-<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>
<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>
-<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">
-<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">
/*
contour.h
*/
-#if ! defined(CELLLINUX64) && ! defined(I386MAC)
-#include <values.h>
-#endif
+#include "genUtil.h"
#ifndef MINFLOAT
#define MINFLOAT (1e-31)
-<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">
/* struct end */
/* prototype begin */
+
+#ifdef __cplusplus
+ extern "C" {
+#endif
extern void crystalInit(CrystalInfo* crystal);
extern void crystalSpaceGroupPrint(FILE* fpt, int mode);
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 */
-<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">
-<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">
typedef char matrix3DEulerAngleMode;
+typedef struct EulerAngleInfo {
+ char EAMode[5];
+ double Rot1;
+ double Rot2;
+ double Rot3;
+} EulerAngleInfo;
+
/* struct end */
/*
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);
-<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">
#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. */
extern Memory memoryByteSwap(Memory src, size_t, int n);
-/* struct end */
+/* prototype end */
#ifdef __cplusplus
};
-<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">
-<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">
-<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">
-<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">
</HEAD>
<BODY BGCOLOR="ffffcc">
<H1> String </H1>
-<H4> Update Time 02/03/13---05:41:16 </H4>
<H2> Member function </H2>
<UL>
<LI> stringGetFromFile
<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">
-<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);
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/Vector.c:
-
-../src/VectorScalarProduct.c:
-
-../src/lVectorSpline2D.c:
</PRE>
<HR>
<A NAME="include">
--- /dev/null
+<<<<<<< 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>
--- /dev/null
+<<<<<<< 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>
--- /dev/null
+<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>
--- /dev/null
+<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>
--- /dev/null
+<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>
--- /dev/null
+<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>
--- /dev/null
+<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>
--- /dev/null
+<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>
-<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">
-<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">
--- /dev/null
+<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>
</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>
<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">
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)*/
--- /dev/null
+<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>
-<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">
-<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">
--- /dev/null
+<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>
--- /dev/null
+<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>
--- /dev/null
+<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>
-<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">
--- /dev/null
+<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>
-<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">
-<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">
-<H4> Update Time 02/03/13---05:38:45 </H4>
<H2> API(Application Interface)</H2>
<UL>
<LI> llDataFileRead
<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">
-<H4> Update Time 02/03/13---05:38:52 </H4>
<HTML>
<HEAD>
<TITLE> ltlgData </TITLE>
<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">
-<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">
</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>
#include <stdio.h>
#include <math.h>
#include "genUtil.h"
+#include "Matrix3D.h"
/* struct begin */
#define MRC_SizeOfZero ((mrcStatusType)0x00000000L|mrcStatusMask_ReferMRCInfo)
+
+extern char* mrcImageGeneralTypeList[];
+
/* constant end */
/* struct begin */
#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)
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];
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 */
/*
*/
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;
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;
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 */
mrcImageParaTypeReal sx; /* Filter kernel size */
mrcImageParaTypeReal sy;
mrcImageParaTypeReal sz;
+ double sigma; /* for Lee-Sigma filter */
} lmrcImageSmoothingInfo;
typedef struct lmrcImageCVEInfo {
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)
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];
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;
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);
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);
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);
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 */
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);
/* 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
-<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">
-<H4> Update Time 02/03/13---05:39:39 </H4>
<H1> pdbFile </H1>
<UL>
<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">
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);
-<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">
-<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">
-<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>
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+<LI> <A HREF="bmp2mrc.html"> bmp2mrc</A>
+<LI> <A HREF="bmpFileInfo.html"> bmpFileInfo</A>
<LI> <A HREF="calcCommonLine.html"> calcCommonLine</A>
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<LI> <A HREF="defocusDeterminationFromThonRing.html"> defocusDeterminationFromThonRing</A>
+<LI> <A HREF="dmInfo.html"> dmInfo</A>
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<LI> <A HREF="electronWaveLength.html"> electronWaveLength</A>
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+<LI> <A HREF="eosPointProjector.html"> eosPointProjector</A>
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+<LI> <A HREF="eosPointTracker.html"> eosPointTracker</A>
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<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>
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<LI> <A HREF="mrc2lattice.html"> mrc2lattice</A>
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+<LI> <A HREF="mrc2mrc.html"> mrc2mrc</A>
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<LI> <A HREF="mrc2tiff.html"> mrc2tiff</A>
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<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>
<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>
<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>
<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>
<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>
<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>
<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>
<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>
<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>
<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>
<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>
<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>
-<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
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
-<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
[-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>
--- /dev/null
+<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>
--- /dev/null
+<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>
-<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
-<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
[-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
--- /dev/null
+<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>
--- /dev/null
+<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>
--- /dev/null
+<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>
--- /dev/null
+<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>
-<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
-<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
-<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
<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]
--- /dev/null
+<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>
<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
-sh: mrc2hdf: not found
+/bin/bash: mrc2hdf: No such file or directory
--- /dev/null
+<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>
<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 -----
<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>
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>
<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>
--- /dev/null
+<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>
--- /dev/null
+<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>
-/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>
--- /dev/null
+<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>
--- /dev/null
+<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>
--- /dev/null
+<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>
--- /dev/null
+<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>
--- /dev/null
+<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>
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
--- /dev/null
+<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>
--- /dev/null
+<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>
--- /dev/null
+<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>
--- /dev/null
+<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>
-<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
[-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>
--- /dev/null
+<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>
--- /dev/null
+<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>
<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.
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]
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>
-/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>
<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
--- /dev/null
+<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>
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>
<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
<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>
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>
--- /dev/null
+<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>
-<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
-/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>
--- /dev/null
+<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>
<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>
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
<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
[-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
--- /dev/null
+<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>
--- /dev/null
+<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>
<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 ...
--- /dev/null
+<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>
<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>
[-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
--- /dev/null
+<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>
-<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
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]
-/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>
[-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
--- /dev/null
+<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>
[-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
<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>
<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>
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>
-<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
-<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
-<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
-<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
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>
-<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
-<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
-<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
-<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
-<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
-<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
[-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 -----
-<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
-<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
--- /dev/null
+/bin/bash: pointsSetToPDB: No such file or directory
-/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>
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