From 159fdcd23501c2ecdac036404a4018fc902655a5 Mon Sep 17 00:00:00 2001
From: Takuo Yasunaga <yasunaga@bio.kyutech.ac.jp>
Date: Tue, 14 Oct 2014 04:50:53 +0900
Subject: [PATCH] Modified: doc

---
 doc/Objects/.list.html                             |  16 +-
 doc/Objects/Cluster.html                           |  10 --
 doc/Objects/Contour.html                           |  10 +-
 doc/Objects/Crystal.html                           |  21 +--
 doc/Objects/Map2D.html                             |   2 -
 doc/Objects/Matrix3D.html                          |  31 ++--
 doc/Objects/Memory.html                            |  19 +--
 doc/Objects/PVM.html                               |   2 -
 doc/Objects/Random.html                            |   6 -
 doc/Objects/Socket.html                            |   4 -
 doc/Objects/SpecialNumber.html                     |   2 -
 doc/Objects/String.html                            |   8 -
 doc/Objects/Vector.html                            |   6 -
 doc/Objects/Vector.html.BACKUP.13752.html          | 110 +++++++++++++
 doc/Objects/Vector.html.BACKUP.13830.html          | 110 +++++++++++++
 doc/Objects/Vector.html.BASE.13752.html            | 106 +++++++++++++
 doc/Objects/Vector.html.BASE.13830.html            | 106 +++++++++++++
 doc/Objects/Vector.html.LOCAL.13752.html           | 106 +++++++++++++
 doc/Objects/Vector.html.LOCAL.13830.html           | 106 +++++++++++++
 doc/Objects/Vector.html.REMOTE.13752.html          | 106 +++++++++++++
 doc/Objects/Vector.html.REMOTE.13830.html          | 106 +++++++++++++
 doc/Objects/alsa.html                              |   2 -
 doc/Objects/avsFile.html                           |   6 -
 doc/Objects/bmpFile.html                           | 122 +++++++++++++++
 doc/Objects/ctfInfo.html                           |  36 +----
 doc/Objects/dmFile.html                            | 118 ++++++++++++++
 doc/Objects/dsn6File.html                          |   4 -
 doc/Objects/emData.html                            |   2 -
 doc/Objects/eosFunc.html                           |  54 +++++++
 doc/Objects/eosPThread.html                        |  84 ++++++++++
 doc/Objects/eosPoint.html                          |  84 ++++++++++
 doc/Objects/gifFile.html                           |  14 --
 doc/Objects/hf2000.html                            | 118 ++++++++++++++
 doc/Objects/khorosData.html                        |   2 -
 doc/Objects/largeIP.html                           |   4 -
 doc/Objects/llData.html                            |  88 -----------
 doc/Objects/ltlgData.html                          |  14 --
 doc/Objects/mapFile.html                           |   2 -
 doc/Objects/mrcImage.html                          | 172 +++++++++++++++++++--
 doc/Objects/openGL.html                            | 104 -------------
 doc/Objects/pdbFile.html                           |  33 +---
 doc/Objects/psFile.html                            |  22 ---
 doc/Objects/tgaFile.html                           |   6 -
 doc/Objects/transform.html                         |  62 --------
 doc/SmallTools/.smallToolList.html                 |  30 ++++
 doc/SmallTools/CheckOrientationByDegree.html       |  25 +--
 doc/SmallTools/Display2.html                       |   2 +-
 doc/SmallTools/anglediffchk.html                   |  17 +-
 doc/SmallTools/array2mrc.html                      |  13 ++
 doc/SmallTools/bmp2mrc.html                        |  26 ++++
 doc/SmallTools/bmpFileInfo.html                    |  18 +++
 doc/SmallTools/calcCommonLine.html                 |  21 +--
 doc/SmallTools/commonLinesSearchByVoting.html      |  55 +------
 doc/SmallTools/ctfDisplay.html                     |   1 +
 doc/SmallTools/dmInfo.html                         |  18 +++
 doc/SmallTools/eosPointProjector.html              |  35 +++++
 doc/SmallTools/eosPointRotation.html               |  31 ++++
 doc/SmallTools/eosPointTracker.html                |  38 +++++
 doc/SmallTools/hf2000Init.html                     |  20 +--
 doc/SmallTools/hf2000LenzCurrent.html              |  23 +--
 doc/SmallTools/hf2000SpecimenPosition.html         |  24 +--
 doc/SmallTools/llExtract.html                      |  45 +++---
 doc/SmallTools/marker2Dto3DEstimator.html          |  30 ++++
 doc/SmallTools/mrc2Dto3D.html                      |  55 ++++---
 doc/SmallTools/mrc2hdf.html                        |   2 +-
 doc/SmallTools/mrc2mrc.html                        |  26 ++++
 doc/SmallTools/mrc3Dto2D.html                      |   6 +-
 doc/SmallTools/mrcFFTInfo.html                     |  16 +-
 doc/SmallTools/mrcImage3DPad.html                  |   6 +-
 doc/SmallTools/mrcImageAddValue.html               |  11 +-
 doc/SmallTools/mrcImageAsProbability.html          |  18 +++
 doc/SmallTools/mrcImageAutoRotationAverage.html    |  41 +++++
 .../mrcImageAutoRotationCorrelation3D.html         |  46 +++++-
 doc/SmallTools/mrcImageBilateralFilter.html        |  36 +++++
 doc/SmallTools/mrcImageBottomHatTransform.html     |  23 +++
 doc/SmallTools/mrcImageClosing.html                |  33 ++++
 doc/SmallTools/mrcImageConvolution.html            |  30 ++++
 doc/SmallTools/mrcImageDeconvolution.html          |  45 ++++++
 doc/SmallTools/mrcImageDensityInfo.html            |   2 +-
 doc/SmallTools/mrcImageDilation.html               |  32 ++++
 doc/SmallTools/mrcImageDividedByFile.html          |  19 +++
 doc/SmallTools/mrcImageEdgeEnhancement.html        |  29 ++++
 doc/SmallTools/mrcImageErosion.html                |  32 ++++
 doc/SmallTools/mrcImageFFT.html                    |  22 +--
 doc/SmallTools/mrcImageFOMCalc.html                |   5 +
 doc/SmallTools/mrcImageFloating.html               |  25 +++
 .../mrcImageFourierNeighborCorrelation.html        |  24 +++
 .../mrcImageFourierShellCorrelation.html           |  25 +--
 doc/SmallTools/mrcImageGaussSphere.html            |   4 +
 doc/SmallTools/mrcImageHighlighting.html           |  23 ++-
 doc/SmallTools/mrcImageInfo.html                   |  36 ++---
 doc/SmallTools/mrcImageLogicalOperation.html       |  34 ++++
 doc/SmallTools/mrcImageModelCreate.html            |   4 +
 doc/SmallTools/mrcImageMultiCTFCompensation.html   |  31 ++--
 .../mrcImageNoiseReductionByRelaxation.html        |  15 +-
 doc/SmallTools/mrcImageNormalizing.html            |   2 +
 doc/SmallTools/mrcImageOpening.html                |  33 ++++
 doc/SmallTools/mrcImageOrientationSearch.html      |  46 +-----
 doc/SmallTools/mrcImagePCA.html                    |  27 +++-
 doc/SmallTools/mrcImagePanoramaCreate.html         |  24 +++
 doc/SmallTools/mrcImagePixelDataGet.html           |  20 ++-
 doc/SmallTools/mrcImagePrint.html                  |   2 +-
 doc/SmallTools/mrcImageROI.html                    |  38 +++--
 doc/SmallTools/mrcImageROIs.html                   |   1 +
 .../mrcImageRandomParticlesImageCreate.html        |  21 +++
 doc/SmallTools/mrcImageShapeOrientation.html       |  19 +++
 doc/SmallTools/mrcImageShapePCA.html               |  12 +-
 doc/SmallTools/mrcImageShapePCAFit.html            |  23 +++
 doc/SmallTools/mrcImageSiemensStar.html            |  22 ++-
 doc/SmallTools/mrcImageSmoothing.html              |  11 +-
 doc/SmallTools/mrcImageSpatialFrequencyFilter.html |  23 +++
 doc/SmallTools/mrcImageSphereCheck.html            |  19 +--
 doc/SmallTools/mrcImageSplit.html                  |   2 +-
 doc/SmallTools/mrcImageStack.html                  |  19 ++-
 doc/SmallTools/mrcImageSuperResolution.html        |   4 +-
 doc/SmallTools/mrcImageTopHatTransform.html        |  23 +++
 doc/SmallTools/mrcImageVolumeCalc.html             |   2 +-
 doc/SmallTools/mrcImageWindowing.html              |  31 ++--
 doc/SmallTools/mrcInfo.html                        |  16 +-
 doc/SmallTools/mrcMeanYlinePos.html                |   3 +-
 doc/SmallTools/pdb2mrc2d.html                      |  37 +----
 doc/SmallTools/pdbChargeFit.html                   |  26 +---
 doc/SmallTools/pdbCrystalCreate.html               |  37 +----
 doc/SmallTools/pdbHelix.html                       |  38 +----
 doc/SmallTools/pdbListRMSDCalc.html                |   8 +-
 doc/SmallTools/pdbMove.html                        |  25 +--
 doc/SmallTools/pdbPCA.html                         |  22 +--
 doc/SmallTools/pdbRhoFit.html                      |  73 +--------
 doc/SmallTools/pdbRhoFitTm.html                    |  77 +--------
 doc/SmallTools/pdbRotation.html                    |  28 +---
 doc/SmallTools/pdbShapeFit.html                    |  74 +--------
 doc/SmallTools/pdbSurface.html                     |   1 +
 doc/SmallTools/pdbTrans.html                       |  29 +---
 doc/SmallTools/pdbTwoProteinFit.html               |  31 +---
 doc/SmallTools/pointsSetToPDB.html                 |   1 +
 .../vectorImageNearestNeighborMethod.html          |  25 ++-
 136 files changed, 2928 insertions(+), 1421 deletions(-)
 create mode 100644 doc/Objects/Vector.html.BACKUP.13752.html
 create mode 100644 doc/Objects/Vector.html.BACKUP.13830.html
 create mode 100644 doc/Objects/Vector.html.BASE.13752.html
 create mode 100644 doc/Objects/Vector.html.BASE.13830.html
 create mode 100644 doc/Objects/Vector.html.LOCAL.13752.html
 create mode 100644 doc/Objects/Vector.html.LOCAL.13830.html
 create mode 100644 doc/Objects/Vector.html.REMOTE.13752.html
 create mode 100644 doc/Objects/Vector.html.REMOTE.13830.html
 create mode 100644 doc/Objects/bmpFile.html
 create mode 100644 doc/Objects/dmFile.html
 create mode 100644 doc/Objects/eosFunc.html
 create mode 100644 doc/Objects/eosPThread.html
 create mode 100644 doc/Objects/eosPoint.html
 create mode 100644 doc/Objects/hf2000.html
 create mode 100644 doc/SmallTools/bmp2mrc.html
 create mode 100644 doc/SmallTools/bmpFileInfo.html
 create mode 100644 doc/SmallTools/dmInfo.html
 create mode 100644 doc/SmallTools/eosPointProjector.html
 create mode 100644 doc/SmallTools/eosPointRotation.html
 create mode 100644 doc/SmallTools/eosPointTracker.html
 create mode 100644 doc/SmallTools/marker2Dto3DEstimator.html
 mode change 100755 => 100644 doc/SmallTools/mrc2hdf.html
 create mode 100644 doc/SmallTools/mrc2mrc.html
 create mode 100644 doc/SmallTools/mrcImageAsProbability.html
 create mode 100644 doc/SmallTools/mrcImageAutoRotationAverage.html
 create mode 100644 doc/SmallTools/mrcImageBilateralFilter.html
 create mode 100644 doc/SmallTools/mrcImageBottomHatTransform.html
 create mode 100644 doc/SmallTools/mrcImageClosing.html
 create mode 100644 doc/SmallTools/mrcImageConvolution.html
 create mode 100644 doc/SmallTools/mrcImageDeconvolution.html
 create mode 100644 doc/SmallTools/mrcImageDilation.html
 create mode 100644 doc/SmallTools/mrcImageDividedByFile.html
 create mode 100644 doc/SmallTools/mrcImageEdgeEnhancement.html
 create mode 100644 doc/SmallTools/mrcImageErosion.html
 create mode 100644 doc/SmallTools/mrcImageFloating.html
 create mode 100644 doc/SmallTools/mrcImageFourierNeighborCorrelation.html
 create mode 100644 doc/SmallTools/mrcImageLogicalOperation.html
 create mode 100644 doc/SmallTools/mrcImageOpening.html
 create mode 100644 doc/SmallTools/mrcImagePanoramaCreate.html
 create mode 100644 doc/SmallTools/mrcImageRandomParticlesImageCreate.html
 create mode 100644 doc/SmallTools/mrcImageShapeOrientation.html
 create mode 100644 doc/SmallTools/mrcImageShapePCAFit.html
 create mode 100644 doc/SmallTools/mrcImageSpatialFrequencyFilter.html
 create mode 100644 doc/SmallTools/mrcImageTopHatTransform.html
 create mode 100644 doc/SmallTools/pointsSetToPDB.html

diff --git a/doc/Objects/.list.html b/doc/Objects/.list.html
index 773c0e0..86676a0 100755
--- a/doc/Objects/.list.html
+++ b/doc/Objects/.list.html
@@ -1,4 +1,4 @@
-<H4> Update Time 02/05/13---08:18:05 </H4>
+<H4> Update Time 10/12/14---15:03:18 </H4>
 <UL> <H2> Alphabetical List </H2>
 <LI> <A HREF="Cluster.html"> Cluster</A>
 <LI> <A HREF="Contour.html"> Contour</A>
@@ -27,20 +27,34 @@
 <LI> <A HREF="SpecialNumber.html"> SpecialNumber</A>
 <LI> <A HREF="String.html"> String</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>
+<LI> <A HREF="Vector.BASE.13752.html.html"> Vector.BASE.13752.html</A>
+<LI> <A HREF="Vector.BASE.13830.html.html"> Vector.BASE.13830.html</A>
+<LI> <A HREF="Vector.LOCAL.13752.html.html"> Vector.LOCAL.13752.html</A>
+<LI> <A HREF="Vector.LOCAL.13830.html.html"> Vector.LOCAL.13830.html</A>
+<LI> <A HREF="Vector.REMOTE.13752.html.html"> Vector.REMOTE.13752.html</A>
+<LI> <A HREF="Vector.REMOTE.13830.html.html"> Vector.REMOTE.13830.html</A>
 <LI> <A HREF="alsa.html"> alsa</A>
 <LI> <A HREF="avsFile.html"> avsFile</A>
 <LI> <A HREF="avsFile.BACKUP.13996.html.html"> avsFile.BACKUP.13996.html</A>
 <LI> <A HREF="avsFile.BASE.13996.html.html"> avsFile.BASE.13996.html</A>
 <LI> <A HREF="avsFile.LOCAL.13996.html.html"> avsFile.LOCAL.13996.html</A>
 <LI> <A HREF="avsFile.REMOTE.13996.html.html"> avsFile.REMOTE.13996.html</A>
+<LI> <A HREF="bmpFile.html"> bmpFile</A>
 <LI> <A HREF="ctfInfo.html"> ctfInfo</A>
+<LI> <A HREF="dmFile.html"> dmFile</A>
 <LI> <A HREF="dsn6File.html"> dsn6File</A>
 <LI> <A HREF="emData.html"> emData</A>
 <LI> <A HREF="emData.BACKUP.14307.html.html"> emData.BACKUP.14307.html</A>
 <LI> <A HREF="emData.BASE.14307.html.html"> emData.BASE.14307.html</A>
 <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="eosPThread.html"> eosPThread</A>
+<LI> <A HREF="eosPoint.html"> eosPoint</A>
 <LI> <A HREF="gifFile.html"> gifFile</A>
+<LI> <A HREF="hf2000.html"> hf2000</A>
 <LI> <A HREF="khorosData.html"> khorosData</A>
 <LI> <A HREF="largeIP.html"> largeIP</A>
 <LI> <A HREF="llData.html"> llData</A>
diff --git a/doc/Objects/Cluster.html b/doc/Objects/Cluster.html
index 7d23035..7eec35f 100644
--- a/doc/Objects/Cluster.html
+++ b/doc/Objects/Cluster.html
@@ -1,18 +1,8 @@
-<H4> Update Time 02/03/13---05:40:14 </H4>
 <HR>
 <A NAME="Information">
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/clusterLogAnalysis.c:
-
-../src/clusterLogInit.c:
-
-../src/clusterLogRead.c:
-
-../src/clusterLogUtil.c:
-
-../src/clusterLogWrite.c:
 </PRE>
 <HR>
 <A NAME="include">
diff --git a/doc/Objects/Contour.html b/doc/Objects/Contour.html
index 338ce3c..be7a953 100644
--- a/doc/Objects/Contour.html
+++ b/doc/Objects/Contour.html
@@ -1,14 +1,8 @@
-<H4> Update Time 02/03/13---05:36:46 </H4>
 <HR>
 <A NAME="Information">
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/contourCreate.c:
-
-../src/lcontour2ps.c:
-
-../src/lmrc2contour.c:
 </PRE>
 <HR>
 <A NAME="include">
@@ -20,9 +14,7 @@
 /*
     contour.h
 */
-#if ! defined(CELLLINUX64) &&  ! defined(I386MAC) 
-#include <values.h>
-#endif
+#include  "genUtil.h"
 
 #ifndef MINFLOAT
 #define MINFLOAT (1e-31)
diff --git a/doc/Objects/Crystal.html b/doc/Objects/Crystal.html
index aeb8aa4..52ea46b 100644
--- a/doc/Objects/Crystal.html
+++ b/doc/Objects/Crystal.html
@@ -1,21 +1,8 @@
-<H4> Update Time 02/03/13---05:40:19 </H4>
 <HR>
 <A NAME="Information">
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/crystalHelix.c:
-     $Revision: 1.1 $
-     $Date: 2002/02/14 10:18:46 $
-     $Author: tacyas $
-     $State: Exp $
-     $Log: crystalHelix.c,v $
-
-../src/crystalInfoFile.c:
-
-../src/crystalInit.c:
-
-../src/crystalUtil.c:
 </PRE>
 <HR>
 <A NAME="include">
@@ -106,6 +93,10 @@ typedef struct CrystalInfo {
 /* struct end */
 
 /* prototype begin */
+
+#ifdef __cplusplus
+	extern "C" {
+#endif
 extern void crystalInit(CrystalInfo* crystal);
 
 extern void crystalSpaceGroupPrint(FILE* fpt, int mode);
@@ -119,6 +110,10 @@ extern void crystalAxisSet(CrystalInfo* C, char axis, CrystalParaTypeReal x, Cry
 extern void crystalCellLengthSetUsingAxis(CrystalInfo* C, char axis, int mode);
 extern void crystalAxisSetUsingCellLength(CrystalInfo* C, char axis, int mode);
 
+#ifdef __cplusplus
+	};	
+#endif
+
 /* prototype end */
 
 #endif /* CRYSTAL_H */
diff --git a/doc/Objects/Map2D.html b/doc/Objects/Map2D.html
index 8162741..efeb1c9 100644
--- a/doc/Objects/Map2D.html
+++ b/doc/Objects/Map2D.html
@@ -1,10 +1,8 @@
-<H4> Update Time 02/03/13---05:40:32 </H4>
 <HR>
 <A NAME="Information">
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/map2DCoordGet.c:
 </PRE>
 <HR>
 <A NAME="include">
diff --git a/doc/Objects/Matrix3D.html b/doc/Objects/Matrix3D.html
index a7b33ed..09e5415 100644
--- a/doc/Objects/Matrix3D.html
+++ b/doc/Objects/Matrix3D.html
@@ -1,28 +1,8 @@
-<H4> Update Time 02/03/13---05:40:40 </H4>
 <HR>
 <A NAME="Information">
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/matrix3DEulerAngleGet.c:
-
-../src/matrix3DEulerAngleSet.c:
-
-../src/matrix3DEulerAngles.c:
-
-../src/matrix3DFile.c:
-
-../src/matrix3DInit.c:
-
-../src/matrix3DMultiply.c:
-
-../src/matrix3DMultiplyVector.c:
-
-../src/matrix3DRotation.c:
-
-../src/matrix3DTranslation.c:
-
-../src/matrix3DUtil.c:
 </PRE>
 <HR>
 <A NAME="include">
@@ -59,6 +39,13 @@ typedef matrix3DParaTypeReal Matrix3D[MATRIX_3D_WIDTH][MATRIX_3D_HEIGHT];
 
 typedef char  matrix3DEulerAngleMode;
 
+typedef struct EulerAngleInfo {
+	char   EAMode[5];
+	double Rot1;
+	double Rot2;
+	double Rot3;
+} EulerAngleInfo;
+
 /* struct end */
 
 /*
@@ -82,13 +69,15 @@ extern "C" {
 extern void matrix3DInit(Matrix3D Matrix);
 
 /* matrix3DUtil.c */
-extern void matrix3DCopy(Matrix3D dst, Matrix3D src);
+#include "Array.h"
+extern void matrix3DFromRotationMatrix(Matrix3D dst, Array a);
 extern void matrix3DInverse(Matrix3D mat);
 
 extern void matrix3DMultiply(Matrix3D A, Matrix3D B);     /* A = A*B */
 extern void matrix3DMultiplyInv(Matrix3D A, Matrix3D B);  /* B = A*B */
 
 extern void matrix3DMultiplyVector(floatVector* v, Matrix3D A);
+extern void matrix3DMultiplyVectors(floatVector* vs, int n, Matrix3D A);
 
 extern void matrix3DFileFormat(FILE* fpt);
 extern void matrix3DFileRead(FILE* fpt, Matrix3D Matrix);
diff --git a/doc/Objects/Memory.html b/doc/Objects/Memory.html
index 84022cf..ff6ff94 100644
--- a/doc/Objects/Memory.html
+++ b/doc/Objects/Memory.html
@@ -1,16 +1,8 @@
-<H4> Update Time 02/03/13---05:40:45 </H4>
 <HR>
 <A NAME="Information">
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/memoryAllocate.c:
-
-../src/memoryByteSwap.c:
-
-../src/memoryClear.c:
-
-../src/memoryCopy.c:
 </PRE>
 <HR>
 <A NAME="include">
@@ -26,13 +18,16 @@
 
 #define MemoryAllocate(type,num,message) (type*)memoryAllocate(sizeof(type)*(num),message)
 
+/* struct begin */
+typedef void* Memory;
+
+/* struct end */
+
+/* prototype begin */
 #ifdef __cplusplus
 extern "C" {
 #endif
 
-/* struct begin */
-typedef void* Memory;
-
 extern Memory memoryAllocate(size_t byte, char* message);
 
 /* This function must be created later in memory object. */
@@ -46,7 +41,7 @@ extern Memory memoryClear(Memory src, size_t, char n);
 
 extern Memory memoryByteSwap(Memory src, size_t, int n);
 
-/* struct end */
+/* prototype end */
 
 #ifdef __cplusplus
 };
diff --git a/doc/Objects/PVM.html b/doc/Objects/PVM.html
index aeaa0f2..3420653 100644
--- a/doc/Objects/PVM.html
+++ b/doc/Objects/PVM.html
@@ -1,10 +1,8 @@
-<H4> Update Time 02/03/13---05:40:49 </H4>
 <HR>
 <A NAME="Information">
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/pvmStart.c:
 </PRE>
 <HR>
 <A NAME="include">
diff --git a/doc/Objects/Random.html b/doc/Objects/Random.html
index a012c35..1dc7173 100644
--- a/doc/Objects/Random.html
+++ b/doc/Objects/Random.html
@@ -1,14 +1,8 @@
-<H4> Update Time 02/03/13---05:40:55 </H4>
 <HR>
 <A NAME="Information">
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/randomNormal.c:
-
-../src/randomUniform.c:
-
-../src/srandom.c:
 </PRE>
 <HR>
 <A NAME="include">
diff --git a/doc/Objects/Socket.html b/doc/Objects/Socket.html
index 7954fcd..fdf0075 100644
--- a/doc/Objects/Socket.html
+++ b/doc/Objects/Socket.html
@@ -1,12 +1,8 @@
-<H4> Update Time 02/03/13---05:41:03 </H4>
 <HR>
 <A NAME="Information">
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/socketClient.c:
-
-../src/socketServer.c:
 </PRE>
 <HR>
 <A NAME="include">
diff --git a/doc/Objects/SpecialNumber.html b/doc/Objects/SpecialNumber.html
index 43dbf00..1801383 100644
--- a/doc/Objects/SpecialNumber.html
+++ b/doc/Objects/SpecialNumber.html
@@ -1,10 +1,8 @@
-<H4> Update Time 02/03/13---05:41:11 </H4>
 <HR>
 <A NAME="Information">
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/pow2nn.c:
 </PRE>
 <HR>
 <A NAME="include">
diff --git a/doc/Objects/String.html b/doc/Objects/String.html
index 42d9d2d..1b64aca 100644
--- a/doc/Objects/String.html
+++ b/doc/Objects/String.html
@@ -4,7 +4,6 @@
 </HEAD>
 <BODY BGCOLOR="ffffcc">
 <H1> String </H1>
-<H4> Update Time 02/03/13---05:41:16 </H4>
 <H2> Member function </H2>
 <UL>
 	<LI> stringGetFromFile
@@ -20,13 +19,6 @@
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/stringGet.c:
-
-../src/stringGetFromFile.c:
-
-../src/stringIsSame.c:
-
-../src/stringUtil.c:
 </PRE>
 <HR>
 <A NAME="include">
diff --git a/doc/Objects/Vector.html b/doc/Objects/Vector.html
index 1656462..6f66ea1 100644
--- a/doc/Objects/Vector.html
+++ b/doc/Objects/Vector.html
@@ -1,4 +1,3 @@
-<H4> Update Time 02/03/13---05:41:18 </H4>
 <ul>
 	<li>extern floatVector* floatVectorAdd(floatVector* v, floatVector* u, floatVector* w);
 	<li>extern floatVector* floatVectorMinus(floatVector* v, floatVector* u, floatVector* w);
@@ -11,11 +10,6 @@
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/Vector.c:
-
-../src/VectorScalarProduct.c:
-
-../src/lVectorSpline2D.c:
 </PRE>
 <HR>
 <A NAME="include">
diff --git a/doc/Objects/Vector.html.BACKUP.13752.html b/doc/Objects/Vector.html.BACKUP.13752.html
new file mode 100644
index 0000000..e1f636e
--- /dev/null
+++ b/doc/Objects/Vector.html.BACKUP.13752.html
@@ -0,0 +1,110 @@
+<<<<<<< HEAD
+<H4> Update Time 06/15/13---00:21:55 </H4>
+=======
+<H4> Update Time 06/15/13---09:36:33 </H4>
+>>>>>>> FETCH_HEAD
+<ul>
+	<li>extern floatVector* floatVectorAdd(floatVector* v, floatVector* u, floatVector* w);
+	<li>extern floatVector* floatVectorMinus(floatVector* v, floatVector* u, floatVector* w);
+	<br>	v = u - w
+	<li>extern double lfloatVectorLength(floatVector* x);
+
+</ul>
+<HR>
+<A NAME="Information">
+<H2>Information from source codes</H2>
+</A>
+<PRE>
+../src/Vector.c:
+
+../src/VectorRead.c:
+
+../src/VectorScalarProduct.c:
+
+../src/lVectorSpline2D.c:
+</PRE>
+<HR>
+<A NAME="include">
+<H2>Vector.h</H2>
+</A>
+<PRE>
+/*
+# %M% %Y% %I%
+# The latest update : %G% at %U%
+#
+#%Z% Vector.h ver %I%
+#%Z% Created by 
+#%Z%
+#%Z% Usage : Vector.h 
+#%Z% Attention
+#%Z%
+*/
+
+#ifndef VECTOR_H
+#define VECTOR_H
+
+/* struct begin */
+typedef struct floatVector {
+	unsigned long size;
+	float*        data;
+} floatVector;
+
+typedef struct intVector {
+	unsigned long size;
+	int*        data;
+} intVector;
+
+/* struct end */
+
+/* prototype begin */
+extern floatVector* floatVectorInit(floatVector* v, long size);
+extern floatVector* floatVectorFree(floatVector* v);
+
+extern intVector* intVectorInit(intVector* v, long size);
+extern intVector* intVectorFree(intVector* v);
+
+
+extern floatVector* floatVectorAdd(floatVector* v, floatVector* u, floatVector* w);
+extern floatVector* floatVectorMinus(floatVector* v, floatVector* u, floatVector* w);
+
+extern double floatVectorScalarProduct(floatVector* x, floatVector* y);
+extern double lfloatVectorLength(floatVector* x);
+
+extern void lVectorSplineTableMake(floatVector* x, floatVector* y, floatVector* z);
+
+extern double lVectorSpline(double t, floatVector* x, floatVector* y, floatVector* z);
+
+extern void lVectorSplineTable2DMake(floatVector* p, floatVector* x, floatVector* y, floatVector* a, floatVector* b);
+extern void lVectorSpline2D(double t, double* px, double* py, 
+floatVector* p, floatVector* x, floatVector* y,
+floatVector* a, floatVector* b);
+/* prototype end */
+
+/* struct begin */
+typedef struct doubleVector {
+	unsigned long size;
+	double*        data;
+} doubleVector;
+/* struct end */
+
+/* prototype begin */
+extern doubleVector* doubleVectorInit(doubleVector* v, long size);
+extern doubleVector* doubleVectorFree(doubleVector* v);
+extern doubleVector* doubleVectorAdd(doubleVector* v, doubleVector* u, doubleVector* w);
+extern doubleVector* doubleVectorMinus(doubleVector* v, doubleVector* u, doubleVector* w);
+
+extern double doubleVectorScalarProduct(doubleVector* x, doubleVector* y);
+extern double ldoubleVectorLength(doubleVector* x);
+
+extern void ldoubleVectorSplineTableMake(doubleVector* x, doubleVector* y, doubleVector* z);
+
+extern double ldoubleVectorSpline(double t, doubleVector* x, doubleVector* y, doubleVector* z);
+
+extern void ldoubleVectorSplineTable2DMake(doubleVector* p, doubleVector* x, doubleVector* y, doubleVector* a, doubleVector* b);
+extern void ldoubleVectorSpline2D(double t, double* px, double* py, 
+doubleVector* p, doubleVector* x, doubleVector* y,
+doubleVector* a, doubleVector* b);
+/* prototype begin */
+
+#endif /* VECTOR_H */
+</PRE>
diff --git a/doc/Objects/Vector.html.BACKUP.13830.html b/doc/Objects/Vector.html.BACKUP.13830.html
new file mode 100644
index 0000000..e1f636e
--- /dev/null
+++ b/doc/Objects/Vector.html.BACKUP.13830.html
@@ -0,0 +1,110 @@
+<<<<<<< HEAD
+<H4> Update Time 06/15/13---00:21:55 </H4>
+=======
+<H4> Update Time 06/15/13---09:36:33 </H4>
+>>>>>>> FETCH_HEAD
+<ul>
+	<li>extern floatVector* floatVectorAdd(floatVector* v, floatVector* u, floatVector* w);
+	<li>extern floatVector* floatVectorMinus(floatVector* v, floatVector* u, floatVector* w);
+	<br>	v = u - w
+	<li>extern double lfloatVectorLength(floatVector* x);
+
+</ul>
+<HR>
+<A NAME="Information">
+<H2>Information from source codes</H2>
+</A>
+<PRE>
+../src/Vector.c:
+
+../src/VectorRead.c:
+
+../src/VectorScalarProduct.c:
+
+../src/lVectorSpline2D.c:
+</PRE>
+<HR>
+<A NAME="include">
+<H2>Vector.h</H2>
+</A>
+<PRE>
+/*
+# %M% %Y% %I%
+# The latest update : %G% at %U%
+#
+#%Z% Vector.h ver %I%
+#%Z% Created by 
+#%Z%
+#%Z% Usage : Vector.h 
+#%Z% Attention
+#%Z%
+*/
+
+#ifndef VECTOR_H
+#define VECTOR_H
+
+/* struct begin */
+typedef struct floatVector {
+	unsigned long size;
+	float*        data;
+} floatVector;
+
+typedef struct intVector {
+	unsigned long size;
+	int*        data;
+} intVector;
+
+/* struct end */
+
+/* prototype begin */
+extern floatVector* floatVectorInit(floatVector* v, long size);
+extern floatVector* floatVectorFree(floatVector* v);
+
+extern intVector* intVectorInit(intVector* v, long size);
+extern intVector* intVectorFree(intVector* v);
+
+
+extern floatVector* floatVectorAdd(floatVector* v, floatVector* u, floatVector* w);
+extern floatVector* floatVectorMinus(floatVector* v, floatVector* u, floatVector* w);
+
+extern double floatVectorScalarProduct(floatVector* x, floatVector* y);
+extern double lfloatVectorLength(floatVector* x);
+
+extern void lVectorSplineTableMake(floatVector* x, floatVector* y, floatVector* z);
+
+extern double lVectorSpline(double t, floatVector* x, floatVector* y, floatVector* z);
+
+extern void lVectorSplineTable2DMake(floatVector* p, floatVector* x, floatVector* y, floatVector* a, floatVector* b);
+extern void lVectorSpline2D(double t, double* px, double* py, 
+floatVector* p, floatVector* x, floatVector* y,
+floatVector* a, floatVector* b);
+/* prototype end */
+
+/* struct begin */
+typedef struct doubleVector {
+	unsigned long size;
+	double*        data;
+} doubleVector;
+/* struct end */
+
+/* prototype begin */
+extern doubleVector* doubleVectorInit(doubleVector* v, long size);
+extern doubleVector* doubleVectorFree(doubleVector* v);
+extern doubleVector* doubleVectorAdd(doubleVector* v, doubleVector* u, doubleVector* w);
+extern doubleVector* doubleVectorMinus(doubleVector* v, doubleVector* u, doubleVector* w);
+
+extern double doubleVectorScalarProduct(doubleVector* x, doubleVector* y);
+extern double ldoubleVectorLength(doubleVector* x);
+
+extern void ldoubleVectorSplineTableMake(doubleVector* x, doubleVector* y, doubleVector* z);
+
+extern double ldoubleVectorSpline(double t, doubleVector* x, doubleVector* y, doubleVector* z);
+
+extern void ldoubleVectorSplineTable2DMake(doubleVector* p, doubleVector* x, doubleVector* y, doubleVector* a, doubleVector* b);
+extern void ldoubleVectorSpline2D(double t, double* px, double* py, 
+doubleVector* p, doubleVector* x, doubleVector* y,
+doubleVector* a, doubleVector* b);
+/* prototype begin */
+
+#endif /* VECTOR_H */
+</PRE>
diff --git a/doc/Objects/Vector.html.BASE.13752.html b/doc/Objects/Vector.html.BASE.13752.html
new file mode 100644
index 0000000..81f1314
--- /dev/null
+++ b/doc/Objects/Vector.html.BASE.13752.html
@@ -0,0 +1,106 @@
+<H4> Update Time 06/12/13---03:58:08 </H4>
+<ul>
+	<li>extern floatVector* floatVectorAdd(floatVector* v, floatVector* u, floatVector* w);
+	<li>extern floatVector* floatVectorMinus(floatVector* v, floatVector* u, floatVector* w);
+	<br>	v = u - w
+	<li>extern double lfloatVectorLength(floatVector* x);
+
+</ul>
+<HR>
+<A NAME="Information">
+<H2>Information from source codes</H2>
+</A>
+<PRE>
+../src/lVectorSpline2D.c:
+
+../src/Vector.c:
+
+../src/VectorRead.c:
+
+../src/VectorScalarProduct.c:
+</PRE>
+<HR>
+<A NAME="include">
+<H2>Vector.h</H2>
+</A>
+<PRE>
+/*
+# %M% %Y% %I%
+# The latest update : %G% at %U%
+#
+#%Z% Vector.h ver %I%
+#%Z% Created by 
+#%Z%
+#%Z% Usage : Vector.h 
+#%Z% Attention
+#%Z%
+*/
+
+#ifndef VECTOR_H
+#define VECTOR_H
+
+/* struct begin */
+typedef struct floatVector {
+	unsigned long size;
+	float*        data;
+} floatVector;
+
+typedef struct intVector {
+	unsigned long size;
+	int*        data;
+} intVector;
+
+/* struct end */
+
+/* prototype begin */
+extern floatVector* floatVectorInit(floatVector* v, long size);
+extern floatVector* floatVectorFree(floatVector* v);
+
+extern intVector* intVectorInit(intVector* v, long size);
+extern intVector* intVectorFree(intVector* v);
+
+
+extern floatVector* floatVectorAdd(floatVector* v, floatVector* u, floatVector* w);
+extern floatVector* floatVectorMinus(floatVector* v, floatVector* u, floatVector* w);
+
+extern double floatVectorScalarProduct(floatVector* x, floatVector* y);
+extern double lfloatVectorLength(floatVector* x);
+
+extern void lVectorSplineTableMake(floatVector* x, floatVector* y, floatVector* z);
+
+extern double lVectorSpline(double t, floatVector* x, floatVector* y, floatVector* z);
+
+extern void lVectorSplineTable2DMake(floatVector* p, floatVector* x, floatVector* y, floatVector* a, floatVector* b);
+extern void lVectorSpline2D(double t, double* px, double* py, 
+floatVector* p, floatVector* x, floatVector* y,
+floatVector* a, floatVector* b);
+/* prototype end */
+
+/* struct begin */
+typedef struct doubleVector {
+	unsigned long size;
+	double*        data;
+} doubleVector;
+/* struct end */
+
+/* prototype begin */
+extern doubleVector* doubleVectorInit(doubleVector* v, long size);
+extern doubleVector* doubleVectorFree(doubleVector* v);
+extern doubleVector* doubleVectorAdd(doubleVector* v, doubleVector* u, doubleVector* w);
+extern doubleVector* doubleVectorMinus(doubleVector* v, doubleVector* u, doubleVector* w);
+
+extern double doubleVectorScalarProduct(doubleVector* x, doubleVector* y);
+extern double ldoubleVectorLength(doubleVector* x);
+
+extern void ldoubleVectorSplineTableMake(doubleVector* x, doubleVector* y, doubleVector* z);
+
+extern double ldoubleVectorSpline(double t, doubleVector* x, doubleVector* y, doubleVector* z);
+
+extern void ldoubleVectorSplineTable2DMake(doubleVector* p, doubleVector* x, doubleVector* y, doubleVector* a, doubleVector* b);
+extern void ldoubleVectorSpline2D(double t, double* px, double* py, 
+doubleVector* p, doubleVector* x, doubleVector* y,
+doubleVector* a, doubleVector* b);
+/* prototype begin */
+
+#endif /* VECTOR_H */
+</PRE>
diff --git a/doc/Objects/Vector.html.BASE.13830.html b/doc/Objects/Vector.html.BASE.13830.html
new file mode 100644
index 0000000..81f1314
--- /dev/null
+++ b/doc/Objects/Vector.html.BASE.13830.html
@@ -0,0 +1,106 @@
+<H4> Update Time 06/12/13---03:58:08 </H4>
+<ul>
+	<li>extern floatVector* floatVectorAdd(floatVector* v, floatVector* u, floatVector* w);
+	<li>extern floatVector* floatVectorMinus(floatVector* v, floatVector* u, floatVector* w);
+	<br>	v = u - w
+	<li>extern double lfloatVectorLength(floatVector* x);
+
+</ul>
+<HR>
+<A NAME="Information">
+<H2>Information from source codes</H2>
+</A>
+<PRE>
+../src/lVectorSpline2D.c:
+
+../src/Vector.c:
+
+../src/VectorRead.c:
+
+../src/VectorScalarProduct.c:
+</PRE>
+<HR>
+<A NAME="include">
+<H2>Vector.h</H2>
+</A>
+<PRE>
+/*
+# %M% %Y% %I%
+# The latest update : %G% at %U%
+#
+#%Z% Vector.h ver %I%
+#%Z% Created by 
+#%Z%
+#%Z% Usage : Vector.h 
+#%Z% Attention
+#%Z%
+*/
+
+#ifndef VECTOR_H
+#define VECTOR_H
+
+/* struct begin */
+typedef struct floatVector {
+	unsigned long size;
+	float*        data;
+} floatVector;
+
+typedef struct intVector {
+	unsigned long size;
+	int*        data;
+} intVector;
+
+/* struct end */
+
+/* prototype begin */
+extern floatVector* floatVectorInit(floatVector* v, long size);
+extern floatVector* floatVectorFree(floatVector* v);
+
+extern intVector* intVectorInit(intVector* v, long size);
+extern intVector* intVectorFree(intVector* v);
+
+
+extern floatVector* floatVectorAdd(floatVector* v, floatVector* u, floatVector* w);
+extern floatVector* floatVectorMinus(floatVector* v, floatVector* u, floatVector* w);
+
+extern double floatVectorScalarProduct(floatVector* x, floatVector* y);
+extern double lfloatVectorLength(floatVector* x);
+
+extern void lVectorSplineTableMake(floatVector* x, floatVector* y, floatVector* z);
+
+extern double lVectorSpline(double t, floatVector* x, floatVector* y, floatVector* z);
+
+extern void lVectorSplineTable2DMake(floatVector* p, floatVector* x, floatVector* y, floatVector* a, floatVector* b);
+extern void lVectorSpline2D(double t, double* px, double* py, 
+floatVector* p, floatVector* x, floatVector* y,
+floatVector* a, floatVector* b);
+/* prototype end */
+
+/* struct begin */
+typedef struct doubleVector {
+	unsigned long size;
+	double*        data;
+} doubleVector;
+/* struct end */
+
+/* prototype begin */
+extern doubleVector* doubleVectorInit(doubleVector* v, long size);
+extern doubleVector* doubleVectorFree(doubleVector* v);
+extern doubleVector* doubleVectorAdd(doubleVector* v, doubleVector* u, doubleVector* w);
+extern doubleVector* doubleVectorMinus(doubleVector* v, doubleVector* u, doubleVector* w);
+
+extern double doubleVectorScalarProduct(doubleVector* x, doubleVector* y);
+extern double ldoubleVectorLength(doubleVector* x);
+
+extern void ldoubleVectorSplineTableMake(doubleVector* x, doubleVector* y, doubleVector* z);
+
+extern double ldoubleVectorSpline(double t, doubleVector* x, doubleVector* y, doubleVector* z);
+
+extern void ldoubleVectorSplineTable2DMake(doubleVector* p, doubleVector* x, doubleVector* y, doubleVector* a, doubleVector* b);
+extern void ldoubleVectorSpline2D(double t, double* px, double* py, 
+doubleVector* p, doubleVector* x, doubleVector* y,
+doubleVector* a, doubleVector* b);
+/* prototype begin */
+
+#endif /* VECTOR_H */
+</PRE>
diff --git a/doc/Objects/Vector.html.LOCAL.13752.html b/doc/Objects/Vector.html.LOCAL.13752.html
new file mode 100644
index 0000000..bcf245a
--- /dev/null
+++ b/doc/Objects/Vector.html.LOCAL.13752.html
@@ -0,0 +1,106 @@
+<H4> Update Time 06/15/13---00:21:55 </H4>
+<ul>
+	<li>extern floatVector* floatVectorAdd(floatVector* v, floatVector* u, floatVector* w);
+	<li>extern floatVector* floatVectorMinus(floatVector* v, floatVector* u, floatVector* w);
+	<br>	v = u - w
+	<li>extern double lfloatVectorLength(floatVector* x);
+
+</ul>
+<HR>
+<A NAME="Information">
+<H2>Information from source codes</H2>
+</A>
+<PRE>
+../src/lVectorSpline2D.c:
+
+../src/Vector.c:
+
+../src/VectorRead.c:
+
+../src/VectorScalarProduct.c:
+</PRE>
+<HR>
+<A NAME="include">
+<H2>Vector.h</H2>
+</A>
+<PRE>
+/*
+# %M% %Y% %I%
+# The latest update : %G% at %U%
+#
+#%Z% Vector.h ver %I%
+#%Z% Created by 
+#%Z%
+#%Z% Usage : Vector.h 
+#%Z% Attention
+#%Z%
+*/
+
+#ifndef VECTOR_H
+#define VECTOR_H
+
+/* struct begin */
+typedef struct floatVector {
+	unsigned long size;
+	float*        data;
+} floatVector;
+
+typedef struct intVector {
+	unsigned long size;
+	int*        data;
+} intVector;
+
+/* struct end */
+
+/* prototype begin */
+extern floatVector* floatVectorInit(floatVector* v, long size);
+extern floatVector* floatVectorFree(floatVector* v);
+
+extern intVector* intVectorInit(intVector* v, long size);
+extern intVector* intVectorFree(intVector* v);
+
+
+extern floatVector* floatVectorAdd(floatVector* v, floatVector* u, floatVector* w);
+extern floatVector* floatVectorMinus(floatVector* v, floatVector* u, floatVector* w);
+
+extern double floatVectorScalarProduct(floatVector* x, floatVector* y);
+extern double lfloatVectorLength(floatVector* x);
+
+extern void lVectorSplineTableMake(floatVector* x, floatVector* y, floatVector* z);
+
+extern double lVectorSpline(double t, floatVector* x, floatVector* y, floatVector* z);
+
+extern void lVectorSplineTable2DMake(floatVector* p, floatVector* x, floatVector* y, floatVector* a, floatVector* b);
+extern void lVectorSpline2D(double t, double* px, double* py, 
+floatVector* p, floatVector* x, floatVector* y,
+floatVector* a, floatVector* b);
+/* prototype end */
+
+/* struct begin */
+typedef struct doubleVector {
+	unsigned long size;
+	double*        data;
+} doubleVector;
+/* struct end */
+
+/* prototype begin */
+extern doubleVector* doubleVectorInit(doubleVector* v, long size);
+extern doubleVector* doubleVectorFree(doubleVector* v);
+extern doubleVector* doubleVectorAdd(doubleVector* v, doubleVector* u, doubleVector* w);
+extern doubleVector* doubleVectorMinus(doubleVector* v, doubleVector* u, doubleVector* w);
+
+extern double doubleVectorScalarProduct(doubleVector* x, doubleVector* y);
+extern double ldoubleVectorLength(doubleVector* x);
+
+extern void ldoubleVectorSplineTableMake(doubleVector* x, doubleVector* y, doubleVector* z);
+
+extern double ldoubleVectorSpline(double t, doubleVector* x, doubleVector* y, doubleVector* z);
+
+extern void ldoubleVectorSplineTable2DMake(doubleVector* p, doubleVector* x, doubleVector* y, doubleVector* a, doubleVector* b);
+extern void ldoubleVectorSpline2D(double t, double* px, double* py, 
+doubleVector* p, doubleVector* x, doubleVector* y,
+doubleVector* a, doubleVector* b);
+/* prototype begin */
+
+#endif /* VECTOR_H */
+</PRE>
diff --git a/doc/Objects/Vector.html.LOCAL.13830.html b/doc/Objects/Vector.html.LOCAL.13830.html
new file mode 100644
index 0000000..bcf245a
--- /dev/null
+++ b/doc/Objects/Vector.html.LOCAL.13830.html
@@ -0,0 +1,106 @@
+<H4> Update Time 06/15/13---00:21:55 </H4>
+<ul>
+	<li>extern floatVector* floatVectorAdd(floatVector* v, floatVector* u, floatVector* w);
+	<li>extern floatVector* floatVectorMinus(floatVector* v, floatVector* u, floatVector* w);
+	<br>	v = u - w
+	<li>extern double lfloatVectorLength(floatVector* x);
+
+</ul>
+<HR>
+<A NAME="Information">
+<H2>Information from source codes</H2>
+</A>
+<PRE>
+../src/lVectorSpline2D.c:
+
+../src/Vector.c:
+
+../src/VectorRead.c:
+
+../src/VectorScalarProduct.c:
+</PRE>
+<HR>
+<A NAME="include">
+<H2>Vector.h</H2>
+</A>
+<PRE>
+/*
+# %M% %Y% %I%
+# The latest update : %G% at %U%
+#
+#%Z% Vector.h ver %I%
+#%Z% Created by 
+#%Z%
+#%Z% Usage : Vector.h 
+#%Z% Attention
+#%Z%
+*/
+
+#ifndef VECTOR_H
+#define VECTOR_H
+
+/* struct begin */
+typedef struct floatVector {
+	unsigned long size;
+	float*        data;
+} floatVector;
+
+typedef struct intVector {
+	unsigned long size;
+	int*        data;
+} intVector;
+
+/* struct end */
+
+/* prototype begin */
+extern floatVector* floatVectorInit(floatVector* v, long size);
+extern floatVector* floatVectorFree(floatVector* v);
+
+extern intVector* intVectorInit(intVector* v, long size);
+extern intVector* intVectorFree(intVector* v);
+
+
+extern floatVector* floatVectorAdd(floatVector* v, floatVector* u, floatVector* w);
+extern floatVector* floatVectorMinus(floatVector* v, floatVector* u, floatVector* w);
+
+extern double floatVectorScalarProduct(floatVector* x, floatVector* y);
+extern double lfloatVectorLength(floatVector* x);
+
+extern void lVectorSplineTableMake(floatVector* x, floatVector* y, floatVector* z);
+
+extern double lVectorSpline(double t, floatVector* x, floatVector* y, floatVector* z);
+
+extern void lVectorSplineTable2DMake(floatVector* p, floatVector* x, floatVector* y, floatVector* a, floatVector* b);
+extern void lVectorSpline2D(double t, double* px, double* py, 
+floatVector* p, floatVector* x, floatVector* y,
+floatVector* a, floatVector* b);
+/* prototype end */
+
+/* struct begin */
+typedef struct doubleVector {
+	unsigned long size;
+	double*        data;
+} doubleVector;
+/* struct end */
+
+/* prototype begin */
+extern doubleVector* doubleVectorInit(doubleVector* v, long size);
+extern doubleVector* doubleVectorFree(doubleVector* v);
+extern doubleVector* doubleVectorAdd(doubleVector* v, doubleVector* u, doubleVector* w);
+extern doubleVector* doubleVectorMinus(doubleVector* v, doubleVector* u, doubleVector* w);
+
+extern double doubleVectorScalarProduct(doubleVector* x, doubleVector* y);
+extern double ldoubleVectorLength(doubleVector* x);
+
+extern void ldoubleVectorSplineTableMake(doubleVector* x, doubleVector* y, doubleVector* z);
+
+extern double ldoubleVectorSpline(double t, doubleVector* x, doubleVector* y, doubleVector* z);
+
+extern void ldoubleVectorSplineTable2DMake(doubleVector* p, doubleVector* x, doubleVector* y, doubleVector* a, doubleVector* b);
+extern void ldoubleVectorSpline2D(double t, double* px, double* py, 
+doubleVector* p, doubleVector* x, doubleVector* y,
+doubleVector* a, doubleVector* b);
+/* prototype begin */
+
+#endif /* VECTOR_H */
+</PRE>
diff --git a/doc/Objects/Vector.html.REMOTE.13752.html b/doc/Objects/Vector.html.REMOTE.13752.html
new file mode 100644
index 0000000..8d0abaa
--- /dev/null
+++ b/doc/Objects/Vector.html.REMOTE.13752.html
@@ -0,0 +1,106 @@
+<H4> Update Time 06/15/13---09:36:33 </H4>
+<ul>
+	<li>extern floatVector* floatVectorAdd(floatVector* v, floatVector* u, floatVector* w);
+	<li>extern floatVector* floatVectorMinus(floatVector* v, floatVector* u, floatVector* w);
+	<br>	v = u - w
+	<li>extern double lfloatVectorLength(floatVector* x);
+
+</ul>
+<HR>
+<A NAME="Information">
+<H2>Information from source codes</H2>
+</A>
+<PRE>
+../src/Vector.c:
+
+../src/VectorRead.c:
+
+../src/VectorScalarProduct.c:
+
+../src/lVectorSpline2D.c:
+</PRE>
+<HR>
+<A NAME="include">
+<H2>Vector.h</H2>
+</A>
+<PRE>
+/*
+# %M% %Y% %I%
+# The latest update : %G% at %U%
+#
+#%Z% Vector.h ver %I%
+#%Z% Created by 
+#%Z%
+#%Z% Usage : Vector.h 
+#%Z% Attention
+#%Z%
+*/
+
+#ifndef VECTOR_H
+#define VECTOR_H
+
+/* struct begin */
+typedef struct floatVector {
+	unsigned long size;
+	float*        data;
+} floatVector;
+
+typedef struct intVector {
+	unsigned long size;
+	int*        data;
+} intVector;
+
+/* struct end */
+
+/* prototype begin */
+extern floatVector* floatVectorInit(floatVector* v, long size);
+extern floatVector* floatVectorFree(floatVector* v);
+
+extern intVector* intVectorInit(intVector* v, long size);
+extern intVector* intVectorFree(intVector* v);
+
+
+extern floatVector* floatVectorAdd(floatVector* v, floatVector* u, floatVector* w);
+extern floatVector* floatVectorMinus(floatVector* v, floatVector* u, floatVector* w);
+
+extern double floatVectorScalarProduct(floatVector* x, floatVector* y);
+extern double lfloatVectorLength(floatVector* x);
+
+extern void lVectorSplineTableMake(floatVector* x, floatVector* y, floatVector* z);
+
+extern double lVectorSpline(double t, floatVector* x, floatVector* y, floatVector* z);
+
+extern void lVectorSplineTable2DMake(floatVector* p, floatVector* x, floatVector* y, floatVector* a, floatVector* b);
+extern void lVectorSpline2D(double t, double* px, double* py, 
+floatVector* p, floatVector* x, floatVector* y,
+floatVector* a, floatVector* b);
+/* prototype end */
+
+/* struct begin */
+typedef struct doubleVector {
+	unsigned long size;
+	double*        data;
+} doubleVector;
+/* struct end */
+
+/* prototype begin */
+extern doubleVector* doubleVectorInit(doubleVector* v, long size);
+extern doubleVector* doubleVectorFree(doubleVector* v);
+extern doubleVector* doubleVectorAdd(doubleVector* v, doubleVector* u, doubleVector* w);
+extern doubleVector* doubleVectorMinus(doubleVector* v, doubleVector* u, doubleVector* w);
+
+extern double doubleVectorScalarProduct(doubleVector* x, doubleVector* y);
+extern double ldoubleVectorLength(doubleVector* x);
+
+extern void ldoubleVectorSplineTableMake(doubleVector* x, doubleVector* y, doubleVector* z);
+
+extern double ldoubleVectorSpline(double t, doubleVector* x, doubleVector* y, doubleVector* z);
+
+extern void ldoubleVectorSplineTable2DMake(doubleVector* p, doubleVector* x, doubleVector* y, doubleVector* a, doubleVector* b);
+extern void ldoubleVectorSpline2D(double t, double* px, double* py, 
+doubleVector* p, doubleVector* x, doubleVector* y,
+doubleVector* a, doubleVector* b);
+/* prototype begin */
+
+#endif /* VECTOR_H */
+</PRE>
diff --git a/doc/Objects/Vector.html.REMOTE.13830.html b/doc/Objects/Vector.html.REMOTE.13830.html
new file mode 100644
index 0000000..8d0abaa
--- /dev/null
+++ b/doc/Objects/Vector.html.REMOTE.13830.html
@@ -0,0 +1,106 @@
+<H4> Update Time 06/15/13---09:36:33 </H4>
+<ul>
+	<li>extern floatVector* floatVectorAdd(floatVector* v, floatVector* u, floatVector* w);
+	<li>extern floatVector* floatVectorMinus(floatVector* v, floatVector* u, floatVector* w);
+	<br>	v = u - w
+	<li>extern double lfloatVectorLength(floatVector* x);
+
+</ul>
+<HR>
+<A NAME="Information">
+<H2>Information from source codes</H2>
+</A>
+<PRE>
+../src/Vector.c:
+
+../src/VectorRead.c:
+
+../src/VectorScalarProduct.c:
+
+../src/lVectorSpline2D.c:
+</PRE>
+<HR>
+<A NAME="include">
+<H2>Vector.h</H2>
+</A>
+<PRE>
+/*
+# %M% %Y% %I%
+# The latest update : %G% at %U%
+#
+#%Z% Vector.h ver %I%
+#%Z% Created by 
+#%Z%
+#%Z% Usage : Vector.h 
+#%Z% Attention
+#%Z%
+*/
+
+#ifndef VECTOR_H
+#define VECTOR_H
+
+/* struct begin */
+typedef struct floatVector {
+	unsigned long size;
+	float*        data;
+} floatVector;
+
+typedef struct intVector {
+	unsigned long size;
+	int*        data;
+} intVector;
+
+/* struct end */
+
+/* prototype begin */
+extern floatVector* floatVectorInit(floatVector* v, long size);
+extern floatVector* floatVectorFree(floatVector* v);
+
+extern intVector* intVectorInit(intVector* v, long size);
+extern intVector* intVectorFree(intVector* v);
+
+
+extern floatVector* floatVectorAdd(floatVector* v, floatVector* u, floatVector* w);
+extern floatVector* floatVectorMinus(floatVector* v, floatVector* u, floatVector* w);
+
+extern double floatVectorScalarProduct(floatVector* x, floatVector* y);
+extern double lfloatVectorLength(floatVector* x);
+
+extern void lVectorSplineTableMake(floatVector* x, floatVector* y, floatVector* z);
+
+extern double lVectorSpline(double t, floatVector* x, floatVector* y, floatVector* z);
+
+extern void lVectorSplineTable2DMake(floatVector* p, floatVector* x, floatVector* y, floatVector* a, floatVector* b);
+extern void lVectorSpline2D(double t, double* px, double* py, 
+floatVector* p, floatVector* x, floatVector* y,
+floatVector* a, floatVector* b);
+/* prototype end */
+
+/* struct begin */
+typedef struct doubleVector {
+	unsigned long size;
+	double*        data;
+} doubleVector;
+/* struct end */
+
+/* prototype begin */
+extern doubleVector* doubleVectorInit(doubleVector* v, long size);
+extern doubleVector* doubleVectorFree(doubleVector* v);
+extern doubleVector* doubleVectorAdd(doubleVector* v, doubleVector* u, doubleVector* w);
+extern doubleVector* doubleVectorMinus(doubleVector* v, doubleVector* u, doubleVector* w);
+
+extern double doubleVectorScalarProduct(doubleVector* x, doubleVector* y);
+extern double ldoubleVectorLength(doubleVector* x);
+
+extern void ldoubleVectorSplineTableMake(doubleVector* x, doubleVector* y, doubleVector* z);
+
+extern double ldoubleVectorSpline(double t, doubleVector* x, doubleVector* y, doubleVector* z);
+
+extern void ldoubleVectorSplineTable2DMake(doubleVector* p, doubleVector* x, doubleVector* y, doubleVector* a, doubleVector* b);
+extern void ldoubleVectorSpline2D(double t, double* px, double* py, 
+doubleVector* p, doubleVector* x, doubleVector* y,
+doubleVector* a, doubleVector* b);
+/* prototype begin */
+
+#endif /* VECTOR_H */
+</PRE>
diff --git a/doc/Objects/alsa.html b/doc/Objects/alsa.html
index 410eee0..a55cd26 100644
--- a/doc/Objects/alsa.html
+++ b/doc/Objects/alsa.html
@@ -1,10 +1,8 @@
-<H4> Update Time 02/03/13---05:36:56 </H4>
 <HR>
 <A NAME="Information">
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/monoSound.c:
 </PRE>
 <HR>
 <A NAME="include">
diff --git a/doc/Objects/avsFile.html b/doc/Objects/avsFile.html
index 3540bf2..f36527e 100644
--- a/doc/Objects/avsFile.html
+++ b/doc/Objects/avsFile.html
@@ -1,14 +1,8 @@
-<H4> Update Time 02/03/13---05:37:02 </H4>
 <HR>
 <A NAME="Information">
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/avsFileInit.c:
-
-../src/avsFileSet.c:
-
-../src/avsFileWrite.c:
 </PRE>
 <HR>
 <A NAME="include">
diff --git a/doc/Objects/bmpFile.html b/doc/Objects/bmpFile.html
new file mode 100644
index 0000000..e1e7f48
--- /dev/null
+++ b/doc/Objects/bmpFile.html
@@ -0,0 +1,122 @@
+<HR>
+<A NAME="Information">
+<H2>Information from source codes</H2>
+</A>
+<PRE>
+</PRE>
+<HR>
+<A NAME="include">
+<H2>bmpFile.h</H2>
+</A>
+<PRE>
+/*
+# bmpFile.h : $Revision$  
+# $Date$ 
+# Created by $Author$
+# Usage : bmpFile.h 
+# Attention
+#   $Loccker$
+#  	$State$ 
+#
+*/
+/* $Log$ */
+#ifndef BMP_FILE_H 
+#define BMP_FILE_H 
+
+#include <stdio.h>
+#include "mrcImage.h"
+
+/* constant begin */
+
+
+/* constant end */
+
+/* struct begin */
+
+typedef struct bmpFileHeader {
+	char  bfType[2]; 		// BM
+	unsigned int   bfSize;			// FileSize [Byte]	
+	char  bfReserved1[2];	
+	char  bfReserved2[2];	
+	unsigned int   bfOffBits;		// ImageOffset [Byte]	
+} bmpFileHeader; /* 14 BYTE */
+
+typedef struct bmpFileInfoHeader {
+	unsigned int biSize;
+	int	biWidth;  // [Pixel]
+	int	biHeight; // [Pixel]
+	unsigned short biPlanes;  // 1
+	unsigned short biBitCount; // bits/pixel
+	unsigned int biCompression;   
+	unsigned int biSizeImage;
+	int biXPixPerMeter;
+	int biYPixPerMeter;
+	unsigned int biCirUsed;
+	unsigned int biCirImportant;
+} bmpFileCoreHeader;
+
+typedef struct bmpFileColorPalette {
+	char rgbBlue;
+	char rgbGreen;
+	char rgbRed;
+	char rgbReserved;
+} bmpFileColorPalette;
+
+typedef struct bmpFile {
+	bmpFileHeader 		 Header;
+	bmpFileCoreHeader 	 Info;
+	bmpFileColorPalette* Palette ;
+	unsigned char*  Image;
+	unsigned char*  ColorImage;
+
+	int Width;
+	int Width4;
+	int Height;
+	int numPixel;
+	int numPixel4; 
+	int BytesPerPixel;
+	int BitsPerPixel;
+	int BytesPerImage;
+} bmpFile;
+
+typedef enum lbmp2mrcInfoMode {
+	lbmp2mrcInfoModeY=0,
+	lbmp2mrcInfoModeR=1,
+	lbmp2mrcInfoModeG=2,
+	lbmp2mrcInfoModeB=3
+} lbmp2mrcInfoMode;
+
+typedef struct lbmp2mrcInfo {
+	mrcImageParaTypeRealCoord Length;	
+	lbmp2mrcInfoMode mode;
+} lbmp2mrcInfo;
+
+/* struct end */
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* prototype begin */
+
+/* bmpFileRead.c */
+extern void bmpFileRead(bmpFile* in, FILE* fpt, int mode);
+
+/* lbmp2mrc.c */
+extern void lbmp2mrc(mrcImage* out, bmpFile* in, lbmp2mrcInfo linfo, int mode);
+extern void lbmp2mrcUsage(FILE* fpt);
+
+/* bmpFileInfo.c */
+extern void bmpFileInfo(FILE* fpt, bmpFile* in, int mode);
+extern void bmpFileFileHeaderInfo(FILE* fpt, bmpFile* in, int mode);
+extern void bmpFileInfoHeaderInfo(FILE* fpt, bmpFile* in, int mode);
+extern void bmpFilePaletteInfo(FILE* fpt, bmpFile* in, int mode);
+
+/* prototype end */
+
+#ifdef __cplusplus
+};
+#endif
+
+#endif  /* XXXX */ 
+</PRE>
diff --git a/doc/Objects/ctfInfo.html b/doc/Objects/ctfInfo.html
index 930bbe2..eeb9421 100644
--- a/doc/Objects/ctfInfo.html
+++ b/doc/Objects/ctfInfo.html
@@ -5,7 +5,6 @@ ctfInfo
 </TITLE>
 </HEAD>
 <BODY bgcolor="#ffffcc">
-<H4> Update Time 02/03/13---05:38:15 </H4>
 <H1> ctfInfo Object </H1>
 
 <H2> <A HREF="#information"> information from souce codes</A></H2>
@@ -15,35 +14,6 @@ ctfInfo
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/ctfDeterminationFromPhaseComparison.c:
-
-../src/ctfFunction.c:
-
-../src/ctfInfoPVM.c:
-
-../src/ctfInfoRead.c:
-
-../src/ctfInfoWrite.c:
-
-../src/ctfInfoWrite2.c:
-
-../src/ctfWeight.c:
-
-../src/ctfZeroPoint.c:
-
-../src/lastigmatismDetection.c:
-
-../src/lctfDetermination.c:
-
-../src/lctfDetermine.c:
-
-../src/lmolecularEnvelope.c:
-
-../src/lmrcFSInfoScatteringAngularDistributionAverageSection.c:
-
-../src/powerspectraTangentLine.c:
-
-../src/thonRing.c:
 </PRE>
 <HR>
 <A NAME="include">
@@ -108,6 +78,12 @@ typedef struct ctfInfo {
 	long  flagWhiteNoiseRaising; 	
 	float WhiteNoiseRaising; /* WhiteNoise Raising depending upon R */
 
+	long  flagMaxWhiteNoise; 	
+	float MaxWhiteNoise; /* max White Noise*/
+
+	long  flagNdependentWhiteNoise; 	
+	float NdependentWhiteNoise; /* max White Noise*/
+
 	float Inoise2; /* Intensity of noise */
 	long  flagWhiteNoise2;
 	float WhiteNoise2; /* Not Affected by MTF(R)*/
diff --git a/doc/Objects/dmFile.html b/doc/Objects/dmFile.html
new file mode 100644
index 0000000..05cd707
--- /dev/null
+++ b/doc/Objects/dmFile.html
@@ -0,0 +1,118 @@
+<HR>
+<A NAME="Information">
+<H2>Information from source codes</H2>
+</A>
+<PRE>
+</PRE>
+<HR>
+<A NAME="include">
+<H2>dmFile.h</H2>
+</A>
+<PRE>
+/*
+# dmFile.h : $Revision$  
+# $Date$ 
+# Created by $Author$
+# Usage : dmFile.h 
+# Attention
+#   $Loccker$
+#  	$State$ 
+#
+*/
+/* $Log$ */
+#ifndef DMFILE_H 
+#define DMFILE_H 
+
+#include <stdio.h>
+
+/* constant begin */
+
+
+/* constant end */
+
+/* struct begin */
+
+typedef __int64_t dmFileInteger8; 
+typedef __int32_t dmFileInteger4; 
+typedef __int16_t dmFileInteger2; 
+typedef __int8_t  dmFileInteger1; 
+
+typedef enum dmFileTagDataType {
+	dmFileTagDataTypeShort=2,
+	dmFileTagDataTypeLong =3,
+	dmFileTagDataTypeUShort =4,
+} dmFileTagDataType;
+
+typedef struct dm3FileHeader {
+	dmFileInteger4 version;
+	dmFileInteger4 rootLength;
+	dmFileInteger4 byteOrder;
+} dm3FileHeader;
+
+typedef struct dm4FileHeader {
+	dmFileInteger4 version;
+	dmFileInteger8 rootLength;
+	dmFileInteger4 byteOrder;
+} dm4FileHeader;
+
+typedef struct dm3FileTagDirectrory {
+	dmFileInteger1 tagID;
+	dmFileInteger2 tagNameLength; // Bytes
+	char*          tagName;
+	dmFileInteger8 tagDataSize;   // Bytes
+} dm3FileTagDirectrory;
+
+typedef struct dm4FileTagDirectrory {
+	dmFileInteger1 tagID;
+	dmFileInteger2 tagNameLength; // Bytes
+	char*          tagName;
+	dmFileInteger8 tagDataSize;   // Bytes
+} dm4FileTagDirectrory;
+
+typedef struct dm3FileRootTagDirectory {
+	dmFileInteger1 sortf;
+	dmFileInteger1 closef;
+	dmFileInteger4 numberOfTags;
+} dm3FileRootTagDirectory;
+
+typedef struct dm4FileRootTagDirectory {
+	dmFileInteger1 sortf;
+	dmFileInteger1 closef;
+	dmFileInteger8 numberOfTags;
+} dm4FileRootTagDirectory;
+
+typedef struct dmFile {
+	// Header
+	dmFileInteger4 version;
+	dm3FileHeader Header3;
+	dm4FileHeader Header4;
+	// Root Tag
+	dm3FileRootTagDirectory RootTag3;
+	dm4FileRootTagDirectory RootTag4;
+
+	dmFileInteger8 Tail;
+} dmFile;
+
+/* struct end */
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* prototype begin */
+
+// in dfFileInfo.c
+extern void dmFileInfo(FILE* fpt, dmFile dm, int mode);
+
+// in dmFileRead.c
+extern void dmFileRead(FILE* fpt, dmFile* dm, char* message, int mode);
+
+
+/* prototype end */
+
+#ifdef __cplusplus
+};
+#endif
+
+#endif  /* DMFILE_H */ 
+</PRE>
diff --git a/doc/Objects/dsn6File.html b/doc/Objects/dsn6File.html
index 7109529..d0d0314 100644
--- a/doc/Objects/dsn6File.html
+++ b/doc/Objects/dsn6File.html
@@ -1,12 +1,8 @@
-<H4> Update Time 02/03/13---05:38:19 </H4>
 <HR>
 <A NAME="Information">
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/dsn6Init.c:
-
-../src/dsn6Write.c:
 </PRE>
 <HR>
 <A NAME="include">
diff --git a/doc/Objects/emData.html b/doc/Objects/emData.html
index 6c1ddb3..73d9c20 100644
--- a/doc/Objects/emData.html
+++ b/doc/Objects/emData.html
@@ -1,10 +1,8 @@
-<H4> Update Time 02/03/13---05:38:24 </H4>
 <HR>
 <A NAME="Information">
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/emDataRead.c:
 </PRE>
 <HR>
 <A NAME="include">
diff --git a/doc/Objects/eosFunc.html b/doc/Objects/eosFunc.html
new file mode 100644
index 0000000..d184578
--- /dev/null
+++ b/doc/Objects/eosFunc.html
@@ -0,0 +1,54 @@
+<HR>
+<A NAME="Information">
+<H2>Information from source codes</H2>
+</A>
+<PRE>
+</PRE>
+<HR>
+<A NAME="include">
+<H2>eosFunc.h</H2>
+</A>
+<PRE>
+/*
+# eosFunc.h : $Revision$  
+# $Date$ 
+# Created by $Author$
+# Usage : eosFunc.h 
+# Attention
+#   $Loccker$
+#  	$State$ 
+#
+*/
+/* $Log$ */
+#ifndef EOS_FUNC_H 
+#define EOS_FUNC_H 
+
+#include <stdio.h>
+
+/* constant begin */
+
+
+/* constant end */
+
+/* struct begin */
+
+
+/* struct end */
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* prototype begin */
+
+double eosSinc(double x);
+double eosRect(double x, double xmax);
+
+/* prototype end */
+
+#ifdef __cplusplus
+};
+#endif
+
+#endif  /* EOS_FUNC_H */ 
+</PRE>
diff --git a/doc/Objects/eosPThread.html b/doc/Objects/eosPThread.html
new file mode 100644
index 0000000..d286259
--- /dev/null
+++ b/doc/Objects/eosPThread.html
@@ -0,0 +1,84 @@
+<HR>
+<A NAME="Information">
+<H2>Information from source codes</H2>
+</A>
+<PRE>
+</PRE>
+<HR>
+<A NAME="include">
+<H2>eosPThread.h</H2>
+</A>
+<PRE>
+/*
+# eosPThread.h : $Revision$  
+# $Date$ 
+# Created by $Author$
+# Usage : eosPThread.h 
+# Attention
+#   $Loccker$
+#  	$State$ 
+#
+*/
+/* $Log$ */
+#ifndef EOS_PTHREAD_H
+#define EOS_PTHREAD_H 
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <pthread.h>
+#include <errno.h>
+
+/* constant begin */
+
+extern int __eosPThread__;
+extern int __eosPThreadNum__;
+
+/* constant end */
+
+/* struct begin */
+
+typedef enum eosPThreadStatus {
+	eosPThreadStatusWaiting = 0,
+	eosPThreadStatusRunning = 1
+} eosPThreadStatus;
+
+typedef struct eosPThread {
+	pthread_t* 			th;         /* [max] thread */
+	eosPThreadStatus* 	status;     /* [max] thread status */
+	long*				id;         /* [max] thread ID indicated by count */
+
+	int 				max;		/* maximum thread number working simultaneously. */ 
+	long				count;		/* count of created threads */	 
+	long				latest;     /* working thread ID which started latest */
+	long				oldest;     /* working thread ID which started oldest */
+
+	pthread_mutex_t     mutex;
+	pthread_mutexattr_t mutex_attr;
+} eosPThread;
+
+/* struct end */
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* prototype begin */
+extern void eosPThreadInit   (eosPThread* t, int max, int mode);
+extern int  eosPThreadCreateOnWaitingThread (eosPThread* t, void* (*start_routine)(void *), void * arg, int mode);
+extern int  eosPThreadCreate (eosPThread* t, int i, void* (*start_routine)(void *), void * arg, int mode);
+extern void eosPThreadJoin   (eosPThread* t, int i, int mode);
+extern void eosPThreadJoinAll(eosPThread* t, int mode);
+
+extern void eosPThreadMutexInit(eosPThread* t);
+extern void eosPThreadMutexDestroy(eosPThread* t);
+extern void eosPThreadMutexLock(eosPThread* t);
+extern void eosPThreadMutexUnlock(eosPThread* t);
+
+/* prototype end */
+
+#ifdef __cplusplus
+};
+#endif
+
+#endif  /* EOS_PTHREAD_H */ 
+</PRE>
diff --git a/doc/Objects/eosPoint.html b/doc/Objects/eosPoint.html
new file mode 100644
index 0000000..d68994b
--- /dev/null
+++ b/doc/Objects/eosPoint.html
@@ -0,0 +1,84 @@
+<HR>
+<A NAME="Information">
+<H2>Information from source codes</H2>
+</A>
+<PRE>
+</PRE>
+<HR>
+<A NAME="include">
+<H2>eosPoint.h</H2>
+</A>
+<PRE>
+#ifndef EOS_POINT_H
+#define EOS_POINT_H
+
+#include <stdio.h>
+#include "Matrix3D.h"
+#include "Vector.h"
+
+/* constant begin */
+
+
+/* constant end */
+
+/* struct begin */
+
+typedef double eosPointParaTypeReal;
+typedef struct eosPointCoord {
+	floatVector coord;
+	eosPointParaTypeReal sigma;  
+	floatVector sig;
+} eosPointCoord;
+
+typedef struct eosPointList {
+	eosPointCoord p;
+	struct eosPointList* next;
+	struct eosPointList* prev;
+} eosPointList ;
+
+typedef struct eosPoint {
+	eosPointList* top;  
+	eosPointList* current;  
+	eosPointList* bottom;  
+} eosPoint;
+
+/* struct end */
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* prototype begin */
+
+extern void eosPointFileFormatUsage(FILE* fpt);
+extern void eosPointRead(FILE* fpt, eosPoint* p, int mode); 
+
+extern void eosPointWrite(FILE* fpt, eosPoint* p, int mode); 
+
+extern void eosPointInit(eosPoint* p, eosPointCoord* pc);
+extern eosPointList* eosPointTop(eosPoint* p);
+extern eosPointList* eosPointBottom(eosPoint* p);
+extern eosPointList* eosPointNext(eosPoint* p);
+extern eosPointList* eosPointPrev(eosPoint* p);
+extern eosPointList* eosPointAppend(eosPoint* p, eosPointCoord* pc, int mode);
+extern void eosPointCoordInit(eosPointCoord* pc, int mode);
+extern void eosPointCoordSet(eosPointCoord* p, eosPointParaTypeReal x, eosPointParaTypeReal y, eosPointParaTypeReal z);
+extern void eosPointCoordSigSet(eosPointCoord* p, eosPointParaTypeReal sigx, eosPointParaTypeReal sigy, eosPointParaTypeReal sigz);
+
+extern void eosPointRotate(eosPoint* p, Matrix3D mat);
+extern void eosPointRotate2(eosPoint* out, eosPoint* in, Matrix3D mat);
+
+extern void eosPointProject(eosPoint* p, int index); // index　0: x-projection, 1: y-projection, 2: z-projection
+extern void eosPointProject2(eosPoint* out, eosPoint* in, int index); 
+
+extern void eosPointCopy(eosPoint* out, eosPoint* in);
+
+/* prototype end */
+
+#ifdef __cplusplus
+};
+#endif
+
+
+#endif  /* EOS_POINT_H */ 
+</PRE>
diff --git a/doc/Objects/gifFile.html b/doc/Objects/gifFile.html
index e6d65b6..9eeabe1 100644
--- a/doc/Objects/gifFile.html
+++ b/doc/Objects/gifFile.html
@@ -1,22 +1,8 @@
-<H4> Update Time 02/03/13---05:37:18 </H4>
 <HR>
 <A NAME="Information">
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/decoder.c:
-
-../src/gifFileInit.c:
-
-../src/gifFileWrite.c:
-
-../src/gifUtil.c:
-
-../src/gifcompr.c:
-
-../src/gifencod.c:
-
-../src/lmrc2gif.c:
 </PRE>
 <HR>
 <A NAME="include">
diff --git a/doc/Objects/hf2000.html b/doc/Objects/hf2000.html
new file mode 100644
index 0000000..a45dd8a
--- /dev/null
+++ b/doc/Objects/hf2000.html
@@ -0,0 +1,118 @@
+<HR>
+<A NAME="Information">
+<H2>Information from source codes</H2>
+</A>
+<PRE>
+</PRE>
+<HR>
+<A NAME="include">
+<H2>hf2000.h</H2>
+</A>
+<PRE>
+#ifndef HF2000_H
+#define HF2000_H
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <fcntl.h>
+#include <termios.h>
+#include <stdio.h>
+
+#define _POSIX_SOURCE 1
+
+/* struct begin */
+typedef int   hf2000ParaTypeInteger;
+typedef float hf2000ParaTypeReal;
+
+typedef struct hf2000Info {
+	char* deviceName;
+	struct termios IO;
+	struct termios prevIO;
+	int fd;
+	int flagClient;	
+	int flagServer;	
+	int serverSocket;
+	int serverFD;
+	char* hostname;
+	u_short port;
+	u_short maxPort;
+	u_short portSpeed;
+} hf2000Info;
+/* struct end */
+
+#ifdef __HF2000INIT__
+/* constant begin */
+hf2000Info __hf2000;
+char* __hf2000CommandList[] = {
+    "*R", /* Initialize */
+	"#Q", /* Specimen Position Get */
+	"#A", /* Absolute Position Set */
+	"#G", /* GO after #A #D #B */
+	"#H", /* Speed down and stop*/
+	"#X", /* Motor Information */
+	"?30", /* C1 Get */   /* Lenz */
+	"?31", /* C2 Get */
+	"?32", /* C3 Get */
+	"?33", /* OBJ Get */
+	"?34", /* I1 Get */
+	"?35", /* I2 Get */
+	"?36", /* P1 Get */
+	"?37", /* P2 Get */
+	"?40", /* OS(X) Get */ /* BD Coil */
+	"?41", /* OS(Y) Get */
+	"?42", /* CS(X) Get */
+	"?43", /* CS(Y) Get */
+	"?44", /* IS(X) Get */
+	"?45", /* IS(Y) Get */
+	"?46", /* BT(X) Get */
+	"?47", /* BT(Y) Get */
+	"?48", /* BH(X) Get */
+	"?49", /* BH(Y) Get */
+	NULL
+};
+/* constant end */
+#else
+extern hf2000Info __hf2000;
+extern char* __hf2000CommandList[]; 
+#endif
+/* constant begin */
+#define HF2000CMD_Initialize   0
+#define HF2000CMD_PositionGet  1
+#define HF2000CMD_PositionSet  2 
+#define HF2000CMD_PositionMove 3 
+#define HF2000CMD_PositionStop 4 
+#define HF2000CMD_PositionMotorInfo 5 
+#define HF2000CMD_C1Get   6 
+#define HF2000CMD_C2Get   7 
+#define HF2000CMD_C3Get   8 
+#define HF2000CMD_OBJGet  9 
+#define HF2000CMD_I1Get   10 
+#define HF2000CMD_I2Get   11 
+#define HF2000CMD_P1Get   12 
+#define HF2000CMD_P2Get   13 
+#define HF2000CMD_OSXGet   14 
+#define HF2000CMD_OSYGet   15 
+#define HF2000CMD_CSXGet   16 
+#define HF2000CMD_CSYGet   17 
+#define HF2000CMD_ISXGet   18 
+#define HF2000CMD_ISYGet   19 
+#define HF2000CMD_BTXGet   18 
+#define HF2000CMD_BTYGet   19 
+#define HF2000CMD_BHXGet   20 
+#define HF2000CMD_BHYGet   21 
+/* constant end */
+
+/* prototype begin */
+extern void hf2000Init(hf2000Info* info);
+extern void hf2000Close(hf2000Info* info);
+extern void hf2000Read(hf2000Info* info, char* s);
+extern void hf2000Write(hf2000Info* info, char* s);
+extern void hf2000Command(hf2000Info* info, char* command, char* result);
+/* prototype end */
+
+#include <tk.h>
+/* prototype begin */
+extern int hf2000_TclAppInit(Tcl_Interp * interp);
+/* prototype end   */
+
+#endif HF2000_H
+</PRE>
diff --git a/doc/Objects/khorosData.html b/doc/Objects/khorosData.html
index 4f6777c..aa13b68 100644
--- a/doc/Objects/khorosData.html
+++ b/doc/Objects/khorosData.html
@@ -1,10 +1,8 @@
-<H4> Update Time 02/03/13---05:38:28 </H4>
 <HR>
 <A NAME="Information">
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/lmrc2viff.c:
 </PRE>
 <HR>
 <A NAME="include">
diff --git a/doc/Objects/largeIP.html b/doc/Objects/largeIP.html
index 65ee802..7b24cd8 100644
--- a/doc/Objects/largeIP.html
+++ b/doc/Objects/largeIP.html
@@ -1,12 +1,8 @@
-<H4> Update Time 02/03/13---05:38:33 </H4>
 <HR>
 <A NAME="Information">
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/largeIPRead.c:
-
-../src/tkImgFmtlargeIP.c:
 </PRE>
 <HR>
 <A NAME="include">
diff --git a/doc/Objects/llData.html b/doc/Objects/llData.html
index cec15fd..415f9ed 100644
--- a/doc/Objects/llData.html
+++ b/doc/Objects/llData.html
@@ -1,4 +1,3 @@
-<H4> Update Time 02/03/13---05:38:45 </H4>
 <H2> API(Application Interface)</H2>
 <UL>
 	<LI> llDataFileRead
@@ -20,93 +19,6 @@
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/llDataCheck.c:
-
-../src/llDataETC.c:
-
-../src/llDataError.c:
-
-../src/llDataGet.c:
-
-../src/llDataInfo.c:
-
-../src/llDataInit.c:
-
-../src/llDataIntensityInformationGet.c:
-
-../src/llDataPVM.c:
-
-../src/llDataRead.c:
-
-../src/llDataSet.c:
-
-../src/llDataUtil.c:
-
-../src/llDataWrite.c:
-
-../src/lll2ltlg.c:
-
-../src/lllDataAdd.c:
-
-../src/lllDataAverage.c:
-
-../src/lllDataAvgTo.c:
-
-../src/lllDataAxisSearch.c:
-
-../src/lllDataAxisSearch2.c:
-
-../src/lllDataAxisSearchAndAverage.c:
-
-../src/lllDataCTFCompensate.c:
-
-../src/lllDataCTFObservation.c:
-
-../src/lllDataCompare.c:
-
-../src/lllDataContributionCalcDifferentN.c:
-
-../src/lllDataDifferenceCalc.c:
-
-../src/lllDataEquatorAdd.c:
-
-../src/lllDataExtract.c:
-
-../src/lllDataFit.c:
-
-../src/lllDataFit2.c:
-
-../src/lllDataFitAndAverage.c:
-
-../src/lllDataFitMergedLL.c:
-
-../src/lllDataFitOut.c:
-
-../src/lllDataFitParamInverse.c:
-
-../src/lllDataFitUtil.c:
-
-../src/lllDataFitUtilPVM.c:
-
-../src/lllDataInterpolate.c:
-
-../src/lllDataLowPassFiltering.c:
-
-../src/lllDataMergeDifferentN.c:
-
-../src/lllDataMultiCTFCompensation.c:
-
-../src/lllDataPhaseShift.c:
-
-../src/lllDataPrint.c:
-
-../src/lllDataRescaling.c:
-
-../src/lllDataSingleCTFCompensation.c:
-
-../src/lllDataWeightSet.c:
-
-../src/lllDatarMaxLimit.c:
 </PRE>
 <HR>
 <A NAME="include">
diff --git a/doc/Objects/ltlgData.html b/doc/Objects/ltlgData.html
index 5a41157..a9bcb9c 100644
--- a/doc/Objects/ltlgData.html
+++ b/doc/Objects/ltlgData.html
@@ -1,4 +1,3 @@
-<H4> Update Time 02/03/13---05:38:52 </H4>
 <HTML>
 <HEAD>
 <TITLE> ltlgData </TITLE>
@@ -13,19 +12,6 @@
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/lltlg2mrc.c:
-
-../src/ltlgDataAllocate.c:
-
-../src/ltlgDataGet.c:
-
-../src/ltlgDataPrint.c:
-
-../src/ltlgDataReadFile.c:
-
-../src/ltlgDataWeightModify.c:
-
-../src/ltlgDataWriteFile.c:
 </PRE>
 <HR>
 <A NAME="include">
diff --git a/doc/Objects/mapFile.html b/doc/Objects/mapFile.html
index a2605a3..d81ebc5 100644
--- a/doc/Objects/mapFile.html
+++ b/doc/Objects/mapFile.html
@@ -1,10 +1,8 @@
-<H4> Update Time 02/03/13---05:38:56 </H4>
 <HR>
 <A NAME="Information">
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/mapFileRead.c:
 </PRE>
 <HR>
 <A NAME="include">
diff --git a/doc/Objects/mrcImage.html b/doc/Objects/mrcImage.html
index 44ac17c..6eed6dd 100644
--- a/doc/Objects/mrcImage.html
+++ b/doc/Objects/mrcImage.html
@@ -4,7 +4,6 @@
 </HEAD>
 <BODY>
 <H1> mrcImage </H1>
-<H4> Update Time 02/05/13---08:18:03 </H4>
 <H2> Concept </H2>
 	<A HREF="#include">mrcImage.h</A>
 <H2> Data Structure </H2>
@@ -139,6 +138,7 @@
 #include <stdio.h>
 #include <math.h>
 #include "genUtil.h"
+#include "Matrix3D.h"
 
 /* struct begin */
 
@@ -193,6 +193,9 @@ typedef unsigned int mrcStatusType;
 
 #define  MRC_SizeOfZero             ((mrcStatusType)0x00000000L|mrcStatusMask_ReferMRCInfo)
 
+
+extern char* mrcImageGeneralTypeList[];
+
 /* constant end */
 
 /* struct begin */
@@ -266,8 +269,12 @@ typedef mrcImageParaTypeInteger mrcImageMode;
 #define	mrcComplexShortFT        ((mrcImageMode)3)
 #define	mrcComplexFloatFT        ((mrcImageMode)4)
 #define	mrcComplexFloatOneDimFT  ((mrcImageMode)5)
-#define	mrcFloatRadonImage       ((mrcImageMode)6)
-#define	mrcFloatRadonFT          ((mrcImageMode)7)
+// Change of IMOD 
+#define	mrcUShortImage           ((mrcImageMode)6)
+#define	mrcCharImageRGB          ((mrcImageMode)16)
+// Change for IMOD: (6,7) -> (26,27) 
+#define	mrcFloatRadonImage       ((mrcImageMode)26)
+#define	mrcFloatRadonFT          ((mrcImageMode)27)
 #define	mrcLongImage	         ((mrcImageMode)101)
 #define	mrcDoubleImage	         ((mrcImageMode)102)
 #define	mrcComplexLongFT         ((mrcImageMode)103)
@@ -340,6 +347,48 @@ typedef struct _mrcImageHeaderCCP4 {
     char                                Label[MRC_MAX_LABEL_N][MRC_MAX_LABEL_LEN];
 } _mrcImageHeaderCCP4;
 
+/* For IMOD: Current New */
+typedef struct _mrcImageHeaderIMOD {
+	mrcImageParaTypeIntegerCoord        N;	    /* Data Numbers */
+	mrcImageMode                        Mode;   /* Data Type */
+	mrcImageParaTypeIntegerCoord        StartN; /* First in map */
+	mrcImageParaTypeIntegerCoord        M;	    /* Number of Intervals */
+	mrcImageParaTypeRealCoord           Length; /* PixelSize=Len/M: Angstrom */
+	mrcImageParaTypeReal                Alpha;  /* Cell Angle : Degree */
+	mrcImageParaTypeReal                Beta;
+	mrcImageParaTypeReal                Gamma;
+	mrcImageParaTypeInteger             MAPC;   /* Which Axis Corresponds to Columns */
+	mrcImageParaTypeInteger             MAPR;   /* Which Axis Corresponds to Rows */
+	mrcImageParaTypeInteger             MAPS;   /* Which Axis Corresponds to Sections */
+	mrcImageParaTypeReal                AMin;   /* Minimum Density Value */
+	mrcImageParaTypeReal                AMax;   /* Maximum Density Value */
+	mrcImageParaTypeReal                AMean;  /* Mean Density Value */
+	mrcImageParaTypeInteger             ISPG;   /* Space Group */
+	mrcImageParaTypeInteger             NSYMBT; /* Number of bytes used for extended header */
+	short                               creatid; /* Flag for Skew transformation */
+	short                               extra1[15]; /* Flag for Skew transformation */
+	short                               nint;
+	short                               nreal; /*l Skew matrix S */
+	mrcImageParaTypeReal                extra2[5]; /* Extra, user defined storage space */
+	mrcImageParaTypeInteger             imodStamp;   
+	mrcImageParaTypeInteger             imodFlags;   
+	short                               idtype;   
+	short                               lnes;   
+	short                               nd1;   
+	short                               nd2;   
+	short                               vd1;   
+	short                               vd2;   
+	mrcImageParaTypeReal                tiltangles[6]; /* Extra, user defined storage space */
+	mrcImageParaTypeReal                xorg; /* Extra, user defined storage space */
+	mrcImageParaTypeReal                yorg; /* Extra, user defined storage space */
+	mrcImageParaTypeReal                zorg; /* Extra, user defined storage space */
+    mrcImageParaTypeCharacter  			MAP[4];
+    mrcImageParaTypeInteger  			MARCHST;
+    mrcImageParaTypeReal                ARMS;
+    mrcImageParaTypeInteger             LabelN;
+    char                                Label[MRC_MAX_LABEL_N][MRC_MAX_LABEL_LEN];
+} _mrcImageHeaderIMOD;
+
 
 typedef union mrcImageHeader {
   unsigned char           All[MRC_HEADER];
@@ -347,8 +396,42 @@ typedef union mrcImageHeader {
   mrcImageParaTypeReal    Real[MRC_HEADER/4];
   _mrcImageHeader         Cont;
   _mrcImageHeaderCCP4     ContCCP4;
+  _mrcImageHeaderIMOD     ContIMOD;
 } mrcImageHeader;
 
+
+#define FEI_EXTENDED_HEADER_EACH (128) 
+
+typedef struct _FEIextendedHeader {
+	mrcImageParaTypeReal aTilt;   // Alpha tilt, in degrees
+	mrcImageParaTypeReal bTilt;   // Beta tilt, in degrees 
+	mrcImageParaTypeReal xStage;  // Stage x position. 
+								  // Normally in SI units (meters), 
+								  // but some older files may be in micrometers. 
+								  // Check by looking at values for x,y,z. 
+								  // If one of these exceeds 1, it will be micrometers.
+	mrcImageParaTypeReal yStage;  // Stage y position. For testing of units see x_stage.
+	mrcImageParaTypeReal zStage;  // Stage z position. For testing of units see x_stage.
+	mrcImageParaTypeReal xShift;  // Image shift x. For testing of units see x_stage.
+	mrcImageParaTypeReal yShift;  // Image shift y. For testing of units see x_stage.
+	mrcImageParaTypeReal defocus;  
+	mrcImageParaTypeReal expTime;  
+	mrcImageParaTypeReal mean;  
+	mrcImageParaTypeReal tiltAxis;  
+	mrcImageParaTypeReal pixelSize;  
+	mrcImageParaTypeReal magnification;  
+	mrcImageParaTypeReal ht;  
+	mrcImageParaTypeReal binning;  
+	mrcImageParaTypeReal appliedDefocus;  
+	mrcImageParaTypeReal reminder[FEI_EXTENDED_HEADER_EACH/4-16];  
+} _FEIextendedHeader;
+
+typedef union FEIextendedHeader {
+	mrcImageParaTypeReal Real[FEI_EXTENDED_HEADER_EACH/4];
+	_FEIextendedHeader   Cont;
+} FEIextendedHeader;
+
+
 /* struct end */
 
 /*
@@ -385,10 +468,10 @@ mrcImage Structure
 */
 typedef struct mrcImage {
     mrcImageHeader          Header;
-    mrcImageParaTypeInteger BytePerImage;
+    size_t BytePerImage;
     mrcImageParaTypeInteger BytePerBand;
     mrcImageParaTypeInteger BandPerPixel;
-    mrcImageParaTypeInteger PixelPerImage;
+    size_t PixelPerImage;
     mrcStatusType           status;
     char*           Image;
     unsigned char*  ImageCharImage;
@@ -396,9 +479,19 @@ typedef struct mrcImage {
     unsigned long*  ImageLongImage;
     float*          ImageFloatImage;
     double*         ImageDoubleImage;
+
+	/* Tailer */
 	mrcImageTailer*         Tailer;	
 	mrcImageParaTypeInteger numTailer;
 
+	/* FEIextendedHeader */
+	FEIextendedHeader*      FEIHeader;
+	mrcImageParaTypeInteger numFEIHeader;
+
+ 	/* Dummy */
+	char*     dummyHeader;
+	mrcImageParaTypeInteger dummyHeaderByte;
+
 	/* Swap Bytes */
 	mrcImageParaTypeInteger flagByteSwap;
 
@@ -430,6 +523,22 @@ typedef struct mrcImageInformation {
 	long flagrmax;
 	double RMS; /* Root mean square */
 	int mode;
+
+	/* For Search Area */
+	int flagXrange;
+	int flagYrange;
+	int flagZrange;
+	double XrangeMin; 
+	double XrangeMax; 
+	double YrangeMin; 
+	double YrangeMax; 
+	double ZrangeMin; 
+	double ZrangeMax; 
+
+	int flagCentre;
+	double CentreX;
+	double CentreY;
+	double CentreZ;
 } mrcImageInformation;
 
 /* struct end */
@@ -497,6 +606,7 @@ typedef struct lmrcImageSmoothingInfo  {
 	mrcImageParaTypeReal sx; /* Filter kernel size */
 	mrcImageParaTypeReal sy;
 	mrcImageParaTypeReal sz;
+	double sigma;            /* for Lee-Sigma filter  */
 } lmrcImageSmoothingInfo;
 
 typedef struct lmrcImageCVEInfo {
@@ -556,10 +666,28 @@ extern void mrcTailerInit(mrcImage* mrc, long mode);
 extern void mrcTailerCopy(mrcImage* dst, mrcImage* src, long mode); 
   /* mode 1: Tailer Memory Allocation */
 /* in mrcRead.c */
+extern mrcStatusType mrcFileReadGeneral  (mrcImage* mrc, char* filename, char* type, char* message, long mode);
+extern mrcStatusType mrcImageReadGeneral  (mrcImage* mrc, char* filename, char* type, char* message, long mode);
+extern mrcStatusType mrcHeaderReadGeneral(mrcImage* mrc, char* filename, char* type, char* message, long mode);
+extern mrcStatusType mrcTailerReadGeneral(mrcImage* mrc, char* filename, char* type, char* message, long mode);
+extern mrcStatusType mrcFileGeneralListPrint(FILE* fpt); 
+
 extern mrcStatusType mrcFileRead  (mrcImage* mrc, char* filename, char* message, long mode);
 extern mrcStatusType mrcImageRead (mrcImage* mrc, char* filename, char* message, long mode);
 extern mrcStatusType mrcHeaderRead(mrcImage* mrc, char* filename, char* message, long mode);
 extern mrcStatusType mrcTailerRead(mrcImage* mrc, char* filename, char* message, long mode);
+
+extern mrcStatusType mrcFileReadFEIextendedMRC  (mrcImage* mrc, char* filename, char* message, long mode);
+extern mrcStatusType mrcImageReadFEIextendedMRC (mrcImage* mrc, char* filename, char* message, long mode);
+extern mrcStatusType mrcHeaderReadFEIextendedMRC(mrcImage* mrc, char* filename, char* message, long mode);
+extern mrcStatusType mrcTailerReadFEIextendedMRC(mrcImage* mrc, char* filename, char* message, long mode);
+
+extern mrcStatusType mrcFileReadIMODextendedMRC  (mrcImage* mrc, char* filename, char* message, long mode);
+extern mrcStatusType mrcImageReadIMODextendedMRC (mrcImage* mrc, char* filename, char* message, long mode);
+extern mrcStatusType mrcHeaderReadIMODextendedMRC(mrcImage* mrc, char* filename, char* message, long mode);
+extern mrcStatusType mrcTailerReadIMODextendedMRC(mrcImage* mrc, char* filename, char* message, long mode);
+
+extern int mrcImageByteSwap(mrcImage* mrc, long mode);
 /* in mrcWrite.c */
 #define mrcFileWriteModeGet(x)     BYTE4GETBYTE(x,0)
 #define mrcImageWriteModeGet(x)    BYTE4GETBYTE(x,1)
@@ -591,18 +719,21 @@ extern double mrcPixelDataGet(mrcImage* mrc,
 			      mrcPixelDataType mode,
 			      mrcPixelDataHowToGet how);
 
-extern inline double mrcPixelDataGetFloatImage(mrcImage* img, 
+extern void mrcPixelsDataGet(float* data, mrcImageParaTypeRealCoord* inCoord, int nPixel, mrcImage* in, mrcPixelDataType type, mrcPixelDataHowToGet howto);
+extern void mrcPixelDataGetbyMatrix3D(mrcImage* out, mrcImage* in, Matrix3D mat, mrcPixelDataHowToGet mode, int mode2);
+
+static inline double mrcPixelDataGetFloatImage(mrcImage* img, 
 		mrcImageParaTypeInteger x, mrcImageParaTypeInteger y, mrcImageParaTypeInteger z)
 {
 	return img->ImageFloatImage[x + y*img->HeaderN.x + z*img->HeaderN.x*img->HeaderN.y];
 }
 
-extern inline double mrcPixelDataGetFloatFTRe(mrcImage* fft, 
+static inline double mrcPixelDataGetFloatFTRe(mrcImage* fft, 
 		mrcImageParaTypeInteger x, mrcImageParaTypeInteger y, mrcImageParaTypeInteger z)
 {
 	return fft->ImageFloatImage[2*(x + y*(fft->HeaderN.x/2+1) + z*(fft->HeaderN.x/2+1)*fft->HeaderN.y)];
 }
-extern inline double mrcPixelDataGetFloatFTIm(mrcImage* fft, 
+static inline double mrcPixelDataGetFloatFTIm(mrcImage* fft, 
 		mrcImageParaTypeInteger x, mrcImageParaTypeInteger y, mrcImageParaTypeInteger z)
 {
 	return fft->ImageFloatImage[2*(x + y*(fft->HeaderN.x/2+1) + z*(fft->HeaderN.x/2+1)*fft->HeaderN.y)+1];
@@ -644,19 +775,19 @@ extern double mrcPixelDataSet(mrcImage* mrc,
 			      double data,
 			      mrcPixelDataType mode);
 
-extern inline void mrcPixelDataSetFloatImage(mrcImage* img, 
+static inline void mrcPixelDataSetFloatImage(mrcImage* img, 
 		mrcImageParaTypeInteger x, mrcImageParaTypeInteger y, mrcImageParaTypeInteger z, double data)
 {
 	img->ImageFloatImage[x + y*img->HeaderN.x + z*img->HeaderN.x*img->HeaderN.y] = (float)data;
 }
 
-extern inline void mrcPixelDataSetFloatFTRe(mrcImage* fft, 
+static inline void mrcPixelDataSetFloatFTRe(mrcImage* fft, 
 		mrcImageParaTypeInteger x, mrcImageParaTypeInteger y, mrcImageParaTypeInteger z, double data)
 {
 	fft->ImageFloatImage[2*(x + y*(fft->HeaderN.x/2+1) + z*(fft->HeaderN.x/2+1)*fft->HeaderN.y)] = (float)data;
 }
 
-extern inline void mrcPixelDataSetFloatFTIm(mrcImage* fft, 
+static inline void mrcPixelDataSetFloatFTIm(mrcImage* fft, 
 		mrcImageParaTypeInteger x, mrcImageParaTypeInteger y, mrcImageParaTypeInteger z, double data)
 {
 	fft->ImageFloatImage[2*(x + y*(fft->HeaderN.x/2+1) + z*(fft->HeaderN.x/2+1)*fft->HeaderN.y)+1] = (float)data;
@@ -700,11 +831,11 @@ extern int IsFFT(mrcImage* mrc, char* message, mrcImageParaTypeInteger mode);
 extern void mrcImageInfoSet(mrcImage* mrc, FILE* fptIn, FILE* fptOut, long mode);
 
 /* in mrcImageOperation.c */
-extern void lmrcImageDevidedByImage(mrcImage* img, mrcImage* i1, mrcImage* i2);
+extern void lmrcImageDividedByImage(mrcImage* img, mrcImage* i1, mrcImage* i2);
 extern void lmrcImagetMapForZero(mrcImage* t, mrcImage* avg, mrcImage* se);
 extern void lmrcImageSN(mrcImage* sn, mrcImage* avg, mrcImage* sig);
-extern void lmrcImageDevidedByReal(mrcImage* img, double d);
-extern void lmrcImageDevidedByRealForOnlyPositive(mrcImage* img, double d);
+extern void lmrcImageDividedByReal(mrcImage* img, double d);
+extern void lmrcImageDividedByRealForOnlyPositive(mrcImage* img, double d);
 extern void lmrcImageAddedByReal(mrcImage* img, double d);
 extern void lmrcImageStdDev(mrcImage* sig, mrcImage* avg, mrcImage* avg2, long num);
 extern void lmrcImageStdErr(mrcImage* sig, mrcImage* avg, mrcImage* avg2, long num);
@@ -713,6 +844,7 @@ extern void lmrcSQRImageAdd(mrcImage* img2, mrcImage* img1, long* num);
 extern void lmrcImageSquare(mrcImage* in);
 extern void lmrcImageRoot(mrcImage* in ,double eps);
 extern void lmrcImageAbs(mrcImage* out, mrcImage* in);
+extern void lmrcImageConvolution(mrcImage* out, mrcImage* in,  mrcImage* kernel, int mode);
 
 /* in mrcImageToIntImage.c */
 extern void lmrcImageToIntImage(mrcImage* dst, mrcImage* src, mrcImageParaTypeInteger mode);
@@ -748,7 +880,10 @@ extern floatVector* lmrcFSInfoScatteringAngularDistribution(mrcImage* fft);
 extern floatVector* lmrcFSInfoScatteringAngularDistributionAverage(mrcImage* fft);
 extern floatVector* lmrcFSInfoScatteringAngularDistributionSD(mrcImage* fft);
 extern floatVector* lmrcFSInfoSpacing(mrcImage* fft);
-
+extern floatVector** lmrcFSInfoScatteringAngularDistributionDivisionAverage(mrcImage* fft, mrcImageParaTypeReal axis, mrcImageParaTypeInteger n, int mode);
+extern floatVector** lmrcFSInfoScatteringAngularDistributionDivisionSD(mrcImage* fft, mrcImageParaTypeReal axis, mrcImageParaTypeInteger n, int mode);
+extern floatVector** lmrcFSInfoScatteringAngularDistributionDivisionAverageDelR(mrcImage* fft, mrcImageParaTypeReal axis, mrcImageParaTypeInteger n, mrcImageParaTypeReal delR, int mode);
+extern floatVector** lmrcFSInfoScatteringAngularDistributionDivisionSDDelR(mrcImage* fft, mrcImageParaTypeReal axis, mrcImageParaTypeInteger n, mrcImageParaTypeReal delR, int mode);
 /* in mrcImageCheckSameSize.c */
 extern void lmrcImageCheckSameSize(mrcImage* in, mrcImage* ref);
 
@@ -756,6 +891,7 @@ extern void lmrcImageCheckSameSize(mrcImage* in, mrcImage* ref);
 extern void lmrcImageCheckFFT(mrcImage* in, mrcImage* ref);
 
 /* in lmrcImageSmoothing */
+extern void lmrcImageSmoothingModeInfo(FILE* fpt);
 extern void lmrcImageSmoothing(mrcImage* dst, mrcImage* src, lmrcImageSmoothingInfo* info, long mode);
 
 /* in lmrcImageCVE */
@@ -861,6 +997,7 @@ extern mrcImageFourierPowerSpectrum lmrcImageFourierPowerSpectrumMakeSpectrum(co
 extern void lmrcImageFourierPowerSpectrumDeleteSpectrum(mrcImageFourierPowerSpectrum theSpectrum);
 extern mrcImageFourierPowerSpectrum lmrcImageFourierPowerSpectrum(const mrcImage *inMrc, lmrcImageFourierPowerSpectrumInfo *info, long mode);
 
+extern void lmrcImageRotation3DModePrint(FILE* fpt);
 extern void lmrcImageRotation3DFollowingEulerAngle(mrcImage* dst, mrcImage* src, const char* m, 
 	mrcImageParaTypeReal rot1, mrcImageParaTypeReal rot2, mrcImageParaTypeReal rot3, mrcPixelDataHowToGet mode, int mode2);
 
@@ -880,9 +1017,12 @@ extern void mrcImageSectionGet(mrcImage* dst, mrcImage* src, mrcImageParaTypeRea
 /* in mrcImageSectionSet.c */
 extern void mrcImageSectionSet(mrcImage* dst, mrcImage* src, mrcImageParaTypeReal z, long mode);
 
-
 extern double lmrcImageMaxDataGet(mrcImage* src, long mode);
 
+/* in lmrcImageStack.c */
+extern void lmrcImageStackAlloc(mrcImage* dst, mrcImage* src, int N, int* sp, int mode);
+extern void lmrcImageStackPush(mrcImage* dst, mrcImage* src, int* sp, int mode);
+
 /* prototype end */
 
 #ifdef __cplusplus
diff --git a/doc/Objects/openGL.html b/doc/Objects/openGL.html
index 0847f74..d07ba5b 100644
--- a/doc/Objects/openGL.html
+++ b/doc/Objects/openGL.html
@@ -1,112 +1,8 @@
-<H4> Update Time 02/03/13---05:37:44 </H4>
 <HR>
 <A NAME="Information">
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/density_sphere.c:
-
-../src/drawWireFrame.c:
-
-../src/lmolvieCamera.c:
-
-../src/lmolvieDisplayLib.c:
-
-../src/lmolvieDisplayListMake.c:
-
-../src/lmolvieDisplayNormal.c:
-
-../src/lmolvieDisplayParallel.c:
-
-../src/lmolvieDockDisplay.c:
-
-../src/lmolvieDockKeyboard.c:
-
-../src/lmolvieFlightDisplay.c:
-
-../src/lmolvieFlightIdle.c:
-
-../src/lmolvieFlightKeyboard.c:
-
-../src/lmolvieIdleNormal.c:
-
-../src/lmolvieInitNormal.c:
-
-../src/lmolvieInitParallel.c:
-
-../src/lmolvieKeyboard.c:
-
-../src/lmolvieKeyboardDrive.c:
-
-../src/lmolvieKeyboardMulti.c:
-
-../src/lmolvieKeyboardNormal.c:
-
-../src/lmolvieKeyboardParallel.c:
-
-../src/lmolvieKeyboardSurface.c:
-
-../src/lmolvieLight.c:
-
-../src/lmolvieMRCread.c:
-
-../src/lmolvieMouse.c:
-
-../src/lmolvieMouseDrive.c:
-
-../src/lmolvieMouseMulti.c:
-
-../src/lmolvieMouseNormal.c:
-
-../src/lmolvieMouseParallel.c:
-
-../src/lmolvieMrcViewerDisplay.c:
-
-../src/lmolvieMrcViewerKeyboard.c:
-
-../src/lmolvieMrcViewerMouse.c:
-
-../src/lmolvieOperation.c:
-
-../src/lmolviePDBread.c:
-
-../src/lmolvieProjectionKeyboard.c:
-
-../src/lmolvieProjectionMouse.c:
-
-../src/lmolvieProteinStatus.c:
-
-../src/lmolvieReshapeNormal.c:
-
-../src/lmolvieReshapeParallel.c:
-
-../src/lmolvieTest.c:
-
-../src/lmolvieTexture.c:
-
-../src/lmolvieViewerDisplay.c:
-
-../src/lmolvieViewerIdle.c:
-
-../src/lmolvieViewerKeyboard.c:
-
-../src/lmolvieViewerMouse.c:
-
-../src/lmolvieViewerSpecial.c:
-
-../src/lmolvieVoice.c:
-
-../src/loadPDB.c:
-
-../src/loadPPM.c:
-
-../src/marching_cubes.c:
-
-../src/multiPDB.c:
-
-../src/openGLKey.c:
-
-../src/savePPM.c:
 </PRE>
 <HR>
 <A NAME="include">
diff --git a/doc/Objects/pdbFile.html b/doc/Objects/pdbFile.html
index a8076c1..e7d9c55 100644
--- a/doc/Objects/pdbFile.html
+++ b/doc/Objects/pdbFile.html
@@ -1,4 +1,3 @@
-<H4> Update Time 02/03/13---05:39:39 </H4>
 <H1> pdbFile </H1>
 
 <UL>
@@ -98,35 +97,6 @@
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/lpdb2mrc2d.c:
-
-../src/lpdb2mrc3d.c:
-
-../src/lpdbCoord.c:
-
-../src/lpdbCoordInfo.c:
-
-../src/lpdbSelectedAtom.c:
-
-../src/lpdbSurface.c:
-
-../src/pdbFileRead.c:
-
-../src/pdbFileWrite.c:
-
-../src/pdbGet.c:
-
-../src/pdbInfoGet.c:
-
-../src/pdbRotation.c:
-
-../src/pdbSecondaryStructure.c:
-
-../src/pdbSet.c:
-
-../src/pdbTrans.c:
-
-../src/pdbUtil.c:
 </PRE>
 <HR>
 <A NAME="include">
@@ -385,7 +355,10 @@ extern void pdbFileWriteSecondaryStructure(FILE* fpt, pdbFileSecondaryStructure*
 extern void pdbMatrixFileFormat(FILE* fpt);
 extern void pdbMatrixFileRead(FILE* fpt, Matrix3D Matrix);
 extern void pdbMatrixFileWrite(FILE* fpt, Matrix3D Matrix);
+
 extern void pdbTrans(pdbFile* pdb, Matrix3D Matrix);
+//extern void pdbTransCuda(pdbFile* pdb, Matrix3D Matrix);
+extern void pdbTransCuda(float* hv, int n, Matrix3D Matrix);
 
 extern void pdbFileResidueSequenceNumberIncrementAll(pdbFile* pdb, int n);
 extern void pdbFileResidueSequenceNumberIncrement(pdbFile* pdb, int n);
diff --git a/doc/Objects/psFile.html b/doc/Objects/psFile.html
index 1774f4f..6f88d1f 100644
--- a/doc/Objects/psFile.html
+++ b/doc/Objects/psFile.html
@@ -1,30 +1,8 @@
-<H4> Update Time 02/03/13---05:37:48 </H4>
 <HR>
 <A NAME="Information">
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/psFileCircle.c:
-
-../src/psFileContour.c:
-
-../src/psFileContour3D.c:
-
-../src/psFileEnd.c:
-
-../src/psFileImage.c:
-
-../src/psFileInit.c:
-
-../src/psFileLine.c:
-
-../src/psFilePage.c:
-
-../src/psFileRead.c:
-
-../src/psFileString.c:
-
-../src/psFileUtil.c:
 </PRE>
 <HR>
 <A NAME="include">
diff --git a/doc/Objects/tgaFile.html b/doc/Objects/tgaFile.html
index 74501cd..3ba22d6 100644
--- a/doc/Objects/tgaFile.html
+++ b/doc/Objects/tgaFile.html
@@ -1,14 +1,8 @@
-<H4> Update Time 02/03/13---05:39:48 </H4>
 <HR>
 <A NAME="Information">
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/tgaFileInit.c:
-
-../src/tgaFilePrint.c:
-
-../src/tgaFileRead.c:
 </PRE>
 <HR>
 <A NAME="include">
diff --git a/doc/Objects/transform.html b/doc/Objects/transform.html
index cddde7a..0096d71 100644
--- a/doc/Objects/transform.html
+++ b/doc/Objects/transform.html
@@ -1,70 +1,8 @@
-<H4> Update Time 02/03/13---05:40:05 </H4>
 <HR>
 <A NAME="Information">
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/lAllCommonLineCalculation.c:
-
-../src/lAngularWeightCalculation.c:
-
-../src/lCommonLineCalculation.c:
-
-../src/lCommonLineDataSetInPlaneRotation.c:
-
-../src/lCommonLinesDataSet.c:
-
-../src/lDescartesIntoPolar.c:
-
-../src/lEvaluateCorrelationMapwithCommonLine.c:
-
-../src/lFETOrientationSearchByAnnealing.c:
-
-../src/lFETOrientationSearchByFeatureAlignment.c:
-
-../src/lFETOrientationSearchByFeatureAlignmentInitSet.c:
-
-../src/lFETOrientationSearchByFeatureAlignmentSphere.c:
-
-../src/lFETmapOrientationSearchBySimultaneousFitting.c:
-
-../src/lFETsmallMapSetCreate_forSimultaneousMinimization.c:
-
-../src/lInitialDataFileRead.c:
-
-../src/lJcalulation.c:
-
-../src/lLcalculation.c:
-
-../src/lPlaneRotationAngleSet.c:
-
-../src/lllDataSeparationInfoPrint.c:
-
-../src/lllDataSeparationInfoRead.c:
-
-../src/lllDataSeparationInfoSet.c:
-
-../src/lllDatarMaxLimitForSeparation.c:
-
-../src/lllExtract.c:
-
-../src/lllExtractCtfinfFileCreate.c:
-
-../src/lllExtractWithSeparation.c:
-
-../src/lllExtractdYEstimate.c:
-
-../src/lmrc2Dto3D.c:
-
-../src/lmrc2Dto3DSIRT.c:
-
-../src/lmrc3Dto2D.c:
-
-../src/lmrcImageFileListAndEulerAngleDataRead.c:
-
-../src/lmrcImageOneLineGet.c:
-
-../src/lmrcImageSinogramCorrelationAdditionalWeight.c:
 </PRE>
 <HR>
 <A NAME="include">
diff --git a/doc/SmallTools/.smallToolList.html b/doc/SmallTools/.smallToolList.html
index 11ea1de..0ab0a14 100755
--- a/doc/SmallTools/.smallToolList.html
+++ b/doc/SmallTools/.smallToolList.html
@@ -33,6 +33,8 @@
 <LI> <A HREF="anglediffchk.html"> anglediffchk</A>
 <LI> <A HREF="array2mrc.html"> array2mrc</A>
 <LI> <A HREF="bin2mrc.html"> bin2mrc</A>
+<LI> <A HREF="bmp2mrc.html"> bmp2mrc</A>
+<LI> <A HREF="bmpFileInfo.html"> bmpFileInfo</A>
 <LI> <A HREF="calcCommonLine.html"> calcCommonLine</A>
 <LI> <A HREF="class.html"> class</A>
 <LI> <A HREF="clusterLog2ToLog.html"> clusterLog2ToLog</A>
@@ -65,11 +67,15 @@
 <LI> <A HREF="dcdTest.html"> dcdTest</A>
 <LI> <A HREF="dcdTimeSeriesBehavior.html"> dcdTimeSeriesBehavior</A>
 <LI> <A HREF="defocusDeterminationFromThonRing.html"> defocusDeterminationFromThonRing</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="eosPointProjector.html"> eosPointProjector</A>
+<LI> <A HREF="eosPointRotation.html"> eosPointRotation</A>
+<LI> <A HREF="eosPointTracker.html"> eosPointTracker</A>
 <LI> <A HREF="fft2d.html"> fft2d</A>
 <LI> <A HREF="geogeoge.html"> geogeoge</A>
 <LI> <A HREF="gmolvie.html"> gmolvie</A>
@@ -131,6 +137,7 @@
 <LI> <A HREF="ltlg2ps.html"> ltlg2ps</A>
 <LI> <A HREF="ltlgDataInfo.html"> ltlgDataInfo</A>
 <LI> <A HREF="mallocCheck.html"> mallocCheck</A>
+<LI> <A HREF="marker2Dto3DEstimator.html"> marker2Dto3DEstimator</A>
 <LI> <A HREF="matrix3DEulerAngleTransform.html"> matrix3DEulerAngleTransform</A>
 <LI> <A HREF="matrix3DFromEulerAngle.html"> matrix3DFromEulerAngle</A>
 <LI> <A HREF="matrix3DInverse.html"> matrix3DInverse</A>
@@ -153,6 +160,7 @@
 <LI> <A HREF="mrc2hdf.html"> mrc2hdf</A>
 <LI> <A HREF="mrc2lattice.html"> mrc2lattice</A>
 <LI> <A HREF="mrc2map.html"> mrc2map</A>
+<LI> <A HREF="mrc2mrc.html"> mrc2mrc</A>
 <LI> <A HREF="mrc2pov.html"> mrc2pov</A>
 <LI> <A HREF="mrc2tiff.html"> mrc2tiff</A>
 <LI> <A HREF="mrc2viff.html"> mrc2viff</A>
@@ -196,17 +204,21 @@
 <LI> <A HREF="mrcImageAdd.html"> mrcImageAdd</A>
 <LI> <A HREF="mrcImageAddValue.html"> mrcImageAddValue</A>
 <LI> <A HREF="mrcImageAreaCalc.html"> mrcImageAreaCalc</A>
+<LI> <A HREF="mrcImageAsProbability.html"> mrcImageAsProbability</A>
 <LI> <A HREF="mrcImageAssignedToTFofPDB.html"> mrcImageAssignedToTFofPDB</A>
 <LI> <A HREF="mrcImageAutoCorrelationWithWindowing.html"> mrcImageAutoCorrelationWithWindowing</A>
 <LI> <A HREF="mrcImageAutoFilamentExtract.html"> mrcImageAutoFilamentExtract</A>
 <LI> <A HREF="mrcImageAutoFilamentExtractResultAnalysis.html"> mrcImageAutoFilamentExtractResultAnalysis</A>
+<LI> <A HREF="mrcImageAutoRotationAverage.html"> mrcImageAutoRotationAverage</A>
 <LI> <A HREF="mrcImageAutoRotationCorrelation.html"> mrcImageAutoRotationCorrelation</A>
 <LI> <A HREF="mrcImageAutoRotationCorrelation3D.html"> mrcImageAutoRotationCorrelation3D</A>
 <LI> <A HREF="mrcImageAutoRotationCorrelationResultPrint.html"> mrcImageAutoRotationCorrelationResultPrint</A>
 <LI> <A HREF="mrcImageAverage.html"> mrcImageAverage</A>
 <LI> <A HREF="mrcImageBandPassFilter.html"> mrcImageBandPassFilter</A>
+<LI> <A HREF="mrcImageBilateralFilter.html"> mrcImageBilateralFilter</A>
 <LI> <A HREF="mrcImageBinalization.html"> mrcImageBinalization</A>
 <LI> <A HREF="mrcImageBlockMerge.html"> mrcImageBlockMerge</A>
+<LI> <A HREF="mrcImageBottomHatTransform.html"> mrcImageBottomHatTransform</A>
 <LI> <A HREF="mrcImageBoundaryInfo.html"> mrcImageBoundaryInfo</A>
 <LI> <A HREF="mrcImageBtest.html"> mrcImageBtest</A>
 <LI> <A HREF="mrcImageCCDNoiseRemove.html"> mrcImageCCDNoiseRemove</A>
@@ -220,6 +232,7 @@
 <LI> <A HREF="mrcImageCenterGet.html"> mrcImageCenterGet</A>
 <LI> <A HREF="mrcImageCenterOfMassCalculate.html"> mrcImageCenterOfMassCalculate</A>
 <LI> <A HREF="mrcImageCircumferentialProjection.html"> mrcImageCircumferentialProjection</A>
+<LI> <A HREF="mrcImageClosing.html"> mrcImageClosing</A>
 <LI> <A HREF="mrcImageClusterAnalysis.html"> mrcImageClusterAnalysis</A>
 <LI> <A HREF="mrcImageColoring.html"> mrcImageColoring</A>
 <LI> <A HREF="mrcImageColorlizing.html"> mrcImageColorlizing</A>
@@ -227,6 +240,7 @@
 <LI> <A HREF="mrcImageConnection.html"> mrcImageConnection</A>
 <LI> <A HREF="mrcImageConnectivityNumberCalc.html"> mrcImageConnectivityNumberCalc</A>
 <LI> <A HREF="mrcImageContourSurfaceCreate.html"> mrcImageContourSurfaceCreate</A>
+<LI> <A HREF="mrcImageConvolution.html"> mrcImageConvolution</A>
 <LI> <A HREF="mrcImageCoordinateChange.html"> mrcImageCoordinateChange</A>
 <LI> <A HREF="mrcImageCoreImageCalc.html"> mrcImageCoreImageCalc</A>
 <LI> <A HREF="mrcImageCorrelation.html"> mrcImageCorrelation</A>
@@ -237,17 +251,22 @@
 <LI> <A HREF="mrcImageCutAndSetInArray.html"> mrcImageCutAndSetInArray</A>
 <LI> <A HREF="mrcImageCylinderSection.html"> mrcImageCylinderSection</A>
 <LI> <A HREF="mrcImageDeadPixelCorrection.html"> mrcImageDeadPixelCorrection</A>
+<LI> <A HREF="mrcImageDeconvolution.html"> mrcImageDeconvolution</A>
 <LI> <A HREF="mrcImageDensityChangeEstimation.html"> mrcImageDensityChangeEstimation</A>
 <LI> <A HREF="mrcImageDensityInfo.html"> mrcImageDensityInfo</A>
 <LI> <A HREF="mrcImageDensityNormalization.html"> mrcImageDensityNormalization</A>
 <LI> <A HREF="mrcImageDensityNormalizationByImage.html"> mrcImageDensityNormalizationByImage</A>
 <LI> <A HREF="mrcImageDevideIntoTwoImages.html"> mrcImageDevideIntoTwoImages</A>
+<LI> <A HREF="mrcImageDilation.html"> mrcImageDilation</A>
 <LI> <A HREF="mrcImageDisplayDensityAsTempFactor.html"> mrcImageDisplayDensityAsTempFactor</A>
 <LI> <A HREF="mrcImageDistanceConversion.html"> mrcImageDistanceConversion</A>
 <LI> <A HREF="mrcImageDivideInfoForTomography.html"> mrcImageDivideInfoForTomography</A>
 <LI> <A HREF="mrcImageDivideIntoTwoImages.html"> mrcImageDivideIntoTwoImages</A>
+<LI> <A HREF="mrcImageDividedByFile.html"> mrcImageDividedByFile</A>
+<LI> <A HREF="mrcImageEdgeEnhancement.html"> mrcImageEdgeEnhancement</A>
 <LI> <A HREF="mrcImageEdgeImageGet.html"> mrcImageEdgeImageGet</A>
 <LI> <A HREF="mrcImageEnhancementWithFuzzySets.html"> mrcImageEnhancementWithFuzzySets</A>
+<LI> <A HREF="mrcImageErosion.html"> mrcImageErosion</A>
 <LI> <A HREF="mrcImageEstimateTiltImage.html"> mrcImageEstimateTiltImage</A>
 <LI> <A HREF="mrcImageExpression.html"> mrcImageExpression</A>
 <LI> <A HREF="mrcImageFFT.html"> mrcImageFFT</A>
@@ -259,6 +278,8 @@
 <LI> <A HREF="mrcImageFilterCreate.html"> mrcImageFilterCreate</A>
 <LI> <A HREF="mrcImageFilteringbyFile.html"> mrcImageFilteringbyFile</A>
 <LI> <A HREF="mrcImageFilteringbyFileForVariance.html"> mrcImageFilteringbyFileForVariance</A>
+<LI> <A HREF="mrcImageFloating.html"> mrcImageFloating</A>
+<LI> <A HREF="mrcImageFourierNeighborCorrelation.html"> mrcImageFourierNeighborCorrelation</A>
 <LI> <A HREF="mrcImageFourierPowerSpectrum.html"> mrcImageFourierPowerSpectrum</A>
 <LI> <A HREF="mrcImageFourierShellCorrelation.html"> mrcImageFourierShellCorrelation</A>
 <LI> <A HREF="mrcImageFractalFourierShellCorrelation.html"> mrcImageFractalFourierShellCorrelation</A>
@@ -277,6 +298,7 @@
 <LI> <A HREF="mrcImageInfo.html"> mrcImageInfo</A>
 <LI> <A HREF="mrcImageInverseRadonTransform.html"> mrcImageInverseRadonTransform</A>
 <LI> <A HREF="mrcImageLabeling.html"> mrcImageLabeling</A>
+<LI> <A HREF="mrcImageLogicalOperation.html"> mrcImageLogicalOperation</A>
 <LI> <A HREF="mrcImageLowPassFilter.html"> mrcImageLowPassFilter</A>
 <LI> <A HREF="mrcImageMagnificationChange.html"> mrcImageMagnificationChange</A>
 <LI> <A HREF="mrcImageMake2DArrayImage.html"> mrcImageMake2DArrayImage</A>
@@ -313,12 +335,14 @@
 <LI> <A HREF="mrcImageNullImageCreate.html"> mrcImageNullImageCreate</A>
 <LI> <A HREF="mrcImageOddBoxel.html"> mrcImageOddBoxel</A>
 <LI> <A HREF="mrcImageOneLineSimilarityCalc.html"> mrcImageOneLineSimilarityCalc</A>
+<LI> <A HREF="mrcImageOpening.html"> mrcImageOpening</A>
 <LI> <A HREF="mrcImageOrientationSearch.html"> mrcImageOrientationSearch</A>
 <LI> <A HREF="mrcImageOrientationSearchByHigherSelection.html"> mrcImageOrientationSearchByHigherSelection</A>
 <LI> <A HREF="mrcImageOrientationSearchByHybridization.html"> mrcImageOrientationSearchByHybridization</A>
 <LI> <A HREF="mrcImageOrientationSearchBySimultaneousMinimization.html"> mrcImageOrientationSearchBySimultaneousMinimization</A>
 <LI> <A HREF="mrcImagePCA.html"> mrcImagePCA</A>
 <LI> <A HREF="mrcImagePad.html"> mrcImagePad</A>
+<LI> <A HREF="mrcImagePanoramaCreate.html"> mrcImagePanoramaCreate</A>
 <LI> <A HREF="mrcImageParticleCandidateExtract.html"> mrcImageParticleCandidateExtract</A>
 <LI> <A HREF="mrcImagePeakSearch.html"> mrcImagePeakSearch</A>
 <LI> <A HREF="mrcImagePhaseCTFCompensationFromCTFINFO.html"> mrcImagePhaseCTFCompensationFromCTFINFO</A>
@@ -335,6 +359,7 @@
 <LI> <A HREF="mrcImageROItoPCAoutputImage.html"> mrcImageROItoPCAoutputImage</A>
 <LI> <A HREF="mrcImageRadialDistribution.html"> mrcImageRadialDistribution</A>
 <LI> <A HREF="mrcImageRadonTransform.html"> mrcImageRadonTransform</A>
+<LI> <A HREF="mrcImageRandomParticlesImageCreate.html"> mrcImageRandomParticlesImageCreate</A>
 <LI> <A HREF="mrcImageRealValueAdd.html"> mrcImageRealValueAdd</A>
 <LI> <A HREF="mrcImageRectangleGet.html"> mrcImageRectangleGet</A>
 <LI> <A HREF="mrcImageRectangleGetByCorrelation.html"> mrcImageRectangleGetByCorrelation</A>
@@ -351,7 +376,9 @@
 <LI> <A HREF="mrcImageScalarAdd.html"> mrcImageScalarAdd</A>
 <LI> <A HREF="mrcImageSectionGet.html"> mrcImageSectionGet</A>
 <LI> <A HREF="mrcImageSetFunction.html"> mrcImageSetFunction</A>
+<LI> <A HREF="mrcImageShapeOrientation.html"> mrcImageShapeOrientation</A>
 <LI> <A HREF="mrcImageShapePCA.html"> mrcImageShapePCA</A>
+<LI> <A HREF="mrcImageShapePCAFit.html"> mrcImageShapePCAFit</A>
 <LI> <A HREF="mrcImageShift.html"> mrcImageShift</A>
 <LI> <A HREF="mrcImageShiftFollowingGC.html"> mrcImageShiftFollowingGC</A>
 <LI> <A HREF="mrcImageShrink.html"> mrcImageShrink</A>
@@ -363,6 +390,7 @@
 <LI> <A HREF="mrcImageSinogramFFT.html"> mrcImageSinogramFFT</A>
 <LI> <A HREF="mrcImageSmoothing.html"> mrcImageSmoothing</A>
 <LI> <A HREF="mrcImageSolventFlattening.html"> mrcImageSolventFlattening</A>
+<LI> <A HREF="mrcImageSpatialFrequencyFilter.html"> mrcImageSpatialFrequencyFilter</A>
 <LI> <A HREF="mrcImageSphere.html"> mrcImageSphere</A>
 <LI> <A HREF="mrcImageSphereCheck.html"> mrcImageSphereCheck</A>
 <LI> <A HREF="mrcImageSplit.html"> mrcImageSplit</A>
@@ -381,6 +409,7 @@
 <LI> <A HREF="mrcImageTiltAxisSearchHelp.html"> mrcImageTiltAxisSearchHelp</A>
 <LI> <A HREF="mrcImageToNAMDConstantForces.html"> mrcImageToNAMDConstantForces</A>
 <LI> <A HREF="mrcImageToPointsSet.html"> mrcImageToPointsSet</A>
+<LI> <A HREF="mrcImageTopHatTransform.html"> mrcImageTopHatTransform</A>
 <LI> <A HREF="mrcImageTrans.html"> mrcImageTrans</A>
 <LI> <A HREF="mrcImageTransepose.html"> mrcImageTransepose</A>
 <LI> <A HREF="mrcImageTransformDescartesIntoPolar.html"> mrcImageTransformDescartesIntoPolar</A>
@@ -490,6 +519,7 @@
 <LI> <A HREF="pgMemoSelectCORBAServer.html"> pgMemoSelectCORBAServer</A>
 <LI> <A HREF="pgSelect.html"> pgSelect</A>
 <LI> <A HREF="pointAffineTransform.html"> pointAffineTransform</A>
+<LI> <A HREF="pointsSetToPDB.html"> pointsSetToPDB</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/CheckOrientationByDegree.html b/doc/SmallTools/CheckOrientationByDegree.html
index 1b2b7ff..bf1fd0a 100644
--- a/doc/SmallTools/CheckOrientationByDegree.html
+++ b/doc/SmallTools/CheckOrientationByDegree.html
@@ -1,24 +1 @@
-<HTML>
-<HEAD>
-<TITLE>CheckOrientationByDegree</TITLE>
-</HEAD>
-<BODY>
-<H1>CheckOrientationByDegree</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: CheckOrientationByDegree
-Options:
-    [-i[nput]b[ase]      Inbase              (NULL      )] :Essential :InputBaseDataFile
-    [-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]c[hanging]   modechanging        (0         )] :Optional  :Mode
-
------ mode changing -----
--mc : 0 : do not chang rotational mode of -i
-      1 :        chang rotational mode of -i
-
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: CheckOrientationByDegree: No such file or directory
diff --git a/doc/SmallTools/Display2.html b/doc/SmallTools/Display2.html
index b4e11a4..8e0568d 100644
--- a/doc/SmallTools/Display2.html
+++ b/doc/SmallTools/Display2.html
@@ -9,7 +9,7 @@
 Usage: Display2
 Options:
     [-i[nput]            In                  (NULL      )] :Optional  :InputDataFile
-    [-t[epmlate]         Template            (85.roi    )] :Optional  :Template for InputFile 
+    [-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 
diff --git a/doc/SmallTools/anglediffchk.html b/doc/SmallTools/anglediffchk.html
index 931ab31..e0fdb4f 100644
--- a/doc/SmallTools/anglediffchk.html
+++ b/doc/SmallTools/anglediffchk.html
@@ -1,16 +1 @@
-<HTML>
-<HEAD>
-<TITLE>anglediffchk</TITLE>
-</HEAD>
-<BODY>
-<H1>anglediffchk</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: anglediffchk
-Options:
-    [-c[heckangle]       Check               (0.0       )] :Essential :check
-    [-o[riginalangle]    Original            (0.0       )] :Essential :original
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: anglediffchk: No such file or directory
diff --git a/doc/SmallTools/array2mrc.html b/doc/SmallTools/array2mrc.html
index 41a54c3..c6464e0 100644
--- a/doc/SmallTools/array2mrc.html
+++ b/doc/SmallTools/array2mrc.html
@@ -15,6 +15,19 @@ Options:
     [-m[ode]m[rcimage]   mm                  (2         )] :Optional  :Mode of mrcImage
     [-l[ength]m[rcimage] lm                  (0         )] :Optional  :Length of mrcImage
 ----- Additional Usage -----
+-- Attension --
+Array format : left-hand
+mrc   format : right-hand
+---------------
+>>> Array Format under Eos <<<<
+ndim N0 N1 N2 ...
+data(0,   0,   0,...,        0) data(1,   0,   0,...,        0) data(2,   0,   0,...,        0) ... data(N0-1,   0,   0,...,        0)
+data(0,   1,   0,...,        0) data(1,   1,   0,...,        0) data(2,   1,   0,...,        0) ... data(N0-1,   1,   0,...,        0)
+..............................................................
+data(0,N1-1,   0,...,        0) data(1,N1-1,   0,...,        0) data(2,N1-1,   0,...,        0) ... data(N0-1,N1-1,   0,...,        0)
+data(0,   0,   1,...,        0) data(1,   0,   1,...,        0) data(2,   0,   1,...,        0) ... data(N0-1,   0,   1,...,        0)
+..............................................................
+data(0,N1-1,N2-1,...,Nndim-1-1) data(1,N1-1,N2-1,...,Nndim-1-1) data(2,N1-1,N2-1,...,Nndim-1-1) ... data(N0-1,N1-1,N2-1,...,Nndim-1-1)
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/bmp2mrc.html b/doc/SmallTools/bmp2mrc.html
new file mode 100644
index 0000000..ea98e9d
--- /dev/null
+++ b/doc/SmallTools/bmp2mrc.html
@@ -0,0 +1,26 @@
+<HTML>
+<HEAD>
+<TITLE>bmp2mrc</TITLE>
+</HEAD>
+<BODY>
+<H1>bmp2mrc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: bmp2mrc
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile::bmpFile     ) ] :Essential :Input: bmpFile
+    [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Essential :Output: mrcImage
+    [-L[ength]           LengthX             (1.0       ).as(Real                ) 
+                         LengthY             (1.0       ).as(Real                ) ] :Optional  :Input: Length
+    [-M[ode]             Mode                (0         ).as(Integer             ) ] :Optional  :Input: Mode
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+-M 
+0: Y to mono
+1: R to mono
+2: G to mono
+3: B to mono
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/bmpFileInfo.html b/doc/SmallTools/bmpFileInfo.html
new file mode 100644
index 0000000..6838634
--- /dev/null
+++ b/doc/SmallTools/bmpFileInfo.html
@@ -0,0 +1,18 @@
+<HTML>
+<HEAD>
+<TITLE>bmpFileInfo</TITLE>
+</HEAD>
+<BODY>
+<H1>bmpFileInfo</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: bmpFileInfo
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile::bmpFile     ) ] :Essential :Input: bmpFile
+    [-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
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/calcCommonLine.html b/doc/SmallTools/calcCommonLine.html
index db6be86..0e167d7 100644
--- a/doc/SmallTools/calcCommonLine.html
+++ b/doc/SmallTools/calcCommonLine.html
@@ -1,20 +1 @@
-<HTML>
-<HEAD>
-<TITLE>calcCommonLine</TITLE>
-</HEAD>
-<BODY>
-<H1>calcCommonLine</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: calcCommonLine
-Options:
-    [-i[nput]            In                  (NULL      )] :Optional  :InputEulerAnglesList
-    [-R[ot]1             EMode1              (YOYS      )Rot1_1              (0.0       )Rot1_2              (0.0       )Rot1_3              (0.0       )] :Optional  :Input: RotAngle1[degree]
-    [-R[ot]2             EMode2              (YOYS      )Rot2_1              (0.0       )Rot2_2              (0.0       )Rot2_3              (0.0       )] :Optional  :Input: RotAngle2[degree]
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output:Degrees
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: calcCommonLine: No such file or directory
diff --git a/doc/SmallTools/commonLinesSearchByVoting.html b/doc/SmallTools/commonLinesSearchByVoting.html
index 224e79f..4279e45 100644
--- a/doc/SmallTools/commonLinesSearchByVoting.html
+++ b/doc/SmallTools/commonLinesSearchByVoting.html
@@ -1,54 +1 @@
-<HTML>
-<HEAD>
-<TITLE>commonLinesSearchByVoting</TITLE>
-</HEAD>
-<BODY>
-<H1>commonLinesSearchByVoting</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: commonLinesSearchByVoting
-Options:
-    [-i[nput]            In                  (NULL      )] :Optional  :InputCorrelationMapList
-    [-i[nput]c[ommonLines]InC                 (NULL      )] :Optional  :InputCommonLinesList
-    [-i[nput]c[orrect]c[ommonLines]InCC                (NULL      )] :Optional  :InputCorrectCommonLinesList
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputFilteredCommonLinesList
-    [-o[utput]a[ll]      OutA                (NULL      )] :Optional  :OutputAllCommonLinesList
-    [-o[utput]d[etecting]r[ate]OutDR               (NULL      )] :Optional  :OutputDetectingRate
-    [-o[utput]d[etecting]r[ate]a[ll]OutDRA              (NULL      )] :Optional  :OutputDetectingRateALL
-    [-o[utput]p[eaks]h[istgram]OutPH               (NULL      )] :Optional  :OutputPeaksHistgram
-    [-e[stimation]n[umber]en                  (1         )] :Optional  :EstimationNumber
-    [-th[resholdLevel]   th                  (1         )] :Optional  :ThresholdLevel
-    [-histgramCreate[Flag]] :Optional  :HistgramCreateFlag
-    [-extend[VotingFlag] ] :Optional  :ExtendVotingFlag
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
------ Additional Usage -----
-Common lines are filtered only top G*100/sqrt(N) %, where N is the number of projections.
--extend Option 
-    Execute extended voting.
--m Option 
-    0: normal
-    1: self voting (each angle histgram peak is multiplyed by its correlation value)
--th Option 
-    : 
-   -1: G = 2^(-1) 
-    0: G = 2^0 
-    1: G = 2^1 
-    2: G = 2^2 
-    : 
--en Option 
-    Estimation number of common line in a map. 
-    Running time is proportional to this number.
-    Default; 1: the largest value in a correlation map is detected as common line.
-MapList Format
-    numOfProjection1 numOfProjection2 mapFileName
-           :                :              :     
-CLinesList Format
-    numOfProjection1 numOfProjection2 [ degOfProjection1 degOfProjection2 degDiff cor ] mapFileName
-           :                :                 :                :            :      :         :     
-Voting Algorithm by Amit Singer et al (2010),
-"Detecting consistent common lines in cryo-EM by voting " (doi:10.1016/j.jsb.2009.11.003)
-----------------------------
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: commonLinesSearchByVoting: No such file or directory
diff --git a/doc/SmallTools/ctfDisplay.html b/doc/SmallTools/ctfDisplay.html
index 4331bd1..f1cef89 100644
--- a/doc/SmallTools/ctfDisplay.html
+++ b/doc/SmallTools/ctfDisplay.html
@@ -13,6 +13,7 @@ Options:
     [-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
diff --git a/doc/SmallTools/dmInfo.html b/doc/SmallTools/dmInfo.html
new file mode 100644
index 0000000..d8c4247
--- /dev/null
+++ b/doc/SmallTools/dmInfo.html
@@ -0,0 +1,18 @@
+<HTML>
+<HEAD>
+<TITLE>dmInfo</TITLE>
+</HEAD>
+<BODY>
+<H1>dmInfo</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: dmInfo
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile::dmFile      ) ] :Essential :Input:dfFile(dm3|dm4)
+    [-o[utput]           Out                 (stdout    ).as(outFile::ASCII      ) ] :Optional  :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/eosPointProjector.html b/doc/SmallTools/eosPointProjector.html
new file mode 100644
index 0000000..83abaa6
--- /dev/null
+++ b/doc/SmallTools/eosPointProjector.html
@@ -0,0 +1,35 @@
+<HTML>
+<HEAD>
+<TITLE>eosPointProjector</TITLE>
+</HEAD>
+<BODY>
+<H1>eosPointProjector</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: eosPointProjector
+Options:
+    [-i[nput]            In                  (stdin     ).as(inFile::ASCII       ) ] :Optional  :Input: eosPoint
+    [-i[nput]t[ype]      InType              (3         ).as(Integer             ) ] :Optional  :Input: eosPointType
+    [-o[utput]           Out                 (stdout    ).as(outFile::ASCII      ) ] :Optional  :Output: eosPoint
+    [-o[utput]t[ype]     OutType             (3         ).as(Integer             ) ] :Optional  :Input: eosPointType
+    [-E[uler]A[ngle]     EAMode              (YOYS      ).as(String              ) 
+                         Rot1                (0.0       ).as(Real                ) 
+                         Rot2                (0.0       ).as(Real                ) 
+                         Rot3                (0.0       ).as(Real                ) ] :Optional  :Input: EulerAngleMode Rot1 Rot2 Rot3
+    [-I[nput]            InList              (NULL      ).as(inFileList::ASCII   ) ] :Optional  :Input:  eosPointFileList
+    [-O[uput]            OutList             (NULL      ).as(outFileList::ASCII  ) ] :Optional  :Output: eosPointFileList
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+>> eosPointFileType
+type-0: x y z
+type-1: x y z sig
+type-2: x y z sigx sigy sigz
+type-3: x y z sig sigx sigy sigz
+>> mode
+0: x-projection
+1: y-projection
+2: z-projection
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/eosPointRotation.html b/doc/SmallTools/eosPointRotation.html
new file mode 100644
index 0000000..8b1de86
--- /dev/null
+++ b/doc/SmallTools/eosPointRotation.html
@@ -0,0 +1,31 @@
+<HTML>
+<HEAD>
+<TITLE>eosPointRotation</TITLE>
+</HEAD>
+<BODY>
+<H1>eosPointRotation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: eosPointRotation
+Options:
+    [-i[nput]            In                  (stdin     ).as(inFile::ASCII       ) ] :Optional  :Input: eosPoint
+    [-i[nput]t[ype]      InType              (3         ).as(Integer             ) ] :Optional  :Input: eosPointType
+    [-o[utput]           Out                 (stdout    ).as(outFile::ASCII      ) ] :Optional  :Output: eosPoint
+    [-o[utput]t[ype]     OutType             (3         ).as(Integer             ) ] :Optional  :Input: eosPointType
+    [-E[uler]A[ngle]     EAMode              (YOYS      ).as(String              ) 
+                         Rot1                (0.0       ).as(Real                ) 
+                         Rot2                (0.0       ).as(Real                ) 
+                         Rot3                (0.0       ).as(Real                ) ] :Optional  :Input: EulerAngleMode Rot1 Rot2 Rot3
+    [-I[nput]            InList              (NULL      ).as(inFileList::ASCII   ) ] :Optional  :Input:  eosPointFileList
+    [-O[uput]            OutList             (NULL      ).as(outFileList::ASCII  ) ] :Optional  :Output: eosPointFileList
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+>> eosPointFileType
+type-0: x y z
+type-1: x y z sig
+type-2: x y z sigx sigy sigz
+type-3: x y z sig sigx sigy sigz
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/eosPointTracker.html b/doc/SmallTools/eosPointTracker.html
new file mode 100644
index 0000000..b94339c
--- /dev/null
+++ b/doc/SmallTools/eosPointTracker.html
@@ -0,0 +1,38 @@
+<HTML>
+<HEAD>
+<TITLE>eosPointTracker</TITLE>
+</HEAD>
+<BODY>
+<H1>eosPointTracker</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: eosPointTracker
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFileList::ASCII::eosPoint) ] :Essential :Input: Tracker2D[eosPoint]
+    [-i[nput]P[arameter] InParam             (NULL      ).as(inFileList::ASCII   ) ] :Essential :Input: InitialParams
+    [-o[utput]           Out                 (NULL      ).as(outFile::ASCII::eosPoint) ] :Essential :Output: Tracker3D[eosPoint]
+    [-o[utput]2D         Out2D               (NULL      ).as(outFileList::ASCII::eosPoint) ] :Essential :Output: Tracker3D[eosPoint]
+    [-o[utput]P[arameter]OutParam            (NULL      ).as(outFileList::ASCII  ) ] :Essential :Output: Params
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+----- input; -i  -----
+-i pointListPerEachImage
+point2d.000
+point2d.001
+.....
+EachFile::eosPoint(type3)
+x0 y0 0 weight0 sigx0 sigy0 0
+x1 y1 0 weight1 sigx1 sigy1 0
+.....
+----- input; -iP  -----
+matInit.000
+matInit.001
+.....
+EachFile:: ex.tiltSeries  tiltInfo Y->X->Z
+image000 YOYS tiltAngle0 tiltAxisBeta0 tiltAxisAlpha0 axisShiftX0 axisShiftY0
+image001 YOYS tiltAngle1 tiltAxisBeta1 tiltAxisAlpha1 axisShiftX1 axisShiftY1
+.....
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/hf2000Init.html b/doc/SmallTools/hf2000Init.html
index cfe38eb..63602bd 100644
--- a/doc/SmallTools/hf2000Init.html
+++ b/doc/SmallTools/hf2000Init.html
@@ -1,19 +1 @@
-<HTML>
-<HEAD>
-<TITLE>hf2000Init</TITLE>
-</HEAD>
-<BODY>
-<H1>hf2000Init</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: hf2000Init
-Options:
-    [-tty                tty                 (/dev/ttyS1)] :Optional  :DeviceFile
-    [-speed              speed               (4800      )] :Optional  :SerialPort Speed
-    [-S[erver]           Host                (tkyemg-pc06)Server              (6000      )] :Optional  :host port: As Server: Default Shell mode
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: hf2000Init: No such file or directory
diff --git a/doc/SmallTools/hf2000LenzCurrent.html b/doc/SmallTools/hf2000LenzCurrent.html
index 60361f4..729cdc6 100644
--- a/doc/SmallTools/hf2000LenzCurrent.html
+++ b/doc/SmallTools/hf2000LenzCurrent.html
@@ -1,22 +1 @@
-<HTML>
-<HEAD>
-<TITLE>hf2000LenzCurrent</TITLE>
-</HEAD>
-<BODY>
-<H1>hf2000LenzCurrent</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: hf2000LenzCurrent
-Options:
-    [-i[nput]            In                  (NULL      )] :Optional  :InputDataFile
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-tty                tty                 (/dev/ttyS1)] :Optional  :TTY
-    [-speed              speed               (4800      )] :Optional  :TTY
-    [-which[Lenz]        which               (OBJ       )] :Optional  :Lenz:C1/C2/C3/OBJ/I1/I2/P1/P2
-    [-I[nteractive]      Interactive         (5         )] :Optional  :[sec]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: hf2000LenzCurrent: No such file or directory
diff --git a/doc/SmallTools/hf2000SpecimenPosition.html b/doc/SmallTools/hf2000SpecimenPosition.html
index 5b975cc..bc6d2f9 100644
--- a/doc/SmallTools/hf2000SpecimenPosition.html
+++ b/doc/SmallTools/hf2000SpecimenPosition.html
@@ -1,23 +1 @@
-<HTML>
-<HEAD>
-<TITLE>hf2000SpecimenPosition</TITLE>
-</HEAD>
-<BODY>
-<H1>hf2000SpecimenPosition</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: hf2000SpecimenPosition
-Options:
-    [-i[nput]            In                  (NULL      )] :Optional  :InputDataFile
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-tty                tty                 (/dev/ttyS1)] :Optional  :TTY
-    [-speed              Speed               (4800      )] :Optional  :Speed
-    [-p[osition]         posX                (0.0       )posY                (0.0       )] :Optional  :Set Position[um,um]
-    [-I[nteractive]      Interactive         (5         )] :Optional  :Interactive[sec]
-    [-S[erver]           Host                (tkyemg-pc06)Port                (6000      )] :Optional  :Host port Server[sec]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: hf2000SpecimenPosition: No such file or directory
diff --git a/doc/SmallTools/llExtract.html b/doc/SmallTools/llExtract.html
index 9ba3524..4e1da99 100644
--- a/doc/SmallTools/llExtract.html
+++ b/doc/SmallTools/llExtract.html
@@ -8,24 +8,33 @@
 <PRE>
 Usage: llExtract
 Options:
-    [-t[itle]            Title               (NULL      )] :Optional  :Title[80]
-    [-s[tep]             xStep               (1.0       )yStep               (1.0       )] :Optional  :Step[A]
-    [-M[ax]              MaxX                (1.0       )MaxY                (1.0       )] :Optional  :Max[GridUnit]
-    [-i[nput]            In                  (NULL      )] :Optional  :InputDataFile[mrcImage]
-    [-1[output]          Nea                 (NULL      )] :Optional  :NearSide[llData]
-    [-2[output]          Far                 (NULL      )] :Optional  :FarSide [llData]
-    [-R[otationAngle]    RotationAngle       (0.0       )] :Optional  :Ratation Angle [Degree]
-    [-O[mega]            Omega               (0.0       )] :Optional  :Omega[Degree]
-    [-S[hear]            Shear               (0.0       )] :Optional  :Shear[Degree]
-    [-I[every]           ievery              (0         )] :Optional  :ievery
-    [-axl                axl                 (0.0       )] :Optional  :axl
-    [-ayl                ayl                 (0.0       )] :Optional  :ayl
-    [-x[Shift]           xShift              (0.0       )] :Optional  :[GridUnit]
-    [-l[lMax]            llMax               (0         )] :Optional  :
-    [-d[elRInv]          delRInv             (0.0       )] :Optional  :[A]
-    [-f[lagOutputInfo]   ] :Optional  :
-    [-L[ayerLineInfo]    n                   (0         )l                   (0         )Y                   (0.0       )leftMin             (0.0       )leftMax             (0.0       )rightMin            (0.0       )rightMax            (0.0       )weight              (1.0       )... ] :Variable  :
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-t[itle]            Title               (NULL      ).as(String              ) ] :Optional  :Title[80]
+    [-s[tep]             xStep               (1.0       ).as(Real                ) 
+                         yStep               (1.0       ).as(Real                ) ] :Optional  :Step[A]
+    [-M[ax]              MaxX                (1.0       ).as(Real                ) 
+                         MaxY                (1.0       ).as(Real                ) ] :Optional  :Max[GridUnit]
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Optional  :InputDataFile[mrcImage]
+    [-1[output]          Nea                 (NULL      ).as(outFile             ) ] :Optional  :NearSide[llData]
+    [-2[output]          Far                 (NULL      ).as(outFile             ) ] :Optional  :FarSide [llData]
+    [-R[otationAngle]    RotationAngle       (0.0       ).as(Real                ) ] :Optional  :Ratation Angle [Degree]
+    [-O[mega]            Omega               (0.0       ).as(Real                ) ] :Optional  :Omega[Degree]
+    [-S[hear]            Shear               (0.0       ).as(Real                ) ] :Optional  :Shear[Degree]
+    [-I[every]           ievery              (0         ).as(Integer             ) ] :Optional  :ievery
+    [-axl                axl                 (0.0       ).as(Real                ) ] :Optional  :axl
+    [-ayl                ayl                 (0.0       ).as(Real                ) ] :Optional  :ayl
+    [-x[Shift]           xShift              (0.0       ).as(Real                ) ] :Optional  :[GridUnit]
+    [-l[lMax]            llMax               (0         ).as(Integer             ) ] :Optional  :
+    [-d[elRInv]          delRInv             (0.0       ).as(Real                ) ] :Optional  :[A]
+    [-f[lagOutputInfo]                                                             ] :Optional  :
+    [-L[ayerLineInfo]    n                   (0         ).as(Integer             ) 
+                         l                   (0         ).as(Integer             ) 
+                         Y                   (0.0       ).as(Real                ) 
+                         leftMin             (0.0       ).as(Real                ) 
+                         leftMax             (0.0       ).as(Real                ) 
+                         rightMin            (0.0       ).as(Real                ) 
+                         rightMax            (0.0       ).as(Real                ) 
+                         weight              (1.0       ).as(Real                ) ... ] :Variable  :
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
 ----- Control File -----
 Title[String:NULL]				#Title[80]
 xStep[Real:1.0]	yStep[Real:1.0]				#Step[A]
diff --git a/doc/SmallTools/marker2Dto3DEstimator.html b/doc/SmallTools/marker2Dto3DEstimator.html
new file mode 100644
index 0000000..6ab13bf
--- /dev/null
+++ b/doc/SmallTools/marker2Dto3DEstimator.html
@@ -0,0 +1,30 @@
+<HTML>
+<HEAD>
+<TITLE>marker2Dto3DEstimator</TITLE>
+</HEAD>
+<BODY>
+<H1>marker2Dto3DEstimator</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: marker2Dto3DEstimator
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFileList::ASCII   ) ] :Essential :Input: 
+    [-i[nput]t[ype]      InType              (2         ).as(Integer             ) ] :Optional  :Input: 
+    [-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: 
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+----- input; -i  -----
+-i pointListPerEachImage
+point2d.000 YOYS tiltAngle0 tiltAxisBeta0 tiltAxisAlpha0 axisShiftX0 axisShiftY0
+point2d.001 YOYS tiltAngle1 tiltAxisBeta1 tiltAxisAlpha1 axisShiftX1 axisShiftY1
+.....
+EachFile::eosPoint(type)
+x0 y0 0 weight0 sigx0 sigy0 0
+x1 y1 0 weight1 sigx1 sigy1 0
+.....
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrc2Dto3D.html b/doc/SmallTools/mrc2Dto3D.html
index 8184e5f..6583451 100644
--- a/doc/SmallTools/mrc2Dto3D.html
+++ b/doc/SmallTools/mrc2Dto3D.html
@@ -8,34 +8,45 @@
 <PRE>
 Usage: mrc2Dto3D
 Options:
-    [-i[nput]            In                  (NULL      )] :Optional  :InputDataFile
-    [-I[nput]            In2                 (NULL      )] :Optional  :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-O[utput]           Out2                (NULL      )] :Optional  :OutputDataFile[2DMulti]
-    [-single             single              (1         )] :Optional  :SingleTiltMode
-    [-InterpolationMode  InterpolationMode   (1         )] :Optional  :InterpolationMode
-    [-Double             ] :Optional  :DoubleTiltMode
-    [-DoubleCounter      DoubleCounter       (NULL      )] :Optional  :DoubleCounter
-    [-CounterThreshold   CounterThreshold    (1e-6      )] :Optional  :CounterThreshold
-    [-CounterThresholdModeCounterThresholdMode(0         )] :Optional  :CounterThresholdMode
-    [-WeightMode         WeightMode          (0         )] :Optional  :WeightMode
-    [-thicknessWeight    ] :Optional  :ThicknessWeight
-    [-Sub[Sampling]      SubSampling         (1         )] :Optional  :SubSampling: [pixel]
-    [-PlusXrot           ] :Optional  :plus x-rotation by 180 for rasmol.
-    [-N                  Nx                  (0         )Ny                  (0         )Nz                  (0         )] :Optional  :OutputSize
-    [-SIRT               ] :Optional  :by SIRT
-    [-max[Iter]          maxIter             (30        )] :Optional  :MaxIteration for SIRT
-    [-rms                rms                 (1.0       )] :Optional  :Ending Conditions: rms for SIRT
-    [-CTF[Info]          CTFInfo             (NULL      )] :Optional  :CTFInfo: for SIRT
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Optional  :InputDataFile
+    [-I[nput]            In2                 (NULL      ).as(inFileListNoOpen    ) ] :Optional  :InputDataFile
+    [-each                                                                         ] :Optional  :Read each projection file if necessary, not at once.
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-O[utput]           Out2                (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile[2DMulti]
+    [-Rmax               Rmax                (1.0       ).as(Real                ) ] :Optional  :Rmax: High Cut [/A]
+    [-single             single              (1         ).as(Integer             ) ] :Optional  :SingleTiltMode
+    [-singleFilter       singleFilter        (0         ).as(Integer             ) ] :Optional  :SingleFilterMode
+    [-InterpolationMode  InterpolationMode   (1         ).as(Integer             ) ] :Optional  :InterpolationMode
+    [-Double                                                                       ] :Optional  :DoubleTiltMode
+    [-DoubleCounter      DoubleCounter       (NULL      ).as(outFile             ) ] :Optional  :DoubleCounter
+    [-CounterThreshold   CounterThreshold    (1e-6      ).as(Real                ) ] :Optional  :CounterThreshold
+    [-CounterThresholdModeCounterThresholdMode(0         ).as(Integer             ) ] :Optional  :CounterThresholdMode
+    [-WeightMode         WeightMode          (0         ).as(Integer             ) ] :Optional  :WeightMode
+    [-thicknessWeight                                                              ] :Optional  :ThicknessWeight
+    [-Sub[Sampling]      SubSampling         (1         ).as(Integer             ) ] :Optional  :SubSampling: [pixel]
+    [-PlusXrot                                                                     ] :Optional  :plus x-rotation by 180 for rasmol.
+    [-N                  Nx                  (0         ).as(Integer             ) 
+                         Ny                  (0         ).as(Integer             ) 
+                         Nz                  (0         ).as(Integer             ) ] :Optional  :OutputSize
+    [-SIRT                                                                         ] :Optional  :by SIRT
+    [-max[Iter]          maxIter             (30        ).as(Integer             ) ] :Optional  :MaxIteration for SIRT
+    [-rms                rms                 (1.0       ).as(Real                ) ] :Optional  :Ending Conditions: rms for SIRT
+    [-CTF[Info]          CTFInfo             (NULL      ).as(inFileList          ) ] :Optional  :CTFInfo: for SIRT
+    [-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 -----
 -m Option
     0:SimpleBackProjection
-    1:FilteredBackProjection
+    1:FilteredBackProjection(Fourier Space)
+    2:WeightedBackProjection(Real Space)
 -single 0|1 
     0: tilt axis is parallel to x-axis
     1: tilt axis is parallel to y-axis
+-singleFilter 0|1|2 
+    0: simple rho filter
+    1: Ram-Lak Filter
+    2: Shepp-Logan Filter
 -Double 
     Double Tilt 
 -WeightMode 
diff --git a/doc/SmallTools/mrc2hdf.html b/doc/SmallTools/mrc2hdf.html
old mode 100755
new mode 100644
index 1a2815f..2436d28
--- a/doc/SmallTools/mrc2hdf.html
+++ b/doc/SmallTools/mrc2hdf.html
@@ -1 +1 @@
-sh: mrc2hdf:  not found
+/bin/bash: mrc2hdf: No such file or directory
diff --git a/doc/SmallTools/mrc2mrc.html b/doc/SmallTools/mrc2mrc.html
new file mode 100644
index 0000000..9b8dfbf
--- /dev/null
+++ b/doc/SmallTools/mrc2mrc.html
@@ -0,0 +1,26 @@
+<HTML>
+<HEAD>
+<TITLE>mrc2mrc</TITLE>
+</HEAD>
+<BODY>
+<H1>mrc2mrc</H1>
+<H2>Usage</H2>
+<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
+----- Additional Usage -----
+>> To be suppoerted (Not all)
+Eos
+CCP4-2000
+IMODextendedMRC
+FEIextendedMRC
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrc3Dto2D.html b/doc/SmallTools/mrc3Dto2D.html
index 0e13bd0..3711c0e 100644
--- a/doc/SmallTools/mrc3Dto2D.html
+++ b/doc/SmallTools/mrc3Dto2D.html
@@ -8,14 +8,16 @@
 <PRE>
 Usage: mrc3Dto2D
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-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
 ----- Additional Usage -----
diff --git a/doc/SmallTools/mrcFFTInfo.html b/doc/SmallTools/mrcFFTInfo.html
index b16b6e0..979e9ba 100644
--- a/doc/SmallTools/mrcFFTInfo.html
+++ b/doc/SmallTools/mrcFFTInfo.html
@@ -8,18 +8,22 @@
 <PRE>
 Usage: mrcFFTInfo
 Options:
-    [-i[nput]            In                  ] :Essential :InputDataFile
-    [-o[utput]           Out                 ] :Essential :OutputDataFile
-    [-c[onfig]           configFile          ] :Optional  :ConfigurationFile
-    [-m[ode]             mode                ] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input
+    [-o[utput]           Out                 (NULL      ).as(outFile::ASCII      ) ] :Essential :Output
+    [-a[ngle]            Angle               (0.0       ).as(Real                ) ] :Optional  :Angle
+    [-nDiv[ision]        nDivision           (18        ).as(Integer             ) ] :Optional  :num of Divsion
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 Mode: 
 	 1 :Scattering Angular Distribution(Sum)
 	 2 :X-axis (OutPut: Mag, Phase)
 	 4 :Y-axis (OutPut: Mag, Phase)
 	 5 :Y-axis (Average:Along X-axis)(OutPut: Mag, Phase)
+	 7 :Scattering Angular Distribution(Average, range(angle, nDivion)xnDiv; e.g. (10, 18) -> range(10-360/18/2, 10+360/18/2) x nDiv
 	 8 :Scattering Angular Distribution(Average)
-	16 :with spacing 
-	32 :with Angular Distribution(SD)
+	+16 :with spacing 
+	+32 :with Angular Distribution(SD)
+	+64 :Log Scaling for |value| 
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImage3DPad.html b/doc/SmallTools/mrcImage3DPad.html
index e89d3a2..b9e1455 100644
--- a/doc/SmallTools/mrcImage3DPad.html
+++ b/doc/SmallTools/mrcImage3DPad.html
@@ -24,8 +24,10 @@ Options:
 0:Default: Out of threshold is avrage of threshold plain.
 1:Mulplying cos function. Default: Out of threshold is avrage of threshold plain.
 ----- mode2 -----
-0:For filaments.  R is calculated from its axis.
-1:For particles.  R is calculated from its center.
+0: Filament-type(cylinder)
+1: SingleParticle-type(sphere)
+2: SigplePartilce-type(ellipsoid)
+3: Rectangle
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageAddValue.html b/doc/SmallTools/mrcImageAddValue.html
index 15bf9d7..99bfc4e 100644
--- a/doc/SmallTools/mrcImageAddValue.html
+++ b/doc/SmallTools/mrcImageAddValue.html
@@ -8,11 +8,12 @@
 <PRE>
 Usage: mrcImageAddValue
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: mrc
-    [-o[utput]           Out                 (NULL      )] :Essential :Output: mrc
-    [-v[alue]            Value               (0.0       )] :Optional  :Value: o=i+v
-    [-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               (0.0       ).as(Real                ) ] :Optional  :Value: o=i+v
+    [-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 -----
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageAsProbability.html b/doc/SmallTools/mrcImageAsProbability.html
new file mode 100644
index 0000000..3958a27
--- /dev/null
+++ b/doc/SmallTools/mrcImageAsProbability.html
@@ -0,0 +1,18 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageAsProbability</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageAsProbability</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageAsProbability
+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/mrcImageAutoRotationAverage.html b/doc/SmallTools/mrcImageAutoRotationAverage.html
new file mode 100644
index 0000000..6c84b11
--- /dev/null
+++ b/doc/SmallTools/mrcImageAutoRotationAverage.html
@@ -0,0 +1,41 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageAutoRotationAverage</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageAutoRotationAverage</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageAutoRotationAverage
+Options:
+    [-i[nput]            In                  (stdin     ).as(inFileList::mrcImage) ] :Essential :Input: Ins
+    [-r[eferenc]         Ref                 (NULL      ).as(inFile::mrcImage    ) ] :Optional  :Input: Ref
+    [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Essential :Output:Average
+    [-range              Min                 (0.0       ).as(Real                ) 
+                         Max                 (360.0     ).as(Real                ) 
+                         Delta               (5.0       ).as(Real                ) 
+                         Iter                (2         ).as(Integer             ) ] :Optional  :Mode
+    [-iter               iter                (2         ).as(Integer             ) ] :Optional  :iteration for rotation
+    [-M[odeCorrelation]  CorMode             (16        ).as(Integer             ) ] :Optional  :Mode: Correlation
+    [-Method[Correlation]Method              (0         ).as(Integer             ) ] :Optional  :Method: Correlation
+    [-Periodic                                                                     ] :Optional  :Periodic
+    [-maxIter[aration]   maxIter             (10        ).as(Integer             ) ] :Optional  :MaxIteration
+    [-rmsd               rmsd                (1e-2      ).as(Real                ) ] :Optional  :rmsd
+    [-log                Log                 (stdout    ).as(outFile::ASCII      ) ] :Optional  :logFile
+    [-thres[hold]        Thres               (0.2       ).as(Real                ) ] :Optional  :threshold: Linear Correlation
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+----- -Mode -----
+0: Normal Correlation FxG*
+1: Phase  Correlation FxG*/     |FxG*|
+2: Phase  Correlation FxG*/sqrt(|FxG*|)
+3: Normalized Normal Correlation FxG*/|F||G|)
+16: (0,0) = 0 
+Refinement Correlation Map
+0: sqrt(Sum |Fi-Gi|^2                 / Sum |Gi|^2)
+1:      Sum |Gi||phaseFi - phaseGi|   / Sum |Gi|  
+2: sqrt(Sum |Gi||phaseFi - phaseGi|^2 / Sum |Gi|  )
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageAutoRotationCorrelation3D.html b/doc/SmallTools/mrcImageAutoRotationCorrelation3D.html
index fff02e9..9d06763 100644
--- a/doc/SmallTools/mrcImageAutoRotationCorrelation3D.html
+++ b/doc/SmallTools/mrcImageAutoRotationCorrelation3D.html
@@ -1 +1,45 @@
-/bin/bash: mrcImageAutoRotationCorrelation3D: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>mrcImageAutoRotationCorrelation3D</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageAutoRotationCorrelation3D</H1>
+<H2>Usage</H2>
+<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
+----- Additional Usage -----
+----- -M  CorrelationMode -----
+0: Normal Correlation FxG*
+1: Phase  Correlation FxG*/     |FxG*|
+2: Phase  Correlation FxG*/sqrt(|FxG*|)
+3: Normalized Normal Correlation FxG*/|F||G|)
+16: (0,0) = 0 
+Refinement Correlation Map
+0: sqrt(Sum |Fi-Gi|^2                 / Sum |Gi|^2)
+1:      Sum |Gi||phaseFi - phaseGi|   / Sum |Gi|  
+2: sqrt(Sum |Gi||phaseFi - phaseGi|^2 / Sum |Gi|  )
+----- -MR RotationMode -----
+ 0: padding 0 
+ 1: padding average 
+ +0:  within ellipsoidal area.
+ +16: within square area.
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageBilateralFilter.html b/doc/SmallTools/mrcImageBilateralFilter.html
new file mode 100644
index 0000000..a68e566
--- /dev/null
+++ b/doc/SmallTools/mrcImageBilateralFilter.html
@@ -0,0 +1,36 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageBilateralFilter</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageBilateralFilter</H1>
+<H2>Usage</H2>
+<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
+----- Additional Usage -----
+Bilateral Filter
+    by Tomashi and Manduchi
+    C. Tomasi and R. Manduchi, Bilateral Filtering for Gray and Color Images, Proceedings of the 1998 IEEE International Conference on Computer Vision, Bombay, India
+ fi = Sigma_j(W(i,j)*Ij)/ Sigma_j(Wj)   
+   ,where W(i,j)=W_x(xi,xj)*W_I(Ii,Ij)    
+------- linfo.mode : 0 
+                 W_x(xi,xj) = exp(-|xi-xj|^2/2 sigmaSpace^2  )
+                 W_I(Ii,Ij) = exp(-|Ii-Ij|^2/2 sigmaDensity^2)
+------- linfo.mode : 1 
+                 W_x(xi,xj) = 1/(1+|xi-xj|^2/sigmaSpace^2  )   
+                 W_I(Ii,Ij) = 1/(1+|Ii-Ij|^2/sigmaDensity^2)   
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageBottomHatTransform.html b/doc/SmallTools/mrcImageBottomHatTransform.html
new file mode 100644
index 0000000..073a813
--- /dev/null
+++ b/doc/SmallTools/mrcImageBottomHatTransform.html
@@ -0,0 +1,23 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageBottomHatTransform</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageBottomHatTransform</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageBottomHatTransform
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-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 -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageClosing.html b/doc/SmallTools/mrcImageClosing.html
new file mode 100644
index 0000000..39073ad
--- /dev/null
+++ b/doc/SmallTools/mrcImageClosing.html
@@ -0,0 +1,33 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageClosing</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageClosing</H1>
+<H2>Usage</H2>
+<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
+----- Additional Usage -----
+----- Structuring Element : Mode 
+0: 2D Cross3x3:  4-neighbour
+1: 2D Square3x3: 8-neighbour
+2: 2D Open Disk , need (radius, n)
+3: 3D Cross3x3x3:   6-neighbour
+4: 3D Cubic3x3x3: 26-neighbour
+5: 3D Open Disk , need (radius, n)
+-----
+Dilation: Max for image : Or  for binary image 
+Erosion:  Min for image : And for binary image 
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageConvolution.html b/doc/SmallTools/mrcImageConvolution.html
new file mode 100644
index 0000000..9c890d4
--- /dev/null
+++ b/doc/SmallTools/mrcImageConvolution.html
@@ -0,0 +1,30 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageConvolution</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageConvolution</H1>
+<H2>Usage</H2>
+<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
+----- Additional Usage -----
+>>> Array Format under Eos <<<<
+ndim N0 N1 N2 ...
+data(0,   0,   0,...,        0) data(1,   0,   0,...,        0) data(2,   0,   0,...,        0) ... data(N0-1,   0,   0,...,        0)
+data(0,   1,   0,...,        0) data(1,   1,   0,...,        0) data(2,   1,   0,...,        0) ... data(N0-1,   1,   0,...,        0)
+..............................................................
+data(0,N1-1,   0,...,        0) data(1,N1-1,   0,...,        0) data(2,N1-1,   0,...,        0) ... data(N0-1,N1-1,   0,...,        0)
+data(0,   0,   1,...,        0) data(1,   0,   1,...,        0) data(2,   0,   1,...,        0) ... data(N0-1,   0,   1,...,        0)
+..............................................................
+data(0,N1-1,N2-1,...,Nndim-1-1) data(1,N1-1,N2-1,...,Nndim-1-1) data(2,N1-1,N2-1,...,Nndim-1-1) ... data(N0-1,N1-1,N2-1,...,Nndim-1-1)
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageDeconvolution.html b/doc/SmallTools/mrcImageDeconvolution.html
new file mode 100644
index 0000000..250b9de
--- /dev/null
+++ b/doc/SmallTools/mrcImageDeconvolution.html
@@ -0,0 +1,45 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageDeconvolution</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageDeconvolution</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageDeconvolution
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input: Src
+    [-k[ernel]           Kernel              (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input: Kernel
+    [-k[ernel]centre     KernelCentre        (1         ).as(Integer             ) ] :Optional  :Input: Kernel Centre
+    [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Essential :Output: Dst
+    [-o[utput]conv       OutConv             (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output: Conv*Dst to compare with in
+    [-O[utput]           OutASCII            (stdout    ).as(outFile::ASCII      ) ] :Optional  :Output: Param
+    [-O[utput]RMSD       OutRMSD             (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output: Param
+    [-thresCTF           thresCTF            (1e-4      ).as(Real                ) ] :Optional  :threshold CTF for InverseFilter
+    [-NSRatio            NSRatio             (0.0       ).as(Real                ) ] :Optional  :N/S Ratio for R-dependent Wiener Filter
+    [-NSCoeff            NSCoeff             (0.0       ).as(Real                ) ] :Optional  :N/S Coeff for R-dependent Wiener Filter
+    [-Pad3DMode          Pad3DMode           (1         ).as(Integer             ) ] :Optional  :lmrcImage3DPad Mode
+    [-r[max]             r                   (0         ).as(Real                ) ] :Optional  :Pad3D: [pix] Threshold radius of signal.Default is min(Nx,Ny).
+    [-w[idth]            w                   (1         ).as(Real                ) ] :Optional  :Pad3D: [pix] Width of slope. For mode 1.
+    [-v[alue]            v                   (0         ).as(Real                ) ] :Optional  :Pad3D: Value of out of threshold.
+    [-Floating                                                                     ] :Optional  :Pad3D: Floating
+    [-maxIter            maxIter             (0         ).as(Integer             ) ] :Optional  :maxIteration for Iterative
+    [-minRMSD            minRMSD             (0.0       ).as(Real                ) ] :Optional  :min of MRSD for Iterative
+    [-lambda             lambda              (0.5       ).as(Real                ) ] :Optional  :lambda for Iterative
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+Deconvolution Mode 
+0: No deconvolution
+1: CTF/|CTF| (phase flipping)
+2: CTF       (CTF-Multi)
+3: 1/CTF     (Inverse Filter)
+4: CTF/(SQR(CTF)+SQR(NS))  (Wiener Filter)
+5: SQR(CTF) x CTF/|CTF|    (phase flipping + ctfWeighted)
+6: 1/|CTF|                   (No phase-flipping: Inverse Filter)
+7: |CTF|/(SQR(CTF)+SQR(NS))  (No phase-flipping: Wiener Filter)
+8:  CTF /(SQR(CTF)+SQR(NS*exp(a*R)))  (phase-flipping:    Wiener Filter + Noise)
+9: |CTF|/(SQR(CTF)+SQR(NS*exp(a*R)))  (No phase-flipping: Wiener Filter + Noise)
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageDensityInfo.html b/doc/SmallTools/mrcImageDensityInfo.html
index 6e1c41e..a3a31a4 100644
--- a/doc/SmallTools/mrcImageDensityInfo.html
+++ b/doc/SmallTools/mrcImageDensityInfo.html
@@ -10,7 +10,7 @@ Usage: mrcImageDensityInfo
 Options:
     [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
     [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-C[ontour]          Contour             (10        )] :Optional  :ContourLevel: 10 2.345000e-310ach
+    [-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
diff --git a/doc/SmallTools/mrcImageDilation.html b/doc/SmallTools/mrcImageDilation.html
new file mode 100644
index 0000000..70fe244
--- /dev/null
+++ b/doc/SmallTools/mrcImageDilation.html
@@ -0,0 +1,32 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageDilation</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageDilation</H1>
+<H2>Usage</H2>
+<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
+----- Additional Usage -----
+----- Structuring Element : Mode 
+0: 2D Cross3x3:  4-neighbour
+1: 2D Square3x3: 8-neighbour
+2: 2D Open Disk , need (radius, n)
+3: 3D Cross3x3x3:   6-neighbour
+4: 3D Cubic3x3x3: 26-neighbour
+5: 3D Open Disk , need (radius, n)
+-----
+Dilation: Max for image : Or  for binary image 
+Erosion:  Min for image : And for binary image 
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageDividedByFile.html b/doc/SmallTools/mrcImageDividedByFile.html
new file mode 100644
index 0000000..4deb380
--- /dev/null
+++ b/doc/SmallTools/mrcImageDividedByFile.html
@@ -0,0 +1,19 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageDividedByFile</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageDividedByFile</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageDividedByFile
+Options:
+    [-i[nput]1           In1                 (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input: In1
+    [-i[nput]2           In2                 (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input: In2
+    [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Essential :Output: In1/In2
+    [-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/mrcImageEdgeEnhancement.html b/doc/SmallTools/mrcImageEdgeEnhancement.html
new file mode 100644
index 0000000..6ff7c44
--- /dev/null
+++ b/doc/SmallTools/mrcImageEdgeEnhancement.html
@@ -0,0 +1,29 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageEdgeEnhancement</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageEdgeEnhancement</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageEdgeEnhancement
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Essential :OutputDataFile
+    [-o[utput]d[irection]OutDirection        (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output: Direction
+    [-M[ode]             NeighborMode        (0         ).as(Integer             ) ] :Optional  :Input: NeighborMode
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+mode: 0 : Differential(SQRT)
+mode: 1 : Differential(ABS)
+mode: 2 : Roberts Cross(SQRT)
+mode: 3 : Roberts Cross(ABS)
+mode: 4 : Prewitt(SQRT)
+mode: 5 : Prewitt(ABS)
+mode: 6 : Sobel(SQRT)
+mode: 7 : Sobel(ABS)
+mode: 8 : NegativeLaplacian
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageErosion.html b/doc/SmallTools/mrcImageErosion.html
new file mode 100644
index 0000000..909d854
--- /dev/null
+++ b/doc/SmallTools/mrcImageErosion.html
@@ -0,0 +1,32 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageErosion</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageErosion</H1>
+<H2>Usage</H2>
+<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
+----- Additional Usage -----
+----- Structuring Element : Mode 
+0: 2D Cross3x3:  4-neighbour
+1: 2D Square3x3: 8-neighbour
+2: 2D Open Disk , need (radius, n)
+3: 3D Cross3x3x3:   6-neighbour
+4: 3D Cubic3x3x3: 26-neighbour
+5: 3D Open Disk , need (radius, n)
+-----
+Dilation: Max for image : Or  for binary image 
+Erosion:  Min for image : And for binary image 
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageFFT.html b/doc/SmallTools/mrcImageFFT.html
index 19054b0..f663df1 100644
--- a/doc/SmallTools/mrcImageFFT.html
+++ b/doc/SmallTools/mrcImageFFT.html
@@ -1,21 +1 @@
-<HTML>
-<HEAD>
-<TITLE>mrcImageFFT</TITLE>
-</HEAD>
-<BODY>
-<H1>mrcImageFFT</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrcImageFFT
-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
------ Additional Usage -----
-x, y and z must be even pixels.
-Excepts for like that 
-(x, y, z)=(100, 1, 1)
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrcImageFFT: No such file or directory
diff --git a/doc/SmallTools/mrcImageFOMCalc.html b/doc/SmallTools/mrcImageFOMCalc.html
index a027ed0..b3ec234 100644
--- a/doc/SmallTools/mrcImageFOMCalc.html
+++ b/doc/SmallTools/mrcImageFOMCalc.html
@@ -24,6 +24,11 @@ Options:
     [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
     [-m[ode]             mode                (0         )] :Optional  :Mode
 ----- Additional Usage -----
+>> -I FileFormat 
+mrc[0]   weight[0]
+mrc[1]   weight[1]
+.....
+mrc[n-1] weight[n-1]
 This algorithm is originated from K. Yonekura for Layer Lines. Nature/SupplmentTable 2 
 </PRE>
 </BODY>
diff --git a/doc/SmallTools/mrcImageFloating.html b/doc/SmallTools/mrcImageFloating.html
new file mode 100644
index 0000000..4000727
--- /dev/null
+++ b/doc/SmallTools/mrcImageFloating.html
@@ -0,0 +1,25 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageFloating</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageFloating</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageFloating
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input: mrcImage
+    [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Essential :Output: mrcImage
+    [-v[alue]            Value               (0.0       ).as(Real                ) ] :Optional  :Input: value
+    [-rmax               rmax                (0.0       ).as(Real                ) ] :Optional  :Input: default: rmax=MIN(Nx,Ny[,Nz])
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+>>> Edge Mode 0xf&mode
+All Mean:                     0
+Sphere Surface Mean (rmax):   1
+Cylinder Surface Mean (rmax): 2
+Edge Pixels:                  3
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageFourierNeighborCorrelation.html b/doc/SmallTools/mrcImageFourierNeighborCorrelation.html
new file mode 100644
index 0000000..614e811
--- /dev/null
+++ b/doc/SmallTools/mrcImageFourierNeighborCorrelation.html
@@ -0,0 +1,24 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageFourierNeighborCorrelation</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageFourierNeighborCorrelation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageFourierNeighborCorrelation
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input
+    [-o[utput]           Out                 (stdout    ).as(outFile::ASCII      ) ] :Optional  :Output:FNC
+    [-d[elta]            delta               (0.0       ).as(Real                ) ] :Optional  :Mode
+    [-C[enter]           Centre              (0         ).as(Integer             ) ] :Optional  :CentreMode
+    [-M[ode]             GetMode             (0         ).as(Integer             ) ] :Optional  :PixelDataGetHowToGet: InterpolationMode 
+    [-FSC                                                                          ] :Optional  :Output:predicted FSC
+    [-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 -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageFourierShellCorrelation.html b/doc/SmallTools/mrcImageFourierShellCorrelation.html
index 2dc688d..798b6a7 100644
--- a/doc/SmallTools/mrcImageFourierShellCorrelation.html
+++ b/doc/SmallTools/mrcImageFourierShellCorrelation.html
@@ -8,16 +8,21 @@
 <PRE>
 Usage: mrcImageFourierShellCorrelation
 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)
-    [-z[position]        z                   (0         )] :Optional  :z position of reference file to correlate.For mode2=1 only
-    [-L[owThreshold]     L                   (0         )] :Optional  :Low threshold for mode +2.
-    [-H[ighThreshold]    H                   (0         )] :Optional  :High threshold for mode +2.
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-M[ode2]            mode2               (0         )] :Optional  :Mode2
-    [-I1[nput array of file]In1Array            (stdin     )] :Optional  :InputDataFiles
+    [-i1[input1]         In1                 (NULL      ).as(inFile::mrcImage    ) ] :Optional  :Input:
+    [-i2[input2]         In2                 (NULL      ).as(inFile::mrcImage    ) ] :Optional  :Input:
+    [-o[utput]           Out                 (stdout    ).as(outFile::ASCII      ) ] :Optional  :Output:FSC
+    [-SNR                                                                          ] :Optional  :flagSNR
+    [-FSCfull                                                                      ] :Optional  :flagFSCfull
+    [-Cref                                                                         ] :Optional  :flagCref
+    [-NoiseWeighted      Brestore            (-1000     ).as(Real                ) ] :Optional  :flagNoiseWeighted: Cref*exp(-Bfactor/(4*d^2)
+    [-d[elta]            delta               (0         ).as(Real                ) ] :Optional  :Interval of output data(1/A). Default 1/(Nx*size of pixel)
+    [-z[position]        z                   (0         ).as(Integer             ) ] :Optional  :z position of reference file to correlate.For mode2=1 only
+    [-L[owThreshold]     L                   (0         ).as(Real                ) ] :Optional  :Low threshold for mode +2.
+    [-H[ighThreshold]    H                   (0         ).as(Real                ) ] :Optional  :High threshold for mode +2.
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-M[ode2]            mode2               (0         ).as(Integer             ) ] :Optional  :Mode2
+    [-I1[nput array of file]In1Array            (stdin     ).as(inFileList          ) ] :Optional  :InputDataFiles
 ----- mode -----
 0: Fourier shell correlation.
 1: Fourier shell phase residual.
diff --git a/doc/SmallTools/mrcImageGaussSphere.html b/doc/SmallTools/mrcImageGaussSphere.html
index c92ad89..d798bc8 100644
--- a/doc/SmallTools/mrcImageGaussSphere.html
+++ b/doc/SmallTools/mrcImageGaussSphere.html
@@ -9,6 +9,8 @@
 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]
@@ -24,6 +26,8 @@ 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) 
 -----------------------------------------------------------------------------------
+-EA: for rotation 
+-----------------------------------------------------------------------------------
 mode 0 char 
 mode 2 float 
 </PRE>
diff --git a/doc/SmallTools/mrcImageHighlighting.html b/doc/SmallTools/mrcImageHighlighting.html
index 28235be..ea7ffa6 100644
--- a/doc/SmallTools/mrcImageHighlighting.html
+++ b/doc/SmallTools/mrcImageHighlighting.html
@@ -1 +1,22 @@
-/bin/bash: mrcImageHighlighting: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>mrcImageHighlighting</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageHighlighting</H1>
+<H2>Usage</H2>
+<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
+---- lmrcImageHighlightInfo ----mode:	0:No Operation 
+	1:ArcTan Filter
+	2:Histgram Equalization
+BiasGrad</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageInfo.html b/doc/SmallTools/mrcImageInfo.html
index 2bf7f18..db9a752 100644
--- a/doc/SmallTools/mrcImageInfo.html
+++ b/doc/SmallTools/mrcImageInfo.html
@@ -8,24 +8,24 @@
 <PRE>
 Usage: mrcImageInfo
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-X[Section]         X                   (0.0       )] :Optional  :X Section at y=X(value)
-    [-Y[Section]         Y                   (0.0       )] :Optional  :Y Section at y=Y(value)
-    [-x[Projection]      ] :Optional  :x Projection[OutPut ASCII FILE]
-    [-y[Projection]      ] :Optional  :y Projection[OutPut ASCII FILE]
-    [-H[istgram]         H                   (256       )] :Optional  :Histgram: Class Number: Normalize
-    [-H[istgram]2        H2                  (1         )] :Optional  :Histgram2: Class Width: Integer: Normalize
-    [-H[istgram]3        H3                  (256       )] :Optional  :Histgram: Class Number: Count
-    [-H[istgram]4        H4                  (1         )] :Optional  :Histgram2: Class Width: Integer: Count
-    [-H[istgram]5        H5                  (1         )] :Optional  :Histgram5: Class Number: Count
-    [-H[istgram]6        H6                  (1         )] :Optional  :Histgram6: Class Width: Integer: Count
-    [-Low                Low                 (1         )] :Optional  :Low : thres
-    [-High               High                (1         )] :Optional  :High: thres
-    [-I[nfo]             ] :Optional  :Information
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-rmax               rmax                (250       )] :Optional  :rmax [A]
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input
+    [-o[utput]           Out                 (stdout    ).as(outFile::ASCII      ) ] :Optional  :Output
+    [-X[Section]         X                   (0.0       ).as(Real                ) ] :Optional  :X Section at y=X(value)
+    [-Y[Section]         Y                   (0.0       ).as(Real                ) ] :Optional  :Y Section at y=Y(value)
+    [-x[Projection]                                                                ] :Optional  :x Projection[OutPut ASCII FILE]
+    [-y[Projection]                                                                ] :Optional  :y Projection[OutPut ASCII FILE]
+    [-H[istgram]         H                   (256       ).as(Integer             ) ] :Optional  :Histgram: Class Number: Normalize
+    [-H[istgram]2        H2                  (1         ).as(Real                ) ] :Optional  :Histgram2: Class Width: Integer: Normalize
+    [-H[istgram]3        H3                  (256       ).as(Integer             ) ] :Optional  :Histgram: Class Number: Count
+    [-H[istgram]4        H4                  (1         ).as(Real                ) ] :Optional  :Histgram2: Class Width: Integer: Count
+    [-H[istgram]5        H5                  (1         ).as(Integer             ) ] :Optional  :Histgram5: Class Number: Count
+    [-H[istgram]6        H6                  (1         ).as(Real                ) ] :Optional  :Histgram6: Class Width: Integer: Count
+    [-Low                Low                 (1         ).as(Real                ) ] :Optional  :Low : thres
+    [-High               High                (1         ).as(Real                ) ] :Optional  :High: thres
+    [-I[nfo]                                                                       ] :Optional  :Information
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-rmax               rmax                (250       ).as(Real                ) ] :Optional  :rmax [A]
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
 The -I option uses -rmax or -m options
 -m 0: mean of all density
diff --git a/doc/SmallTools/mrcImageLogicalOperation.html b/doc/SmallTools/mrcImageLogicalOperation.html
new file mode 100644
index 0000000..4c18cc0
--- /dev/null
+++ b/doc/SmallTools/mrcImageLogicalOperation.html
@@ -0,0 +1,34 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageLogicalOperation</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageLogicalOperation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageLogicalOperation
+Options:
+    [-i[nput]1           In1                 (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input: P
+    [-i[nput]2           In2                 (NULL      ).as(inFile::mrcImage    ) ] :Optional  :Input: Q
+    [-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: AND(P*Q)
+mode 1: OR(P+Q)
+mode 2: ^(1-P)
+mode 3: XOR
+mode 4: XNOR
+mode 5: NAND
+mode 6: NOR
+mode 7: False
+mode 8: True
+mode 9: P
+mode 10: Q
+mode 11: IMP(^P+Q)   : Implication: P -> Q
+mode 12: NIMP(P*^Q)  : Not Implication: P -\-> Q
+mode 13: IIMP(P+^Q)  : Inverse Implication: Q -> P
+mode 14: NIIMP(^P*Q) : Not Inverse Implication: Q -\-> P
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageModelCreate.html b/doc/SmallTools/mrcImageModelCreate.html
index 100db4e..b32cb2b 100644
--- a/doc/SmallTools/mrcImageModelCreate.html
+++ b/doc/SmallTools/mrcImageModelCreate.html
@@ -75,6 +75,10 @@ Options:
        Optional argument : -nx -ny   
 5: Another Projection of 2 Sphere for 2D 
        Optional argument : -nx -ny   
+6: SheppLogan 2D 
+       Optional argument : -nx -ny   
+7: SheppLogan 3D 
+       Optional argument : -nx -ny -nz  
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageMultiCTFCompensation.html b/doc/SmallTools/mrcImageMultiCTFCompensation.html
index b63a4ab..be927bc 100644
--- a/doc/SmallTools/mrcImageMultiCTFCompensation.html
+++ b/doc/SmallTools/mrcImageMultiCTFCompensation.html
@@ -8,20 +8,23 @@
 <PRE>
 Usage: mrcImageMultiCTFCompensation
 Options:
-    [-i[nput]            In                  (stdin     )] :Essential :Input: filename ...
-    [-info2              CTF                 (stdin     )] :Optional  :InputFileList: the same order as the input: ctfinfo from Display2/ctfDisplay
-    [-o[utput]           Out                 (stdout    )] :Essential :OutputDataFile(average file)
-    [-f[ft]              fftOut              (stdout    )] :Optional  :OutputDataFile(averaged fft file)
-    [-W[hiteNoise]       WhiteNoise          (1.0       )] :Optional  :
-    [-W[hiteNoise]R[aising]WhiteNoiseRaising   (1.0       )] :Optional  :Weight:W*exp(WR*R)
-    [-SinWin             SinWinRmin          (0.1       )SinWinRmax          (1.0       )] :Optional  :Windowing by sine function from Rmin[/A] to Rmax[/A]
-    [-MaxIter[ation]     MaxIter             (10        )] :Optional  :Max Iteration
-    [-ctfMode            CTFMode             (1         )] :Optional  :CTFMode: refer to mrcImageCTFObservation
-    [-solventMode        solventMode         (0         )] :Optional  :If solvent flatterning is used, NEED
-    [-solventSTD         solventSTD          (-1.0      )] :Optional  :If solvent flatterning is used as mode=1, NEED 
-    [-log[file]          Log                 (stderr    )] :Optional  :Log File Name
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-i[nput]            In                  (stdin     ).as(inFileList          ) ] :Essential :Input: filename ...
+    [-info2              CTF                 (stdin     ).as(inFileList          ) ] :Optional  :InputFileList: the same order as the input: ctfinfo from Display2/ctfDisplay
+    [-o[utput]           Out                 (stdout    ).as(outFile             ) ] :Essential :OutputDataFile(average file)
+    [-f[ft]              fftOut              (stdout    ).as(outFile             ) ] :Optional  :OutputDataFile(averaged fft file)
+    [-W[hiteNoise]       WhiteNoise          (1.0       ).as(Real                ) ] :Optional  :
+    [-W[hiteNoise]R[aising]WhiteNoiseRaising   (1.0       ).as(Real                ) ] :Optional  :Weight:W*exp(WR*R)
+    [-maxW[hiteNoise]R[aising]MaxWhiteNoise       (1.0       ).as(Real                ) ] :Optional  :max(W*exp(WR*R),maxWhiteNoise)
+    [-Ndep[endent]W[hiteNoise]R[aising]NdependentWhiteNoise(1         ).as(Integer             ) ] :Optional  :W*exp(WR*R)/sqrt(N)
+    [-SinWin             SinWinRmin          (0.1       ).as(Real                ) 
+                         SinWinRmax          (1.0       ).as(Real                ) ] :Optional  :Windowing by sine function from Rmin[/A] to Rmax[/A]
+    [-MaxIter[ation]     MaxIter             (10        ).as(Integer             ) ] :Optional  :Max Iteration
+    [-ctfMode            CTFMode             (1         ).as(Integer             ) ] :Optional  :CTFMode: refer to mrcImageCTFObservation
+    [-solventMode        solventMode         (0         ).as(Real                ) ] :Optional  :If solvent flatterning is used, NEED
+    [-solventSTD         solventSTD          (-1.0      ).as(Real                ) ] :Optional  :If solvent flatterning is used as mode=1, NEED 
+    [-log[file]          Log                 (stderr    ).as(outFile             ) ] :Optional  :Log File Name
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- InputFileFormat -----
 filename0 deltaF[A] Cs[mm] kV[kV] ratioOfAmpToPhase
 filename1 deltaF[A] Cs[mm] kV[kV] ratioOfAmpToPhase
diff --git a/doc/SmallTools/mrcImageNoiseReductionByRelaxation.html b/doc/SmallTools/mrcImageNoiseReductionByRelaxation.html
index 0cf89e4..846d3ca 100644
--- a/doc/SmallTools/mrcImageNoiseReductionByRelaxation.html
+++ b/doc/SmallTools/mrcImageNoiseReductionByRelaxation.html
@@ -8,17 +8,18 @@
 <PRE>
 Usage: mrcImageNoiseReductionByRelaxation
 Options:
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
     [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
     [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
     [-n[umber]           Nlab                (8         )] :Optional  :Number of Density Level
-    [-max[imum]          max                 (NULL      )] :Optional  :Maximum of Density Level
-    [-min[imum]          min                 (NULL      )] :Optional  :Minimum of Density Level
-    [-m[ode1]            mode1               (1         )] :Optional  :Dij Modeof Personal Style
-    [-m[ode2]            mode2               (1         )] :Optional  :Dij Mode of Figure Style
-    [-m[ode3]            mode3               (1         )] :Optional  :Dij Mode of Dimension Style
-    [-o[ptionalmode]     mode                (0         )] :Optional  :Optional Mode of Noise Reduction
+    [-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
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageNormalizing.html b/doc/SmallTools/mrcImageNormalizing.html
index 3ccf915..8554985 100644
--- a/doc/SmallTools/mrcImageNormalizing.html
+++ b/doc/SmallTools/mrcImageNormalizing.html
@@ -31,6 +31,8 @@ Options:
 		   data = A*(data-ContourMin)/(ContourMax-ContourMin) + B 
   4: No Estimation
 		   data = A*data + B 
+  5: Assume the density as gaussion.
+		   data = A*Normalized(data) + B , where normalized means (average=0, SD=1)
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageOpening.html b/doc/SmallTools/mrcImageOpening.html
new file mode 100644
index 0000000..0896254
--- /dev/null
+++ b/doc/SmallTools/mrcImageOpening.html
@@ -0,0 +1,33 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageOpening</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageOpening</H1>
+<H2>Usage</H2>
+<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
+----- Additional Usage -----
+----- Structuring Element : Mode 
+0: 2D Cross3x3:  4-neighbour
+1: 2D Square3x3: 8-neighbour
+2: 2D Open Disk , need (radius, n)
+3: 3D Cross3x3x3:   6-neighbour
+4: 3D Cubic3x3x3: 26-neighbour
+5: 3D Open Disk , need (radius, n)
+-----
+Dilation: Max for image : Or  for binary image 
+Erosion:  Min for image : And for binary image 
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageOrientationSearch.html b/doc/SmallTools/mrcImageOrientationSearch.html
index df0ed67..09d9ad3 100644
--- a/doc/SmallTools/mrcImageOrientationSearch.html
+++ b/doc/SmallTools/mrcImageOrientationSearch.html
@@ -1,45 +1 @@
-<HTML>
-<HEAD>
-<TITLE>mrcImageOrientationSearch</TITLE>
-</HEAD>
-<BODY>
-<H1>mrcImageOrientationSearch</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrcImageOrientationSearch
-Options:
-    [-I[nputFileList]1   In1                 (NULL      )] :Essential :InputDataFileList1
-    [-I[nputFileList]2   In2                 (NULL      )] :Essential :InputDataFileList2
-    [-o[utputFile]       Out                 (NULL      )] :Essential :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-T[hreshold]        threshold           (0         )] :Optional  :Threshold
-
------ mode -----
--m : 0 : There is one common line position in input file (using Test)
-     1 : There is    correlation file name in input file (common line position is determined Max correlation)
-     2 : There is    correlation file name in input file (common line position is determined Threshold), -T
-
------ input file 1 format -----
--m : 0 : filename1 filename2 commonlineposition1 commonlineposition2 commonlinepositionMode
-             .         .             .                   .                     .           
-             .         .             .                   .                     .           
-             .         .             .                   .                     .           
-             .         .             .                   .                     .           
-
-     1 : correlationfilename filename1 filename2
-     2 :         .               .         .    
-                 .               .         .    
-                 .               .         .    
-                 .               .         .    
-
------ input file 2 format -----
--m : 0 : filename 
-     1 :    .     
-     2 :    .     
-            .     
-            .     
-
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrcImageOrientationSearch: No such file or directory
diff --git a/doc/SmallTools/mrcImagePCA.html b/doc/SmallTools/mrcImagePCA.html
index c535729..fd8625c 100644
--- a/doc/SmallTools/mrcImagePCA.html
+++ b/doc/SmallTools/mrcImagePCA.html
@@ -1 +1,26 @@
-/bin/bash: mrcImagePCA: No such file or directory
+Program Start
+<HTML>
+<HEAD>
+<TITLE>mrcImagePCA</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImagePCA</H1>
+<H2>Usage</H2>
+<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
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImagePanoramaCreate.html b/doc/SmallTools/mrcImagePanoramaCreate.html
new file mode 100644
index 0000000..9f62bb4
--- /dev/null
+++ b/doc/SmallTools/mrcImagePanoramaCreate.html
@@ -0,0 +1,24 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImagePanoramaCreate</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImagePanoramaCreate</H1>
+<H2>Usage</H2>
+<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
+----- Additional Usage -----
+>>>InputFileList Format
+FileName OffsetX OffsetY OffsetZ
+.....
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImagePixelDataGet.html b/doc/SmallTools/mrcImagePixelDataGet.html
index 5ceaccd..19b6822 100644
--- a/doc/SmallTools/mrcImagePixelDataGet.html
+++ b/doc/SmallTools/mrcImagePixelDataGet.html
@@ -8,14 +8,20 @@
 <PRE>
 Usage: mrcImagePixelDataGet
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-x                  x                   (0.0       )] :Optional  :Input: x
-    [-y                  y                   (0.0       )] :Optional  :Input: y
-    [-z                  z                   (0.0       )] :Optional  :Input: z
-    [-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                 (stdout    ).as(outFile::ASCII      ) ] :Optional  :OutputDataFile
+    [-x                  x                   (0.0       ).as(Real                ) ] :Optional  :Input: x
+    [-y                  y                   (0.0       ).as(Real                ) ] :Optional  :Input: y
+    [-z                  z                   (0.0       ).as(Real                ) ] :Optional  :Input: z
+    [-In[put]            InCoord             (stdin     ).as(inFile::ASCII       ) ] :Optional  :Input:eosPoint
+    [-cuda               cudaDeviceID        (0         ).as(Integer             ) ] :Optional  :cudaDeviceID
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-o[utput]m[ode]     outMode             (0         ).as(Integer             ) ] :Optional  :Mode:Output
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode:Interpolation
 ----- Additional Usage -----
+-m InterpolationMode ; refer to mrcImageROI 
+-om outputMode
+ +1 : with coordinates
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImagePrint.html b/doc/SmallTools/mrcImagePrint.html
index 1cd603a..7d1db30 100644
--- a/doc/SmallTools/mrcImagePrint.html
+++ b/doc/SmallTools/mrcImagePrint.html
@@ -9,7 +9,7 @@
 Usage: mrcImagePrint
 Options:
     [-i[nput]            In                  (NULL      )] :Essential :InputImageFile
-    [-o[utput]           Out                 (NULL      )] :Optional  :OutputImageFile
+    [-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
diff --git a/doc/SmallTools/mrcImageROI.html b/doc/SmallTools/mrcImageROI.html
index b47c276..94e3006 100644
--- a/doc/SmallTools/mrcImageROI.html
+++ b/doc/SmallTools/mrcImageROI.html
@@ -8,26 +8,34 @@
 <PRE>
 Usage: mrcImageROI
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-r[oi]              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 
-    [-x                  WidthBeforeExpansion(1.0/* Default is set by -r */)] :Optional  :Width  before expansion
-    [-y                  HeightBeforeExpansion(1.0/* Default is set by -r */)] :Optional  :Height before expansion
-    [-a[ngle]            Angle               (0.0       )] :Optional  :This value [degree] is added to angle of current source image.
-    [-W                  WidthAfterExpansion (1.0       )] :Optional  :Width  after expansion[Pixel]
-    [-H                  HeightAfterExpansion(1.0       )] :Optional  :Height after expansion[Pixel]: 
+    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input
+    [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Essential :Output
+    [-r[oi]              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 
+    [-x                  WidthBeforeExpansion(1.0       ).as(Real                ) ] :Optional  :Width  before expansion: /* Default is set by -r */
+    [-y                  HeightBeforeExpansion(1.0       ).as(Real                ) ] :Optional  :Height before expansion: /* Default is set by -r */
+    [-a[ngle]            Angle               (0.0       ).as(Real                ) ] :Optional  :This value [degree] is added to angle of current source image.
+    [-W                  WidthAfterExpansion (1.0       ).as(Real                ) ] :Optional  :Width  after expansion[Pixel]
+    [-H                  HeightAfterExpansion(1.0       ).as(Real                ) ] :Optional  :Height after expansion[Pixel]: 
 		ROI Size is (10,20):
 			If -W 30 -H 40, out (30,40)
 			If -W 30, out (30, 20*30/10)
 			If -H 40, out (10*40/20,40)
 				If omitted, out (10,20)
-    [-Shift              ShiftX              (0.0       )ShiftY              (0.0       )] :Optional  :ROI ARea Shift [Pixel]
-    [-turePitch          truePitch           (430.0     )] :Optional  :truePitch [A]
-    [-dY                 dY                  (0.0       )] :Optional  :Number of turePitch
-    [-Ly                 Ly                  (5.0       )] :Optional  :Header Length y [A/Pixel]
-    [-S[hrink]           Shrink              (1         )] :Optional  :When inputfile is shrinked
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-Shift              ShiftX              (0.0       ).as(Real                ) 
+                         ShiftY              (0.0       ).as(Real                ) ] :Optional  :ROI ARea Shift [Pixel]
+    [-turePitch          truePitch           (430.0     ).as(Real                ) ] :Optional  :truePitch [A]
+    [-dY                 dY                  (0.0       ).as(Real                ) ] :Optional  :Number of turePitch
+    [-Ly                 Ly                  (5.0       ).as(Real                ) ] :Optional  :Header Length y [A/Pixel]
+    [-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
 ---- mode ----
 	0: Nearest Neighbor Method
 	1: Bilinear method
diff --git a/doc/SmallTools/mrcImageROIs.html b/doc/SmallTools/mrcImageROIs.html
index 5ad82c5..35fb82d 100644
--- a/doc/SmallTools/mrcImageROIs.html
+++ b/doc/SmallTools/mrcImageROIs.html
@@ -14,6 +14,7 @@ Options:
     [-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
diff --git a/doc/SmallTools/mrcImageRandomParticlesImageCreate.html b/doc/SmallTools/mrcImageRandomParticlesImageCreate.html
new file mode 100644
index 0000000..fa38638
--- /dev/null
+++ b/doc/SmallTools/mrcImageRandomParticlesImageCreate.html
@@ -0,0 +1,21 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageRandomParticlesImageCreate</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageRandomParticlesImageCreate</H1>
+<H2>Usage</H2>
+<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
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageShapeOrientation.html b/doc/SmallTools/mrcImageShapeOrientation.html
new file mode 100644
index 0000000..0606b4b
--- /dev/null
+++ b/doc/SmallTools/mrcImageShapeOrientation.html
@@ -0,0 +1,19 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageShapeOrientation</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageShapeOrientation</H1>
+<H2>Usage</H2>
+<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
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageShapePCA.html b/doc/SmallTools/mrcImageShapePCA.html
index 7ec0fcd..3bd6a0e 100644
--- a/doc/SmallTools/mrcImageShapePCA.html
+++ b/doc/SmallTools/mrcImageShapePCA.html
@@ -8,15 +8,15 @@
 <PRE>
 Usage: mrcImageShapePCA
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input: mrcImage
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output: ASCII
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-C[ontour]          Contour             (0.0       )... ] :Variable  :Contour
+    [-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
+    [-C[ontour]          Contour             (1.0       ).as(Real                ) ... ] :Variable  :Contour
 ----- Additional Usage -----
 -C : ContourLevels
    e.g. -C  20  30  40 
-           100% 40%
+           100% 60% 40%
 ----- Objectives -----
 Determine the orientations/molecular axis by PCA alogrism
   $ mrcImagePCA -i mrc -o parameter -C C1 C2 C3 ...
diff --git a/doc/SmallTools/mrcImageShapePCAFit.html b/doc/SmallTools/mrcImageShapePCAFit.html
new file mode 100644
index 0000000..f85451a
--- /dev/null
+++ b/doc/SmallTools/mrcImageShapePCAFit.html
@@ -0,0 +1,23 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageShapePCAFit</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageShapePCAFit</H1>
+<H2>Usage</H2>
+<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)
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageSiemensStar.html b/doc/SmallTools/mrcImageSiemensStar.html
index 2724b2b..412421e 100644
--- a/doc/SmallTools/mrcImageSiemensStar.html
+++ b/doc/SmallTools/mrcImageSiemensStar.html
@@ -8,14 +8,22 @@
 <PRE>
 Usage: mrcImageSiemensStar
 Options:
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-N[umber]           Nx                  (256       )Ny                  (256       )] :Optional  :Number[pixel]
-    [-R[adius]           R                   (64        )] :Optional  :Radius[pixel]
-    [-n[umber]           nRadial             (18        )] :Optional  :nOfRadial
-    [-delta              Delta               (1.72      )] :Optional  :Delta[A]
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-o[utput]           Out                 (stdout    ).as(outFile::ASCII      ) ] :Essential :OutputDataFile
+    [-N[umber]           Nx                  (256       ).as(Integer             ) 
+                         Ny                  (256       ).as(Integer             ) ] :Optional  :Number[pixel]
+    [-R[adius]           R                   (64        ).as(Integer             ) ] :Optional  :Radius[pixel]
+    [-n[umber]           nRadial             (18        ).as(Integer             ) ] :Optional  :nOfRadial
+    [-delta              Delta               (1.72      ).as(Real                ) ] :Optional  :Delta[A]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-Shape              Shape               (0         ).as(Integer             ) ] :Optional  :Mode
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 ----- Additional Usage -----
+-mode : mrcImageHeaderMode: 2 float
+                            0 char
+-Shape  0 : SiemensStar(Step)
+-Shape  1 : SiemensStar(Cos)
+-Shape  2 : Linear(Step)
+-Shape  3 : Linear(Cos)
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcImageSmoothing.html b/doc/SmallTools/mrcImageSmoothing.html
index f07c762..886a7ec 100644
--- a/doc/SmallTools/mrcImageSmoothing.html
+++ b/doc/SmallTools/mrcImageSmoothing.html
@@ -14,13 +14,20 @@ Options:
     [-sy                 sy                  (3         )] :Optional  :y of Kernel Size
     [-sz                 sz                  (3         )] :Optional  :z of Kernel Size
     [-r                  r                   (1         )] :Optional  :Radius of Kernel Size
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-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
 >>> Mode <<<< 
     1: Median filter
     2: Mean filter 
-    3: Surface FIt  filter
+    3: Surface Fit filter
+    4: Lee-Sigma filter(Use sigma)
+    5: Local weighted mean filter
+    6: Edge and line weights smoothing filter(3x3)
+    7: Contrast-sensitiveline weights smoothing filter(3x3:Use sigma)
+    8: Gradient inverse weighted smoothing filter(3x3)
 >>> Mode2 <<<< 
     0: Kernel is cube. : required argumnent: -sx, -sy, [-sz]
     1: Kernel is sphere.(Only mode 1 supported) : required argumnent: -r 
diff --git a/doc/SmallTools/mrcImageSpatialFrequencyFilter.html b/doc/SmallTools/mrcImageSpatialFrequencyFilter.html
new file mode 100644
index 0000000..4658ea6
--- /dev/null
+++ b/doc/SmallTools/mrcImageSpatialFrequencyFilter.html
@@ -0,0 +1,23 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageSpatialFrequencyFilter</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageSpatialFrequencyFilter</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageSpatialFrequencyFilter
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input: mrcImage
+    [-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
+    [-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
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageSphereCheck.html b/doc/SmallTools/mrcImageSphereCheck.html
index 060cc89..9af5e8b 100644
--- a/doc/SmallTools/mrcImageSphereCheck.html
+++ b/doc/SmallTools/mrcImageSphereCheck.html
@@ -1,18 +1 @@
-<HTML>
-<HEAD>
-<TITLE>mrcImageSphereCheck</TITLE>
-</HEAD>
-<BODY>
-<H1>mrcImageSphereCheck</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrcImageSphereCheck
-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
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrcImageSphereCheck: No such file or directory
diff --git a/doc/SmallTools/mrcImageSplit.html b/doc/SmallTools/mrcImageSplit.html
index d2c31c2..ffbffea 100644
--- a/doc/SmallTools/mrcImageSplit.html
+++ b/doc/SmallTools/mrcImageSplit.html
@@ -11,7 +11,7 @@ Usage: mrcImageSplit
 Options:
     [-i[nput]            In                  (NULL      )] :Essential :Input: mrcImage
     [-o[utput]           Out                 (          )] :Optional  :Output: Basename
-    [-s[uffix]           Suffix              (0088-10790097604276224.splt)] :Optional  :Output: Suffix
+    [-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]
diff --git a/doc/SmallTools/mrcImageStack.html b/doc/SmallTools/mrcImageStack.html
index 3bf1f05..da058f5 100644
--- a/doc/SmallTools/mrcImageStack.html
+++ b/doc/SmallTools/mrcImageStack.html
@@ -1 +1,18 @@
-/bin/bash: mrcImageStack: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>mrcImageStack</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageStack</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageStack
+Options:
+    [-I[nput array of file]In                  (stdin     ).as(inFileListNoOpen::mrcImage) ] :Optional  :InputDataFiles
+    [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :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/mrcImageSuperResolution.html b/doc/SmallTools/mrcImageSuperResolution.html
index 06885fe..8fe5a02 100644
--- a/doc/SmallTools/mrcImageSuperResolution.html
+++ b/doc/SmallTools/mrcImageSuperResolution.html
@@ -20,8 +20,8 @@ Options:
     [-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(%) 
+    [-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
diff --git a/doc/SmallTools/mrcImageTopHatTransform.html b/doc/SmallTools/mrcImageTopHatTransform.html
new file mode 100644
index 0000000..9011525
--- /dev/null
+++ b/doc/SmallTools/mrcImageTopHatTransform.html
@@ -0,0 +1,23 @@
+<HTML>
+<HEAD>
+<TITLE>mrcImageTopHatTransform</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageTopHatTransform</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageTopHatTransform
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-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 -----
+</PRE>
+</BODY>
+</HTML>
diff --git a/doc/SmallTools/mrcImageVolumeCalc.html b/doc/SmallTools/mrcImageVolumeCalc.html
index 424033c..3410319 100644
--- a/doc/SmallTools/mrcImageVolumeCalc.html
+++ b/doc/SmallTools/mrcImageVolumeCalc.html
@@ -14,7 +14,7 @@ Options:
     [-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%
+    [-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
diff --git a/doc/SmallTools/mrcImageWindowing.html b/doc/SmallTools/mrcImageWindowing.html
index dd88dc7..a1afdf4 100644
--- a/doc/SmallTools/mrcImageWindowing.html
+++ b/doc/SmallTools/mrcImageWindowing.html
@@ -8,23 +8,36 @@
 <PRE>
 Usage: mrcImageWindowing
 Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-W[indowing]        Wx                  (0.1       )WxMax               (0.0       )Wy                  (0.1       )WyMax               (0.0       )] :Optional  :Windowsing 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
+    [-W[indowing]        Wx                  (0.1       ).as(Real                ) 
+                         WxMax               (0.0       ).as(Real                ) 
+                         Wy                  (0.1       ).as(Real                ) 
+                         WyMax               (0.0       ).as(Real                ) ] :Optional  :Windowsing Size:
+    [-W[indowing]x       WX                  (0.1       ).as(Real                ) ] :Optional  :Windowsing Size:
+    [-W[indowing]y       WY                  (0.1       ).as(Real                ) ] :Optional  :Windowsing Size:
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
 >>> Mode
     0: If 0<x<0.1*nx or 0.9*nx<x<nx, then cos windowing, else original.
-0: 90% windowing:         fixed.   
-1: Wy: Settings:          variable.
-2: WxMax and Wx                    
+0: Cos Window (Fixed)
+   90% windowing:         fixed.   
+1: Cos Window (Y-variable)
+   Wy: Settings:          variable.
+2: Cos Window XY-variable
+   WxMax and Wx                    
    WyMax and Wy Settings: variables
            x/Nx < WxMax   or    1-WxMax < x/Nx           : 0 
    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.  
-+16: Contrast down around mean. 
+3: Rectangle Window
+4: Hanning Window
+5: Hamming Window
+6: Blackman Window
++0 : To Zero.  
++16: Contrast down around mean.
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcInfo.html b/doc/SmallTools/mrcInfo.html
index 775aac2..88be6a4 100644
--- a/doc/SmallTools/mrcInfo.html
+++ b/doc/SmallTools/mrcInfo.html
@@ -8,12 +8,18 @@
 <PRE>
 Usage: mrcInfo
 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::mrcImage    ) ] :Essential :Input::mrcImage
+    [-i[nput]t[ype]      InType              (Eos       ).as(String              ) ] :Optional  :InputType
+    [-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
 -mode
   +16: one line Tailer information 
- </PRE>
+ >> MRC Mode
+ Eos
+CCP4-2000
+IMODextendedMRC
+FEIextendedMRC
+</PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/mrcMeanYlinePos.html b/doc/SmallTools/mrcMeanYlinePos.html
index 279b806..208ce05 100644
--- a/doc/SmallTools/mrcMeanYlinePos.html
+++ b/doc/SmallTools/mrcMeanYlinePos.html
@@ -9,7 +9,8 @@
 Usage: mrcMeanYlinePos
 Options:
     [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-w[idth]            width               (1         )] :Essential :GetMeanWidth
+    [-w[idth]            width               (-1        )] :Optional  :GetMeanWidth
+    [-o[utput]           Out                 (stdout    )] :Optional  :Output
     [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
     [-m[ode]             mode                (0         )] :Optional  :Mode
 </PRE>
diff --git a/doc/SmallTools/pdb2mrc2d.html b/doc/SmallTools/pdb2mrc2d.html
index 54b26c0..f600fec 100644
--- a/doc/SmallTools/pdb2mrc2d.html
+++ b/doc/SmallTools/pdb2mrc2d.html
@@ -1,36 +1 @@
-<HTML>
-<HEAD>
-<TITLE>pdb2mrc2d</TITLE>
-</HEAD>
-<BODY>
-<H1>pdb2mrc2d</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: pdb2mrc2d
-Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Optional  :OutputDataFile(2D)
-    [-O[utput]           Out3D               (NULL      )] :Optional  :OutputDataFile(3D)
-    [-d[elta]            dx                  (5.0       )dy                  (5.0       )] :Essential :delta: dx[A] dy[A]
-    [-s[tart]            sx                  (0.0       )sy                  (0.0       )] :Optional  :start: startx[A] starty[A]: When -s was not set, image centre is the origin(0,0,0)
-    [-n[umber]           nx                  (0         )ny                  (0         )] :Essential :N:     nx ny (image size)
-    [-Rot[ation]         rotnx               (1         )rotny               (1         )] :Optional  :rotnx rotny
-    [-S[tart]            srotx               (0.0       )sroty               (0.0       )srotz               (0.0       )] :Optional  :start(rotx roty rotz):ZXY
-    [-startE[uler]A[ngle]sRotMode            (YOYS      )sRot1               (0.0       )sRot2               (0.0       )sRot3               (0.0       )] :Optional  :EulerAngle: Start Angle
-    [-E[uler]A[ngle]Mode RotMode             (YOYS      )] :Optional  :RotationMode
-    [-E[uler]A[ngle]Rot1 dRot1               (5.0       )minRot1             (0.0       )maxRot1             (180.0     )] :Optional  :FirstRotation
-    [-E[uler]A[ngle]Rot2 dRot2               (5.0       )minRot2             (0.0       )maxRot2             (180.0     )] :Optional  :SecondRotation
-    [-w[eight]           Weight              (1.0       )] :Optional  :weight
-    [-sig[ma]            Sigma               (0.0       )] :Optional  :Sigma[A]:Atom radius
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :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>
+/bin/bash: pdb2mrc2d: No such file or directory
diff --git a/doc/SmallTools/pdbChargeFit.html b/doc/SmallTools/pdbChargeFit.html
index 028e4cd..2622898 100644
--- a/doc/SmallTools/pdbChargeFit.html
+++ b/doc/SmallTools/pdbChargeFit.html
@@ -1,25 +1 @@
-<HTML>
-<HEAD>
-<TITLE>pdbChargeFit</TITLE>
-</HEAD>
-<BODY>
-<H1>pdbChargeFit</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: pdbChargeFit
-Options:
-    [-i[nput]f[ixed pdb] InFix               (NULL      )] :Essential :InputFixedPdbFile
-    [-i[nput]m[oved pdb] InMove              (NULL      )] :Essential :InputMovedPdbFile
-    [-o[utput]           OutTxt              (NULL      )] :Essential :OutputTextFile
-    [-s[ymmetry of helix(degree/A)]symmetry            (0.47096   )] :Optional  :default: 13/28
-    [-zmin               zmin                (-28       )] :Optional  :minimum z
-    [-zmax               zmax                (28        )] :Optional  :maximum z
-    [-zDel[ta]           zDel                (1         )] :Optional  :delta z
-    [-mind[istance]      mind                (1         )] :Optional  :set atoms distance to mind
-    [-maxd[istance]      maxd                (5         )] :Optional  :ignore atoms distance
-    [-a[xis coordinate]  axisX               (70        )axisY               (70        )] :Optional  :(x, y)
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: pdbChargeFit: No such file or directory
diff --git a/doc/SmallTools/pdbCrystalCreate.html b/doc/SmallTools/pdbCrystalCreate.html
index 479b9d4..076ce13 100644
--- a/doc/SmallTools/pdbCrystalCreate.html
+++ b/doc/SmallTools/pdbCrystalCreate.html
@@ -1,36 +1 @@
-<HTML>
-<HEAD>
-<TITLE>pdbCrystalCreate</TITLE>
-</HEAD>
-<BODY>
-<H1>pdbCrystalCreate</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: pdbCrystalCreate
-Options:
-    [-i[nput]            In                  (NULL      )] :Essential :Input:PDB
-    [-I[nfo]             Info                (NULL      )] :Essential :Input:Crystal Information
-    [-o[utput]           Out                 (NULL      )] :Essential :Output:PDB
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :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>
+/bin/bash: pdbCrystalCreate: No such file or directory
diff --git a/doc/SmallTools/pdbHelix.html b/doc/SmallTools/pdbHelix.html
index 46738b8..0ec5a3f 100644
--- a/doc/SmallTools/pdbHelix.html
+++ b/doc/SmallTools/pdbHelix.html
@@ -1,37 +1 @@
-<HTML>
-<HEAD>
-<TITLE>pdbHelix</TITLE>
-</HEAD>
-<BODY>
-<H1>pdbHelix</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: pdbHelix
-Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Optional  :OutputDataFile
-    [-3[D]               Out3D               (NULL      )] :Optional  :OutputDataFile(3D-mrc)
-    [-2[D]               Out2D               (NULL      )] :Optional  :OutputDataFile(2D-mrc projection(y-z))
-    [-d[elta]            delta               (5         )] :Optional  :delta[A](mrc-file)
-    [-p[delphi]          delphi              (165       )] :Essential :deltaPhi
-    [-dp[delphi]         deldelphi           (5         )] :Optional  :deltaDeltaPhi
-    [-z[deltaz]          delz                (5         )] :Essential :deltaz
-    [-n[Molecule]        nMolecule           (1         )] :Essential :NumberOfMolecules
-    [-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]
-    [-w[eight]           Weight              (1.0       )] :Optional  :Weight
-    [-dx                 dx                  (2.5       )] :Optional  :dx
-    [-dy                 dy                  (2.5       )] :Optional  :dy
-    [-dz                 dz                  (2.5       )] :Optional  :dz
-    [-startn             startn              (0         )] :Optional  :start molecule's index
-    [-startC             startID             (A         )] :Optional  :start chain ID
-    [-deltaSeq           deltaSeq            (1000      )] :Optional  :start chain ID
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: pdbHelix: No such file or directory
diff --git a/doc/SmallTools/pdbListRMSDCalc.html b/doc/SmallTools/pdbListRMSDCalc.html
index 8f37263..de6bc0c 100644
--- a/doc/SmallTools/pdbListRMSDCalc.html
+++ b/doc/SmallTools/pdbListRMSDCalc.html
@@ -9,11 +9,17 @@
 Usage: pdbListRMSDCalc
 Options:
     [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-r[ef]              Ref                 (NULL      )] :Essential :ReferenceDataFile
+    [-r[ef]              Ref                 (NULL      )] :Optional  :ReferenceDataFile
     [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
     [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
     [-m[ode]             mode                (0         )] :Optional  :Mode
 ----- Additional Usage -----
+>> -m  
+ 0: -i only   : against average 
+ 1: -i and -r : against reference 
+>> -o 
+ Coord: Averged Coord
+ TempFactor: against average or reference
 </PRE>
 </BODY>
 </HTML>
diff --git a/doc/SmallTools/pdbMove.html b/doc/SmallTools/pdbMove.html
index 36ba6cb..9a2b54e 100644
--- a/doc/SmallTools/pdbMove.html
+++ b/doc/SmallTools/pdbMove.html
@@ -1,24 +1 @@
-<HTML>
-<HEAD>
-<TITLE>pdbMove</TITLE>
-</HEAD>
-<BODY>
-<H1>pdbMove</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: pdbMove
-Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-x                  X                   (0.0       )] :Optional  :Move X[A]
-    [-y                  Y                   (0.0       )] :Optional  :Move Y[A]
-    [-z                  Z                   (0.0       )] :Optional  :Move Z[A]
-    [-originTo           toX                 (0.0       )toY                 (0.0       )toZ                 (0.0       )] :Optional  :move (0,0,0) to (X,Y,Z)
-    [-toOrigin           fromX               (0.0       )fromY               (0.0       )fromZ               (0.0       )] :Optional  :move (X,Y,Z) to (0,0,0)
-    [-GCtoOrigin         ] :Optional  :GC(Gravity Centre) to origin
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: pdbMove: No such file or directory
diff --git a/doc/SmallTools/pdbPCA.html b/doc/SmallTools/pdbPCA.html
index f2cedb4..cc39266 100644
--- a/doc/SmallTools/pdbPCA.html
+++ b/doc/SmallTools/pdbPCA.html
@@ -1,21 +1 @@
-<HTML>
-<HEAD>
-<TITLE>pdbPCA</TITLE>
-</HEAD>
-<BODY>
-<H1>pdbPCA</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: pdbPCA
-Options:
-    [-i[nput]            In                  (stdin     )] :Optional  :InputDataFile
-    [-o[utput]           Out                 (stdout    )] :Optional  :Output: Result
-    [-o[utput]U[nit]     OutUnit             (NULL      )] :Optional  :Output: Unit Vector Array
-    [-o[utput]M[atrix3D] OutMat3D            (NULL      )] :Optional  :Output: Matrix3D from Unit Vector Array
-    [-o[utput]PDB        OutPDB              (NULL      )] :Optional  :Output: PDB rotated from Unit Vector Array
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: pdbPCA: No such file or directory
diff --git a/doc/SmallTools/pdbRhoFit.html b/doc/SmallTools/pdbRhoFit.html
index eca7042..22baa00 100644
--- a/doc/SmallTools/pdbRhoFit.html
+++ b/doc/SmallTools/pdbRhoFit.html
@@ -1,72 +1 @@
-<HTML>
-<HEAD>
-<TITLE>pdbRhoFit</TITLE>
-</HEAD>
-<BODY>
-<H1>pdbRhoFit</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: pdbRhoFit
-Options:
-    [-i[nput]pdb[File]   InPdb               (NULL      )] :Essential :InputDataFile
-    [-i[nput]mrc[File]   InMrc               (NULL      )] :Essential :InputDataFile
-    [-o[utput of ]mrc    OutMrc              (NULL      )] :Essential :OutputDataFile
-    [-o[utput of ]txt    OutTxt              (NULL      )] :Optional  :OutputDataFile
-    [-o[utput of ]par    OutPar              (stdout    )] :Optional  :OutputDataFile
-    [-o[utput of ]pdb    OutPDB              (NULL      )] :Optional  :OutputDataFile
-    [-xmin               xmin                (0         )] :Optional  :xmin for fitting
-    [-xmax               xmax                (0         )] :Optional  :xmax for fitting
-    [-xd[elta]           xDelta              (1         )] :Optional  :delta x for fitting
-    [-ymin               ymin                (0         )] :Optional  :ymin for fitting
-    [-ymax               ymax                (0         )] :Optional  :ymax for fitting
-    [-yd[elta]           yDelta              (1         )] :Optional  :delta y for fitting
-    [-zmin               zmin                (0         )] :Optional  :zmin for fitting
-    [-zmax               zmax                (82        )] :Optional  :zmax for fitting
-    [-zd[elta]           zDelta              (1         )] :Optional  :delta z for fitting
-    [-E[uler]A[ngle]     EulerAngle          (ZOYS      )] :Optional  :Euler Angle for three-angle
-    [-phimin             phimin              (0         )] :Optional  :phimin for fitting(degree)
-    [-phimax             phimax              (194       )] :Optional  :phimax for fitting(degree)
-    [-phid[elta]         phiDelta            (2         )] :Optional  :delta phi for fitting(degree)
-    [-psimin             psimin              (0         )] :Optional  :psimin for fitting(degree)
-    [-psimax             psimax              (0         )] :Optional  :psimax for fitting(degree)
-    [-psid[elta]         psiDelta            (2         )] :Optional  :delta psi for fitting(degree)
-    [-thetamin           thetamin            (0         )] :Optional  :thetamin for fitting(degree)
-    [-thetamax           thetamax            (0         )] :Optional  :thetamax for fitting(degree)
-    [-thetad[elta]       thetaDelta          (2         )] :Optional  :delta theta for fitting(degree)
-    [-n[ormalize]w[eight]normalizeWeight     (100000000.0)] :Optional  :weight for normalize
-    [-n[ormalize]C[ontour]normalizeContour    (0.0       )] :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        )] :Optional  :The atom will be neglected
-    [-Centre             ] :Optional  :Filament-axis is x=0, y=0
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-C[ontour]          contourLevel        (0.0       )... ] :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>
+/bin/bash: pdbRhoFit: No such file or directory
diff --git a/doc/SmallTools/pdbRhoFitTm.html b/doc/SmallTools/pdbRhoFitTm.html
index c8ba78b..a1c79f5 100644
--- a/doc/SmallTools/pdbRhoFitTm.html
+++ b/doc/SmallTools/pdbRhoFitTm.html
@@ -1,76 +1 @@
-<HTML>
-<HEAD>
-<TITLE>pdbRhoFitTm</TITLE>
-</HEAD>
-<BODY>
-<H1>pdbRhoFitTm</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: pdbRhoFitTm
-Options:
-    [-i[nput]pdb[File]   InPdb               (NULL      )] :Essential :InputDataFile
-    [-i[nput]mrc[File]   InMrc               (NULL      )] :Essential :InputDataFile
-    [-o[utput of ]mrc    OutMrc              (NULL      )] :Essential :OutputDataFile
-    [-Sx                 Sx                  (50        )] :Essential :x of rotation axis
-    [-Sy                 Sy                  (110       )] :Essential :y of rotation axis
-    [-Sz                 Sz                  (110       )] :Essential :z of rotation axis
-    [-o[utput of ]txt    OutTxt              (NULL      )] :Optional  :OutputDataFile
-    [-o[utput of ]pdb    OutPDB              (NULL      )] :Optional  :OutputDataFile
-    [-xmin               xmin                (0         )] :Optional  :xmin for fitting
-    [-xmax               xmax                (0         )] :Optional  :xmax for fitting
-    [-xd[elta]           xDelta              (1         )] :Optional  :delta x for fitting
-    [-ymin               ymin                (0         )] :Optional  :ymin for fitting
-    [-ymax               ymax                (0         )] :Optional  :ymax for fitting
-    [-yd[elta]           yDelta              (1         )] :Optional  :delta y for fitting
-    [-zmin               zmin                (0         )] :Optional  :zmin for fitting
-    [-zmax               zmax                (82        )] :Optional  :zmax for fitting
-    [-zd[elta]           zDelta              (1         )] :Optional  :delta z for fitting
-    [-E[uler]A[ngle]     EulerAngle          (ZOYS      )] :Optional  :Euler Angle for three-angle
-    [-phimin             phimin              (0         )] :Optional  :phimin for fitting(degree)
-    [-phimax             phimax              (194       )] :Optional  :phimax for fitting(degree)
-    [-phid[elta]         phiDelta            (2         )] :Optional  :delta phi for fitting(degree)
-    [-psimin             psimin              (0         )] :Optional  :psimin for fitting(degree)
-    [-psimax             psimax              (0         )] :Optional  :psimax for fitting(degree)
-    [-psid[elta]         psiDelta            (2         )] :Optional  :delta psi for fitting(degree)
-    [-thetamin           thetamin            (0         )] :Optional  :thetamin for fitting(degree)
-    [-thetamax           thetamax            (0         )] :Optional  :thetamax for fitting(degree)
-    [-thetad[elta]       thetaDelta          (2         )] :Optional  :delta theta for fitting(degree)
-    [-n[ormalize]w[eight]normalizeWeight     (100000000.0)] :Optional  :weight for normalize
-    [-n[ormalize]C[ontour]normalizeContour    (0.0       )] :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        )] :Optional  :The atom will be neglected
-    [-Centre             ] :Optional  :Filament-axis is x=0, y=0
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-C[ontour]          contourLevel        (0.0       )... ] :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>
+/bin/bash: pdbRhoFitTm: No such file or directory
diff --git a/doc/SmallTools/pdbRotation.html b/doc/SmallTools/pdbRotation.html
index b780f5b..5e1a16e 100644
--- a/doc/SmallTools/pdbRotation.html
+++ b/doc/SmallTools/pdbRotation.html
@@ -1,27 +1 @@
-<HTML>
-<HEAD>
-<TITLE>pdbRotation</TITLE>
-</HEAD>
-<BODY>
-<H1>pdbRotation</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: pdbRotation
-Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-ZXY                ZXYrotx             (0.0       )ZXYroty             (0.0       )ZXYrotz             (0.0       )] :Optional  :ZXY*pdb: rotz(rotz)rotx(rotx)roty(roty) 
-    [-ZYX                ZYXrotx             (0.0       )ZYXroty             (0.0       )ZYXrotz             (0.0       )] :Optional  :ZYX*pdb: rotz(rotz)roty(roty)rotx(rotx) 
-    [-YXZ                YXZrotx             (0.0       )YXZroty             (0.0       )YXZrotz             (0.0       )] :Optional  :YXZ*pdb: roty(roty)rotx(rotx)rotz(rotz) 
-    [-XYZ                XYZrotx             (0.0       )XYZroty             (0.0       )XYZrotz             (0.0       )] :Optional  :XYZ*pdb: rotx(rotx)roty(roty)rotz(rotz) 
-    [-E[uler]A[ngle]     RotMode             (YOYS      )Rot1                (0.0       )Rot2                (0.0       )Rot3                (0.0       )] :Optional  :EA*pdb: EA=rot(rot3)rot(rot2)rot(rot1) 
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :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>
+/bin/bash: pdbRotation: No such file or directory
diff --git a/doc/SmallTools/pdbShapeFit.html b/doc/SmallTools/pdbShapeFit.html
index a5faa3f..91488a3 100644
--- a/doc/SmallTools/pdbShapeFit.html
+++ b/doc/SmallTools/pdbShapeFit.html
@@ -1,73 +1 @@
-<HTML>
-<HEAD>
-<TITLE>pdbShapeFit</TITLE>
-</HEAD>
-<BODY>
-<H1>pdbShapeFit</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: pdbShapeFit
-Options:
-    [-i[nput]pdb[File]   InPDB               (NULL      )] :Essential :InputDataFile
-    [-i[nput]mrc[File]   InMRC               (NULL      )] :Essential :InputDataFile
-    [-C[ontour]          Contour             (0.0       )] :Essential :Contour
-    [-C[ontour]M[ode]    ContourMode         (0         )] :Optional  :ContourMode: refer to mrcImageContourSurfaceCreate
-    [-o[utput of ]mrc    OutMRC              (NULL      )] :Optional  :OutputDataFile
-    [-o[utput of ]txt    OutTxt              (stdout    )] :Optional  :OutputDataFile
-    [-o[utput of ]pdb    OutPDB              (NULL      )] :Optional  :OutputDataFile
-    [-xmin               xmin                (0         )] :Optional  :xmin for fitting
-    [-xmax               xmax                (0         )] :Optional  :xmax for fitting
-    [-xd[elta]           xDelta              (1         )] :Optional  :delta x for fitting
-    [-ymin               ymin                (0         )] :Optional  :ymin for fitting
-    [-ymax               ymax                (0         )] :Optional  :ymax for fitting
-    [-yd[elta]           yDelta              (1         )] :Optional  :delta y for fitting
-    [-zmin               zmin                (0         )] :Optional  :zmin for fitting
-    [-zmax               zmax                (82        )] :Optional  :zmax for fitting
-    [-zd[elta]           zDelta              (1         )] :Optional  :delta z for fitting
-    [-E[uler]A[ngle]     EulerAngle          (ZOYS      )] :Optional  :Euler Angle for three-angle
-    [-phimin             phimin              (0         )] :Optional  :phimin for fitting(degree)
-    [-phimax             phimax              (194       )] :Optional  :phimax for fitting(degree)
-    [-phid[elta]         phiDelta            (2         )] :Optional  :delta phi for fitting(degree)
-    [-psimin             psimin              (0         )] :Optional  :psimin for fitting(degree)
-    [-psimax             psimax              (0         )] :Optional  :psimax for fitting(degree)
-    [-psid[elta]         psiDelta            (2         )] :Optional  :delta psi for fitting(degree)
-    [-thetamin           thetamin            (0         )] :Optional  :thetamin for fitting(degree)
-    [-thetamax           thetamax            (0         )] :Optional  :thetamax for fitting(degree)
-    [-thetad[elta]       thetaDelta          (2         )] :Optional  :delta theta for fitting(degree)
-    [-P[DB]C[ontour]M[ode]surfaceMode         (0         )] :Optional  :PDB SurfaceMode: refer to pdbSurface
-    [-order              order               (1.7       )] :Optional  :order: refer to pdbSurface
-    [-refine             refine              (2         )] :Optional  :refine: refer to pdbSurface
-    [-size               size                (3         )] :Optional  :size: refer to pdbSurface
-    [-weight             weight              (100       )] :Optional  :weight: refer to pdbSurface
-    [-mergin             mergin              (3.0       )] :Optional  :mergin: refer to pdbSurface
-    [-thres              thresHold           (0.0       )] :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      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :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>
+/bin/bash: pdbShapeFit: No such file or directory
diff --git a/doc/SmallTools/pdbSurface.html b/doc/SmallTools/pdbSurface.html
index 53a2f2c..50f06e4 100644
--- a/doc/SmallTools/pdbSurface.html
+++ b/doc/SmallTools/pdbSurface.html
@@ -16,6 +16,7 @@ Options:
     [-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
 ----- Additional Usage -----
diff --git a/doc/SmallTools/pdbTrans.html b/doc/SmallTools/pdbTrans.html
index 4be2579..4d26a75 100644
--- a/doc/SmallTools/pdbTrans.html
+++ b/doc/SmallTools/pdbTrans.html
@@ -1,28 +1 @@
-<HTML>
-<HEAD>
-<TITLE>pdbTrans</TITLE>
-</HEAD>
-<BODY>
-<H1>pdbTrans</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: pdbTrans
-Options:
-    [-i[nput]            inFile              (NULL      )] :Essential :Input: DataFile
-    [-o[utput]           outFile             (NULL      )] :Essential :Output: DataFile
-    [-M[atrix]           matFile             (NULL      )] :Optional  :Input: MatrixFile[4][4]
-    [-E[uler]A[ngle]     RotMode             (YOYS      )Rot1                (0.0       )Rot2                (0.0       )Rot3                (0.0       )] :Optional  :Input: 
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :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>
+/bin/bash: pdbTrans: No such file or directory
diff --git a/doc/SmallTools/pdbTwoProteinFit.html b/doc/SmallTools/pdbTwoProteinFit.html
index 56cdc28..3b7dbb2 100644
--- a/doc/SmallTools/pdbTwoProteinFit.html
+++ b/doc/SmallTools/pdbTwoProteinFit.html
@@ -1,30 +1 @@
-<HTML>
-<HEAD>
-<TITLE>pdbTwoProteinFit</TITLE>
-</HEAD>
-<BODY>
-<H1>pdbTwoProteinFit</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: pdbTwoProteinFit
-Options:
-    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
-    [-i[nput]res[idue]   InResidue           (NULL      )] :Optional  :ResidueInformationOfInputData
-    [-i[nput]sel[ectResidue]SelectIn            (NULL      )] :Optional  :Output: Selected residue of in after fitting
-    [-r[ef]              Ref                 (NULL      )] :Essential :ReferenceDataFile
-    [-r[ef]res[idue]     RefResidue          (NULL      )] :Optional  :ResidueInfomationOfReferenceData
-    [-r[ef]sel[ectResidue]SelectRef           (NULL      )] :Optional  :Output: Selected residue of after fitting
-    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
-    [-o[utput]Matrix     Matrix              (stdout    )] :Optional  :OutputMatrix
-    [-o[utput]Param      Param               (stdout    )] :Optional  :OutputParam
-    [-o[utput]Dis[tance] outDis              (stdout    )] :Optional  :Output: PDB Distance as Temp
-    [-o[utput]Dis[tance]2outDis2             (stdout    )] :Optional  :Output: Distance List for Ca
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
->>>> Input and Reference File Format<<<<
-ResidueNumberToBeFitted
-...
-If |, all residules are sellected till the residue in the next line
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: pdbTwoProteinFit: No such file or directory
diff --git a/doc/SmallTools/pointsSetToPDB.html b/doc/SmallTools/pointsSetToPDB.html
new file mode 100644
index 0000000..3b652c9
--- /dev/null
+++ b/doc/SmallTools/pointsSetToPDB.html
@@ -0,0 +1 @@
+/bin/bash: pointsSetToPDB: No such file or directory
diff --git a/doc/SmallTools/vectorImageNearestNeighborMethod.html b/doc/SmallTools/vectorImageNearestNeighborMethod.html
index e87e3d5..d7fd4e8 100644
--- a/doc/SmallTools/vectorImageNearestNeighborMethod.html
+++ b/doc/SmallTools/vectorImageNearestNeighborMethod.html
@@ -1 +1,24 @@
-/bin/bash: vectorImageNearestNeighborMethod: No such file or directory
+Program Start
+<HTML>
+<HEAD>
+<TITLE>vectorImageNearestNeighborMethod</TITLE>
+</HEAD>
+<BODY>
+<H1>vectorImageNearestNeighborMethod</H1>
+<H2>Usage</H2>
+<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
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-- 
2.11.0