ).as(Real                ) ] :Optional  :Move X[A]
+    [-y                  Y                   (0.0       ).as(Real                ) ] :Optional  :Move Y[A]
+    [-z                  Z                   (0.0       ).as(Real                ) ] :Optional  :Move Z[A]
+    [-originTo           toX                 (0.0       ).as(Real                ) 
+                         toY                 (0.0       ).as(Real                ) 
+                         toZ                 (0.0       ).as(Real                ) ] :Optional  :move (0,0,0) to (X,Y,Z)
+    [-toOrigin           fromX               (0.0       ).as(Real                ) 
+                         fromY               (0.0       ).as(Real                ) 
+                         fromZ               (0.0       ).as(Real                ) ] :Optional  :move (X,Y,Z) to (0,0,0)
+    [-GCtoOrigin                                                                   ] :Optional  :GC(Gravity Centre) to origin
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/pdbNAMDRestraintCreate.html b/doc/SmallTools/pdbNAMDRestraintCreate.html
index cbff00c..f09b54c 100644
--- a/doc/SmallTools/pdbNAMDRestraintCreate.html
+++ b/doc/SmallTools/pdbNAMDRestraintCreate.html
@@ -8,15 +8,15 @@
 <PRE>
 Usage: pdbNAMDRestraintCreate
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input:PDB
-    [-r[efrence]         Ref                 (NULL      )] :Essential :Input:PDB
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output: NAMD Restraint
-    [-O[utput]           Out2                (stdout    )] :Optional  :Output: NAMD PDB Force
-    [-kf                 Kf                  (1.0       )] :Optional  :Input: Kf kcal/mol/A^2
-    [-autokf             AutoKf              (1.0       )] :Optional  :Input: Kf kcal/mol for averaged length
-    [-seg[name]          SegName             (EXAMPLE   )] :Optional  :Input: segment name
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input:PDB
+    [-r[efrence]         Ref                 (NULL      ).as(inFile              ) ] :Essential :Input:PDB
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output: NAMD Restraint
+    [-O[utput]           Out2                (stdout    ).as(outFile             ) ] :Optional  :Output: NAMD PDB Force
+    [-kf                 Kf                  (1.0       ).as(Real                ) ] :Optional  :Input: Kf kcal/mol/A^2
+    [-autokf             AutoKf              (1.0       ).as(Real                ) ] :Optional  :Input: Kf kcal/mol for averaged length
+    [-seg[name]          SegName             (EXAMPLE   ).as(String              ) ] :Optional  :Input: segment name
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 -autokf is prior to -kf.
 </PRE>
diff --git a/doc/SmallTools/pdbNearAtomListShow.html b/doc/SmallTools/pdbNearAtomListShow.html
index f42eb75..347ad3d 100644
--- a/doc/SmallTools/pdbNearAtomListShow.html
+++ b/doc/SmallTools/pdbNearAtomListShow.html
@@ -8,14 +8,16 @@
 <PRE>
 Usage: pdbNearAtomListShow
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: pdbFile
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output: Coordinates List
-    [-P[ointOfInterest]  Px                  (0.0       )Py                  (0.0       )Pz                  (0.0       )] :Optional  :PointOfInterest: Coordinates 
-    [-V[olumeOfInterest] MRC                 (NULL      )] :Optional  :VolumeOfInterest: MRC
-    [-C[outourLevel]     Contour             (0.0       )] :Optional  :ContourLevel for VolumeOfInterest: MRC
-    [-d[istance]         distance            (0.0       )] :Optional  :Distance [A]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: pdbFile
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output: Coordinates List
+    [-P[ointOfInterest]  Px                  (0.0       ).as(Real                ) 
+                         Py                  (0.0       ).as(Real                ) 
+                         Pz                  (0.0       ).as(Real                ) ] :Optional  :PointOfInterest: Coordinates 
+    [-V[olumeOfInterest] MRC                 (NULL      ).as(inFile              ) ] :Optional  :VolumeOfInterest: MRC
+    [-C[outourLevel]     Contour             (0.0       ).as(Real                ) ] :Optional  :ContourLevel for VolumeOfInterest: MRC
+    [-d[istance]         distance            (0.0       ).as(Real                ) ] :Optional  :Distance [A]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/pdbOneProteinGet.html b/doc/SmallTools/pdbOneProteinGet.html
index 2b41b61..39b67ac 100644
--- a/doc/SmallTools/pdbOneProteinGet.html
+++ b/doc/SmallTools/pdbOneProteinGet.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: pdbOneProteinGet
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-N[umber]           Num                 (0         )] :Optional  :Number[0->]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-N[umber]           Num                 (0         ).as(Integer             ) ] :Optional  :Number[0->]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/pdbPCA.html b/doc/SmallTools/pdbPCA.html
index cc39266..7a915a8 100644
--- a/doc/SmallTools/pdbPCA.html
+++ b/doc/SmallTools/pdbPCA.html
@@ -1 +1,21 @@
-/bin/bash: pdbPCA: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbPCA</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbPCA</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbPCA
+Options:
+    [-i[nput]            In                  (stdin     ).as(inFile              ) ] :Optional  :InputDataFile
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output: Result
+    [-o[utput]U[nit]     OutUnit             (NULL      ).as(outFile             ) ] :Optional  :Output: Unit Vector Array
+    [-o[utput]M[atrix3D] OutMat3D            (NULL      ).as(outFile             ) ] :Optional  :Output: Matrix3D from Unit Vector Array
+    [-o[utput]PDB        OutPDB              (NULL      ).as(outFile             ) ] :Optional  :Output: PDB rotated from Unit Vector Array
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/pdbProteinIDSet.html b/doc/SmallTools/pdbProteinIDSet.html
index 446d719..4851d2e 100644
--- a/doc/SmallTools/pdbProteinIDSet.html
+++ b/doc/SmallTools/pdbProteinIDSet.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: pdbProteinIDSet
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-ID                 ID                  (A         )] :Essential :ChainID
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-ID                 ID                  (A         ).as(Character           ) ] :Essential :ChainID
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/pdbRhoFit.html b/doc/SmallTools/pdbRhoFit.html
index 22baa00..9811048 100644
--- a/doc/SmallTools/pdbRhoFit.html
+++ b/doc/SmallTools/pdbRhoFit.html
@@ -1 +1,72 @@
-/bin/bash: pdbRhoFit: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbRhoFit</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbRhoFit</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbRhoFit
+Options:
+    [-i[nput]pdb[File]   InPdb               (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-i[nput]mrc[File]   InMrc               (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput of ]mrc    OutMrc              (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-o[utput of ]txt    OutTxt              (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-o[utput of ]par    OutPar              (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-o[utput of ]pdb    OutPDB              (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-xmin               xmin                (0         ).as(Real                ) ] :Optional  :xmin for fitting
+    [-xmax               xmax                (0         ).as(Real                ) ] :Optional  :xmax for fitting
+    [-xd[elta]           xDelta              (1         ).as(Real                ) ] :Optional  :delta x for fitting
+    [-ymin               ymin                (0         ).as(Real                ) ] :Optional  :ymin for fitting
+    [-ymax               ymax                (0         ).as(Real                ) ] :Optional  :ymax for fitting
+    [-yd[elta]           yDelta              (1         ).as(Real                ) ] :Optional  :delta y for fitting
+    [-zmin               zmin                (0         ).as(Real                ) ] :Optional  :zmin for fitting
+    [-zmax               zmax                (82        ).as(Real                ) ] :Optional  :zmax for fitting
+    [-zd[elta]           zDelta              (1         ).as(Real                ) ] :Optional  :delta z for fitting
+    [-E[uler]A[ngle]     EulerAngle          (ZOYS      ).as(String              ) ] :Optional  :Euler Angle for three-angle
+    [-phimin             phimin              (0         ).as(Real                ) ] :Optional  :phimin for fitting(degree)
+    [-phimax             phimax              (194       ).as(Real                ) ] :Optional  :phimax for fitting(degree)
+    [-phid[elta]         phiDelta            (2         ).as(Real                ) ] :Optional  :delta phi for fitting(degree)
+    [-psimin             psimin              (0         ).as(Real                ) ] :Optional  :psimin for fitting(degree)
+    [-psimax             psimax              (0         ).as(Real                ) ] :Optional  :psimax for fitting(degree)
+    [-psid[elta]         psiDelta            (2         ).as(Real                ) ] :Optional  :delta psi for fitting(degree)
+    [-thetamin           thetamin            (0         ).as(Real                ) ] :Optional  :thetamin for fitting(degree)
+    [-thetamax           thetamax            (0         ).as(Real                ) ] :Optional  :thetamax for fitting(degree)
+    [-thetad[elta]       thetaDelta          (2         ).as(Real                ) ] :Optional  :delta theta for fitting(degree)
+    [-n[ormalize]w[eight]normalizeWeight     (100000000.0).as(Real                ) ] :Optional  :weight for normalize
+    [-n[ormalize]C[ontour]normalizeContour    (0.0       ).as(Real                ) ] :Optional  :Contour Level for Normalize
+    [-I[nverse]                                                                    ] :Optional  :Black is High Density.
+    [-Zminus                                                                       ] :Optional  :Shift to -z
+    [-Tfactor                                                                      ] :Optional  :Consider T factor
+    [-T[ factor ]lim[it] Tlim                (60        ).as(Real                ) ] :Optional  :The atom will be neglected
+    [-Centre                                                                       ] :Optional  :Filament-axis is x=0, y=0
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-C[ontour]          contourLevel        (0.0       ).as(Real                ) ... ] :Variable  :ContourLevel
+
+
+Usage of pdbRhoFit:
+    -ipdb   : Filename of pdb file of atomic model
+    -imrc   : Filename of mrc file of contour map
+    -omrc   : Filename of mrc file of fitting results
+    -otxt   : Filename of text file of fitting results
+    -opar   : Filename of text file of fitting results
+    -opdb   : Filename of pdb file with a max score after fitting results
+    -zmin   : Initial value of z (should <= zmax)
+    -zmax   : Final value of z
+    -zd     : Delta z for fitting (should >0)
+    -phimin : Initial value of phi (should <= phimax; initial value of phi is 0)
+    -phimax : Final value of phi (should >0)
+    -phid   : Delta phi for fitting (should >0)
+    -C      : Contour level (variable and MUST be last option)
+    -Inverse: Protein has high density on the image
+    -Zminus : Atomic model shift to -z while fitting
+    -Tfactor: Consider temperature factor
+    -Tlim   : The atoms whose T factor is above Tlim will be neglected
+    -Centre : Filament-axis is x=0, y=0
+    -c      : Not used now
+    -m   0 : Count the atom number inside the contour.
+         1 : Add the densities of atoms.
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/pdbRhoFitCoiledCoil.html b/doc/SmallTools/pdbRhoFitCoiledCoil.html
index 13ab40d..1e54b59 100644
--- a/doc/SmallTools/pdbRhoFitCoiledCoil.html
+++ b/doc/SmallTools/pdbRhoFitCoiledCoil.html
@@ -1 +1,18 @@
-/bin/bash: pdbRhoFitCoiledCoil: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbRhoFitCoiledCoil</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbRhoFitCoiledCoil</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbRhoFitCoiledCoil
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/pdbRhoFitTm.html b/doc/SmallTools/pdbRhoFitTm.html
index a1c79f5..a0c20a4 100644
--- a/doc/SmallTools/pdbRhoFitTm.html
+++ b/doc/SmallTools/pdbRhoFitTm.html
@@ -1 +1,76 @@
-/bin/bash: pdbRhoFitTm: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbRhoFitTm</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbRhoFitTm</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbRhoFitTm
+Options:
+    [-i[nput]pdb[File]   InPdb               (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-i[nput]mrc[File]   InMrc               (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput of ]mrc    OutMrc              (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-Sx                 Sx                  (50        ).as(Real                ) ] :Essential :x of rotation axis
+    [-Sy                 Sy                  (110       ).as(Real                ) ] :Essential :y of rotation axis
+    [-Sz                 Sz                  (110       ).as(Real                ) ] :Essential :z of rotation axis
+    [-o[utput of ]txt    OutTxt              (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-o[utput of ]pdb    OutPDB              (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-xmin               xmin                (0         ).as(Real                ) ] :Optional  :xmin for fitting
+    [-xmax               xmax                (0         ).as(Real                ) ] :Optional  :xmax for fitting
+    [-xd[elta]           xDelta              (1         ).as(Real                ) ] :Optional  :delta x for fitting
+    [-ymin               ymin                (0         ).as(Real                ) ] :Optional  :ymin for fitting
+    [-ymax               ymax                (0         ).as(Real                ) ] :Optional  :ymax for fitting
+    [-yd[elta]           yDelta              (1         ).as(Real                ) ] :Optional  :delta y for fitting
+    [-zmin               zmin                (0         ).as(Real                ) ] :Optional  :zmin for fitting
+    [-zmax               zmax                (82        ).as(Real                ) ] :Optional  :zmax for fitting
+    [-zd[elta]           zDelta              (1         ).as(Real                ) ] :Optional  :delta z for fitting
+    [-E[uler]A[ngle]     EulerAngle          (ZOYS      ).as(String              ) ] :Optional  :Euler Angle for three-angle
+    [-phimin             phimin              (0         ).as(Real                ) ] :Optional  :phimin for fitting(degree)
+    [-phimax             phimax              (194       ).as(Real                ) ] :Optional  :phimax for fitting(degree)
+    [-phid[elta]         phiDelta            (2         ).as(Real                ) ] :Optional  :delta phi for fitting(degree)
+    [-psimin             psimin              (0         ).as(Real                ) ] :Optional  :psimin for fitting(degree)
+    [-psimax             psimax              (0         ).as(Real                ) ] :Optional  :psimax for fitting(degree)
+    [-psid[elta]         psiDelta            (2         ).as(Real                ) ] :Optional  :delta psi for fitting(degree)
+    [-thetamin           thetamin            (0         ).as(Real                ) ] :Optional  :thetamin for fitting(degree)
+    [-thetamax           thetamax            (0         ).as(Real                ) ] :Optional  :thetamax for fitting(degree)
+    [-thetad[elta]       thetaDelta          (2         ).as(Real                ) ] :Optional  :delta theta for fitting(degree)
+    [-n[ormalize]w[eight]normalizeWeight     (100000000.0).as(Real                ) ] :Optional  :weight for normalize
+    [-n[ormalize]C[ontour]normalizeContour    (0.0       ).as(Real                ) ] :Optional  :Contour Level for Normalize
+    [-I[nverse]                                                                    ] :Optional  :Black is High Density.
+    [-Zminus                                                                       ] :Optional  :Shift to -z
+    [-Tfactor                                                                      ] :Optional  :Consider T factor
+    [-T[ factor ]lim[it] Tlim                (60        ).as(Real                ) ] :Optional  :The atom will be neglected
+    [-Centre                                                                       ] :Optional  :Filament-axis is x=0, y=0
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-C[ontour]          contourLevel        (0.0       ).as(Real                ) ... ] :Variable  :ContourLevel
+
+
+Usage of pdbRhoFitTm:
+    -ipdb   : Filename of pdb file of atomic model
+    -imrc   : Filename of mrc file of contour map
+    -omrc   : Filename of mrc file of fitting results
+    -otxt   : Filename of text file of fitting results
+    -opdb   : Filename of pdb file with a max score after fitting results
+    -zmin   : Initial value of z (should <= zmax)
+    -zmax   : Final value of z
+    -zd     : Delta z for fitting (should >0)
+    -phimin : Initial value of phi (should <= phimax; initial value of phi is 0)
+    -phimax : Final value of phi (should >0)
+    -phid   : Delta phi for fitting (should >0)
+    -C      : Contour level (variable and MUST be last option)
+    -Inverse: Protein has high density on the image
+    -Sx	    : x of rotation axis
+    -Sy     : y of rotation axis
+    -Sz     : z of rotation axis
+    -Zminus : Atomic model shift to -z while fitting
+    -Tfactor: Consider temperature factor
+    -Tlim   : The atoms whose T factor is above Tlim will be neglected
+    -Centre : Filament-axis is x=0, y=0
+    -c      : Not used now
+    -m   0 : Count the atom number inside the contour.
+         1 : Add the densities of atoms.
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/pdbRotation.html b/doc/SmallTools/pdbRotation.html
index 5e1a16e..e6ab3b8 100644
--- a/doc/SmallTools/pdbRotation.html
+++ b/doc/SmallTools/pdbRotation.html
@@ -1 +1,39 @@
-/bin/bash: pdbRotation: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbRotation</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbRotation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbRotation
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-ZXY                ZXYrotx             (0.0       ).as(Real                ) 
+                         ZXYroty             (0.0       ).as(Real                ) 
+                         ZXYrotz             (0.0       ).as(Real                ) ] :Optional  :ZXY*pdb: rotz(rotz)rotx(rotx)roty(roty) 
+    [-ZYX                ZYXrotx             (0.0       ).as(Real                ) 
+                         ZYXroty             (0.0       ).as(Real                ) 
+                         ZYXrotz             (0.0       ).as(Real                ) ] :Optional  :ZYX*pdb: rotz(rotz)roty(roty)rotx(rotx) 
+    [-YXZ                YXZrotx             (0.0       ).as(Real                ) 
+                         YXZroty             (0.0       ).as(Real                ) 
+                         YXZrotz             (0.0       ).as(Real                ) ] :Optional  :YXZ*pdb: roty(roty)rotx(rotx)rotz(rotz) 
+    [-XYZ                XYZrotx             (0.0       ).as(Real                ) 
+                         XYZroty             (0.0       ).as(Real                ) 
+                         XYZrotz             (0.0       ).as(Real                ) ] :Optional  :XYZ*pdb: rotx(rotx)roty(roty)rotz(rotz) 
+    [-E[uler]A[ngle]     RotMode             (YOYS      ).as(String              ) 
+                         Rot1                (0.0       ).as(Real                ) 
+                         Rot2                (0.0       ).as(Real                ) 
+                         Rot3                (0.0       ).as(Real                ) ] :Optional  :EA*pdb: EA=rot(rot3)rot(rot2)rot(rot1) 
+    [-cuda               cudaDeviceID        (0         ).as(Integer             ) ] :Optional  :UseCuda
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+
+ZXY : y-axis -> x-axis -> z->axis 
+ZYX : x-axis -> y-axis -> z->axis 
+ZXY -> ZYX -> XYZ ->YXZ -> EU
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/pdbSecondaryStructurePrint.html b/doc/SmallTools/pdbSecondaryStructurePrint.html
index 8e620b4..4052b0e 100644
--- a/doc/SmallTools/pdbSecondaryStructurePrint.html
+++ b/doc/SmallTools/pdbSecondaryStructurePrint.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: pdbSecondaryStructurePrint
 Options:
-    [-i[nput]            In                  (stdin     )] :Optional  :Input: pdb
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output: pdb
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (stdin     ).as(inFile              ) ] :Optional  :Input: pdb
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output: pdb
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/pdbShapeFit.html b/doc/SmallTools/pdbShapeFit.html
index 91488a3..8ea14d0 100644
--- a/doc/SmallTools/pdbShapeFit.html
+++ b/doc/SmallTools/pdbShapeFit.html
@@ -1 +1,73 @@
-/bin/bash: pdbShapeFit: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbShapeFit</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbShapeFit</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbShapeFit
+Options:
+    [-i[nput]pdb[File]   InPDB               (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-i[nput]mrc[File]   InMRC               (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-C[ontour]          Contour             (0.0       ).as(Real                ) ] :Essential :Contour
+    [-C[ontour]M[ode]    ContourMode         (0         ).as(Integer             ) ] :Optional  :ContourMode: refer to mrcImageContourSurfaceCreate
+    [-o[utput of ]mrc    OutMRC              (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-o[utput of ]txt    OutTxt              (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-o[utput of ]pdb    OutPDB              (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-xmin               xmin                (0         ).as(Real                ) ] :Optional  :xmin for fitting
+    [-xmax               xmax                (0         ).as(Real                ) ] :Optional  :xmax for fitting
+    [-xd[elta]           xDelta              (1         ).as(Real                ) ] :Optional  :delta x for fitting
+    [-ymin               ymin                (0         ).as(Real                ) ] :Optional  :ymin for fitting
+    [-ymax               ymax                (0         ).as(Real                ) ] :Optional  :ymax for fitting
+    [-yd[elta]           yDelta              (1         ).as(Real                ) ] :Optional  :delta y for fitting
+    [-zmin               zmin                (0         ).as(Real                ) ] :Optional  :zmin for fitting
+    [-zmax               zmax                (82        ).as(Real                ) ] :Optional  :zmax for fitting
+    [-zd[elta]           zDelta              (1         ).as(Real                ) ] :Optional  :delta z for fitting
+    [-E[uler]A[ngle]     EulerAngle          (ZOYS      ).as(String              ) ] :Optional  :Euler Angle for three-angle
+    [-phimin             phimin              (0         ).as(Real                ) ] :Optional  :phimin for fitting(degree)
+    [-phimax             phimax              (194       ).as(Real                ) ] :Optional  :phimax for fitting(degree)
+    [-phid[elta]         phiDelta            (2         ).as(Real                ) ] :Optional  :delta phi for fitting(degree)
+    [-psimin             psimin              (0         ).as(Real                ) ] :Optional  :psimin for fitting(degree)
+    [-psimax             psimax              (0         ).as(Real                ) ] :Optional  :psimax for fitting(degree)
+    [-psid[elta]         psiDelta            (2         ).as(Real                ) ] :Optional  :delta psi for fitting(degree)
+    [-thetamin           thetamin            (0         ).as(Real                ) ] :Optional  :thetamin for fitting(degree)
+    [-thetamax           thetamax            (0         ).as(Real                ) ] :Optional  :thetamax for fitting(degree)
+    [-thetad[elta]       thetaDelta          (2         ).as(Real                ) ] :Optional  :delta theta for fitting(degree)
+    [-P[DB]C[ontour]M[ode]surfaceMode         (0         ).as(Integer             ) ] :Optional  :PDB SurfaceMode: refer to pdbSurface
+    [-order              order               (1.7       ).as(Real                ) ] :Optional  :order: refer to pdbSurface
+    [-refine             refine              (2         ).as(Integer             ) ] :Optional  :refine: refer to pdbSurface
+    [-size               size                (3         ).as(Integer             ) ] :Optional  :size: refer to pdbSurface
+    [-weight             weight              (100       ).as(Real                ) ] :Optional  :weight: refer to pdbSurface
+    [-mergin             mergin              (3.0       ).as(Real                ) ] :Optional  :mergin: refer to pdbSurface
+    [-thres              thresHold           (0.0       ).as(Real                ) ] :Optional  :threshold: refer to pdbSurface
+    [-I[nverse]                                                                    ] :Optional  :Black is High Density.
+    [-Centre                                                                       ] :Optional  :Filament-axis is x=0, y=0
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+    -ipdb   : Filename : An atomic model to be fitted (PDB) 
+    -imrc   : Filename : 3-D density map (mrc-formated) 
+    -omrc   : Filename : fitting score map (MRC) 
+                         z=0: a max-score map of an phi-z plane which includes a max score point.
+                              The max score mean a maximum score in all x-y-psi-theta plane with specific values of phi and z.
+                         z=1: a max-score map of an psi-theta plane which includes a max score point.
+                              The max score mean a maximum score in all x-y plane with specific values of psi, theta, phi and z.
+                         z=2: a score map of an x-y plane which includes a max score point.
+    -otxt   : Filename : fitting results (Text)
+    -opdb   : Filename : An atomic model with a maximum score after fitting 
+    -x|y|zmin   : Initial value of z (should <= zmax)
+    -x|y|zmax   : Final   value of z
+    -x|y|zd     : Delta z for fitting (should !=0)
+    -phi|psi|thetamin : Initial value of phi (should <= phimax; initial value of phi is 0)
+    -phi|psi|thetamax : Final value of phi  (should !=0)
+    -phi|psi|thetad   : Delta phi for fitting (should >0)
+    -C      : Contour level of map file
+    -Inverse: Protein has high density on the image
+    -Centre : Filament-axis in an inPDBFile is along the line of x=0, y=0
+    -EA     : Euler Angle Set : ZOYS: z -> y -> x 
+    -c      : Not used now
+    -m   0 : Count the atom number inside the contour.
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/pdbSurface.html b/doc/SmallTools/pdbSurface.html
index 50f06e4..a6e1f94 100644
--- a/doc/SmallTools/pdbSurface.html
+++ b/doc/SmallTools/pdbSurface.html
@@ -8,17 +8,17 @@
 <PRE>
 Usage: pdbSurface
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: pdbFile
-    [-o[utput]           Out                 (NULL      )] :Essential :Output: pdbFile
-    [-order              order               (1.7       )] :Optional  :Order: [A]
-    [-refine             refine              (2         )] :Optional  :Refine: Meshsize = Order/Refine
-    [-size               size                (3         )] :Optional  :Refine: Shell thickness = Order/Refine*Size
-    [-weight             weight              (100.0     )] :Optional  :Weight
-    [-mergin             mergin              (3.0       )] :Optional  :SearchArea
-    [-thres              thresHold           (0.0       )] :Optional  :thresHold
-    [-densityMode        DensityMode         (0         )] :Optional  :DensityMode
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: pdbFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output: pdbFile
+    [-order              order               (1.7       ).as(Real                ) ] :Optional  :Order: [A]
+    [-refine             refine              (2         ).as(Integer             ) ] :Optional  :Refine: Meshsize = Order/Refine
+    [-size               size                (3         ).as(Integer             ) ] :Optional  :Refine: Shell thickness = Order/Refine*Size
+    [-weight             weight              (100.0     ).as(Real                ) ] :Optional  :Weight
+    [-mergin             mergin              (3.0       ).as(Real                ) ] :Optional  :SearchArea
+    [-thres              thresHold           (0.0       ).as(Real                ) ] :Optional  :thresHold
+    [-densityMode        DensityMode         (0         ).as(Integer             ) ] :Optional  :DensityMode
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/pdbTempFactorSet.html b/doc/SmallTools/pdbTempFactorSet.html
index a1154ff..fd03bee 100644
--- a/doc/SmallTools/pdbTempFactorSet.html
+++ b/doc/SmallTools/pdbTempFactorSet.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: pdbTempFactorSet
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: pdbFile
-    [-r[eference]        Ref                 (stdin     )] :Optional  :Input: selectionFile
-    [-o[utput]           Out                 (NULL      )] :Essential :Output: pdbFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: pdbFile
+    [-r[eference]        Ref                 (stdin     ).as(inFile              ) ] :Optional  :Input: selectionFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output: pdbFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/pdbTrans.html b/doc/SmallTools/pdbTrans.html
index 4d26a75..7305b20 100644
--- a/doc/SmallTools/pdbTrans.html
+++ b/doc/SmallTools/pdbTrans.html
@@ -1 +1,32 @@
-/bin/bash: pdbTrans: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbTrans</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbTrans</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbTrans
+Options:
+    [-i[nput]            inFile              (NULL      ).as(inFile              ) ] :Essential :Input: DataFile
+    [-o[utput]           outFile             (NULL      ).as(outFile             ) ] :Essential :Output: DataFile
+    [-M[atrix]           matFile             (NULL      ).as(inFile              ) ] :Optional  :Input: MatrixFile[4][4]
+    [-E[uler]A[ngle]     RotMode             (YOYS      ).as(String              ) 
+                         Rot1                (0.0       ).as(Real                ) 
+                         Rot2                (0.0       ).as(Real                ) 
+                         Rot3                (0.0       ).as(Real                ) ] :Optional  :Input: 
+    [-cuda               cudaDeviceID        (0         ).as(Integer             ) ] :Optional  :cuda
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+>>> Matrix3D File Format y = Ax + b<<<
+a11 a21 a31 : Rotation Array : y=Ax
+a12 a22 a32 
+a13 a23 a33 
+b1  b2  b3  : Translation Array : y = x + b
+--- Attention ---
+If both options of -M and -EA are set, 
+    first, translation and rotation by -M will be performed 
+    then,  rotation by -EA will be done.
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/pdbTwoProteinFit.html b/doc/SmallTools/pdbTwoProteinFit.html
index 3b7dbb2..204e3c2 100644
--- a/doc/SmallTools/pdbTwoProteinFit.html
+++ b/doc/SmallTools/pdbTwoProteinFit.html
@@ -1 +1,30 @@
-/bin/bash: pdbTwoProteinFit: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbTwoProteinFit</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbTwoProteinFit</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbTwoProteinFit
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-i[nput]res[idue]   InResidue           (NULL      ).as(inFile              ) ] :Optional  :ResidueInformationOfInputData
+    [-i[nput]sel[ectResidue]SelectIn            (NULL      ).as(outFile             ) ] :Optional  :Output: Selected residue of in after fitting
+    [-r[ef]              Ref                 (NULL      ).as(inFile              ) ] :Essential :ReferenceDataFile
+    [-r[ef]res[idue]     RefResidue          (NULL      ).as(inFile              ) ] :Optional  :ResidueInfomationOfReferenceData
+    [-r[ef]sel[ectResidue]SelectRef           (NULL      ).as(outFile             ) ] :Optional  :Output: Selected residue of after fitting
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-o[utput]Matrix     Matrix              (stdout    ).as(outFile             ) ] :Optional  :OutputMatrix
+    [-o[utput]Param      Param               (stdout    ).as(outFile             ) ] :Optional  :OutputParam
+    [-o[utput]Dis[tance] outDis              (stdout    ).as(outFile             ) ] :Optional  :Output: PDB Distance as Temp
+    [-o[utput]Dis[tance]2outDis2             (stdout    ).as(outFile             ) ] :Optional  :Output: Distance List for Ca
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+>>>> Input and Reference File Format<<<<
+ResidueNumberToBeFitted
+...
+If |, all residules are sellected till the residue in the next line
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/pdbWaterAdd.html b/doc/SmallTools/pdbWaterAdd.html
index d58a656..618f04e 100644
--- a/doc/SmallTools/pdbWaterAdd.html
+++ b/doc/SmallTools/pdbWaterAdd.html
@@ -8,15 +8,17 @@
 <PRE>
 Usage: pdbWaterAdd
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-d[ensity]          Density             (55.55555  )] :Optional  :[M]: Density of Water
-    [-r[adius]           Radius              (100.      )] :Optional  :[A]: Radius of Water Volume: Sphere, Cylinder
-    [-height             Height              (100.      )] :Optional  :[A]: Height of Water Volume : Cylinder
-    [-cube               X                   (100.      )Y                   (100.      )Z                   (100.      )] :Optional  :[A]: Cube
-    [-edge               Edge                (3.        )] :Optional  :layer number: Edge
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-d[ensity]          Density             (55.55555  ).as(Real                ) ] :Optional  :[M]: Density of Water
+    [-r[adius]           Radius              (100.      ).as(Real                ) ] :Optional  :[A]: Radius of Water Volume: Sphere, Cylinder
+    [-height             Height              (100.      ).as(Real                ) ] :Optional  :[A]: Height of Water Volume : Cylinder
+    [-cube               X                   (100.      ).as(Real                ) 
+                         Y                   (100.      ).as(Real                ) 
+                         Z                   (100.      ).as(Real                ) ] :Optional  :[A]: Cube
+    [-edge               Edge                (3.        ).as(Integer             ) ] :Optional  :layer number: Edge
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 ----- Mode: -m  -----
 -m 0 :  sphere   
diff --git a/doc/SmallTools/pointAffineTransform.html b/doc/SmallTools/pointAffineTransform.html
index 59cdfcf..0d7f637 100644
--- a/doc/SmallTools/pointAffineTransform.html
+++ b/doc/SmallTools/pointAffineTransform.html
@@ -8,12 +8,19 @@
 <PRE>
 Usage: pointAffineTransform
 Options:
-    [-p[oint]            X                   (0         )Y                   (0         )Z                   (0         )] :Essential :Input: Points
-    [-Euler              Euler               (YOYS      )Rot1                (0         )Rot2                (0         )Rot3                (0         )] :Optional  :Input: EuerAngle
-    [-shift              dX                  (0         )dY                  (0         )dZ                  (0         )] :Optional  :Input: shift[pixel]
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-p[oint]            X                   (0         ).as(Real                ) 
+                         Y                   (0         ).as(Real                ) 
+                         Z                   (0         ).as(Real                ) ] :Essential :Input: Points
+    [-Euler              Euler               (YOYS      ).as(String              ) 
+                         Rot1                (0         ).as(Real                ) 
+                         Rot2                (0         ).as(Real                ) 
+                         Rot3                (0         ).as(Real                ) ] :Optional  :Input: EuerAngle
+    [-shift              dX                  (0         ).as(Real                ) 
+                         dY                  (0         ).as(Real                ) 
+                         dZ                  (0         ).as(Real                ) ] :Optional  :Input: shift[pixel]
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/pointsSetToPDB.html b/doc/SmallTools/pointsSetToPDB.html
index 3b652c9..7aeaf77 100644
--- a/doc/SmallTools/pointsSetToPDB.html
+++ b/doc/SmallTools/pointsSetToPDB.html
@@ -1 +1,18 @@
-/bin/bash: pointsSetToPDB: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pointsSetToPDB</TITLE>
+</HEAD>
+<BODY>
+<H1>pointsSetToPDB</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pointsSetToPDB
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: PointsSet
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output: PDB
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/probabilityDensityFunction.html b/doc/SmallTools/probabilityDensityFunction.html
new file mode 100644
index 0000000..03a3a9f
--- /dev/null
+++ b/doc/SmallTools/probabilityDensityFunction.html
@@ -0,0 +1,18 @@
+<HTML>
+<HEAD>
+<TITLE>probabilityDensityFunction</TITLE>
+</HEAD>
+<BODY>
+<H1>probabilityDensityFunction</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: probabilityDensityFunction
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/psFileMerge.html b/doc/SmallTools/psFileMerge.html
index 78702ff..e2f5ad9 100644
--- a/doc/SmallTools/psFileMerge.html
+++ b/doc/SmallTools/psFileMerge.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: psFileMerge
 Options:
-    [-i[nput file]1      In1                 (NULL      )] :Essential :InputDataFile1
-    [-i[nput file]2      In2                 (NULL      )] :Essential :InputDataFile2
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput file]1      In1                 (NULL      ).as(inFile              ) ] :Essential :InputDataFile1
+    [-i[nput file]2      In2                 (NULL      ).as(inFile              ) ] :Essential :InputDataFile2
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/psFilePageMerge.html b/doc/SmallTools/psFilePageMerge.html
index 75f961c..2343c49 100644
--- a/doc/SmallTools/psFilePageMerge.html
+++ b/doc/SmallTools/psFilePageMerge.html
@@ -8,11 +8,11 @@
 <PRE>
 Usage: psFilePageMerge
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-p[age]             Page                (2         )] :Optional  :PageNumberToBeMerged
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-p[age]             Page                (2         ).as(Integer             ) ] :Optional  :PageNumberToBeMerged
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/randomNormalGet.html b/doc/SmallTools/randomNormalGet.html
index 922f59e..abdd892 100644
--- a/doc/SmallTools/randomNormalGet.html
+++ b/doc/SmallTools/randomNormalGet.html
@@ -8,13 +8,13 @@
 <PRE>
 Usage: randomNormalGet
 Options:
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-O[utput]           OutMRC              (NULL      )] :Optional  :OutputDataFile(mrcImage)
-    [-n                  N                   (100       )] :Optional  :number
-    [-a[verage]          Ave                 (0.0       )] :Optional  :average
-    [-sd                 SD                  (1.0       )] :Optional  :SD
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-O[utput]           OutMRC              (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile(mrcImage)
+    [-n                  N                   (100       ).as(Integer             ) ] :Optional  :number
+    [-a[verage]          Ave                 (0.0       ).as(Real                ) ] :Optional  :average
+    [-sd                 SD                  (1.0       ).as(Real                ) ] :Optional  :SD
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/randomUniformGet.html b/doc/SmallTools/randomUniformGet.html
index 3c40701..105101c 100644
--- a/doc/SmallTools/randomUniformGet.html
+++ b/doc/SmallTools/randomUniformGet.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: randomUniformGet
 Options:
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-min                min                 (0.0       )] :Optional  :Minimum of Number
-    [-max                max                 (1.0       )] :Optional  :Maximum of Number
-    [-n[umber]           num                 (1         )] :Optional  :Number
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile
+    [-min                min                 (0.0       ).as(Real                ) ] :Optional  :Minimum of Number
+    [-max                max                 (1.0       ).as(Real                ) ] :Optional  :Maximum of Number
+    [-n[umber]           num                 (1         ).as(Integer             ) ] :Optional  :Number
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/rasmonyo.html b/doc/SmallTools/rasmonyo.html
index 3807fb5..ad4f032 100644
--- a/doc/SmallTools/rasmonyo.html
+++ b/doc/SmallTools/rasmonyo.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: rasmonyo
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/tgaInfo.html b/doc/SmallTools/tgaInfo.html
index 4f9d86a..45bea64 100644
--- a/doc/SmallTools/tgaInfo.html
+++ b/doc/SmallTools/tgaInfo.html
@@ -8,10 +8,10 @@
 <PRE>
 Usage: tgaInfo
 Options:
-    [-i[nput]            In                  (stdin     )] :Optional  :Input: tgaFile or Pipe
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output: ASCII
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (stdin     ).as(inFile              ) ] :Optional  :Input: tgaFile or Pipe
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output: ASCII
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/tiff2mrc.html b/doc/SmallTools/tiff2mrc.html
index 7e09f0f..3e4f47f 100644
--- a/doc/SmallTools/tiff2mrc.html
+++ b/doc/SmallTools/tiff2mrc.html
@@ -8,24 +8,24 @@
 <PRE>
 Usage: tiff2mrc
 Options:
-    [-i[nput]            inFile              (NULL      )] :Essential :InputDataFile
-    [-o[utput]           outFile             (NULL      )] :Essential :OutputDataFile
-    [-r[esolution]       Resolution          (2.5       )] :Optional  :Resolution[A]
-    [-t[ime]             time                (1.0       )] :Optional  :x OptimalTime
-    [-d[irnum]           dirnum              (0         )] :Optional  :tiffDirectoryNumber
-    [-I[nverse]          ] :Optional  :Black<->White
-    [-Signed             ] :Optional  :Original image is Signed or Not: Default unsigned
-    [-Offset             Offset              (0.0       )] :Optional  :OffsetValue
-    [-Max                Max                 (16        )] :Optional  :MaxValue:2^Max
-    [-Min                Min                 (1         )] :Optional  :MinValue:2^Min: without 0
-    [-realMin            realMin             (0.0       )] :Optional  :Real MinValue
-    [-realMax            realMax             (0.0       )] :Optional  :Real MaxValue
-    [-realMaxBit         realMaxBit          (14        )] :Optional  :Real MaxValue Bit
-    [-sin                sinFile             (NULL      )] :Optional  :sin file from Zeiss
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-S[hrink]           Shrink              (8         )] :Optional  :ShrinkMode
-    [-M[ode]             Mode                (0         )] :Optional  :Mode: mrcMode: Def: if -m 0, -M 0. if -m 1 -M 2
-    [-m[ode]             mode                (0         )] :Optional  :Mode: 0 (Direct), 1(Log10(65535/data))
+    [-i[nput]            inFile              (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           outFile             (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-r[esolution]       Resolution          (2.5       ).as(Real                ) ] :Optional  :Resolution[A]
+    [-t[ime]             time                (1.0       ).as(Real                ) ] :Optional  :x OptimalTime
+    [-d[irnum]           dirnum              (0         ).as(Integer             ) ] :Optional  :tiffDirectoryNumber
+    [-I[nverse]                                                                    ] :Optional  :Black<->White
+    [-Signed                                                                       ] :Optional  :Original image is Signed or Not: Default unsigned
+    [-Offset             Offset              (0.0       ).as(Real                ) ] :Optional  :OffsetValue
+    [-Max                Max                 (16        ).as(Real                ) ] :Optional  :MaxValue:2^Max
+    [-Min                Min                 (1         ).as(Real                ) ] :Optional  :MinValue:2^Min: without 0
+    [-realMin            realMin             (0.0       ).as(Real                ) ] :Optional  :Real MinValue
+    [-realMax            realMax             (0.0       ).as(Real                ) ] :Optional  :Real MaxValue
+    [-realMaxBit         realMaxBit          (14        ).as(Real                ) ] :Optional  :Real MaxValue Bit
+    [-sin                sinFile             (NULL      ).as(inFile              ) ] :Optional  :sin file from Zeiss
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-S[hrink]           Shrink              (8         ).as(Integer             ) ] :Optional  :ShrinkMode
+    [-M[ode]             Mode                (0         ).as(Integer             ) ] :Optional  :Mode: mrcMode: Def: if -m 0, -M 0. if -m 1 -M 2
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode: 0 (Direct), 1(Log10(65535/data))
 ---- mode ----
 0x0000000f bits: Direct or Log
 0x000000f0 bits: Which Color
diff --git a/doc/SmallTools/tiltInfoDetermine.html b/doc/SmallTools/tiltInfoDetermine.html
index 00d3e50..b07e8c2 100644
--- a/doc/SmallTools/tiltInfoDetermine.html
+++ b/doc/SmallTools/tiltInfoDetermine.html
@@ -8,12 +8,12 @@
 <PRE>
 Usage: tiltInfoDetermine
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-defocusIn[put]     defocus             (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-M[ag]              mag                 (2.4       )] :Optional  :Mag
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-defocusIn[put]     defocus             (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-M[ag]              mag                 (2.4       ).as(Real                ) ] :Optional  :Mag
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/vector2pdb.html b/doc/SmallTools/vector2pdb.html
index c391f2f..7957d96 100644
--- a/doc/SmallTools/vector2pdb.html
+++ b/doc/SmallTools/vector2pdb.html
@@ -8,18 +8,27 @@
 <PRE>
 Usage: vector2pdb
 Options:
-    [-v[ector]           vx                  (1         )vy                  (0         )vz                  (0         )] :Optional  :Input: vector
-    [-polar[vector]      phi                 (0         )theta               (0         )] :Optional  :Input: vector[degree]
-    [-polarz[axis]       zx                  (0         )zy                  (0         )zz                  (1         )] :Optional  :Input: z-axis for polar
-    [-polarx[axis]       xx                  (1         )xy                  (0         )xz                  (0         )] :Optional  :Input: x-axis for polar
-    [-ori[ginal]         sx                  (0         )sy                  (3         )sz                  (0         )] :Optional  :Input: origin
-    [-step               step                (1.6       )] :Optional  :Input: step [A]
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output: pdbFile
-    [-n                  n                   (20        )] :Optional  :Input: Number Of CA
-    [-ID                 ID                  (A         )] :Optional  :Input: Chain ID
-    [-Res                Res                 (GLY       )] :Optional  :Input: Chain ID
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-v[ector]           vx                  (1         ).as(Real                ) 
+                         vy                  (0         ).as(Real                ) 
+                         vz                  (0         ).as(Real                ) ] :Optional  :Input: vector
+    [-polar[vector]      phi                 (0         ).as(Real                ) 
+                         theta               (0         ).as(Real                ) ] :Optional  :Input: vector[degree]
+    [-polarz[axis]       zx                  (0         ).as(Real                ) 
+                         zy                  (0         ).as(Real                ) 
+                         zz                  (1         ).as(Real                ) ] :Optional  :Input: z-axis for polar
+    [-polarx[axis]       xx                  (1         ).as(Real                ) 
+                         xy                  (0         ).as(Real                ) 
+                         xz                  (0         ).as(Real                ) ] :Optional  :Input: x-axis for polar
+    [-ori[ginal]         sx                  (0         ).as(Real                ) 
+                         sy                  (3         ).as(Real                ) 
+                         sz                  (0         ).as(Real                ) ] :Optional  :Input: origin
+    [-step               step                (1.6       ).as(Real                ) ] :Optional  :Input: step [A]
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Optional  :Output: pdbFile
+    [-n                  n                   (20        ).as(Integer             ) ] :Optional  :Input: Number Of CA
+    [-ID                 ID                  (A         ).as(Character           ) ] :Optional  :Input: Chain ID
+    [-Res                Res                 (GLY       ).as(String              ) ] :Optional  :Input: Chain ID
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/vectorImageNearestNeighborMethod.html b/doc/SmallTools/vectorImageNearestNeighborMethod.html
index d7fd4e8..258c0ef 100644
--- a/doc/SmallTools/vectorImageNearestNeighborMethod.html
+++ b/doc/SmallTools/vectorImageNearestNeighborMethod.html
@@ -9,15 +9,15 @@ Program Start
 <PRE>
 Usage: vectorImageNearestNeighborMethod
 Options:
-    [-i[nput]            InList              (NULL      )] :Essential :Input: filelist
-    [-O[utput]           Outclassification   (NULL      )] :Essential :Output: ClassificationDataFile
-    [-o[utput]c[lassification]i[ntegration]r[ate]OutClassificationIntegrationRate(NULL      )] :Optional  :OutputClassificationIntegrationRate: classificationIntegrationRatefile
-    [-o[utput]d[istance] OutDistance         (NULL      )] :Optional  :OutputDistance: distancefile
-    [-o[utput]d[istance]r[ate]OutDistanceRate     (NULL      )] :Optional  :OutputDistanceRate: distanceRatefile
-    [-o[utput]u[pper]d[istance]n[umberOfClasses]OutUpperDistanceRate(NULL      )] :Optional  :OutputUpperDistanceNumberOfClasses: upperDistanceRatefile
-    [-o[utput]u[pper]d[istance]c[lassificationDatafile]OutClassName        (NULL      )] :Optional  :OutputUpperDistanceClassificationDatafile: ClassificationDatafile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            InList              (NULL      ).as(inFileListNoOpen    ) ] :Essential :Input: filelist
+    [-O[utput]           Outclassification   (NULL      ).as(outFile             ) ] :Essential :Output: ClassificationDataFile
+    [-o[utput]c[lassification]i[ntegration]r[ate]OutClassificationIntegrationRate(NULL      ).as(outFile             ) ] :Optional  :OutputClassificationIntegrationRate: classificationIntegrationRatefile
+    [-o[utput]d[istance] OutDistance         (NULL      ).as(outFile             ) ] :Optional  :OutputDistance: distancefile
+    [-o[utput]d[istance]r[ate]OutDistanceRate     (NULL      ).as(outFile             ) ] :Optional  :OutputDistanceRate: distanceRatefile
+    [-o[utput]u[pper]d[istance]n[umberOfClasses]OutUpperDistanceRate(NULL      ).as(outFile             ) ] :Optional  :OutputUpperDistanceNumberOfClasses: upperDistanceRatefile
+    [-o[utput]u[pper]d[istance]c[lassificationDatafile]OutClassName        (NULL      ).as(outFile             ) ] :Optional  :OutputUpperDistanceClassificationDatafile: ClassificationDatafile
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 </PRE>
 </BODY>