SOURCE=\
Integration \
bin \
+data \
env \
hostdepend \
include \
lib \
+optional \
+others \
sbin \
src \
+tutorial \
util \
#LastSource
SOURCE=\
Integration \
bin \
-data \
env \
hostdepend \
include \
lib \
-optional \
-others \
sbin \
src \
-tutorial \
util \
-zephyr \
#LastSource
+++ /dev/null
-/Applications/Eos
\ No newline at end of file
git-merge-all:: git-merge git-merge-zephyr git-merge-data git-merge-optional git-merge-tutorial git-merge-others
git-merge::
- cd . ; git log -1; git merge FETCH_HEAD
+ #cd . ; git log -1; git merge FETCH_HEAD
+ cd . ; git log -1; git merge
git-merge-zephyr::
- cd zephyr ; git log -1; git merge FETCH_HEAD
+ #cd zephyr ; git log -1; git merge FETCH_HEAD
+ cd zephyr ; git log -1; git merge
git-merge-data::
- cd data ; git log -1; git merge FETCH_HEAD
+ #cd data ; git log -1; git merge FETCH_HEAD
+ cd data ; git log -1; git merge
git-merge-optional::
- cd optional; git log -1; git merge FETCH_HEAD
+ #cd optional; git log -1; git merge FETCH_HEAD
+ cd optional; git log -1; git merge
git-merge-tutorial::
- cd tutorial; git log -1; git merge FETCH_HEAD
+ #cd tutorial; git log -1; git merge FETCH_HEAD
+ cd tutorial; git log -1; git merge
git-merge-others::
- cd others ; git log -1; git merge FETCH_HEAD
+ #cd others ; git log -1; git merge FETCH_HEAD
+ cd others ; git log -1; git merge
#
# Nickname
--- /dev/null
+../sbin/MachineIndependent
\ No newline at end of file
--- /dev/null
+../sbin/MachineIndependent
\ No newline at end of file
# element name is the name of a command and the value is
# a script that loads the command.
-set auto_index(roiAreaSelectStart) [list source [file join $dir RoiAreaSelect.wish]]
-set auto_index(roiAreaSelectMotion) [list source [file join $dir RoiAreaSelect.wish]]
-set auto_index(roiAreaSelectEnd) [list source [file join $dir RoiAreaSelect.wish]]
-set auto_index(roiAreaSelectOK) [list source [file join $dir RoiAreaSelect.wish]]
-set auto_index(projectionRecreate) [list source [file join $dir ProjectionUtil.wish]]
-set auto_index(projectionCreate) [list source [file join $dir ProjectionUtil.wish]]
-set auto_index(projectionClear) [list source [file join $dir ProjectionUtil.wish]]
-set auto_index(projectionChange) [list source [file join $dir ProjectionUtil.wish]]
+set auto_index(display2BindingSet) [list source [file join $dir Display2Binding.wish]]
+set auto_index(colormapChange) [list source [file join $dir Display2Colormap.wish]]
+set auto_index(display2DesktopSet) [list source [file join $dir Display2Desktop.wish]]
+set auto_index(display2ETCSet) [list source [file join $dir Display2ETCSet.wish]]
+set auto_index(fileOpenWinCreate) [list source [file join $dir Display2File.wish]]
+set auto_index(fileNewWinCreate) [list source [file join $dir Display2File.wish]]
+set auto_index(seqFileOpenWinCreate) [list source [file join $dir Display2File.wish]]
+set auto_index(seqFileNewWinCreate) [list source [file join $dir Display2File.wish]]
set auto_index(fileOpen) [list source [file join $dir Display2Image.wish]]
set auto_index(mainImagePut) [list source [file join $dir Display2Image.wish]]
set auto_index(overviewImagePut) [list source [file join $dir Display2Image.wish]]
-set auto_index(roiAreaFFT) [list source [file join $dir RoiAreaUtil.wish]]
-set auto_index(splineNearPoint) [list source [file join $dir RoiAreaUtil.wish]]
-set auto_index(rectangleNearPoint) [list source [file join $dir RoiAreaUtil.wish]]
-set auto_index(lineNearPoint) [list source [file join $dir RoiAreaUtil.wish]]
-set auto_index(pointDistance) [list source [file join $dir RoiAreaUtil.wish]]
-set auto_index(pointDistance2) [list source [file join $dir RoiAreaUtil.wish]]
-set auto_index(vectorAngle) [list source [file join $dir RoiAreaUtil.wish]]
-set auto_index(coordGetInMainImageToReal) [list source [file join $dir RoiAreaUtil.wish]]
-set auto_index(coordGetInMainImageToCanvas) [list source [file join $dir RoiAreaUtil.wish]]
-set auto_index(dataGetInMainImageToReal) [list source [file join $dir RoiAreaUtil.wish]]
-set auto_index(dataGetInMainImageToCanvas) [list source [file join $dir RoiAreaUtil.wish]]
-set auto_index(pointSet) [list source [file join $dir RoiAreaUtil.wish]]
-set auto_index(roiAreaZoomIn) [list source [file join $dir RoiAreaZoom.wish]]
-set auto_index(roiAreaZoomOut) [list source [file join $dir RoiAreaZoom.wish]]
-set auto_index(roiAreaZoom) [list source [file join $dir RoiAreaZoom.wish]]
-set auto_index(colormapChange) [list source [file join $dir Display2Colormap.wish]]
-set auto_index(display2SetVar) [list source [file join $dir Display2Init.wish]]
-set auto_index(display2InitVar) [list source [file join $dir Display2Init.wish]]
-set auto_index(display2InitVarSet) [list source [file join $dir Display2Init.wish]]
-set auto_index(diplay2CanvasInit) [list source [file join $dir Display2Init.wish]]
-set auto_index(display2Init) [list source [file join $dir Display2Init.wish]]
-set auto_index(roiInformationWinCreate) [list source [file join $dir Display2InfoROI.wish]]
-set auto_index(roiLineInfoFrameCreate) [list source [file join $dir Display2InfoROI.wish]]
-set auto_index(roiSplineInfoFrameCreate) [list source [file join $dir Display2InfoROI.wish]]
-set auto_index(roiRectangleInfoFrameCreate) [list source [file join $dir Display2InfoROI.wish]]
-set auto_index(roiAnalysisFrameCreate) [list source [file join $dir Display2InfoROI.wish]]
set auto_index(histgramGraphCreate) [list source [file join $dir Display2Info.wish]]
set auto_index(display2InformationWinCreate) [list source [file join $dir Display2Info.wish]]
set auto_index(fileReopen) [list source [file join $dir Display2Info.wish]]
set auto_index(ctfInformationWinCreate) [list source [file join $dir Display2Info.wish]]
set auto_index(unitCellInformationWinCreate) [list source [file join $dir Display2Info.wish]]
set auto_index(scaleInfoWinCreate) [list source [file join $dir Display2Info.wish]]
+set auto_index(roiInformationWinCreate) [list source [file join $dir Display2InfoROI.wish]]
+set auto_index(roiLineInfoFrameCreate) [list source [file join $dir Display2InfoROI.wish]]
+set auto_index(roiSplineInfoFrameCreate) [list source [file join $dir Display2InfoROI.wish]]
+set auto_index(roiRectangleInfoFrameCreate) [list source [file join $dir Display2InfoROI.wish]]
+set auto_index(roiAnalysisFrameCreate) [list source [file join $dir Display2InfoROI.wish]]
+set auto_index(display2SetVar) [list source [file join $dir Display2Init.wish]]
+set auto_index(display2InitVar) [list source [file join $dir Display2Init.wish]]
+set auto_index(display2InitVarSet) [list source [file join $dir Display2Init.wish]]
+set auto_index(diplay2CanvasInit) [list source [file join $dir Display2Init.wish]]
+set auto_index(display2Init) [list source [file join $dir Display2Init.wish]]
+set auto_index(display2MenuSet) [list source [file join $dir Display2Menu.wish]]
+set auto_index(menuFileCreate) [list source [file join $dir Display2Menu.wish]]
+set auto_index(menuSeqFileCreate) [list source [file join $dir Display2Menu.wish]]
+set auto_index(menuWindowCreate) [list source [file join $dir Display2Menu.wish]]
+set auto_index(menuInfoCreate) [list source [file join $dir Display2Menu.wish]]
+set auto_index(menuHelpCreate) [list source [file join $dir Display2Menu.wish]]
+set auto_index(menuExitCreate) [list source [file join $dir Display2Menu.wish]]
+set auto_index(display2MenuSet2) [list source [file join $dir Display2Menu2.wish]]
+set auto_index(roiRelatedObjectRecreate) [list source [file join $dir Display2MenuROI.wish]]
+set auto_index(menuRoiCreate) [list source [file join $dir Display2MenuROI.wish]]
+set auto_index(menuRoiCancelCommand) [list source [file join $dir Display2MenuROI.wish]]
+set auto_index(menuRoiSingleMultiTransform) [list source [file join $dir Display2MenuROI.wish]]
+set auto_index(menuMultiRoiOKCommand) [list source [file join $dir Display2MenuROI.wish]]
+set auto_index(menuMultiRoiAllDeleteCommand) [list source [file join $dir Display2MenuROI.wish]]
+set auto_index(menuMultiRoiDeleteCommand) [list source [file join $dir Display2MenuROI.wish]]
+set auto_index(menuEditCreate) [list source [file join $dir Display2MenuROI.wish]]
set auto_index(fft2dCmd) [list source [file join $dir fft2dCmd.wish]]
+set auto_index(layerLineRecreate) [list source [file join $dir LayerLineUtil.wish]]
+set auto_index(layerLineCreate) [list source [file join $dir LayerLineUtil.wish]]
+set auto_index(layerLineClear) [list source [file join $dir LayerLineUtil.wish]]
+set auto_index(layerLineChange) [list source [file join $dir LayerLineUtil.wish]]
+set auto_index(projectionRecreate) [list source [file join $dir ProjectionUtil.wish]]
+set auto_index(projectionCreate) [list source [file join $dir ProjectionUtil.wish]]
+set auto_index(projectionClear) [list source [file join $dir ProjectionUtil.wish]]
+set auto_index(projectionChange) [list source [file join $dir ProjectionUtil.wish]]
set auto_index(roiAreaCreateStart) [list source [file join $dir RoiAreaCreate.wish]]
set auto_index(roiAreaCreateMotion) [list source [file join $dir RoiAreaCreate.wish]]
set auto_index(roiAreaCreateEnd) [list source [file join $dir RoiAreaCreate.wish]]
set auto_index(splineCreate) [list source [file join $dir RoiAreaCreate.wish]]
set auto_index(knobShow) [list source [file join $dir RoiAreaCreate.wish]]
set auto_index(knobHide) [list source [file join $dir RoiAreaCreate.wish]]
-set auto_index(display2BindingSet) [list source [file join $dir Display2Binding.wish]]
-set auto_index(display2MenuSet) [list source [file join $dir Display2Menu.wish]]
-set auto_index(menuFileCreate) [list source [file join $dir Display2Menu.wish]]
-set auto_index(menuSeqFileCreate) [list source [file join $dir Display2Menu.wish]]
-set auto_index(menuWindowCreate) [list source [file join $dir Display2Menu.wish]]
-set auto_index(menuInfoCreate) [list source [file join $dir Display2Menu.wish]]
-set auto_index(menuHelpCreate) [list source [file join $dir Display2Menu.wish]]
-set auto_index(menuExitCreate) [list source [file join $dir Display2Menu.wish]]
-set auto_index(roiRelatedObjectRecreate) [list source [file join $dir Display2MenuROI.wish]]
-set auto_index(menuRoiCreate) [list source [file join $dir Display2MenuROI.wish]]
-set auto_index(menuRoiCancelCommand) [list source [file join $dir Display2MenuROI.wish]]
-set auto_index(menuRoiSingleMultiTransform) [list source [file join $dir Display2MenuROI.wish]]
-set auto_index(menuMultiRoiOKCommand) [list source [file join $dir Display2MenuROI.wish]]
-set auto_index(menuMultiRoiAllDeleteCommand) [list source [file join $dir Display2MenuROI.wish]]
-set auto_index(menuMultiRoiDeleteCommand) [list source [file join $dir Display2MenuROI.wish]]
-set auto_index(menuEditCreate) [list source [file join $dir Display2MenuROI.wish]]
+set auto_index(roiMultiAreaInfoSave) [list source [file join $dir RoiAreaFile.wish]]
+set auto_index(roiMultiAreaInfoLoad) [list source [file join $dir RoiAreaFile.wish]]
+set auto_index(roiAreaFileSave) [list source [file join $dir RoiAreaFile.wish]]
+set auto_index(roiAreaMoveStart) [list source [file join $dir RoiAreaMove.wish]]
+set auto_index(roiAreaMoveMotion) [list source [file join $dir RoiAreaMove.wish]]
+set auto_index(roiAreaMoveEnd) [list source [file join $dir RoiAreaMove.wish]]
+set auto_index(rectangleMove) [list source [file join $dir RoiAreaMove.wish]]
+set auto_index(lineMove) [list source [file join $dir RoiAreaMove.wish]]
+set auto_index(splineMove) [list source [file join $dir RoiAreaMove.wish]]
set auto_index(roiAreaResizeStart) [list source [file join $dir RoiAreaResize.wish]]
set auto_index(roiAreaResizeMotion) [list source [file join $dir RoiAreaResize.wish]]
set auto_index(roiAreaResizeEnd) [list source [file join $dir RoiAreaResize.wish]]
set auto_index(lineRotateCalc) [list source [file join $dir RoiAreaRotate.wish]]
set auto_index(splineRotate) [list source [file join $dir RoiAreaRotate.wish]]
set auto_index(splineRotateCalc) [list source [file join $dir RoiAreaRotate.wish]]
-set auto_index(roiMultiAreaInfoSave) [list source [file join $dir RoiAreaFile.wish]]
-set auto_index(roiMultiAreaInfoLoad) [list source [file join $dir RoiAreaFile.wish]]
-set auto_index(roiAreaFileSave) [list source [file join $dir RoiAreaFile.wish]]
-set auto_index(layerLineRecreate) [list source [file join $dir LayerLineUtil.wish]]
-set auto_index(layerLineCreate) [list source [file join $dir LayerLineUtil.wish]]
-set auto_index(layerLineClear) [list source [file join $dir LayerLineUtil.wish]]
-set auto_index(layerLineChange) [list source [file join $dir LayerLineUtil.wish]]
-set auto_index(fileOpenWinCreate) [list source [file join $dir Display2File.wish]]
-set auto_index(fileNewWinCreate) [list source [file join $dir Display2File.wish]]
-set auto_index(seqFileOpenWinCreate) [list source [file join $dir Display2File.wish]]
-set auto_index(seqFileNewWinCreate) [list source [file join $dir Display2File.wish]]
-set auto_index(display2DesktopSet) [list source [file join $dir Display2Desktop.wish]]
+set auto_index(roiAreaSelectStart) [list source [file join $dir RoiAreaSelect.wish]]
+set auto_index(roiAreaSelectMotion) [list source [file join $dir RoiAreaSelect.wish]]
+set auto_index(roiAreaSelectEnd) [list source [file join $dir RoiAreaSelect.wish]]
+set auto_index(roiAreaSelectOK) [list source [file join $dir RoiAreaSelect.wish]]
+set auto_index(roiAreaFFT) [list source [file join $dir RoiAreaUtil.wish]]
+set auto_index(splineNearPoint) [list source [file join $dir RoiAreaUtil.wish]]
+set auto_index(rectangleNearPoint) [list source [file join $dir RoiAreaUtil.wish]]
+set auto_index(lineNearPoint) [list source [file join $dir RoiAreaUtil.wish]]
+set auto_index(pointDistance) [list source [file join $dir RoiAreaUtil.wish]]
+set auto_index(pointDistance2) [list source [file join $dir RoiAreaUtil.wish]]
+set auto_index(vectorAngle) [list source [file join $dir RoiAreaUtil.wish]]
+set auto_index(coordGetInMainImageToReal) [list source [file join $dir RoiAreaUtil.wish]]
+set auto_index(coordGetInMainImageToCanvas) [list source [file join $dir RoiAreaUtil.wish]]
+set auto_index(dataGetInMainImageToReal) [list source [file join $dir RoiAreaUtil.wish]]
+set auto_index(dataGetInMainImageToCanvas) [list source [file join $dir RoiAreaUtil.wish]]
+set auto_index(pointSet) [list source [file join $dir RoiAreaUtil.wish]]
+set auto_index(roiAreaZoomIn) [list source [file join $dir RoiAreaZoom.wish]]
+set auto_index(roiAreaZoomOut) [list source [file join $dir RoiAreaZoom.wish]]
+set auto_index(roiAreaZoom) [list source [file join $dir RoiAreaZoom.wish]]
+set auto_index(ScaleRecreate) [list source [file join $dir ScaleUtil.wish]]
+set auto_index(ScaleCreate) [list source [file join $dir ScaleUtil.wish]]
+set auto_index(ScaleClear) [list source [file join $dir ScaleUtil.wish]]
+set auto_index(ScaleChange) [list source [file join $dir ScaleUtil.wish]]
set auto_index(sectionInit) [list source [file join $dir SectionUtil.wish]]
set auto_index(sectionRecreateAll) [list source [file join $dir SectionUtil.wish]]
set auto_index(sectionRecreate) [list source [file join $dir SectionUtil.wish]]
set auto_index(sectionClearAll) [list source [file join $dir SectionUtil.wish]]
set auto_index(sectionClear) [list source [file join $dir SectionUtil.wish]]
set auto_index(sectionChange) [list source [file join $dir SectionUtil.wish]]
-set auto_index(ScaleRecreate) [list source [file join $dir ScaleUtil.wish]]
-set auto_index(ScaleCreate) [list source [file join $dir ScaleUtil.wish]]
-set auto_index(ScaleClear) [list source [file join $dir ScaleUtil.wish]]
-set auto_index(ScaleChange) [list source [file join $dir ScaleUtil.wish]]
set auto_index(unitCellRecreate) [list source [file join $dir UnitCell.wish]]
-set auto_index(display2MenuSet2) [list source [file join $dir Display2Menu2.wish]]
-set auto_index(roiAreaMoveStart) [list source [file join $dir RoiAreaMove.wish]]
-set auto_index(roiAreaMoveMotion) [list source [file join $dir RoiAreaMove.wish]]
-set auto_index(roiAreaMoveEnd) [list source [file join $dir RoiAreaMove.wish]]
-set auto_index(rectangleMove) [list source [file join $dir RoiAreaMove.wish]]
-set auto_index(lineMove) [list source [file join $dir RoiAreaMove.wish]]
-set auto_index(splineMove) [list source [file join $dir RoiAreaMove.wish]]
-set auto_index(display2ETCSet) [list source [file join $dir Display2ETCSet.wish]]
--- /dev/null
+/*
+# leosPointPositionCorrection.h : $Revision$
+# $Date$
+# Created by $Author$
+# Usage : leosPointPositionCorrection.h
+# Attention
+# $Loccker$
+# $State$
+#
+*/
+/* $Log$ */
+#ifndef LEOSPOINT_POSITION_CORRECTION_H
+#define LEOSPOINT_POSITION_CORRECTION_H
+
+#include <stdio.h>
+
+/* constant begin */
+
+typedef enum leosPointPositionCorrectionMode {
+ a=0,
+ b=1
+} leosPointPositionCorrectionMode;
+
+/* constant end */
+
+/* struct begin */
+
+typedef struct leosPointPositionCorrectionInfo {
+ // Input
+ int n;
+
+ // Output
+ int m;
+ eosPoint db;
+} leosPointPositionCorrectionInfo;
+
+/* struct end */
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* prototype begin */
+
+extern int leosPointPositionCorrection(eosPoint* outP, eosPoint* inP, leosPointPositionCorrectionInfo* linfo, int mode);
+
+/* prototype end */
+
+#ifdef __cplusplus
+};
+#endif
+
+#endif /* LEOSPOINT_POSITION_CORRECTION_H*/
+
char* Image;
unsigned char* ImageCharImage;
unsigned short* ImageShortImage;
- unsigned long* ImageLongImage;
+ signed long* ImageLongImage;
+ unsigned long* ImageULongImage;
float* ImageFloatImage;
double* ImageDoubleImage;
int flagSigned;
} mrcImage;
+typedef struct mrcImagePyramidList {
+ mrcImage mrc;
+ mrcImage* up;
+ mrcImage* down;
+} mrcImagePyramidList;
+
+typedef struct mrcImagePyramid {
+ mrcImagePyramidList* top;
+ mrcImagePyramidList* current;
+} mrcImagePyramid;
+
typedef struct mrcImageInformation {
double mean;
double rootMeanSquare;
/* Frequency */
extern void lmrcImageHistgram3(double** hist, unsigned long nlevel, mrcImage* img);
extern void lmrcImageHistgram4(double** hist, double delta, mrcImage* img);
-extern void lmrcImageHistgram6(double** hist, unsigned long nlevel, double Low, double High, mrcImage* img);
+extern void lmrcImageHistgram6(double** hist, double delta, double Low, double High, mrcImage* img);
extern void lmrcImageInformation(mrcImageInformation* info, mrcImage* img);
<H2>Information from source codes</H2>
</A>
<PRE>
+../src/contourCreate.c:
+
+../src/lcontour2ps.c:
+
+../src/lmrc2contour.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
+../src/tkImgFmtMRC.c:
+
+../src/tkImgFmtlargeIP.c:
+
+../src/tkctfInfo.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
+../src/avsFileInit.c:
+
+../src/avsFileSet.c:
+
+../src/avsFileWrite.c:
</PRE>
<HR>
<A NAME="include">
<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">
<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">
<H2>Information from source codes</H2>
</A>
<PRE>
+../src/lmrc2png.c:
+
+../src/pngFileInit.c:
+
+../src/pngFileWrite.c:
</PRE>
<HR>
<A NAME="include">
<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">
<H2>Information from source codes</H2>
</A>
<PRE>
+../src/lmrc2bild.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
+../src/bmpFileInfo.c:
+
+../src/bmpFileRead.c:
+
+../src/lbmp2mrc.c:
</PRE>
<HR>
<A NAME="include">
<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/ctfforbayes.c:
+
+../src/ctfforbayescheck.c:
+
+../src/defocuslikelihood.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">
<H2>Information from source codes</H2>
</A>
<PRE>
+../src/dmFileInfo.c:
+
+../src/dmFileInit.c:
+
+../src/dmFileRead.c:
+
+../src/dmFileUtil.c:
+
+../src/ldm2mrc.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
+../src/dsn6Init.c:
+
+../src/dsn6Write.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
+../src/emDataRead.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
+../src/lmrc2viff.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
+../src/largeIPRead.c:
+
+../src/tkImgFmtlargeIP.c:
</PRE>
<HR>
<A NAME="include">
<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">
<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">
<H2>Information from source codes</H2>
</A>
<PRE>
+../src/mapFileRead.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
+../src/fftn.c:
+
+../src/lmrcFETnormalizeBySD.c:
+
+../src/lmrcFFTCentralSection.c:
+
+../src/lmrcFFTCentralSectionCompare.c:
+
+../src/lmrcFFTCentralSectionCompareInfoWrite.c:
+
+../src/lmrcFFTCentralSectionsGet.c:
+
+../src/lmrcFFTExpression.c:
+
+../src/lmrcFFTFGconj.c:
+
+../src/lmrcFFTFxG.c:
+
+../src/lmrcFFTInfo.c:
+
+../src/lmrcImage3DPad.c:
+
+../src/lmrcImage3DWindowing.c:
+
+../src/lmrcImageAddValue.c:
+
+../src/lmrcImageAsProbability.c:
+
+../src/lmrcImageAverage.c:
+
+../src/lmrcImageBandPassFilter.c:
+
+../src/lmrcImageBilateralFilter.c:
+
+../src/lmrcImageBinarization.c:
+
+../src/lmrcImageBottomHatTransform.c:
+
+../src/lmrcImageBoundaryInfo.c:
+
+../src/lmrcImageCTFCompensation.c:
+
+../src/lmrcImageCTFDetermination.c:
+
+../src/lmrcImageCTFObservation.c:
+
+../src/lmrcImageCTFSN.c:
+
+../src/lmrcImageCVE.c:
+
+../src/lmrcImageCalcArea.c:
+
+../src/lmrcImageCenterGet.c:
+
+../src/lmrcImageCentre.c:
+
+../src/lmrcImageClosing.c:
+
+../src/lmrcImageClusterAnalysis.c:
+
+../src/lmrcImageCommonLine.c:
+
+../src/lmrcImageConnection.c:
+
+../src/lmrcImageConnectivityNumberCalc.c:
+
+../src/lmrcImageContourSurface.c:
+
+../src/lmrcImageContraction.c:
+
+../src/lmrcImageCorrelation.c:
+ $lmrcImageEuclidDistanceCalc: Calculate Euclid distance between two images $
+ $arg: in1: input mrcImage1 $
+ $arg: in2: input mrcImage2 $
+ $arg: mode: input int $
+ $mode: 0 Sum of SQR $
+ $mode: 1 Distance $
+ $return: EuclidDistance $
+
+../src/lmrcImageCorrelationPVM.c:
+
+../src/lmrcImageCorrelationWithCTFCompensation.c:
+
+../src/lmrcImageCorrelationinSpace.c:
+
+../src/lmrcImageCrystalCreate.c:
+
+../src/lmrcImageDataMaxAndMinGetByImage.c:
+
+../src/lmrcImageDataStraightCopy.c:
+
+../src/lmrcImageDeconvolution.c:
+
+../src/lmrcImageDensity.c:
+
+../src/lmrcImageDensityInverse.c:
+
+../src/lmrcImageDensityNormalizationByImage.c:
+
+../src/lmrcImageDifferential.c:
+
+../src/lmrcImageDilation.c:
+
+../src/lmrcImageDistanceConversion.c:
+
+../src/lmrcImageEdge.c:
+
+../src/lmrcImageEdgeAverage.c:
+
+../src/lmrcImageEdgeEnhancement.c:
+
+../src/lmrcImageErosion.c:
+
+../src/lmrcImageFFT.c:
+
+../src/lmrcImageFOMCalc.c:
+
+../src/lmrcImageFeatureCalc.c:
+
+../src/lmrcImageFeatureExtraction.c:
+
+../src/lmrcImageFeatureExtractionCoOccurrence.c:
+
+../src/lmrcImageFeatureExtractionRunLength.c:
+
+../src/lmrcImageFilterCreate.c:
+
+../src/lmrcImageFirstNoiseReductionByRelaxation.c:
+
+../src/lmrcImageFloating.c:
+
+../src/lmrcImageFourierNeighborCorrelation.c:
+
+../src/lmrcImageFourierPowerSpectrum.c:
+
+../src/lmrcImageFourierShellCorrelation.c:
+
+../src/lmrcImageHighPassFilter.c:
+
+../src/lmrcImageHighlighting.c:
+
+../src/lmrcImageHoleFilling.c:
+
+../src/lmrcImageHoughTransform.c:
+
+../src/lmrcImageLabeling.c:
+
+../src/lmrcImageLocalMaximumValuesFind.c:
+
+../src/lmrcImageLogicalOperation.c:
+
+../src/lmrcImageLowPassFilter.c:
+
+../src/lmrcImageMasking.c:
+
+../src/lmrcImageMaxDataGet.c:
+
+../src/lmrcImageMirroring.c:
+ $lmrcImageMirroring: (mrcImage* out, mrcImage* in, lmrcImageMirroring mode) $
+
+../src/lmrcImageModeChange.c:
+
+../src/lmrcImageModelCreate.c:
+
+../src/lmrcImageMontageCreate.c:
+
+../src/lmrcImageMorphology.c:
+
+../src/lmrcImageMove.c:
+
+../src/lmrcImageMultiCTFCompensation.c:
+
+../src/lmrcImageMultiplying.c:
+
+../src/lmrcImageNegativeLaplacian.c:
+
+../src/lmrcImageNoiseCreate.c:
+
+../src/lmrcImageNormalizing.c:
+
+../src/lmrcImageOneLineSimilarityCalc.c:
+
+../src/lmrcImageOpening.c:
+
+../src/lmrcImagePad.c:
+
+../src/lmrcImagePartImageSegmentation.c:
+
+../src/lmrcImagePattersonFunctionCalc.c:
+
+../src/lmrcImagePixelSummationOfProbabilityGetByImage.c:
+
+../src/lmrcImagePosterization.c:
+
+../src/lmrcImagePrewitt.c:
+
+../src/lmrcImageProjection.c:
+
+../src/lmrcImageProportionalDensityLevelSetByImage.c:
+
+../src/lmrcImageROI2D.c:
+
+../src/lmrcImageROI3D.c:
+
+../src/lmrcImageROInotChangeHeaderLength.c:
+
+../src/lmrcImageRadialDistribution.c:
+
+../src/lmrcImageRhoFiltering.c:
+
+../src/lmrcImageRoberts.c:
+
+../src/lmrcImageRotation.c:
+
+../src/lmrcImageSSDA.c:
+
+../src/lmrcImageSamplingUnitChange.c:
+
+../src/lmrcImageSecondNoiseReductionByRelaxation.c:
+
+../src/lmrcImageSecondNoiseReductionByRelaxationDijDimensionSet.c:
+
+../src/lmrcImageSecondNoiseReductionByRelaxationDijValueCalculate.c:
+
+../src/lmrcImageSecondNoiseReductionByRelaxationDijValueSet.c:
+
+../src/lmrcImageSecondNoiseReductionByRelaxationQValueSet.c:
+
+../src/lmrcImageSecondNoiseReductionByRelaxationRValueSet.c:
+
+../src/lmrcImageShapePCA.c:
+
+../src/lmrcImageShift.c:
+
+../src/lmrcImageShrink.c:
+
+../src/lmrcImageSigmaCalculate.c:
+
+../src/lmrcImageSinogram.c:
+
+../src/lmrcImageSinogramCorrelation.c:
+
+../src/lmrcImageSinogramFFT.c:
+
+../src/lmrcImageSmoothing.c:
+
+../src/lmrcImageSobel.c:
+
+../src/lmrcImageSoftEdge.c:
+
+../src/lmrcImageSolventFlattening.c:
+
+../src/lmrcImageSpatialFrequencyFilter.c:
+
+../src/lmrcImageSphere.c:
+
+../src/lmrcImageSplit.c:
+
+../src/lmrcImageStack.c:
+
+../src/lmrcImageStudentCalculate.c:
+
+../src/lmrcImageSubtractionCalc.c:
+
+../src/lmrcImageSummationCalculate.c:
+
+../src/lmrcImageSurfaceAreaCalc.c:
+
+../src/lmrcImageSymmetryFind.c:
+
+../src/lmrcImageTfunction.c:
+
+../src/lmrcImageToneReversal.c:
+
+../src/lmrcImageTopHatTransform.c:
+
+../src/lmrcImageTrans.c:
+
+../src/lmrcImageTransformDescartesIntoPolar.c:
+
+../src/lmrcImageTranspose.c:
+
+../src/lmrcImageTriming.c:
+
+../src/lmrcImageUnsharpening.c:
+
+../src/lmrcImageVolumeCalc.c:
+
+../src/lmrcImageWindowing.c:
+
+../src/lmrcImagesFTest.c:
+
+../src/lmrcImagesStatDataGet.c:
+
+../src/lmrcImagesTTest.c:
+
+../src/lmrcImagesVarianceAnalysis.c:
+
+../src/lmrcImagesVarianceMap.c:
+
+../src/lmrcMultiFFTCentralSectionsCompare.c:
+
+../src/lmrcMultiFFTCentralSectionsSigma.c:
+
+../src/lmrcSinogramFET.c:
+
+../src/lmrcSinogramFETPCA.c:
+
+../src/lmrcSinogramFETcalcWeight.c:
+
+../src/lmrcSinogramFETcorrelationMap.c:
+
+../src/lmrcSinogramFETnormalizedMap.c:
+
+../src/lmrcSinogramFETreferredCorrelation.c:
+
+../src/lmrcSinogramFETsmoothParameterMatching.c:
+
+../src/mrcImageCheckFFT.c:
+
+../src/mrcImageCheckSameSize.c:
+
+../src/mrcImageCopy.c:
+
+../src/mrcImageDataSet.c:
+
+../src/mrcImageError.c:
+
+../src/mrcImageGet.c:
+
+../src/mrcImageGetPixels.c:
+
+../src/mrcImageInfo.c:
+
+../src/mrcImageInit.c:
+
+../src/mrcImageOperation.c:
+
+../src/mrcImagePVM.c:
+
+../src/mrcImagePrint.c:
+
+../src/mrcImageRead.c:
+
+../src/mrcImageSectionGet.c:
+
+../src/mrcImageSectionSet.c:
+
+../src/mrcImageSet.c:
+
+../src/mrcImageTailer.c:
+
+../src/mrcImageToIntImage.c:
+
+../src/mrcImageUtil.c:
+
+../src/mrcImageUtilityforVariance.c:
+
+../src/mrcImageWrite.c:
+
+../src/mrcImageWrite2.c:
+
+../src/mrcImagefuncmin.c:
+
+../src/mrcRefUtil.c:
</PRE>
<HR>
<A NAME="include">
char* Image;
unsigned char* ImageCharImage;
unsigned short* ImageShortImage;
- unsigned long* ImageLongImage;
+ signed long* ImageLongImage;
+ unsigned long* ImageULongImage;
float* ImageFloatImage;
double* ImageDoubleImage;
int flagSigned;
} mrcImage;
+typedef struct mrcImagePyramidList {
+ mrcImage mrc;
+ mrcImage* up;
+ mrcImage* down;
+} mrcImagePyramidList;
+
+typedef struct mrcImagePyramid {
+ mrcImagePyramidList* top;
+ mrcImagePyramidList* current;
+} mrcImagePyramid;
+
typedef struct mrcImageInformation {
double mean;
double rootMeanSquare;
/* Frequency */
extern void lmrcImageHistgram3(double** hist, unsigned long nlevel, mrcImage* img);
extern void lmrcImageHistgram4(double** hist, double delta, mrcImage* img);
-extern void lmrcImageHistgram6(double** hist, unsigned long nlevel, double Low, double High, mrcImage* img);
+extern void lmrcImageHistgram6(double** hist, double delta, double Low, double High, mrcImage* img);
extern void lmrcImageInformation(mrcImageInformation* info, mrcImage* img);
char* Image;
unsigned char* ImageCharImage;
unsigned short* ImageShortImage;
- unsigned long* ImageLongImage;
+ signed long* ImageLongImage;
+ unsigned long* ImageULongImage;
float* ImageFloatImage;
double* ImageDoubleImage;
int flagSigned;
} mrcImage;
+typedef struct mrcImagePyramidList {
+ mrcImage mrc;
+ mrcImage* up;
+ mrcImage* down;
+} mrcImagePyramidList;
+
+typedef struct mrcImagePyramid {
+ mrcImagePyramidList* top;
+ mrcImagePyramidList* current;
+} mrcImagePyramid;
+
typedef struct mrcImageInformation {
double mean;
double rootMeanSquare;
/* Frequency */
extern void lmrcImageHistgram3(double** hist, unsigned long nlevel, mrcImage* img);
extern void lmrcImageHistgram4(double** hist, double delta, mrcImage* img);
-extern void lmrcImageHistgram6(double** hist, unsigned long nlevel, double Low, double High, mrcImage* img);
+extern void lmrcImageHistgram6(double** hist, double delta, double Low, double High, mrcImage* img);
extern void lmrcImageInformation(mrcImageInformation* info, mrcImage* img);
--- /dev/null
+#ifndef MRC_IMAGE_H
+#define MRC_IMAGE_H
+/*
+# %M% %Y% %I%
+# The latest update : %G% at %U%
+#
+#%Z% mrcImage.h ver %I%
+#%Z% Created by tacyas
+#%Z%
+#%Z% Usage : mrcImage.h
+#%Z% Attention
+#%Z%
+*/
+
+/* mrcImage.h
+* Language: C or CC(c++)
+* Editor : tacyas.tkyemg.u_tokyo
+* Date : 1990-1992
+* Modified: 2012 for CCP4(2000)
+*/
+
+/*
+* Header File for MRC Format
+* Edited by Tac
+*/
+
+#include <stdio.h>
+#include <math.h>
+#include "genUtil.h"
+#include "Matrix3D.h"
+
+/* struct begin */
+
+/* Status Mask */
+#ifdef M68
+typedef unsigned int mrcStatusMask;
+#else
+typedef unsigned int mrcStatusMask;
+#endif
+
+/* Status */
+#ifdef M68
+typedef unsigned int mrcStatusType;
+#else
+typedef unsigned int mrcStatusType;
+#endif
+
+/* struct end */
+
+/* constant begin */
+
+#define mrcStatusMask_ExitFailure ((mrcStatusMask)0x80000000L)
+#define mrcStatusMask_Warning ((mrcStatusMask)0x40000000L)
+#define mrcStatusMask_Information ((mrcStatusMask)0x20000000L)
+#define mrcStatusMask_Message ((mrcStatusMask)0x10000000L)
+#define mrcStatusMask_1B ((mrcStatusMask)0x08000000L)
+#define mrcStatusMask_1A ((mrcStatusMask)0x04000000L)
+#define mrcStatusMask_19 ((mrcStatusMask)0x02000000L)
+#define mrcStatusMask_18 ((mrcStatusMask)0x01000000L)
+#define mrcStatusMask_17 ((mrcStatusMask)0x00800000L)
+#define mrcStatusMask_16 ((mrcStatusMask)0x00400000L)
+#define mrcStatusMask_15 ((mrcStatusMask)0x00200000L)
+#define mrcStatusMask_14 ((mrcStatusMask)0x00100000L)
+#define mrcStatusMask_ReferMRCInfo ((mrcStatusMask)0x00080000L)
+#define mrcStatusMask_Mode ((mrcStatusMask)0x00040000L)
+#define mrcStatusMask_ReferMemory ((mrcStatusMask)0x00020000L)
+#define mrcStatusMask_ReferFile ((mrcStatusMask)0x00010000L)
+
+#define MRC_Status_OK ((mrcStatusType)0x00000000L)
+
+#define MRC_FileCanNotOpened ((mrcStatusType)0x00000000L|mrcStatusMask_ReferFile)
+#define MRC_ImageHeaderCanNotRead ((mrcStatusType)0x00000001L|mrcStatusMask_ReferFile)
+#define MRC_ImageDataCanNotRead ((mrcStatusType)0x00000002L|mrcStatusMask_ReferFile)
+#define MRC_ImageHeaderCanNotWrite ((mrcStatusType)0x00000003L|mrcStatusMask_ReferFile)
+#define MRC_ImageDataCanNotWrite ((mrcStatusType)0x00000004L|mrcStatusMask_ReferFile)
+#define MRC_FileCanNotClosed ((mrcStatusType)0x00000005L|mrcStatusMask_ReferFile)
+
+#define MRC_MemoryNotAllocate ((mrcStatusType)0x00000000L|mrcStatusMask_ReferMemory)
+
+#define MRC_ModeNotSupported ((mrcStatusType)0x00000000L|mrcStatusMask_Mode)
+#define MRC_ModeZNot1FFTMode ((mrcStatusType)0x00000001L|mrcStatusMask_Mode)
+
+#define MRC_SizeOfZero ((mrcStatusType)0x00000000L|mrcStatusMask_ReferMRCInfo)
+
+
+extern char* mrcImageGeneralTypeList[];
+
+/* constant end */
+
+/* struct begin */
+typedef union MRC_Status_t {
+ mrcStatusType all;
+ struct Content {
+#ifdef M68
+ unsigned char level;
+ unsigned char category;
+ short detail;
+#else
+ short detail;
+ unsigned char category;
+ unsigned char level;
+#endif
+ } status;
+} MRC_Status_t;
+
+#ifdef M68
+typedef int mrcImageParaTypeInteger;
+#else
+typedef int mrcImageParaTypeInteger;
+#endif
+
+typedef float mrcImageParaTypeReal;
+typedef unsigned char mrcImageParaTypeCharacter;
+
+typedef struct mrcImageParaTypeIntegerCoord {
+ mrcImageParaTypeInteger x;
+ mrcImageParaTypeInteger y;
+ mrcImageParaTypeInteger z;
+} mrcImageParaTypeIntegerCoord;
+
+typedef struct mrcImageParaTypeRealCoord {
+ mrcImageParaTypeReal x;
+ mrcImageParaTypeReal y;
+ mrcImageParaTypeReal z;
+} mrcImageParaTypeRealCoord;
+/* struct end */
+
+/*
+* MRC Image Header
+* Edited by Tac
+*/
+/* Header Size */
+/* constant begin */
+#define MRC_HEADER (1024)
+#define MRC_TAILER (1024)
+
+/* Image Data Type */
+/* for compatibility */
+typedef mrcImageParaTypeInteger mrcImageMode;
+#define MRC_char_image ((mrcImageMode)0)
+#define MRC_short_image ((mrcImageMode)1)
+#define MRC_float_image ((mrcImageMode)2)
+#define MRC_complex_short_ft ((mrcImageMode)3)
+#define MRC_complex_float_ft ((mrcImageMode)4)
+#define MRC_long_image ((mrcImageMode)101)
+#define MRC_double_image ((mrcImageMode)102)
+#define MRC_complex_long_ft ((mrcImageMode)103)
+#define MRC_complex_double_ft ((mrcImageMode)104)
+#define MRC_complex_short_fft ((mrcImageMode)1003)
+#define MRC_complex_float_fft ((mrcImageMode)1004)
+#define MRC_complex_long_fft ((mrcImageMode)1103)
+#define MRC_complex_double_fft ((mrcImageMode)1104)
+#define MRC_NotSuppotedMode ((mrcImageMode)0xffffffffL)
+
+#define mrcCharImage ((mrcImageMode)0)
+#define mrcShortImage ((mrcImageMode)1)
+#define mrcFloatImage ((mrcImageMode)2)
+#define mrcComplexShortFT ((mrcImageMode)3)
+#define mrcComplexFloatFT ((mrcImageMode)4)
+#define mrcComplexFloatOneDimFT ((mrcImageMode)5)
+// 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)
+#define mrcComplexDoubleFT ((mrcImageMode)104)
+#define mrcComplexShortFFT ((mrcImageMode)1003)
+#define mrcComplexFloatFFT ((mrcImageMode)1004)
+#define mrcComplexLongFFT ((mrcImageMode)1103)
+#define mrcComplexDoubleFFT ((mrcImageMode)1104)
+#define mrcNotSuppotedMode ((mrcImageMode)0xffffffffL)
+
+#define MRC_MAX_LABEL_N (10)
+#define MRC_MAX_LABEL_LEN (80)
+#define MRC_MAX_EXTRA (29)
+#define MRC_MAX_EXTRA_CCP4 (15)
+/* constant end */
+
+/* struct begin */
+
+/* Image Header */
+typedef struct _mrcImageHeader {
+ mrcImageParaTypeIntegerCoord N; /* Data Numbers */
+ mrcImageMode Mode; /* Data Type */
+ mrcImageParaTypeIntegerCoord StartN; /* First in map */
+ mrcImageParaTypeIntegerCoord M; /* Number of Intervals */
+ mrcImageParaTypeRealCoord Length; /* Cell Dimensions : 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 */
+ mrcImageParaTypeReal EXTRA[MRC_MAX_EXTRA]; /* Extra, user defined storage space */
+ mrcImageParaTypeReal OriginX;
+ mrcImageParaTypeReal OriginY;
+ mrcImageParaTypeInteger LabelN;
+ char Label[MRC_MAX_LABEL_N][MRC_MAX_LABEL_LEN];
+} _mrcImageHeader;
+
+/* For CCP4 2000 : Current New */
+typedef struct _mrcImageHeaderCCP4 {
+ mrcImageParaTypeIntegerCoord N; /* Data Numbers */
+ mrcImageMode Mode; /* Data Type */
+ mrcImageParaTypeIntegerCoord StartN; /* First in map */
+ mrcImageParaTypeIntegerCoord NI; /* Number of Intervals */
+ mrcImageParaTypeRealCoord Length; /* Cell Dimensions : 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 storing symmetry operators */
+ mrcImageParaTypeInteger LSKFLG; /* Flag for Skew transformation */
+ mrcImageParaTypeReal SKWMAT[9]; /* Skew matrix S */
+ mrcImageParaTypeReal SKWTRN[3]; /* Skew translation */
+ mrcImageParaTypeReal EXTRA[MRC_MAX_EXTRA_CCP4]; /* Extra, user defined storage space */
+ mrcImageParaTypeCharacter MAP[4];
+ mrcImageParaTypeInteger MARCHST;
+ mrcImageParaTypeReal ARMS;
+ mrcImageParaTypeInteger LabelN;
+ 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];
+ mrcImageParaTypeInteger Int[MRC_HEADER/4];
+ 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;
+
+typedef struct mrcImagePyramidList {
+ mrcImage mrc;
+ mrcImage* up;
+ mrcImage* down;
+} mrcImagePyramidList;
+
+typedef struct mrcImagePyramid {
+ mrcImagePyramidList* top;
+ mrcImagePyramidList* current;
+} mrcImagePyramid;
+
+/* struct end */
+
+/*
+ Tailer
+*/
+/* constant begin */
+#define mrcImageTailerMode2DProjection 0
+/* constant end */
+
+/* struct begin */
+typedef struct _mrcImageTailer {
+ char Code[4];
+ mrcImageParaTypeInteger Mode;
+ char EulerAngleMode[4];
+ mrcImageParaTypeReal Rot1;
+ mrcImageParaTypeReal Rot2;
+ mrcImageParaTypeReal Rot3;
+ mrcImageParaTypeInteger Mirror;
+} _mrcImageTailer;
+
+
+typedef union mrcImageTailer {
+ unsigned char All[MRC_TAILER];
+ mrcImageParaTypeInteger Int[MRC_TAILER/4];
+ mrcImageParaTypeReal Real[MRC_TAILER/4];
+ _mrcImageTailer Cont;
+} mrcImageTailer;
+
+
+typedef char mrcImageSymmetryOperator;
+
+/*
+mrcImage Structure
+*/
+typedef struct mrcImage {
+ mrcImageHeader Header;
+ size_t BytePerImage;
+ mrcImageParaTypeInteger BytePerBand;
+ mrcImageParaTypeInteger BandPerPixel;
+ size_t PixelPerImage;
+ mrcStatusType status;
+ char* Image;
+ unsigned char* ImageCharImage;
+ unsigned short* ImageShortImage;
+ signed long* ImageLongImage;
+ unsigned long* ImageULongImage;
+ float* ImageFloatImage;
+ double* ImageDoubleImage;
+
+ /* Tailer */
+ mrcImageTailer* Tailer;
+ mrcImageParaTypeInteger numTailer;
+
+ /* FEIextendedHeader */
+ FEIextendedHeader* FEIHeader;
+ mrcImageParaTypeInteger numFEIHeader;
+
+ /* Dummy */
+ char* dummyHeader;
+ mrcImageParaTypeInteger dummyHeaderByte;
+
+ /* Swap Bytes */
+ mrcImageParaTypeInteger flagByteSwap;
+
+ /* flag CCP4-2000 */
+ mrcImageParaTypeInteger flagCCP4;
+ mrcImageParaTypeInteger ImageOffset;
+ mrcImageSymmetryOperator* SymmetryOperator;
+
+ /* flag signed char/short */
+ int flagSigned;
+} mrcImage;
+
+typedef struct mrcImageInformation {
+ double mean;
+ double rootMeanSquare;
+ double meanOfSphereSurface;
+ double sdOfSphereSurface;
+ double seOfSphereSurface;
+ double meanOfCylinderSurface;
+ double sdOfCylinderSurface;
+ double seOfCylinderSurface;
+ double meanOfEdge;
+ double sdOfEdge;
+ double seOfEdge;
+ double max;
+ mrcImageParaTypeRealCoord maxCoord;
+ double min;
+ mrcImageParaTypeRealCoord minCoord;
+ double sd;
+ double se;
+ double rmax;
+ long flagrmax;
+ double RMS; /* Root mean square */
+ int mode;
+ mrcImageParaTypeRealCoord sdOfAllAxis;
+ mrcImageParaTypeRealCoord aveOfAllAxis;
+
+ /* 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 */
+
+/* constant begin */
+typedef enum mrcImageInformationMode {
+ meanOfAll = 0,
+ meanOfSphereSurface = 1,
+ meanOfCylinderSurface = 2,
+ meanOfEdge = 3,
+ meanOfCentre = 4,
+ meanOfSparse = 5,
+ meanOf2DEdgeY = 6,
+ RMSofAllPixels = 7,
+ sdOfAllAxis = 8
+} mrcImageInformationMode;
+
+/*
+* Define
+*/
+#define HeaderN Header.Cont.N
+#define HeaderMode Header.Cont.Mode
+#define HeaderStartN Header.Cont.StartN
+#define HeaderM Header.Cont.M
+#define HeaderLength Header.Cont.Length
+#define HeaderAlpha Header.Cont.Alpha
+#define HeaderBeta Header.Cont.Beta
+#define HeaderGamma Header.Cont.Gamma
+#define HeaderMAPC Header.Cont.MAPC
+#define HeaderMAPR Header.Cont.MAPR
+#define HeaderMAPS Header.Cont.MAPS
+#define HeaderAMin Header.Cont.AMin
+#define HeaderAMax Header.Cont.AMax
+#define HeaderAMean Header.Cont.AMean
+#define HeaderISPG Header.Cont.ISPG
+#define HeaderNSYMBT Header.Cont.NSYMBT
+#define HeaderLSKFLG Header.ContCCP4.LSKFLG
+#define HeaderEXTRA Header.Cont.EXTRA
+#define HeaderOriginX Header.Cont.OriginX
+#define HeaderOriginY Header.Cont.OriginY
+#define HeaderLabelN Header.Cont.LabelN
+#define HeaderLabel Header.Cont.Label
+
+typedef enum mrcPixelDataType {
+ mrcPixelRePart = 0,
+ mrcPixelImPart,
+ mrcPixelSigmaPart,
+ mrcPixelMag,
+ mrcPixelPow,
+ mrcPixelLogMag,
+ mrcPixelLogPow,
+ mrcPixelPhase
+} mrcPixelDataType;
+
+typedef enum mrcPixelDataHowToGet {
+ mrcPixelHowNearest = 0,
+ mrcPixelHowLinear,
+ mrcPixelHowCubicConv,
+ mrcPixelHowPolySig
+} mrcPixelDataHowToGet;
+
+/* constant end */
+
+/* struct begin */
+typedef struct lmrcImageSmoothingInfo {
+ long mode;
+ mrcImageParaTypeReal sx; /* Filter kernel size */
+ mrcImageParaTypeReal sy;
+ mrcImageParaTypeReal sz;
+ double sigma; /* for Lee-Sigma filter */
+} lmrcImageSmoothingInfo;
+
+typedef struct lmrcImageCVEInfo {
+ long sx; /* CVE domain size. */
+ long sy; /* Apr.30,1996 */
+ long sz;
+} lmrcImageCVEInfo;
+
+typedef struct lmrcImageTfunctionInfo {
+ long sx; /* Tfunction domain size. */
+ long sy; /* June 11,1996 */
+ long sz;
+} lmrcImageTfunctionInfo;
+
+typedef struct lmrcImageHighlightInfo {
+ long mode;
+ float Bias; /* May 1,1996 */
+ float Grad;
+} lmrcImageHighlightInfo;
+
+typedef struct lmrcImageLowPassFilterInfo
+{
+ long mode; /* June 4,1996 */
+ float hvp, width;
+} lmrcImageLowPassFilterInfo;
+
+typedef struct lmrcImageHighPassFilterInfo
+{
+ long mode; /* June 5,1996 */
+ float hvp, width;
+ float pathWindowLow;
+ float pathWindowHigh;
+} lmrcImageHighPassFilterInfo;
+
+typedef struct lmrcImageBandPassFilterInfo
+{
+ long mode; /* June 5,1996 */
+ float hvl, hvh, wl, wh;
+ int flagLowWeight;
+ double lowWeight;
+} lmrcImageBandPassFilterInfo;
+
+/* struct end */
+/* Utility Routines */
+#ifdef __cplusplus
+extern "C" {
+#endif
+/* prototype begin */
+/* in mrcInit.c */
+extern mrcStatusType mrcInit(mrcImage* mrc, char* filaname);
+extern mrcStatusType mrcDefaultHeaderValueSet(mrcImage* mrc);
+extern mrcStatusType mrcDefaultHeaderValueSetOnlyFixedValue(mrcImage* mrc);
+extern mrcStatusType mrcHiddenDataSet(mrcImage* mrc, long mode);
+extern void mrcImageFree(mrcImage* mrc, char* message);
+/* in mrcTailer.c */
+extern void mrcTailerInit(mrcImage* mrc, long mode);
+extern void mrcTailerCopy(mrcImage* dst, mrcImage* src, long mode);
+ /* mode 1: Tailer Memory Allocation */
+/* in mrcRead.c */
+extern mrcStatusType mrcFileReadGeneral (mrcImage* mrc, char* filename, char* type, char* message, long mode);
+extern mrcStatusType mrcImageReadGeneral (mrcImage* mrc, char* filename, char* type, char* message, long mode);
+extern mrcStatusType mrcHeaderReadGeneral(mrcImage* mrc, char* filename, char* type, char* message, long mode);
+extern mrcStatusType mrcTailerReadGeneral(mrcImage* mrc, char* filename, char* type, char* message, long mode);
+extern mrcStatusType mrcFileGeneralListPrint(FILE* fpt);
+
+extern mrcStatusType mrcFileRead (mrcImage* mrc, char* filename, char* message, long mode);
+extern mrcStatusType mrcImageRead (mrcImage* mrc, char* filename, char* message, long mode);
+extern mrcStatusType mrcHeaderRead(mrcImage* mrc, char* filename, char* message, long mode);
+extern mrcStatusType mrcTailerRead(mrcImage* mrc, char* filename, char* message, long mode);
+
+extern mrcStatusType mrcFileReadFEIextendedMRC (mrcImage* mrc, char* filename, char* message, long mode);
+extern mrcStatusType mrcImageReadFEIextendedMRC (mrcImage* mrc, char* filename, char* message, long mode);
+extern mrcStatusType mrcHeaderReadFEIextendedMRC(mrcImage* mrc, char* filename, char* message, long mode);
+extern mrcStatusType mrcTailerReadFEIextendedMRC(mrcImage* mrc, char* filename, char* message, long mode);
+
+extern mrcStatusType mrcFileReadIMODextendedMRC (mrcImage* mrc, char* filename, char* message, long mode);
+extern mrcStatusType mrcImageReadIMODextendedMRC (mrcImage* mrc, char* filename, char* message, long mode);
+extern mrcStatusType mrcHeaderReadIMODextendedMRC(mrcImage* mrc, char* filename, char* message, long mode);
+extern mrcStatusType mrcTailerReadIMODextendedMRC(mrcImage* mrc, char* filename, char* message, long mode);
+
+extern int mrcImageByteSwap(mrcImage* mrc, long mode);
+/* in mrcWrite.c */
+#define mrcFileWriteModeGet(x) BYTE4GETBYTE(x,0)
+#define mrcImageWriteModeGet(x) BYTE4GETBYTE(x,1)
+#define mrcHeaderWriteModeGet(x) BYTE4GETBYTE(x,2)
+#define mrcTailerWriteModeGet(x) BYTE4GETBYTE(x,3)
+
+#define mrcFileWriteMode_InfoPrint 1
+#define mrcFileWriteMode_NoCallForStatData 2
+
+extern mrcStatusType mrcFileWrite (mrcImage* mrc, char* filename, char* message, long mode);
+extern mrcStatusType mrcImageWrite (mrcImage* mrc, char* filename, char* message, long mode);
+extern mrcStatusType mrcHeaderWrite(mrcImage* mrc, char* filename, char* message, long mode);
+extern mrcStatusType mrcTailerWrite(mrcImage* mrc, char* filename, char* message, long mode);
+/* in mrcWrite.c */
+extern mrcStatusType mrcFileWriteLowerResolution(mrcImage* mrc, char* filename, char* message, long sample , long mode);
+/* in mrcGet.c */
+extern double mrcImageDataGetbyAU(mrcImage* mrc,
+ mrcImageParaTypeReal x /* Angstrom */,
+ mrcImageParaTypeReal y /* Angstrom */,
+ mrcImageParaTypeReal z /* Angstrom */,
+ double* data,
+ mrcPixelDataType mode,
+ mrcPixelDataHowToGet how);
+extern double mrcPixelDataGet(mrcImage* mrc,
+ mrcImageParaTypeReal x /* Pixel Unit */,
+ mrcImageParaTypeReal y /* Pixel Unit */,
+ mrcImageParaTypeReal z /* Pixel Unit */,
+ double* data,
+ mrcPixelDataType mode,
+ mrcPixelDataHowToGet how);
+
+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];
+}
+
+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)];
+}
+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];
+}
+
+/* in mrcImageSet.c */
+extern void mrcInfoSet(mrcImage* mrc, FILE* fptIn, FILE* fptOut, mrcImageParaTypeInteger mode);
+
+/* prototype end */
+
+/* struct begin */
+/* in mrcImageDataSet.c */
+typedef enum mrcImageDataSetMode {
+ mrcImageDataSetModeCentre = 0,
+ mrcImageDataSetModeOrigin = 1
+} mrcImageDataSetMode;
+/* struct end */
+
+/* prototype begin */
+extern void mrcImageDataSet(mrcImage* out,
+ mrcImage* in,
+ mrcImageParaTypeReal x,
+ mrcImageParaTypeReal y,
+ mrcImageParaTypeReal z,
+ float phi,
+ mrcImageDataSetMode mode);
+
+/* in mrcSet.c */
+extern double mrcImageDataSetbyAU(mrcImage* mrc,
+ mrcImageParaTypeReal x /* Angstrom */,
+ mrcImageParaTypeReal y /* Angstrom */,
+ mrcImageParaTypeReal z /* Angstrom */,
+ double data,
+ mrcPixelDataType mode);
+extern double mrcPixelDataSet(mrcImage* mrc,
+ mrcImageParaTypeReal x /* Pixel Unit */,
+ mrcImageParaTypeReal y /* Pixel Unit */,
+ mrcImageParaTypeReal z /* Pixel Unit */,
+ double data,
+ mrcPixelDataType mode);
+
+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;
+}
+
+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;
+}
+
+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 mrcStatDataSet(mrcImage* mrc, mrcImageParaTypeInteger mode);
+
+
+
+/* in mrcImageInfo.c */
+extern void lmrcImageXSection(mrcImage* proj, mrcImage* img, double Y);
+extern void lmrcImageYSection(mrcImage* proj, mrcImage* img, double X);
+extern void lmrcImageXProjection(mrcImage* proj, mrcImage* img);
+extern void lmrcImageYProjection(mrcImage* proj, mrcImage* img);
+extern void lmrcImageZProjection(mrcImage* proj, mrcImage* img);
+extern void lmrcImageXYProjection(mrcImage* proj, mrcImage* img);
+extern void lmrcImageYZProjection(mrcImage* proj, mrcImage* img);
+extern void lmrcImageZXProjection(mrcImage* proj, mrcImage* img);
+ /* Histgram */
+ /* Frequecy max -> 1 */
+extern void lmrcImageHistgram(double** hist, unsigned long nlevel, mrcImage* img);
+extern void lmrcImageHistgram2(double** hist, double delta, mrcImage* img);
+extern void lmrcImageHistgram5(double** hist, unsigned long nlevel, double Low, double High, mrcImage* img);
+ /* Frequency */
+extern void lmrcImageHistgram3(double** hist, unsigned long nlevel, mrcImage* img);
+extern void lmrcImageHistgram4(double** hist, double delta, mrcImage* img);
+extern void lmrcImageHistgram6(double** hist, unsigned long nlevel, double Low, double High, mrcImage* img);
+extern void lmrcImageInformation(mrcImageInformation* info, mrcImage* img);
+
+
+/* in mrcImageCopy.c */
+extern void lmrcImageCopy(mrcImage* dst, mrcImage* src, mrcImageParaTypeRealCoord to);
+
+/* in mrcUtil.c */
+extern int IsFloatImage(mrcImage* mrc, char* message, mrcImageParaTypeInteger mode);
+extern int IsFloatFT(mrcImage* mrc, char* message, mrcImageParaTypeInteger mode);
+extern int IsImage(mrcImage* mrc, char* message, mrcImageParaTypeInteger mode);
+extern int IsFT(mrcImage* mrc, char* message, mrcImageParaTypeInteger mode);
+extern int IsFFT(mrcImage* mrc, char* message, mrcImageParaTypeInteger mode);
+extern void mrcImageInfoSet(mrcImage* mrc, FILE* fptIn, FILE* fptOut, long mode);
+
+/* in mrcImageOperation.c */
+extern void 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 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 lmrcImageAdd(mrcImage* img2, mrcImage* img1, long* num);
+extern void lmrcSQRImageAdd(mrcImage* img2, mrcImage* img1, long* num);
+extern void lmrcImageSquare(mrcImage* in);
+extern void lmrcImageRoot(mrcImage* in ,double eps);
+extern void lmrcImageAbs(mrcImage* out, mrcImage* in);
+extern void lmrcImageConvolution(mrcImage* out, mrcImage* in, mrcImage* kernel, int mode);
+
+/* in mrcImageToIntImage.c */
+extern void lmrcImageToIntImage(mrcImage* dst, mrcImage* src, mrcImageParaTypeInteger mode);
+
+
+extern void lfft2d(mrcImage* fft, mrcImage* img);
+
+extern void lmrcImageFFT(mrcImage* fft, mrcImage* img, long mode);
+extern void lmrcImageFFTFirstDimensionOnly(mrcImage* fft, mrcImage* img, long mode);
+#ifdef FFTW
+extern void lmrcImageFFTWFlagSet(unsigned int flag);
+#endif
+extern void lmrcFFTFGconj(mrcImage* out, mrcImage* in1, mrcImage* in2);
+extern void lmrcFFTFxG(mrcImage* out, mrcImage* in1, mrcImage* in2);
+extern void lmrcImageCorrelation(mrcImage* out, mrcImage* in, mrcImage* ref, long mode);
+extern void lmrcImageCorrelationModePrint(FILE* fpt);
+
+extern void lmrcImageFFTCenterChange(mrcImage* fft, int mode);
+
+/* in lMrcImagePattersonFunctionCalc.c */
+extern void lmrcImagePattersonFunctionCalc(mrcImage* out, mrcImage* outFFT, mrcImage* in);
+extern void lmrcImagePattersonFunctionPrint(FILE* fpt, mrcImage* in, int mode);
+extern void lmrcImageGuinierFunctionPrint(FILE* fpt, mrcImage* in, int mode);
+
+#include "ctfInfo.h"
+extern void lmrcImageCorrelationWithCTFCompensation(mrcImage* out, mrcImage* in, ctfInfo* inctf, mrcImage* ref, ctfInfo* refctf, long mode);
+
+
+/* in mrcError.c */
+extern mrcStatusType mrcError(char* message, char* inRtnName, char* callRtnName, mrcStatusType status);
+extern mrcStatusType mrcErrorMsg(FILE* fpt, char* message, char* inRtnName, char* callRtnName, mrcStatusType status);
+/* in lmrcFFTInfo.c */
+#include "Vector.h"
+extern floatVector* lmrcFSInfoXAxisMag(mrcImage* fft);
+extern floatVector* lmrcFSInfoXAxisPhase(mrcImage* fft);
+extern floatVector* lmrcFSInfoYAxisMag(mrcImage* fft);
+extern floatVector* lmrcFSInfoYAxisPhase(mrcImage* fft);
+/* The returned values are not magnitudes but powers */
+extern floatVector* lmrcFSInfoScatteringAngularDistribution(mrcImage* fft);
+extern floatVector* lmrcFSInfoScatteringAngularDistributionAverage(mrcImage* fft);
+extern floatVector* lmrcFSInfoScatteringAngularDistributionSD(mrcImage* fft);
+extern floatVector* lmrcFSInfoSpacing(mrcImage* fft);
+extern floatVector** lmrcFSInfoScatteringAngularDistributionDivisionAverage(mrcImage* fft, mrcImageParaTypeReal axis, mrcImageParaTypeInteger n, int mode);
+extern floatVector** lmrcFSInfoScatteringAngularDistributionDivisionSD(mrcImage* fft, mrcImageParaTypeReal axis, mrcImageParaTypeInteger n, int mode);
+extern floatVector** lmrcFSInfoScatteringAngularDistributionDivisionAverageDelR(mrcImage* fft, mrcImageParaTypeReal axis, mrcImageParaTypeInteger n, mrcImageParaTypeReal delR, int mode);
+extern floatVector** lmrcFSInfoScatteringAngularDistributionDivisionSDDelR(mrcImage* fft, mrcImageParaTypeReal axis, mrcImageParaTypeInteger n, mrcImageParaTypeReal delR, int mode);
+/* in mrcImageCheckSameSize.c */
+extern void lmrcImageCheckSameSize(mrcImage* in, mrcImage* ref);
+
+/* in mrcImageCheckFFT.c */
+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 lmrcImageCVE(mrcImage* dst, mrcImage* src, lmrcImageCVEInfo* info);
+
+/* in lmrcImageTfunction */
+extern void lmrcImageTfunction(mrcImage* dst, mrcImage* src, lmrcImageTfunctionInfo* info, long mode);
+
+/* in lmrcImageHighlighting */
+extern void lmrcImageHighlightingInfoPrint(FILE* fpt);
+extern void lmrcImageHighlighting(mrcImage* dst, mrcImage* src, lmrcImageHighlightInfo* info);
+
+/* in lmrcImageLowPassFilter */
+extern void lmrcImageLowPassFilter(mrcImage* dst, mrcImage* src, lmrcImageLowPassFilterInfo* info, long mode);
+
+/* in lmrcImageHighPassFilter */
+extern void lmrcImageHighPassFilter(mrcImage* dst, mrcImage* src, lmrcImageHighPassFilterInfo* info, long mode);
+
+/* in lmrcImageBandPassFilter */
+extern void lmrcImageBandPassFilter(mrcImage* dst, mrcImage* src, lmrcImageBandPassFilterInfo* info, long mode);
+
+/* in lmrcImageShrink */
+extern void lmrcImageShrink(mrcImage* dst, mrcImage* src, mrcImageParaTypeIntegerCoord S, long mode);
+
+/* in lmrcImageShift */
+extern void lmrcImageShift(mrcImage* out, mrcImage* in, mrcImageParaTypeRealCoord shift, mrcPixelDataHowToGet mode);
+extern void lmrcImageShiftFollowingGC(mrcImage* out, mrcImage* in, int mode);
+
+/* in mrcImagePrint */
+extern void mrcInfoPrint(FILE* fpt, mrcImage* mrc, mrcImageParaTypeInteger mode);
+
+
+/* prototype end */
+
+/* in lmrcImageMultiCTFCompensation.c */
+/* struct begin */
+#include "ctfInfo.h"
+typedef enum lmrcImageMultiCTFCompensationSolventFlatteningMode {
+ lmrcImageMultiCTFCompensationSolventFlatteningModeDensityPeakIsSolvent=0,
+ lmrcImageMultiCTFCompensationSolventFlatteningModeDefinedSTDIsSolvent=1
+} lmrcImageMultiCTFCompensationSolventFlatteningMode;
+
+typedef struct lmrcImageMultiCTFCompensationInfo {
+ long maxiteration;
+ double okrms;
+ long diversefactor;
+ double z;
+ long nhist;
+ FILE* logfile;
+ lmrcImageMultiCTFCompensationSolventFlatteningMode solventMode;
+ float definedSTD;
+} lmrcImageMultiCTFCompensationInfo;
+/* struct end */
+
+#include "ctfInfo.h"
+
+/* prototype begin */
+
+extern void lmrcImageMultiCTFCompensationInfoInit(lmrcImageMultiCTFCompensationInfo* info);
+extern void lmrcImageMultiCTFCompensationInfoSet(lmrcImageMultiCTFCompensationInfo* info);
+extern void lmrcImageMultiCTFCompensation(mrcImage* dst, mrcImage* src, ctfInfo* ctf, long nfile, lmrcImageMultiCTFCompensationInfo info, long mode);
+
+/* in lmrcImageCTFObservation.c */
+extern void lmrcImageCTFObservation(mrcImage* dst, mrcImage* src, ctfInfo* ctf, long mode);
+extern void lmrcImagesCTFObservation(mrcImage* dst, mrcImage* src, ctfInfo* ctf, long mode);
+
+/* in lmrcImageCTFCompensation.c */
+extern void lmrcImageCTFCompensation(mrcImage* src, ctfInfo* ctf, long mode);
+
+/* prototype end */
+
+
+/* in lmrcImageCTFSN.c */
+/* struct begin */
+typedef struct lmrcImageCTFSNInfo
+{
+ long mode, deg1, deg2;
+ ctfInfo ctf;
+} lmrcImageCTFSNInfo;
+/* struct end */
+
+/* prototype begin */
+extern void lmrcImageCTFSN(mrcImage *outMrc, const mrcImage *inMrc, lmrcImageCTFSNInfo *info, long mode);
+/* prototype end */
+
+/* in lmrcImageFourierPowerSpectrum.c */
+/* struct begin */
+typedef struct mrcImageFourierPowerSpectrum
+{
+ long n;
+ double d, *h;
+} mrcImageFourierPowerSpectrum;
+
+typedef struct lmrcImageFourierPowerSpectrumInfo
+{
+ double dX, dY, dZ;
+} lmrcImageFourierPowerSpectrumInfo;
+/* struct end */
+
+/* prototype begin */
+
+extern mrcImageFourierPowerSpectrum lmrcImageFourierPowerSpectrumMakeSpectrum(const mrcImage *inFFT, lmrcImageFourierPowerSpectrumInfo *info);
+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);
+
+#include "Matrix3D.h"
+extern void lmrcImageRotation3DFollowingMatrix3D(mrcImage* dst, mrcImage* src, Matrix3D mat, mrcPixelDataHowToGet mode, int mode2);
+
+extern void lmrcImageRotation3DFollowingEulerAngle2(mrcImage* dst, mrcImage* src, const char* m,
+ mrcImageParaTypeReal rot1, mrcImageParaTypeReal rot2, mrcImageParaTypeReal rot3, mrcPixelDataHowToGet mode, int mode2);
+
+#include "Matrix3D.h"
+extern void lmrcImageRotation3DFollowingMatrix3D2(mrcImage* dst, mrcImage* src, Matrix3D mat, mrcPixelDataHowToGet mode, int mode2);
+
+extern void lmrcImageRotation3DZXY(mrcImage* dst, mrcImage* src,
+ mrcImageParaTypeReal rotx, mrcImageParaTypeReal roty, mrcImageParaTypeReal rotz, mrcPixelDataHowToGet mode, int mode2);
+
+extern void lmrcImageRotation2D(mrcImage* dst, mrcImage* src, double angle, mrcPixelDataHowToGet mode);
+extern void lmrcImageRotation2DPeriodicBoundary(mrcImage* dst, mrcImage* src, double angle, mrcPixelDataHowToGet mode);
+
+/* in mrcImageSectionGet.c */
+extern char* mrcImageSectionGetModeDescription(long mode);
+extern void mrcImageSectionGet(mrcImage* dst, mrcImage* src, mrcImageParaTypeReal z, long mode);
+
+/* 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
+};
+#endif
+
+#endif /* MRC_IMAGE_H */
--- /dev/null
+/*
+# %M% %Y% %I%
+# The latest update : %G% at %U%
+#
+#%Z% lmrcImagePyramidver %I%
+#%Z% Created by
+#%Z%
+#%Z% Usage : lmrcImagePyramid
+#%Z% Attention
+#%Z%
+*/
+static char __sccs_id[] = "%Z%lmrcImagePyramid ver%I%; Date:%D% %Z%";
+
+#include "../inc/mrcImage.h"
+
+void
+{
+ while(1) {
+ }
+}
static char __sccs_id[] = "%Z%mrcImageInfo ver%I%; Date:%D% %Z%";
-#undef DEBUG
+#define DEBUG
#undef UNDEBUG2
#include "genUtil.h"
#include <math.h>
*/
void
-lmrcImageHistgram6(double** hist, unsigned long nlevel, double Low, double High, mrcImage* img)
+lmrcImageHistgram6(double** hist, double delta, double Low, double High, mrcImage* img)
{
mrcImage tmp;
-
+ unsigned int nLevel;
tmp = *img;
tmp.HeaderAMin = Low;
tmp.HeaderAMax = High;
- lmrcImageHistgram3(hist, nlevel, &tmp);
+ nLevel = (int)((High-Low)/delta);
+ DEBUGPRINT3("%f %f %d\n", High, Low, nLevel);
+ lmrcImageHistgram3(hist, nLevel, &tmp);
}
void
<H2>Information from source codes</H2>
</A>
<PRE>
+../src/lmrcImageMeanFreePath.c:
+
+../src/lmrcImageShapeModePrint.c:
+
+../src/lmrcImageShapeSearch.c:
</PRE>
<HR>
<A NAME="include">
<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">
<H2>Information from source codes</H2>
</A>
<PRE>
+../src/rigakuImageRead.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
+../src/tgaFileInit.c:
+
+../src/tgaFilePrint.c:
+
+../src/tgaFileRead.c:
</PRE>
<HR>
<A NAME="include">
<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/lmrc3Dto2DFFT.c:
+
+../src/lmrcImageFileListAndEulerAngleDataRead.c:
+
+../src/lmrcImageOneLineGet.c:
+
+../src/lmrcImageSinogramCorrelationAdditionalWeight.c:
+
+../src/lmrcImageToFFT.c:
</PRE>
<HR>
<A NAME="include">
<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">
<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">
<H2>Information from source codes</H2>
</A>
<PRE>
+../src/map2DCoordGet.c:
</PRE>
<HR>
<A NAME="include">
<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/matrix3DMultiplyMatrix.c:
+
+../src/matrix3DMultiplyVector.c:
+
+../src/matrix3DRotation.c:
+
+../src/matrix3DTranslation.c:
+
+../src/matrix3DUtil.c:
</PRE>
<HR>
<A NAME="include">
<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">
<H2>Information from source codes</H2>
</A>
<PRE>
+../src/pvmStart.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
+../src/randomNormal.c:
+
+../src/randomUniform.c:
+
+../src/srandom.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
+../src/socketClient.c:
+
+../src/socketServer.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
+../src/pow2nn.c:
</PRE>
<HR>
<A NAME="include">
<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>Information from source codes</H2>
</A>
<PRE>
+../src/eosBayesCondition.c:
+
+../src/eosBayesDistributionInit.c:
+
+../src/eosBayesDistributionInitialProbabilitySet.c:
+
+../src/eosBayesEstimation.c:
+
+../src/eosBayesFree.c:
+
+../src/eosBayesParameterOfMaxPosterior.c:
+
+../src/eosBayesRead.c:
+
+../src/eosBayesWrite.c:
+
+../src/eosBayesflag.c:
+
+../src/leosBayesInit.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
+../src/eosFunc.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
+../src/eosMathStatistics.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
+../src/eosPThread.c:
+
+../src/eosPThreadCreate.c:
+
+../src/eosPThreadInit.c:
+
+../src/eosPThreadJoin.c:
+
+../src/eosPThreadMutex.c:
</PRE>
<HR>
<A NAME="include">
CHeader = \
+leosPointPositionCorrection.h \
*/
static char __sccs_id[] = "%Z%eosPointUtil ver%I%; Date:%D% %Z%";
+#include "genUtil.h"
#include "Memory.h"
#include "../inc/eosPoint.h"
void
eosPointCoordSigSet(eosPointCoord* pc, eosPointParaTypeReal x, eosPointParaTypeReal y, eosPointParaTypeReal z)
{
+ pc->sigma = sqrt(SQR(x) + SQR(y) + SQR(z));
pc->sig.data[0] = x;
pc->sig.data[1] = y;
pc->sig.data[2] = z;
--- /dev/null
+/*
+# %M% %Y% %I%
+# The latest update : %G% at %U%
+#
+#%Z% leosPointPositionCorrection ver %I%
+#%Z% Created by
+#%Z%
+#%Z% Usage : leosPointPositionCorrection
+#%Z% Attention
+#%Z%
+*/
+static char __sccs_id[] = "%Z%leosPointPositionCorrection ver%I%; Date:%D% %Z%";
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#define GLOBAL_DECLARATION
+
+#undef DEBUG
+#include "genUtil.h"
+#include "../inc/eosPoint.h"
+#include "./leosPointPositionCorrection.h"
+#include "gsl/gsl_math.h"
+#include "gsl/gsl_vector.h"
+#include "gsl/gsl_matrix.h"
+#include "gsl/gsl_permutation.h"
+#include "gsl/gsl_blas.h"
+#include "gsl/gsl_linalg.h"
+
+int
+leosPointPositionCorrection(eosPoint* outP, eosPoint* inP, leosPointPositionCorrectionInfo* linfo, int mode)
+{
+ gsl_vector* r;
+ gsl_vector* dr;
+ gsl_vector* b;
+ gsl_vector* db;
+ gsl_matrix* A;
+ gsl_matrix* AtA;
+ gsl_permutation* p;
+ int signum;
+ gsl_matrix* AtAInv;
+ gsl_matrix* AtAInvAt;
+ int count = 0;
+ int i, j, k, l;
+ eosPointCoord pc;
+
+ linfo->m = linfo->n*(linfo->n - 1)/2;
+
+ DEBUGPRINT1("VECTOR: %d \n", (linfo->n-1)*3);
+ r = gsl_vector_alloc((linfo->n-1)*3);
+ dr = gsl_vector_alloc((linfo->n-1)*3);
+ DEBUGPRINT1("VECTOR: %d \n", linfo->m*3);
+ b = gsl_vector_alloc(linfo->m*3);
+ db = gsl_vector_alloc(linfo->m*3);
+
+ eosPointCoordInit(&pc, 0);
+ eosPointTop(inP);
+ count=0;
+ while(inP->current != NULL){
+ count++;
+ eosPointNext(inP);
+ }
+ if(count!=linfo->m) {
+ fprintf(stderr, "n %d: m %d is different from data number %d\n", linfo->n, linfo->m, count);
+ return -1;
+ }
+ eosPointTop(inP);
+ count=0;
+ while(inP->current != NULL){
+ DEBUGPRINT4("%d: %f %f %f\n", count, inP->current->p.coord.data[0], inP->current->p.coord.data[1], inP->current->p.coord.data[2])
+ gsl_vector_set(b, count*3, inP->current->p.coord.data[0]);
+ gsl_vector_set(b, count*3+1, inP->current->p.coord.data[1]);
+ gsl_vector_set(b, count*3+2, inP->current->p.coord.data[2]);
+ count++;
+ eosPointNext(inP);
+ }
+
+/*
+ ri = shift(i, i+1)
+ i = 1...n;
+
+ B1 = b12 = r1
+ B2 = b13 = r1 + r2
+ ...
+ b23 = r2
+ b24 = r2 + r3
+ b25 = r2 + r3 + r4
+ ...
+ Bk = bij = ri + ...+ rj-1
+...
+ Bm = rn-1
+ m = 1...n(n-1)/2
+
+ b = A r
+ r <- (At A)-1 At b
+
+*/
+ A = gsl_matrix_calloc(linfo->m*3, (linfo->n-1)*3);
+ DEBUGPRINT2("MATRIX: %d %d\n", linfo->m*3, (linfo->n-1)*3);
+ k = 0;
+ for(i=0; i< linfo->n-1; i++) {
+ for(j=i+1; j< linfo->n; j++) { // bij
+ DEBUGPRINT3("%d (%d, %d)\n", k, i, j);
+ for(l=i; l<j; l++) { //ri+...+rj-1
+ DEBUGPRINT5("(%d %d) - %d mean shift(%d, %d)\n", i, j, l, l, l+1);
+ gsl_matrix_set(A, k*3, l*3, 1);
+ gsl_matrix_set(A, k*3+1, l*3+1, 1);
+ gsl_matrix_set(A, k*3+2, l*3+2, 1);
+ }
+ k++;
+ }
+ }
+ if(k==linfo->m) {
+ DEBUGPRINT("SUCCESS\n");
+ DEBUGPRINT1("Count: %d\n", k);
+#ifdef DEBUG
+ //gsl_matrix_fprintf(stderr, A, "%g");
+#endif
+ } else {
+ return -1;
+ }
+
+ // Least Square
+ // r = (At A)-1 At b
+ AtA = gsl_matrix_calloc((linfo->n-1)*3, (linfo->n-1)*3);
+ p = gsl_permutation_alloc((linfo->n-1)*3);
+ AtAInv = gsl_matrix_calloc((linfo->n-1)*3, (linfo->n-1)*3);
+ AtAInvAt = gsl_matrix_calloc((linfo->n-1)*3, linfo->m*3);
+
+ gsl_blas_dgemm(CblasTrans, CblasNoTrans, 1, A, A, 0.0, AtA);
+ gsl_linalg_LU_decomp(AtA, p, &signum); // LU decomp
+ gsl_linalg_LU_invert(AtA, p, AtAInv); // Inv
+ gsl_blas_dgemm(CblasNoTrans, CblasTrans, 1, AtAInv, A, 0.0, AtAInvAt);
+ gsl_blas_dgemv(CblasNoTrans, 1.0, AtAInvAt, b, 1.0, r);
+
+ // db = A r - b
+ gsl_blas_dgemv(CblasNoTrans, 1.0, A, r, 0.0, db);
+ gsl_blas_daxpy(-1.0, b, db);
+
+ eosPointInit(&(linfo->db), NULL);
+ for(k=0; k<linfo->m; k++) {
+ eosPointCoordSet(&pc, fabs(gsl_vector_get(db, k*3)),
+ fabs(gsl_vector_get(db, k*3+1)),
+ fabs(gsl_vector_get(db, k*3+2)));
+ eosPointAppend(&(linfo->db), &pc, 0);
+ }
+ // r = (At A)-1 At b
+ // |dr| = sqrt((At A)-1) At |db|^2)
+ gsl_vector_mul(db, db);
+ gsl_matrix_mul_elements(AtAInvAt, AtAInvAt);
+ gsl_blas_dgemv(CblasNoTrans, 1.0, AtAInvAt, db, 0.0, dr);
+
+ // eosPoint
+ eosPointInit(outP, NULL);
+ for(k=0; k<linfo->n-1; k++) {
+ eosPointCoordSet(&pc, gsl_vector_get(r, k*3),
+ gsl_vector_get(r, k*3+1),
+ gsl_vector_get(r, k*3+2));
+ eosPointCoordSigSet(&pc, sqrt(gsl_vector_get(dr, k*3 )),
+ sqrt(gsl_vector_get(dr, k*3+1)),
+ sqrt(gsl_vector_get(dr, k*3+2)));
+ eosPointAppend(outP, &pc, 0);
+ }
+
+ gsl_vector_free(r);
+ gsl_vector_free(dr);
+ gsl_vector_free(b);
+ gsl_vector_free(db);
+ gsl_matrix_free(A);
+ gsl_matrix_free(AtA);
+ gsl_matrix_free(AtAInv);
+ gsl_matrix_free(AtAInvAt);
+ gsl_permutation_free(p);
+ return count;
+}
--- /dev/null
+/*
+# leosPointPositionCorrection.h : $Revision$
+# $Date$
+# Created by $Author$
+# Usage : leosPointPositionCorrection.h
+# Attention
+# $Loccker$
+# $State$
+#
+*/
+/* $Log$ */
+#ifndef LEOSPOINT_POSITION_CORRECTION_H
+#define LEOSPOINT_POSITION_CORRECTION_H
+
+#include <stdio.h>
+
+/* constant begin */
+
+typedef enum leosPointPositionCorrectionMode {
+ a=0,
+ b=1
+} leosPointPositionCorrectionMode;
+
+/* constant end */
+
+/* struct begin */
+
+typedef struct leosPointPositionCorrectionInfo {
+ // Input
+ int n;
+
+ // Output
+ int m;
+ eosPoint db;
+} leosPointPositionCorrectionInfo;
+
+/* struct end */
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* prototype begin */
+
+extern int leosPointPositionCorrection(eosPoint* outP, eosPoint* inP, leosPointPositionCorrectionInfo* linfo, int mode);
+
+/* prototype end */
+
+#ifdef __cplusplus
+};
+#endif
+
+#endif /* LEOSPOINT_POSITION_CORRECTION_H*/
+
random \
rec3d \
simulation \
-test \
tiffFileUtil \
timeSeries \
transform \
ctfInfo \
database \
eosBayes \
+eosMath \
eosPoint \
filter \
hf2000 \
random \
rec3d \
simulation \
+test \
tiffFileUtil \
timeSeries \
transform \
WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-WORLDNAME=Tools
-/bin/bash: dcdCompareCA: No such file or directory
+/bin/bash: dcdCompareCA: そのようなファイルやディレクトリはありません
-/bin/bash: dcdDistanceAtomBetweenAtom: No such file or directory
+/bin/bash: dcdDistanceAtomBetweenAtom: そのようなファイルやディレクトリはありません
-/bin/bash: Display3: No such file or directory
+/bin/bash: Display3: そのようなファイルやディレクトリはありません
-/bin/bash: Eos: No such file or directory
+/bin/bash: Eos: そのようなファイルやディレクトリはありません
-/bin/bash: StereoDisplay: No such file or directory
+/bin/bash: StereoDisplay: そのようなファイルやディレクトリはありません
-/bin/bash: Visualmake: No such file or directory
+/bin/bash: Visualmake: そのようなファイルやディレクトリはありません
-/bin/bash: imagesClustering: No such file or directory
+/bin/bash: imagesClustering: そのようなファイルやディレクトリはありません
-/bin/bash: obj3Don2DImageView: No such file or directory
+/bin/bash: obj3Don2DImageView: そのようなファイルやディレクトリはありません
-/bin/bash: smolet: No such file or directory
+/bin/bash: smolet: そのようなファイルやディレクトリはありません
-<<<<<<< HEAD
-<HTML>
-<HEAD>
-<TITLE>crystalGetLatticeVolume</TITLE>
-</HEAD>
-<BODY>
-<H1>crystalGetLatticeVolume</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: crystalGetLatticeVolume
-Options:
- [-i[nput] In (stdin ).as(inFile ) ] :Optional :Input:
- [-a[Axis] ax (2 ).as(Real )
- ay (3 ).as(Real )
- az (0 ).as(Real ) ] :Optional :Input:
- [-b[Axis] bx (2 ).as(Real )
- by (3 ).as(Real )
- bz (0 ).as(Real ) ] :Optional :Input:
- [-c[Axis] cx (2 ).as(Real )
- cy (3 ).as(Real )
- cz (1 ).as(Real ) ] :Optional :Input:
- [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output:
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Additional Usage -----
-> crystaInfo
-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
-</PRE>
-</BODY>
-</HTML>
-=======
/bin/bash: crystalGetLatticeVolume: そのようなファイルやディレクトリはありません
->>>>>>> 05144f7ae9b3e43a94f011609484b025af01d7ae
-<<<<<<< HEAD
-<HTML>
-<HEAD>
-<TITLE>crystalGetReciprocalLattice</TITLE>
-</HEAD>
-<BODY>
-<H1>crystalGetReciprocalLattice</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: crystalGetReciprocalLattice
-Options:
- [-i[nput] In (stdin ).as(inFile::ASCII ) ] :Optional :Input
- [-a[Axis] ax (1 ).as(Real )
- ay (0 ).as(Real )
- az (0 ).as(Real ) ] :Optional :Asix[A]
- [-b[Axis] bx (0 ).as(Real )
- by (1 ).as(Real )
- bz (0 ).as(Real ) ] :Optional :Asix[A]
- [-c[Axis] cx (0 ).as(Real )
- cy (0 ).as(Real )
- cz (1 ).as(Real ) ] :Optional :Asix[A]
- [-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>
-=======
/bin/bash: crystalGetReciprocalLattice: そのようなファイルやディレクトリはありません
->>>>>>> 05144f7ae9b3e43a94f011609484b025af01d7ae
-<HTML>
-<HEAD>
-<TITLE>ctfDeterminationByBayes</TITLE>
-</HEAD>
-<BODY>
-<H1>ctfDeterminationByBayes</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: ctfDeterminationByBayes
-Options:
- [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
- [-i[nput]2 In2 (NULL ).as(inFile ) ] :Essential :InputDataFile
- [-i[nput]3 In3 (NULL ).as(inFile ) ] :Essential :InputDataFile
- [-i[nput]4 In4 (NULL ).as(inFileListNoOpen ) ] :Essential :InputDataFile
- [-n[um] numDistribution (3 ).as(Integer )
- numLikelihood (3 ).as(Integer ) ] :Essential :Integer
- [-rmax rmax (250 ).as(Real ) ] :Optional :rmax[1/A]
- [-rintermediate rintermediate (250 ).as(Real ) ] :Optional :rintermediate[1/A]
- [-rfiestpeak rfirstpeak (0.001 ).as(Real ) ] :Optional :rfirstpeak[1/A]
- [-rmin rmin (0 ).as(Real ) ] :Optional :rmin[1/A]
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
- [-MTFmode MTFmode (0 ).as(Integer ) ] :Optional :MTFmode
- [-Ainmode Ainmode (0 ).as(Integer ) ] :Optional :Ainmode
- [-Intensitymode Intensitymode (0 ).as(Integer ) ] :Optional :Intensitymode
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: ctfDeterminationByBayes: そのようなファイルやディレクトリはありません
-/bin/bash: ctfDeterminationFromPhaseComparison: No such file or directory
+/bin/bash: ctfDeterminationFromPhaseComparison: そのようなファイルやディレクトリはありません
-/bin/bash: ctfDeterminationFromThonRing: No such file or directory
+/bin/bash: ctfDeterminationFromThonRing: そのようなファイルやディレクトリはありません
-/bin/bash: ctfFunctionServer: No such file or directory
+/bin/bash: ctfFunctionServer: そのようなファイルやディレクトリはありません
-/bin/bash: ctfMultiFunction: No such file or directory
+/bin/bash: ctfMultiFunction: そのようなファイルやディレクトリはありません
-/bin/bash: ctfZeroPoint: No such file or directory
+/bin/bash: ctfZeroPoint: そのようなファイルやディレクトリはありません
-/bin/bash: defocusDeterminationFromThonRing: No such file or directory
+/bin/bash: defocusDeterminationFromThonRing: そのようなファイルやディレクトリはありません
-<HTML>
-<HEAD>
-<TITLE>tiltInfoDetermine</TITLE>
-</HEAD>
-<BODY>
-<H1>tiltInfoDetermine</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: tiltInfoDetermine
-Options:
- [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
- [-defocusIn[put] defocus (NULL ).as(inFile ) ] :Essential :InputDataFile
- [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
- [-M[ag] mag (2.4 ).as(Real ) ] :Optional :Mag
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: tiltInfoDetermine: そのようなファイルやディレクトリはありません
-/bin/bash: homology2PG: No such file or directory
+/bin/bash: homology2PG: そのようなファイルやディレクトリはありません
-/bin/bash: pgDataBaseSelectServer: No such file or directory
+/bin/bash: pgDataBaseSelectServer: そのようなファイルやディレクトリはありません
-/bin/bash: pgJournalSelect: No such file or directory
+/bin/bash: pgJournalSelect: そのようなファイルやディレクトリはありません
-/bin/bash: pgJournalSelectCORBAClient: No such file or directory
+/bin/bash: pgJournalSelectCORBAClient: そのようなファイルやディレクトリはありません
-/bin/bash: pgJournalSelectCORBAServer: No such file or directory
+/bin/bash: pgJournalSelectCORBAServer: そのようなファイルやディレクトリはありません
-/bin/bash: pgMemoSelectCORBAServer: No such file or directory
+/bin/bash: pgMemoSelectCORBAServer: そのようなファイルやディレクトリはありません
-/bin/bash: pgSelect: No such file or directory
+/bin/bash: pgSelect: そのようなファイルやディレクトリはありません
-/bin/bash: eosBayesInit: No such file or directory
+/bin/bash: eosBayesInit: そのようなファイルやディレクトリはありません
-m 0 : Average
-m 1 : WeightedAverage
-m 0 -trim xx: Trimming
+-m 1 -trim xx: Trimming
</PRE>
</BODY>
</HTML>
--- /dev/null
+OBJECTNAME = eosPointAffineTransform
+EXTRA_LIB =
+EXTRA_CCOPTS =
+EXTRA_INC =
--- /dev/null
+# OptionControlFile
+# FileFormat
+"-i","-i[nput]","InputDataFile","Essential","1","1","In","inFile","NULL"
+"-o","-o[utput]","OutputDataFile","Essential","1","1","Out","outFile","NULL"
+"-c","-c[onfig]","ConfigurationFile","Optional","1","1","configFile","inFile","NULL"
+"-m","-m[ode]","Mode","Optional","1","1","mode","Integer","0"
--- /dev/null
+include ../../../Config/Define.inc
+include ../../Config/Define.inc
+include ../Config/Define.inc
+include Config/Define.inc
+
+all:
+ cd src; make all; cd ..
+
+install:
+ cd src; make install; cd ..
+
+
+putSF:
+ if [ -f private ] ; \
+ then \
+ echo "$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME) is private"; \
+ else \
+ cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE commit || cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE import src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME); \
+ fi
+
+put:
+ cd src; make put; cd ..
+
+clean:
+ cd src; make clean; cd ..
+
+depend:
+ cd src; make depend; cd ..
+
+check:
+ @if [ ! -d $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) ] ; then \
+ echo making directory; \
+ mkdir -p $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE); \
+ fi
+ ln -sf ../../../../../hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) src/$(OSTYPE);
+ @$(RM) src/Makefile
+ @echo "New src/Makefile"
+ @$(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/src/Makefile src/Makefile
+ @cd src; rm -f $(OSTYPE)/.Depend; touch $(OSTYPE)/.Depend; make depend
+
+update:
+ @if [ ! -d $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) ] ; then \
+ echo making directory; \
+ mkdir -p $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE); \
+ fi
+ ln -sf ../../../../../hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) src/$(OSTYPE);
+ @$(RM) src/Makefile
+ @echo "New src/Makefile"
+ @$(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/src/Makefile src/Makefile
+ @cd src; rm -f $(OSTYPE)/.Depend; touch $(OSTYPE)/.Depend; echo "Y" | make update
+
+cvsupdate::
+ cvs -d $(EOS_CVSROOT) update -d
+
+cvscommit::
+ cvs -d $(EOS_CVSROOT) commit
+
+backup:
+ @cd ../../../..; \
+ echo $(OBJECTNAME) ; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile
+
+backup-all:
+ @cd ../../../..; \
+ echo $(OBJECTNAME) ; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile
+
+distribute:
+ cd ../../../..; \
+ echo $(OBJECTNAME) ; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
+
+distribute-all:
+ @cd ../../../..; \
+ echo $(OBJECTNAME) ; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
+
+eosintroduce:
+ ${EOS_HOME}/sbin/eosintroduce ${WORLDNAME} ${CLASSNAME} ${OBJECTNAME} ./
+
+include Config/Target.inc
--- /dev/null
+install:
+ cd ../src; make install-doc; cd ../doc
--- /dev/null
+#ifndef CONFIG_H
+#define CONFIG_H
+
+#include "../inc/eosPointAffineTransform.h"
+
+#endif /* CONFIG_H */
--- /dev/null
+#ifndef EOSPOINTAFFINETRANSFORM_H
+#define EOSPOINTAFFINETRANSFORM_H
+#include <stdio.h>
+#include <stdlib.h>
+
+#define OPTION_FLAG '-'
+#define OPTION_FLAG_POS (0)
+#define OPTION_POS (1)
+
+
+
+
+typedef struct eosPointAffineTransformInfo {
+ long flagRedirect;
+
+ long flagIn;
+ char* In;
+ FILE* fptIn;
+
+ long flagOut;
+ char* Out;
+ FILE* fptOut;
+
+ long flagconfigFile;
+ char* configFile;
+ FILE* fptconfigFile;
+
+ long flagmode;
+ long mode;
+
+} eosPointAffineTransformInfo;
+#ifdef __cplusplus
+extern "C" {
+#endif
+extern void argCheck(eosPointAffineTransformInfo* info, int argc, char* avgv[]);
+extern void khorosInit(int argc, char* avgv[]);
+extern void init0(eosPointAffineTransformInfo* info);
+extern void init1(eosPointAffineTransformInfo* info);
+extern void usage(char* usage);
+extern void additionalUsage(void);
+extern void htmlBeforeUsage(char* usage);
+extern void htmlAfterUsage(char* usage);
+#ifdef __cplusplus
+};
+#endif
+#endif /* EOSPOINTAFFINETRANSFORM_H */
--- /dev/null
+include ../Config/Define.inc
+include ../../Config/Define.inc
+include ../../../Config/Define.inc
+include ../../../../Config/Define.inc
+
+EOSHOME=../../../../../
+DSTDIR=$(EOSHOME)/bin
+DSTDOC=$(EOSHOME)/doc
+DSTTAR=$(EOSHOME)/tar
+
+INCFILES =
+
+LIBFILES = \
+ $(LIBPREFIX)EosObjects$(LIBSUFFIX)
+
+LIBFILESDEBUG = \
+ $(LIBPREFIX)EosObjects.debug$(LIBSUFFIX)
+
+SRCC = \
+ $(OBJECTNAME).c \
+ init.c \
+ argCheck.c \
+ usage.c \
+ util.c \
+
+SRCCXX = \
+ $(OBJECTNAME).cc \
+ init.cc \
+ argCheck.cc \
+ usage.cc \
+ util.cc \
+
+MODULES = \
+ $(OBJECTNAME).o \
+ init.o \
+ argCheck.o \
+ usage.o \
+ util.o \
+
+REALMODULES = \
+ $(OSTYPE)/$(OBJECTNAME).o \
+ $(OSTYPE)/init.o \
+ $(OSTYPE)/argCheck.o \
+ $(OSTYPE)/usage.o \
+ $(OSTYPE)/util.o
+
+MODULESDEBUG = \
+ $(OBJECTNAME).debugo \
+ init.debugo \
+ argCheck.debugo \
+ usage.debugo \
+ util.debugo \
+
+REALMODULESDEBUG = \
+ $(OSTYPE)/$(OBJECTNAME).debugo \
+ $(OSTYPE)/init.debugo \
+ $(OSTYPE)/argCheck.debugo \
+ $(OSTYPE)/usage.debugo \
+ $(OSTYPE)/util.debugo
+
+
+all: $(OSTYPE)/$(OBJECTNAME)
+ if [ ! -L $(OSTYPE) ] ; then \
+ moveHostdependent; \
+ fi
+
+debug: $(OSTYPE)/$(OBJECTNAME).debug
+
+cudagdb: $(OSTYPE)/$(OBJECTNAME).cudagdb
+
+
+$(OSTYPE)/$(OBJECTNAME)::
+ @$(RM) -f $(OSTYPE)/Makefile ; \
+ $(CP) $(EOS_HOME)/src/Config/Template/$(WORLDNAME)Template.Dir/src/ARCH/Makefile $(OSTYPE)/Makefile ; \
+ cd $(OSTYPE); \
+ $(MAKE) $(OBJECTNAME) WORLDNAME=$(WORLDNAME) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME)
+
+$(OSTYPE)/$(OBJECTNAME).debug::
+ @$(RM) -f $(OSTYPE)/Makefile ; \
+ $(CP) $(EOS_HOME)/src/Config/Template/$(WORLDNAME)Template.Dir/src/ARCH/Makefile $(OSTYPE)/Makefile ; \
+ cd $(OSTYPE); \
+ $(MAKE) $(OBJECTNAME).debug WORLDNAME=$(WORLDNAME) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME)
+
+$(OSTYPE)/$(OBJECTNAME).cudagdb::
+ @$(RM) -f $(OSTYPE)/Makefile ; \
+ $(CP) $(EOS_HOME)/src/Config/Template/$(WORLDNAME)Template.Dir/src/ARCH/Makefile $(OSTYPE)/Makefile ; \
+ cd $(OSTYPE); \
+ $(MAKE) $(OBJECTNAME).cudagdb WORLDNAME=$(WORLDNAME) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME)
+
+cvsupdate::
+ cvs -d $(EOS_CVSROOT) update -d
+
+cvscommit::
+ cvs -d $(EOS_CVSROOT) commit
+
+edit:
+ @if [ -r $(OBJECTNAME).c ]; \
+ then \
+ sccsEdit $(OBJECTNAME).c; \
+ else \
+ echo "Source files are already editable"; \
+ fi
+ @if [ -r wish/$(OBJECTNAME).wish ]; \
+ then \
+ cd wish; sccsEdit $(OBJECTNAME).wish; \
+ else \
+ echo "Source files (wish) are already editable."; \
+ fi
+ @if [ -r ruby/$(OBJECTNAME).rb ]; \
+ then \
+ cd ruby; sccsEdit $(OBJECTNAME).rb; \
+ else \
+ echo "Source files (ruby) are already editable."; \
+ fi
+ @if [ -r perl/$(OBJECTNAME).pl ]; \
+ then \
+ cd perl; sccsEdit $(OBJECTNAME).pl ; \
+ else \
+ echo "Source files (perl) are already editable."; \
+ fi
+ @if [ -r ../Config/OptionControlFile ]; \
+ then \
+ cd ../Config; sccsEdit OptionControlFile; \
+ else \
+ echo "OptionControlFile are already editable."; \
+ fi
+
+unedit:
+ @if [ -w $(OBJECTNAME).c ]; \
+ then \
+ sccsUnedit $(OBJECTNAME).c; \
+ else \
+ echo "Source files are not editable"; \
+ fi
+ @if [ -w wish/$(OBJECTNAME).wish ]; \
+ then \
+ cd wish; sccsUnedit $(OBJECTNAME).wish; \
+ else \
+ echo "Source files (wish) are not editable."; \
+ fi
+ @if [ -w ruby/$(OBJECTNAME).rb]; \
+ then \
+ cd ruby; sccsUnedit $(OBJECTNAME).rb; \
+ else \
+ echo "Source files (ruby) are not editable."; \
+ fi
+ @if [ -w perl/$(OBJECTNAME).pl ]; \
+ then \
+ cd perl; sccsUnedit $(OBJECTNAME).pl ; \
+ else \
+ echo "Source files (ruby) are not editable."; \
+ fi
+ @if [ -w ../Config/OptionControlFile ]; \
+ then \
+ cd ../Config; sccsUnedit OptionControlFile; \
+ else \
+ echo "OptionControlFile are not editable."; \
+ fi
+
+report:
+ @if [ -r $(OBJECTNAME).c ]; \
+ then \
+ sccsReport $(OBJECTNAME).c; \
+ else \
+ echo "Source files are already editable"; \
+ fi
+ @if [ -r wish/$(OBJECTNAME).wish ]; \
+ then \
+ cd wish; sccsReport $(OBJECTNAME).wish; \
+ else \
+ echo "Source files (wish) are already editable."; \
+ fi
+ @if [ -r ruby/$(OBJECTNAME).rb ]; \
+ then \
+ cd ruby; sccsReport $(OBJECTNAME).rb; \
+ else \
+ echo "Source files (ruby) are already editable."; \
+ fi
+ @if [ -r perl/$(OBJECTNAME).pl ] ; \
+ then \
+ cd perl; sccsReport $(OBJECTNAME).pl ; \
+ else \
+ echo "Source files (perl) are already editable."; \
+ fi
+ @if [ -r ../Config/OptionControlFile ]; \
+ then \
+ cd ../Config; sccsReport OptionControlFile; \
+ else \
+ echo "OptionControlFile are already editable."; \
+ fi
+
+clean :
+ rm -f *.debugo $(OSTYPE)/*.debugo *.cudagdbo $(OSTYPE)/*.cudagdbo *.o $(OSTYPE)/*.o *.linkinfo $(OSTYPE)/*.linkinfo \
+ $(OSTYPE)/$(OBJECTNAME) $(OSTYPE)/*.$(OSTYPE) \
+ $(OSTYPE)/$(OBJECTNAME).debug $(OSTYPE)/*.$(OSTYPE).debug \
+ $(OSTYPE)/$(OBJECTNAME).cudagdb $(OSTYPE)/*.$(OSTYPE).cudagdb \
+ $(OSTYPE)/$(OBJECTNAME).linkinfo $(OSTYPE)/*.$(OSTYPE).linkinfo \
+ *.bak *.$(OSTYPE) core
+
+install: install-bin install-doc install-wish install-ruby install-shell install-perl
+ @if [ dummy$(KHOROS_KENGOBJ) != dummy ] ; \
+ then \
+ if [ -x $(KHOROS_KGENOBJ) ] ; \
+ then \
+ make install-khoros ; \
+ fi; \
+ fi
+
+install-bin:$(DSTDIR)/$(OSTYPE)/$(OBJECTNAME)
+
+$(DSTDIR)/$(OSTYPE)/$(OBJECTNAME):$(OSTYPE)/$(OBJECTNAME) $(DSTDIR)/$(OBJECTNAME)
+ @echo ---- Installing to bin
+ @echo $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME)
+ @if [ ! -d $(DSTDIR)/$(OSTYPE) ]; \
+ then \
+ mkdir $(DSTDIR)/$(OSTYPE); \
+ fi
+ @if [ -x $(OSTYPE)/$(OBJECTNAME) ]; \
+ then \
+ echo "Compilation is complete"; \
+ $(RM) -f $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME); \
+ $(CD) $(OSTYPE); $(INSTALL) -m 555 $(OBJECTNAME) ../$(DSTDIR)/$(OSTYPE); \
+ $(CHMOD) 555 ../$(DSTDIR)/$(OSTYPE)/$(OBJECTNAME); \
+ else \
+ echo "Compilation is incomplete. $(OBJECTNAME)"; \
+ fi
+ @echo ---- end of bin
+
+install-wish:
+ @if [ -d wish ]; \
+ then \
+ echo "---- Tcl/Tk file Install"; \
+ if [ ! -d $(DSTDIR)/wish/$(OBJECTNAME) ]; \
+ then \
+ mkdir $(DSTDIR)/wish/$(OBJECTNAME) ; \
+ fi ; \
+ $(CP) -f wish/* $(DSTDIR)/wish/$(OBJECTNAME); \
+ $(CHMOD) 555 $(DSTDIR)/wish/$(OBJECTNAME)/* ;\
+ touch $(DSTDIR)/wish/$(OBJECTNAME)/tclIndex;\
+ $(CHMOD) 666 $(DSTDIR)/wish/$(OBJECTNAME)/tclIndex;\
+ echo "---- Tcl/Tk file Installed";\
+ fi
+
+install-ruby:
+ @if [ -d ruby ]; \
+ then \
+ echo "---- Ruby/Tk file Install"; \
+ if [ ! -d $(DSTDIR)/ruby/$(OBJECTNAME) ]; \
+ then \
+ mkdir $(DSTDIR)/ruby/$(OBJECTNAME) ; \
+ fi ; \
+ $(CP) -f ruby/* $(DSTDIR)/ruby/$(OBJECTNAME); \
+ $(CHMOD) 555 $(DSTDIR)/ruby/$(OBJECTNAME)/* ; \
+ echo "---- Ruby/Tk file Installed"; \
+ fi
+
+install-perl:
+ @if [ -d perl ]; \
+ then \
+ echo "---- Perl/Tk file Install"; \
+ if [ ! -d $(DSTDIR)/perl/$(OBJECTNAME) ]; \
+ then \
+ mkdir $(DSTDIR)/perl/$(OBJECTNAME) ; \
+ fi; \
+ $(CP) -f perl/* $(DSTDIR)/perl/$(OBJECTNAME); \
+ $(CHMOD) 555 $(DSTDIR)/perl/$(OBJECTNAME)/* ; \
+ echo "---- Perl/Tk file Installed"; \
+ fi
+
+install-shell:
+ @if [ ! -d $(DSTDIR)/shell/$(OBJECTNAME) ]; \
+ then \
+ mkdir $(DSTDIR)/shell/$(OBJECTNAME) ; \
+ fi
+ @if [ -d shell ]; \
+ then \
+ echo "---- Shell file Install"; \
+ if [ ! -d $(DSTDIR)/shell/$(OBJECTNAME) ]; \
+ then \
+ mkdir $(DSTDIR)/shell/$(OBJECTNAME) ; \
+ fi ; \
+ $(CP) -f shell/* $(DSTDIR)/shell/$(OBJECTNAME); \
+ $(CHMOD) 555 $(DSTDIR)/shell/$(OBJECTNAME)/*; \
+ echo "---- Shell file Installed"; \
+ fi
+
+install-khoros:
+ @echo Installing to khoros
+ @if [ ! -d ../../../../../objects/script/$(OBJECTNAME) -a -f $(KHOROS_KGENOBJ) ]; \
+ then \
+ echo kgenobj;\
+ $(KHOROS_KGENOBJ) -tb Eos -oname $(OBJECTNAME) -type script -pane -cantata true -cat Eos -subcat $(CLASSNAME) -description $(OBJECTNAME) -bname $(OBJECTNAME) -form -lang ksh ; \
+ fi
+ @if [ ! -d ../../../../../objects/script/$(OBJECTNAME) -a -f $(KHOROS_KSET) ]; \
+ then \
+ $(KHOROS_KSET) -tb Eos -oname $(OBJECTNAME) -icon $(OBJECTNAME) ; \
+ fi
+ @if [ -d ../../../../../objects/script/$(OBJECTNAME) -a -f $(KHOROS_KSET) ]; \
+ then \
+ $(CHMOD) -R 775 ../../../../../objects/script/$(OBJECTNAME) ; \
+ if [ $? ] ; \
+ then \
+ echo "-- setting khoros ---" ; \
+ if [ -d ../../../../../objects/script/$(OBJECTNAME)/uis/ ] ; \
+ then \
+ $(CD) ../../../../../objects/script/$(OBJECTNAME)/uis/ ; \
+ $(RM) -f $(OBJECTNAME).pane ; \
+ $(LN) -s ../../../../src/Tools/$(CLASSNAME)/$(OBJECTNAME)/src/$(OBJECTNAME).pane $(OBJECTNAME).pane; \
+ $(CD) ../../ ; \
+ $(CHMOD) -R 555 $(OBJECTNAME); \
+ else \
+ echo "../../../../../objects/script/$(OBJECTNAME)/uis/ does not exist."; \
+ fi ; \
+ else \
+ echo "Failed !!: Cannot chage mode in installing $(OBJECTNAME) to khoros system"; \
+ fi ; \
+ echo "-- end of khoros-installing"; \
+ fi
+
+install-doc: html
+ @if [ ! -d $(DSTDOC)/SmallTools ]; \
+ then \
+ mkdir $(DSTDOC)/SmallTools ;\
+ fi
+ @if [ -f $(DSTDOC)/SmallTools/$(OBJECTNAME).html ]; \
+ then \
+ $(RM) -f $(DSTDOC)/SmallTools/$(OBJECTNAME).html ;\
+ fi
+ @$(CP) $(OBJECTNAME).html $(DSTDOC)/SmallTools/$(OBJECTNAME).html
+ @$(CHMOD) 444 $(DSTDOC)/SmallTools/$(OBJECTNAME).html
+ @if [ -f ../doc/*.html ]; \
+ then \
+ $(CP) ../doc/*.html $(DSTDOC)/SmallTools/ ;\
+ fi
+ @$(CHMOD) 444 $(DSTDOC)/SmallTools/$(OBJECTNAME).html
+ @if [ -f $(DSTDOC)/SmallTools/Makefile ]; \
+ then \
+ cd $(DSTDOC)/SmallTools; $(MAKE); \
+ fi
+
+html: $(OBJECTNAME).html
+
+configFileRead:
+ @ctrl2configFileRead $(CLASSNAME) $(OBJECTNAME) ../Config/OptionControlFile
+
+$(OBJECTNAME).html: $(OSTYPE)/$(OBJECTNAME)
+ @echo creating html
+ @$(OSTYPE)/$(OBJECTNAME) -html 2> $(OBJECTNAME).html.tmp
+ @sed -e s/$(OSTYPE)\\/// $(OBJECTNAME).html.tmp > $(OBJECTNAME).html
+ @$(RM) $(OBJECTNAME).html.tmp
+
+$(DSTDIR)/$(OBJECTNAME): $(OSTYPE)/$(OBJECTNAME)
+ @ln -s -f ../sbin/MachineIndependent $@
+
+depend::
+ @echo dependency checking now
+ @if [ ! -L $(OSTYPE) ] ; then \
+ moveHostdependent; \
+ fi
+ rm -f $(OSTYPE)/.Depend
+ #echo C
+ @if [ -f $(OBJECTNAME).c ] ; \
+ then \
+ echo "dependency: *.c"; \
+ echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) *.c ; \
+ $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) *.c >> $(OSTYPE)/.Depend ; \
+ fi
+ #echo CC
+ @if [ -f $(OBJECTNAME).cc ] ; \
+ then \
+ echo "dependency: *.cc"; \
+ echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cc ; \
+ $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cc >> $(OSTYPE)/.Depend ; \
+ fi
+ @if [ -f $(OBJECTNAME).ccm ] ; \
+ then \
+ echo "dependency: *.ccm"; \
+ echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.ccm ; \
+ $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.ccm >> $(OSTYPE)/.Depend ; \
+ fi
+ @if [ -f $(OBJECTNAME).cu ] ; \
+ then \
+ echo "dependency: *.cu"; \
+ echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cu ; \
+ $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cu >> $(OSTYPE)/.Depend ; \
+ fi
+
+update:../Config/OptionControlFile
+ maketool $(CLASSNAME) $(OBJECTNAME) update
+
+updateNoAns:../Config/OptionControlFile
+ maketool $(CLASSNAME) $(OBJECTNAME) update N
+
+changeName::
+
+Test:$(OSTYPE)/$(OBJECTNAME) TestDir
+ @if [ -f test/Makefile ] ; \
+ then \
+ cd test; make ; \
+ else \
+ echo "No test Makefile"; \
+ fi
+
+TestDir::
+ @if [ ! -d test ] ; \
+ then \
+ echo "Creating test dir"; \
+ mkdir test; \
+ fi
+ @if [ ! -f test/Makefile ] ; \
+ then \
+ echo "Creating Makefile"; \
+ cd test; \
+ protoTestMakefileCreate; \
+ fi
+ @if [ ! -d test/data ]; \
+ then \
+ mkdir $(EOSHOME)/data/$(OBJECTNAME); \
+ cd test; \
+ ln -sf ../$(EOSHOME)/data/$(OBJECTNAME) data; \
+ fi
+
+tar::
+ cd $(DSTTAR); tar cvf Tools.$(CLASSNAME).$(OBJECTNAME).tar ../bin/$(OBJECTNAME) \
+ ../bin/*/$(OBJECTNAME).* \
+ ../src/Tools/$(CLASSNAME)/$(OBJECTNAME) \
+ ; gzip Tools.$(CLASSNAME).$(OBJECTNAME).tar
+
+-include $(OSTYPE)/.Depend
+-include ../Config/Target.inc
--- /dev/null
+../../../../../hostdepend/X86MAC64/src/Tools/eosPoint/eosPointAffineTransform/src/X86MAC64
\ No newline at end of file
--- /dev/null
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#include "../inc/config.h"
+#include "genUtil.h"
+#include "eosString.h"
+#include "File.h"
+#include "Memory.h"
+
+
+void
+argCheck(eosPointAffineTransformInfo* info, int argc, char* argv[])
+{
+ long i;
+ char s[1024];
+ FILE* fpt;
+
+ if(NULL==(fpt=fopen(".EosLog", "a+"))) {
+
+ } else {
+ for(i=0; i<argc; i++) {
+ fprintf(fpt, "%s ", argv[i]);
+ }
+ fprintf(fpt, "\n");
+ fclose(fpt);
+ }
+ for(i=1; i<argc; i++) {
+ if(OPTION_FLAG==argv[i][OPTION_FLAG_POS]) {
+ SSWITCH(argv[i]+OPTION_POS)
+ SCASE("i") {
+ if(i+1<argc) {
+ info->In = stringGetNthWord(argv[i+1], 1, " ,");
+ i++;
+ info->flagIn++;
+ } else {
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ }
+ SBREAK;
+ }
+ SCASE("o") {
+ if(i+1<argc) {
+ info->Out = stringGetNthWord(argv[i+1], 1, " ,");
+ i++;
+ info->flagOut++;
+ } else {
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ }
+ SBREAK;
+ }
+ SCASE("c") {
+ if(i+1<argc) {
+ info->configFile = stringGetNthWord(argv[i+1], 1, " ,");
+ i++;
+ info->flagconfigFile++;
+ } else {
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ }
+ SBREAK;
+ }
+ SCASE("m") {
+ if(i+1<argc) {
+ info->mode = stringGetNthIntegerData(argv[i+1], 1, " ,");
+ i++;
+ info->flagmode++;
+ } else {
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ }
+ SBREAK;
+ }
+ SCASE("h") {
+ usage(argv[0]);
+ exit(EXIT_SUCCESS);
+ break;
+ }
+ SCASE("html") {
+ htmlBeforeUsage(argv[0]);
+ usage(argv[0]);
+ htmlAfterUsage(argv[0]);
+ exit(EXIT_SUCCESS);
+ break;
+ }
+ SDEFAULT {
+ fprintf(stderr, "Not Supported Options: :%s\n", argv[i]);
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ break;
+ }
+ SSWITCHEND;
+ }
+ }
+}
--- /dev/null
+//出力されるアフィン変換の行列をつかって，座標を変換するためのプログラム
+
+/*
+# eosPointAffineTransform : $Revision$
+# $Date$
+# Created by $Author$
+# Usage : eosPointAffineTransform
+# Attention
+# $Loccker$
+# $State$
+#
+*/
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#define GLOBAL_DECLARATION
+#include "../inc/config.h"
+
+#define DEBUG
+#include "genUtil.h"
+#include "eosPoint.h"
+
+/*
+Example:
+typedef struct leosPointAffineTransformInfo {
+ float a;
+ int b;
+} leosPointAffineTransformInfo;
+
+typedef enum leosPointAffineTransformMode {
+ a=0,
+ b=1
+} leosPointAffineTransformMode;
+*/
+
+int countPoint(eosPoint point)
+{
+ int count = 0;
+ eosPointTop(&point);
+ while(point.current != NULL){
+ count++;
+ eosPointNext(&point);
+ }
+ return count;
+}
+
+//アフィン変換行列を計算
+void MakeAffine(eosPointIcpResult* icp_result_set, double rotation_matrix[3][3], double* translation)
+{
+ int i,j;
+ Matrix3D affine_matrix;
+ matrix3DInit(affine_matrix);
+ for(i=0;i<3;i++){
+ for(j=0;j<3;j++){
+ affine_matrix[i][j] = rotation_matrix[j][i];
+ }
+ affine_matrix[3][i] = translation[i];
+ }
+ matrix3DMultiplyInv(affine_matrix, icp_result_set->matrix);
+}
+
+//変換行列を適用
+void applyMatrix(eosPoint *inP_upd, double rotation_mat[3][3], double qt[3], int cnt_in_point)
+{
+ int i = 0;
+ eosPoint cacheP;
+ eosPointCopy(&cacheP, inP_upd);
+ eosPointTop(inP_upd);
+ eosPointTop(&cacheP);
+ for (i = 0; i < cnt_in_point; i++){
+ inP_upd->current->p.coord.data[0] = rotation_mat[0][0] * cacheP.current->p.coord.data[0] +
+ rotation_mat[0][1] * cacheP.current->p.coord.data[1] +
+ rotation_mat[0][2] * cacheP.current->p.coord.data[2] +
+ qt[0];
+
+ inP_upd->current->p.coord.data[1] = rotation_mat[1][0] * cacheP.current->p.coord.data[0] +
+ rotation_mat[1][1] * cacheP.current->p.coord.data[1] +
+ rotation_mat[1][2] * cacheP.current->p.coord.data[2] +
+ qt[1];
+
+ inP_upd->current->p.coord.data[2] = rotation_mat[2][0] * cacheP.current->p.coord.data[0] +
+ rotation_mat[2][1] * cacheP.current->p.coord.data[1] +
+ rotation_mat[2][2] * cacheP.current->p.coord.data[2] +
+ qt[2];
+ eosPointNext(inP_upd);
+ eosPointNext(&cacheP);
+ }
+}
+
+int
+main(int argc, char* argv[])
+{
+ eosPointAffineTransformInfo info;
+
+ init0(&info);
+ argCheck(&info, argc, argv);
+ init1(&info);
+
+ DEBUGPRINT("Program Start\n");
+
+ exit(EXIT_SUCCESS);
+}
+
+void
+additionalUsage()
+{
+ fprintf(stderr, "----- Additional Usage -----\n");
+}
--- /dev/null
+/bin/bash: eosPointAffineTransform: No such file or directory
--- /dev/null
+-F 4.3 1 0 52x1+0+0 +0+0 'Cantata' cantata
+ -M 1 1 52x1+0+0 +1+0 ' ' subform
+ -P 1 0 52x1+0+1 +0+0 ' ' eosPointAffineTransform
+ -D 1 0 9x1+0+0 'Options' _gui_options
+ -H 1 6x1+0+0 'License' 'license' $BOOTSTRAP/repos/license/License license
+ -E
+ -R 1 0 1 5x1+35+0 'Run' 'execute operation' $EOS/bin/eosPointAffineTransform
+ -H 1 5x1+41+0 'Help' 'help page' $EOS/src/Tools/eosPoint/eosPointAffineTransform/doc/eosPointAffineTransform.doc help
+ -Q 1 0 5.25x1+47+0 'Close'
+ -I 1 0 1 1 0 1 -1x1+1+1.500000 ' ' 'In' 'InputDataFile' i
+ -O 1 0 1 1 0 1 -1x1+1+3.000000 ' ' 'Out' 'OutputDataFile' o
+ -I 1 0 1 0 0 1 -1x1+1+4.500000 ' ' 'configFile' 'ConfigurationFile' c
+ -i 1 0 1 0 0 -1x1+1+6.000000 0 0 0 0 0 'mode' 'Mode' m
+ -E
+ -E
+-E
--- /dev/null
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#include "../inc/config.h"
+#include "genUtil.h"
+#include "eosString.h"
+#include "File.h"
+#include "Memory.h"
+
+
+void
+init0(eosPointAffineTransformInfo* info)
+{
+ info->fptIn = NULL; info->flagIn = 0;
+ info->fptOut = NULL; info->flagOut = 0;
+ info->fptconfigFile = NULL; info->flagconfigFile = 0;
+ info->mode = 0; info->flagmode = 0;
+}
+
+void
+init1(eosPointAffineTransformInfo* info)
+{
+ char s[1024];
+ int i;
+ if(!info->flagIn) {
+ stringGetFromFile(s, "In", stdin, stdout, 0);
+ info->In = stringGetNthWord(s, 1, " ,\t");
+ info->flagIn++;
+ }
+ if(info->flagIn) {
+ info->fptIn = fileOpen(info->In, "r");
+ }
+
+ if(!info->flagOut) {
+ stringGetFromFile(s, "Out", stdin, stdout, 0);
+ info->Out = stringGetNthWord(s, 1, " ,\t");
+ info->flagOut++;
+ }
+ if(info->flagOut) {
+ info->fptOut = fileOpen(info->Out, "w");
+ }
+
+ if(info->flagconfigFile) {
+ info->fptconfigFile = fileOpen(info->configFile, "r");
+ }
+
+ if(info->flagmode) {
+ }
+
+}
+#ifdef KHOROS
+#include <stdio.h>
+#include "bootstrap.h"
+#include "dataserv.h"
+#include "datamanip.h"
+extern void func_usage_additions(void);
+extern void func_free_args(kexit_status status, kaddr client_data);
+extern void func_get_args(kform* pane);
+
+void
+func_usage_additions(void)
+{
+}
+void
+func_free_args(kexit_status status, kaddr client_data)
+{
+}
+void
+func_get_args(kform* pane)
+{
+}
+void
+khorosInit(int argc, char* argv[])
+{
+ char* eospath;
+ char panepath[1024];
+ FILE* fpt;
+
+ eospath = getenv("EOS_HOME");
+ sprintf(panepath, "%s/src/Tools/eosPoint/eosPointAffineTransform/src/eosPointAffineTransform.pane", eospath);
+ khoros_initialize(argc, argv, "EOS");
+ fpt = fopen(panepath, "r"); if(NULL!=fpt) {
+ fclose(fpt);
+ kclui_initialize(panepath, KGEN_NONE, "EOS", "eosPointAffineTransform",
+ func_usage_additions,
+ func_get_args,
+ func_free_args);
+ }
+}
+#endif /* KHOROS */
--- /dev/null
+include ../../Config/Define.inc
+include ../../../Config/Define.inc
+include ../../../../Config/Define.inc
+include ../../../../../Config/Define.inc
+
+all: help exec
+
+help:
+ @echo "----- Help Message Check -----"
+ @../$(OSTYPE)/$(OBJECTNAME) -h
+
+exec:
+ @echo "----- Execution Check -----"
+ ../$(OSTYPE)/$(OBJECTNAME)
+ @echo "----- Calc check -----"
+
+clean:
--- /dev/null
+../../../../../..//data/eosPointAffineTransform
\ No newline at end of file
--- /dev/null
+#include <stdio.h>
+#include <stdlib.h>
+#include "../inc/config.h"
+
+void
+usage(char* thisProgram)
+{
+ fprintf(stderr, "Usage: %s\n", thisProgram);
+ fprintf(stderr, "Options:\n");
+ fprintf(stderr, " [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile\n");
+ fprintf(stderr, " [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile\n");
+ fprintf(stderr, " [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile\n");
+ fprintf(stderr, " [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode\n");
+ additionalUsage();
+}
+
+void
+htmlBeforeUsage(char* thisProgram)
+{
+ fprintf(stderr, "<HTML>\n");
+ fprintf(stderr, "<HEAD>\n");
+ fprintf(stderr, "<TITLE>%s</TITLE>\n", thisProgram);
+ fprintf(stderr, "</HEAD>\n");
+ fprintf(stderr, "<BODY>\n");
+ fprintf(stderr, "<H1>%s</H1>\n", thisProgram);
+ fprintf(stderr, "<H2>Usage</H2>\n");
+ fprintf(stderr, "<PRE>\n");
+}
+
+void
+htmlAfterUsage(char* thisProgram)
+{
+ fprintf(stderr, "</PRE>\n");
+ fprintf(stderr, "</BODY>\n");
+ fprintf(stderr, "</HTML>\n");
+}
--- /dev/null
+#include <stdio.h>
+#include <stdlib.h>
+#include "../inc/config.h"
+
-/bin/bash: eosPointCurvatureInfo: No such file or directory
+/bin/bash: eosPointCurvatureInfo: そのようなファイルやディレクトリはありません
--- /dev/null
+OBJECTNAME = eosPointPositionCorrection
+EXTRA_LIB = -lgsl -lcblas -lm
+EXTRA_CCOPTS =
+EXTRA_INC =
--- /dev/null
+# OptionControlFile
+# FileFormat
+"-i","-i[nput]","Input:eosPoint","Essential","1","1","In","inFile::eosPoint","NULL"
+"-it","-i[nput]t[ype]","Input:eosPointMode","Optional","1","1","InType","Integer","0"
+"-n","-n[umber]","Input:number of Point, n, dependent upon m=n/(n-1)/2, a point number in In","Optional","1","1","N","Integer","-1"
+"-o","-o[utput]","Output:eosPoint","Optional","1","1","Out","outFile::eosPoint","stdout"
+"-ot","-o[utput]t[ype]","Output:eosPoint","Optional","1","1","OutType","Integer","0"
+"-delta","-delta","Output:eosPoint","Optional","1","1","OutDelta","outFile::eosPoint","stdout"
+"-c","-c[onfig]","ConfigurationFile","Optional","1","1","configFile","inFile","NULL"
+"-m","-m[ode]","Mode","Optional","1","1","mode","Integer","0"
--- /dev/null
+include ../../../Config/Define.inc
+include ../../Config/Define.inc
+include ../Config/Define.inc
+include Config/Define.inc
+
+all:
+ cd src; make all; cd ..
+
+install:
+ cd src; make install; cd ..
+
+
+putSF:
+ if [ -f private ] ; \
+ then \
+ echo "$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME) is private"; \
+ else \
+ cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE commit || cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE import src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME); \
+ fi
+
+put:
+ cd src; make put; cd ..
+
+clean:
+ cd src; make clean; cd ..
+
+depend:
+ cd src; make depend; cd ..
+
+check:
+ @if [ ! -d $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) ] ; then \
+ echo making directory; \
+ mkdir -p $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE); \
+ fi
+ ln -sf ../../../../../hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) src/$(OSTYPE);
+ @$(RM) src/Makefile
+ @echo "New src/Makefile"
+ @$(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/src/Makefile src/Makefile
+ @cd src; rm -f $(OSTYPE)/.Depend; touch $(OSTYPE)/.Depend; make depend
+
+update:
+ @if [ ! -d $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) ] ; then \
+ echo making directory; \
+ mkdir -p $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE); \
+ fi
+ ln -sf ../../../../../hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) src/$(OSTYPE);
+ @$(RM) src/Makefile
+ @echo "New src/Makefile"
+ @$(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/src/Makefile src/Makefile
+ @cd src; rm -f $(OSTYPE)/.Depend; touch $(OSTYPE)/.Depend; echo "Y" | make update
+
+cvsupdate::
+ cvs -d $(EOS_CVSROOT) update -d
+
+cvscommit::
+ cvs -d $(EOS_CVSROOT) commit
+
+backup:
+ @cd ../../../..; \
+ echo $(OBJECTNAME) ; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile
+
+backup-all:
+ @cd ../../../..; \
+ echo $(OBJECTNAME) ; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile
+
+distribute:
+ cd ../../../..; \
+ echo $(OBJECTNAME) ; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
+
+distribute-all:
+ @cd ../../../..; \
+ echo $(OBJECTNAME) ; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
+
+eosintroduce:
+ ${EOS_HOME}/sbin/eosintroduce ${WORLDNAME} ${CLASSNAME} ${OBJECTNAME} ./
+
+include Config/Target.inc
--- /dev/null
+install:
+ cd ../src; make install-doc; cd ../doc
--- /dev/null
+#ifndef CONFIG_H
+#define CONFIG_H
+
+#include "../inc/eosPointPositionCorrection.h"
+
+#endif /* CONFIG_H */
--- /dev/null
+#ifndef EOSPOINTPOSITIONCORRECTION_H
+#define EOSPOINTPOSITIONCORRECTION_H
+#include <stdio.h>
+#include <stdlib.h>
+
+#define OPTION_FLAG '-'
+#define OPTION_FLAG_POS (0)
+#define OPTION_POS (1)
+
+
+
+
+typedef struct eosPointPositionCorrectionInfo {
+ long flagRedirect;
+
+ long flagIn;
+ char* In;
+ FILE* fptIn;
+
+ long flagInType;
+ long InType;
+
+ long flagN;
+ long N;
+
+ long flagOut;
+ char* Out;
+ FILE* fptOut;
+
+ long flagOutType;
+ long OutType;
+
+ long flagOutDelta;
+ char* OutDelta;
+ FILE* fptOutDelta;
+
+ long flagconfigFile;
+ char* configFile;
+ FILE* fptconfigFile;
+
+ long flagmode;
+ long mode;
+
+} eosPointPositionCorrectionInfo;
+#ifdef __cplusplus
+extern "C" {
+#endif
+extern void argCheck(eosPointPositionCorrectionInfo* info, int argc, char* avgv[]);
+extern void khorosInit(int argc, char* avgv[]);
+extern void init0(eosPointPositionCorrectionInfo* info);
+extern void init1(eosPointPositionCorrectionInfo* info);
+extern void usage(char* usage);
+extern void additionalUsage(void);
+extern void htmlBeforeUsage(char* usage);
+extern void htmlAfterUsage(char* usage);
+#ifdef __cplusplus
+};
+#endif
+#endif /* EOSPOINTPOSITIONCORRECTION_H */
--- /dev/null
+include ../Config/Define.inc
+include ../../Config/Define.inc
+include ../../../Config/Define.inc
+include ../../../../Config/Define.inc
+
+EOSHOME=../../../../../
+DSTDIR=$(EOSHOME)/bin
+DSTDOC=$(EOSHOME)/doc
+DSTTAR=$(EOSHOME)/tar
+
+INCFILES =
+
+LIBFILES = \
+ $(LIBPREFIX)EosObjects$(LIBSUFFIX)
+
+LIBFILESDEBUG = \
+ $(LIBPREFIX)EosObjects.debug$(LIBSUFFIX)
+
+SRCC = \
+ $(OBJECTNAME).c \
+ init.c \
+ argCheck.c \
+ usage.c \
+ util.c \
+
+SRCCXX = \
+ $(OBJECTNAME).cc \
+ init.cc \
+ argCheck.cc \
+ usage.cc \
+ util.cc \
+
+MODULES = \
+ $(OBJECTNAME).o \
+ init.o \
+ argCheck.o \
+ usage.o \
+ util.o \
+
+REALMODULES = \
+ $(OSTYPE)/$(OBJECTNAME).o \
+ $(OSTYPE)/init.o \
+ $(OSTYPE)/argCheck.o \
+ $(OSTYPE)/usage.o \
+ $(OSTYPE)/util.o
+
+MODULESDEBUG = \
+ $(OBJECTNAME).debugo \
+ init.debugo \
+ argCheck.debugo \
+ usage.debugo \
+ util.debugo \
+
+REALMODULESDEBUG = \
+ $(OSTYPE)/$(OBJECTNAME).debugo \
+ $(OSTYPE)/init.debugo \
+ $(OSTYPE)/argCheck.debugo \
+ $(OSTYPE)/usage.debugo \
+ $(OSTYPE)/util.debugo
+
+
+all: $(OSTYPE)/$(OBJECTNAME)
+ if [ ! -L $(OSTYPE) ] ; then \
+ moveHostdependent; \
+ fi
+
+debug: $(OSTYPE)/$(OBJECTNAME).debug
+
+cudagdb: $(OSTYPE)/$(OBJECTNAME).cudagdb
+
+
+$(OSTYPE)/$(OBJECTNAME)::
+ @$(RM) -f $(OSTYPE)/Makefile ; \
+ $(CP) $(EOS_HOME)/src/Config/Template/$(WORLDNAME)Template.Dir/src/ARCH/Makefile $(OSTYPE)/Makefile ; \
+ cd $(OSTYPE); \
+ $(MAKE) $(OBJECTNAME) WORLDNAME=$(WORLDNAME) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME)
+
+$(OSTYPE)/$(OBJECTNAME).debug::
+ @$(RM) -f $(OSTYPE)/Makefile ; \
+ $(CP) $(EOS_HOME)/src/Config/Template/$(WORLDNAME)Template.Dir/src/ARCH/Makefile $(OSTYPE)/Makefile ; \
+ cd $(OSTYPE); \
+ $(MAKE) $(OBJECTNAME).debug WORLDNAME=$(WORLDNAME) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME)
+
+$(OSTYPE)/$(OBJECTNAME).cudagdb::
+ @$(RM) -f $(OSTYPE)/Makefile ; \
+ $(CP) $(EOS_HOME)/src/Config/Template/$(WORLDNAME)Template.Dir/src/ARCH/Makefile $(OSTYPE)/Makefile ; \
+ cd $(OSTYPE); \
+ $(MAKE) $(OBJECTNAME).cudagdb WORLDNAME=$(WORLDNAME) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME)
+
+cvsupdate::
+ cvs -d $(EOS_CVSROOT) update -d
+
+cvscommit::
+ cvs -d $(EOS_CVSROOT) commit
+
+edit:
+ @if [ -r $(OBJECTNAME).c ]; \
+ then \
+ sccsEdit $(OBJECTNAME).c; \
+ else \
+ echo "Source files are already editable"; \
+ fi
+ @if [ -r wish/$(OBJECTNAME).wish ]; \
+ then \
+ cd wish; sccsEdit $(OBJECTNAME).wish; \
+ else \
+ echo "Source files (wish) are already editable."; \
+ fi
+ @if [ -r ruby/$(OBJECTNAME).rb ]; \
+ then \
+ cd ruby; sccsEdit $(OBJECTNAME).rb; \
+ else \
+ echo "Source files (ruby) are already editable."; \
+ fi
+ @if [ -r perl/$(OBJECTNAME).pl ]; \
+ then \
+ cd perl; sccsEdit $(OBJECTNAME).pl ; \
+ else \
+ echo "Source files (perl) are already editable."; \
+ fi
+ @if [ -r ../Config/OptionControlFile ]; \
+ then \
+ cd ../Config; sccsEdit OptionControlFile; \
+ else \
+ echo "OptionControlFile are already editable."; \
+ fi
+
+unedit:
+ @if [ -w $(OBJECTNAME).c ]; \
+ then \
+ sccsUnedit $(OBJECTNAME).c; \
+ else \
+ echo "Source files are not editable"; \
+ fi
+ @if [ -w wish/$(OBJECTNAME).wish ]; \
+ then \
+ cd wish; sccsUnedit $(OBJECTNAME).wish; \
+ else \
+ echo "Source files (wish) are not editable."; \
+ fi
+ @if [ -w ruby/$(OBJECTNAME).rb]; \
+ then \
+ cd ruby; sccsUnedit $(OBJECTNAME).rb; \
+ else \
+ echo "Source files (ruby) are not editable."; \
+ fi
+ @if [ -w perl/$(OBJECTNAME).pl ]; \
+ then \
+ cd perl; sccsUnedit $(OBJECTNAME).pl ; \
+ else \
+ echo "Source files (ruby) are not editable."; \
+ fi
+ @if [ -w ../Config/OptionControlFile ]; \
+ then \
+ cd ../Config; sccsUnedit OptionControlFile; \
+ else \
+ echo "OptionControlFile are not editable."; \
+ fi
+
+report:
+ @if [ -r $(OBJECTNAME).c ]; \
+ then \
+ sccsReport $(OBJECTNAME).c; \
+ else \
+ echo "Source files are already editable"; \
+ fi
+ @if [ -r wish/$(OBJECTNAME).wish ]; \
+ then \
+ cd wish; sccsReport $(OBJECTNAME).wish; \
+ else \
+ echo "Source files (wish) are already editable."; \
+ fi
+ @if [ -r ruby/$(OBJECTNAME).rb ]; \
+ then \
+ cd ruby; sccsReport $(OBJECTNAME).rb; \
+ else \
+ echo "Source files (ruby) are already editable."; \
+ fi
+ @if [ -r perl/$(OBJECTNAME).pl ] ; \
+ then \
+ cd perl; sccsReport $(OBJECTNAME).pl ; \
+ else \
+ echo "Source files (perl) are already editable."; \
+ fi
+ @if [ -r ../Config/OptionControlFile ]; \
+ then \
+ cd ../Config; sccsReport OptionControlFile; \
+ else \
+ echo "OptionControlFile are already editable."; \
+ fi
+
+clean :
+ rm -f *.debugo $(OSTYPE)/*.debugo *.cudagdbo $(OSTYPE)/*.cudagdbo *.o $(OSTYPE)/*.o *.linkinfo $(OSTYPE)/*.linkinfo \
+ $(OSTYPE)/$(OBJECTNAME) $(OSTYPE)/*.$(OSTYPE) \
+ $(OSTYPE)/$(OBJECTNAME).debug $(OSTYPE)/*.$(OSTYPE).debug \
+ $(OSTYPE)/$(OBJECTNAME).cudagdb $(OSTYPE)/*.$(OSTYPE).cudagdb \
+ $(OSTYPE)/$(OBJECTNAME).linkinfo $(OSTYPE)/*.$(OSTYPE).linkinfo \
+ *.bak *.$(OSTYPE) core
+
+install: install-bin install-doc install-wish install-ruby install-shell install-perl
+ @if [ dummy$(KHOROS_KENGOBJ) != dummy ] ; \
+ then \
+ if [ -x $(KHOROS_KGENOBJ) ] ; \
+ then \
+ make install-khoros ; \
+ fi; \
+ fi
+
+install-bin:$(DSTDIR)/$(OSTYPE)/$(OBJECTNAME)
+
+$(DSTDIR)/$(OSTYPE)/$(OBJECTNAME):$(OSTYPE)/$(OBJECTNAME) $(DSTDIR)/$(OBJECTNAME)
+ @echo ---- Installing to bin
+ @echo $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME)
+ @if [ ! -d $(DSTDIR)/$(OSTYPE) ]; \
+ then \
+ mkdir $(DSTDIR)/$(OSTYPE); \
+ fi
+ @if [ -x $(OSTYPE)/$(OBJECTNAME) ]; \
+ then \
+ echo "Compilation is complete"; \
+ $(RM) -f $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME); \
+ $(CD) $(OSTYPE); $(INSTALL) -m 555 $(OBJECTNAME) ../$(DSTDIR)/$(OSTYPE); \
+ $(CHMOD) 555 ../$(DSTDIR)/$(OSTYPE)/$(OBJECTNAME); \
+ else \
+ echo "Compilation is incomplete. $(OBJECTNAME)"; \
+ fi
+ @echo ---- end of bin
+
+install-wish:
+ @if [ -d wish ]; \
+ then \
+ echo "---- Tcl/Tk file Install"; \
+ if [ ! -d $(DSTDIR)/wish/$(OBJECTNAME) ]; \
+ then \
+ mkdir $(DSTDIR)/wish/$(OBJECTNAME) ; \
+ fi ; \
+ $(CP) -f wish/* $(DSTDIR)/wish/$(OBJECTNAME); \
+ $(CHMOD) 555 $(DSTDIR)/wish/$(OBJECTNAME)/* ;\
+ touch $(DSTDIR)/wish/$(OBJECTNAME)/tclIndex;\
+ $(CHMOD) 666 $(DSTDIR)/wish/$(OBJECTNAME)/tclIndex;\
+ echo "---- Tcl/Tk file Installed";\
+ fi
+
+install-ruby:
+ @if [ -d ruby ]; \
+ then \
+ echo "---- Ruby/Tk file Install"; \
+ if [ ! -d $(DSTDIR)/ruby/$(OBJECTNAME) ]; \
+ then \
+ mkdir $(DSTDIR)/ruby/$(OBJECTNAME) ; \
+ fi ; \
+ $(CP) -f ruby/* $(DSTDIR)/ruby/$(OBJECTNAME); \
+ $(CHMOD) 555 $(DSTDIR)/ruby/$(OBJECTNAME)/* ; \
+ echo "---- Ruby/Tk file Installed"; \
+ fi
+
+install-perl:
+ @if [ -d perl ]; \
+ then \
+ echo "---- Perl/Tk file Install"; \
+ if [ ! -d $(DSTDIR)/perl/$(OBJECTNAME) ]; \
+ then \
+ mkdir $(DSTDIR)/perl/$(OBJECTNAME) ; \
+ fi; \
+ $(CP) -f perl/* $(DSTDIR)/perl/$(OBJECTNAME); \
+ $(CHMOD) 555 $(DSTDIR)/perl/$(OBJECTNAME)/* ; \
+ echo "---- Perl/Tk file Installed"; \
+ fi
+
+install-shell:
+ @if [ ! -d $(DSTDIR)/shell/$(OBJECTNAME) ]; \
+ then \
+ mkdir $(DSTDIR)/shell/$(OBJECTNAME) ; \
+ fi
+ @if [ -d shell ]; \
+ then \
+ echo "---- Shell file Install"; \
+ if [ ! -d $(DSTDIR)/shell/$(OBJECTNAME) ]; \
+ then \
+ mkdir $(DSTDIR)/shell/$(OBJECTNAME) ; \
+ fi ; \
+ $(CP) -f shell/* $(DSTDIR)/shell/$(OBJECTNAME); \
+ $(CHMOD) 555 $(DSTDIR)/shell/$(OBJECTNAME)/*; \
+ echo "---- Shell file Installed"; \
+ fi
+
+install-khoros:
+ @echo Installing to khoros
+ @if [ ! -d ../../../../../objects/script/$(OBJECTNAME) -a -f $(KHOROS_KGENOBJ) ]; \
+ then \
+ echo kgenobj;\
+ $(KHOROS_KGENOBJ) -tb Eos -oname $(OBJECTNAME) -type script -pane -cantata true -cat Eos -subcat $(CLASSNAME) -description $(OBJECTNAME) -bname $(OBJECTNAME) -form -lang ksh ; \
+ fi
+ @if [ ! -d ../../../../../objects/script/$(OBJECTNAME) -a -f $(KHOROS_KSET) ]; \
+ then \
+ $(KHOROS_KSET) -tb Eos -oname $(OBJECTNAME) -icon $(OBJECTNAME) ; \
+ fi
+ @if [ -d ../../../../../objects/script/$(OBJECTNAME) -a -f $(KHOROS_KSET) ]; \
+ then \
+ $(CHMOD) -R 775 ../../../../../objects/script/$(OBJECTNAME) ; \
+ if [ $? ] ; \
+ then \
+ echo "-- setting khoros ---" ; \
+ if [ -d ../../../../../objects/script/$(OBJECTNAME)/uis/ ] ; \
+ then \
+ $(CD) ../../../../../objects/script/$(OBJECTNAME)/uis/ ; \
+ $(RM) -f $(OBJECTNAME).pane ; \
+ $(LN) -s ../../../../src/Tools/$(CLASSNAME)/$(OBJECTNAME)/src/$(OBJECTNAME).pane $(OBJECTNAME).pane; \
+ $(CD) ../../ ; \
+ $(CHMOD) -R 555 $(OBJECTNAME); \
+ else \
+ echo "../../../../../objects/script/$(OBJECTNAME)/uis/ does not exist."; \
+ fi ; \
+ else \
+ echo "Failed !!: Cannot chage mode in installing $(OBJECTNAME) to khoros system"; \
+ fi ; \
+ echo "-- end of khoros-installing"; \
+ fi
+
+install-doc: html
+ @if [ ! -d $(DSTDOC)/SmallTools ]; \
+ then \
+ mkdir $(DSTDOC)/SmallTools ;\
+ fi
+ @if [ -f $(DSTDOC)/SmallTools/$(OBJECTNAME).html ]; \
+ then \
+ $(RM) -f $(DSTDOC)/SmallTools/$(OBJECTNAME).html ;\
+ fi
+ @$(CP) $(OBJECTNAME).html $(DSTDOC)/SmallTools/$(OBJECTNAME).html
+ @$(CHMOD) 444 $(DSTDOC)/SmallTools/$(OBJECTNAME).html
+ @if [ -f ../doc/*.html ]; \
+ then \
+ $(CP) ../doc/*.html $(DSTDOC)/SmallTools/ ;\
+ fi
+ @$(CHMOD) 444 $(DSTDOC)/SmallTools/$(OBJECTNAME).html
+ @if [ -f $(DSTDOC)/SmallTools/Makefile ]; \
+ then \
+ cd $(DSTDOC)/SmallTools; $(MAKE); \
+ fi
+
+html: $(OBJECTNAME).html
+
+configFileRead:
+ @ctrl2configFileRead $(CLASSNAME) $(OBJECTNAME) ../Config/OptionControlFile
+
+$(OBJECTNAME).html: $(OSTYPE)/$(OBJECTNAME)
+ @echo creating html
+ @$(OSTYPE)/$(OBJECTNAME) -html 2> $(OBJECTNAME).html.tmp
+ @sed -e s/$(OSTYPE)\\/// $(OBJECTNAME).html.tmp > $(OBJECTNAME).html
+ @$(RM) $(OBJECTNAME).html.tmp
+
+$(DSTDIR)/$(OBJECTNAME): $(OSTYPE)/$(OBJECTNAME)
+ @ln -s -f ../sbin/MachineIndependent $@
+
+depend::
+ @echo dependency checking now
+ @if [ ! -L $(OSTYPE) ] ; then \
+ moveHostdependent; \
+ fi
+ rm -f $(OSTYPE)/.Depend
+ #echo C
+ @if [ -f $(OBJECTNAME).c ] ; \
+ then \
+ echo "dependency: *.c"; \
+ echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) *.c ; \
+ $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) *.c >> $(OSTYPE)/.Depend ; \
+ fi
+ #echo CC
+ @if [ -f $(OBJECTNAME).cc ] ; \
+ then \
+ echo "dependency: *.cc"; \
+ echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cc ; \
+ $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cc >> $(OSTYPE)/.Depend ; \
+ fi
+ @if [ -f $(OBJECTNAME).ccm ] ; \
+ then \
+ echo "dependency: *.ccm"; \
+ echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.ccm ; \
+ $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.ccm >> $(OSTYPE)/.Depend ; \
+ fi
+ @if [ -f $(OBJECTNAME).cu ] ; \
+ then \
+ echo "dependency: *.cu"; \
+ echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cu ; \
+ $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cu >> $(OSTYPE)/.Depend ; \
+ fi
+
+update:../Config/OptionControlFile
+ maketool $(CLASSNAME) $(OBJECTNAME) update
+
+updateNoAns:../Config/OptionControlFile
+ maketool $(CLASSNAME) $(OBJECTNAME) update N
+
+changeName::
+
+Test:$(OSTYPE)/$(OBJECTNAME) TestDir
+ @if [ -f test/Makefile ] ; \
+ then \
+ cd test; make ; \
+ else \
+ echo "No test Makefile"; \
+ fi
+
+TestDir::
+ @if [ ! -d test ] ; \
+ then \
+ echo "Creating test dir"; \
+ mkdir test; \
+ fi
+ @if [ ! -f test/Makefile ] ; \
+ then \
+ echo "Creating Makefile"; \
+ cd test; \
+ protoTestMakefileCreate; \
+ fi
+ @if [ ! -d test/data ]; \
+ then \
+ mkdir $(EOSHOME)/data/$(OBJECTNAME); \
+ cd test; \
+ ln -sf ../$(EOSHOME)/data/$(OBJECTNAME) data; \
+ fi
+
+tar::
+ cd $(DSTTAR); tar cvf Tools.$(CLASSNAME).$(OBJECTNAME).tar ../bin/$(OBJECTNAME) \
+ ../bin/*/$(OBJECTNAME).* \
+ ../src/Tools/$(CLASSNAME)/$(OBJECTNAME) \
+ ; gzip Tools.$(CLASSNAME).$(OBJECTNAME).tar
+
+-include $(OSTYPE)/.Depend
+-include ../Config/Target.inc
--- /dev/null
+../../../../../hostdepend/X86MAC64/src/Tools/eosPoint/eosPointPositionCorrection/src/X86MAC64
\ No newline at end of file
--- /dev/null
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#include "../inc/config.h"
+#include "genUtil.h"
+#include "eosString.h"
+#include "File.h"
+#include "Memory.h"
+
+
+void
+argCheck(eosPointPositionCorrectionInfo* info, int argc, char* argv[])
+{
+ long i;
+ char s[1024];
+ FILE* fpt;
+
+ if(NULL==(fpt=fopen(".EosLog", "a+"))) {
+
+ } else {
+ for(i=0; i<argc; i++) {
+ fprintf(fpt, "%s ", argv[i]);
+ }
+ fprintf(fpt, "\n");
+ fclose(fpt);
+ }
+ for(i=1; i<argc; i++) {
+ if(OPTION_FLAG==argv[i][OPTION_FLAG_POS]) {
+ SSWITCH(argv[i]+OPTION_POS)
+ SCASE("i") {
+ if(i+1<argc) {
+ info->In = stringGetNthWord(argv[i+1], 1, " ,");
+ i++;
+ info->flagIn++;
+ } else {
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ }
+ SBREAK;
+ }
+ SCASE("it") {
+ if(i+1<argc) {
+ info->InType = stringGetNthIntegerData(argv[i+1], 1, " ,");
+ i++;
+ info->flagInType++;
+ } else {
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ }
+ SBREAK;
+ }
+ SCASE("n") {
+ if(i+1<argc) {
+ info->N = stringGetNthIntegerData(argv[i+1], 1, " ,");
+ i++;
+ info->flagN++;
+ } else {
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ }
+ SBREAK;
+ }
+ SCASE("o") {
+ if(i+1<argc) {
+ info->Out = stringGetNthWord(argv[i+1], 1, " ,");
+ i++;
+ info->flagOut++;
+ } else {
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ }
+ SBREAK;
+ }
+ SCASE("ot") {
+ if(i+1<argc) {
+ info->OutType = stringGetNthIntegerData(argv[i+1], 1, " ,");
+ i++;
+ info->flagOutType++;
+ } else {
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ }
+ SBREAK;
+ }
+ SCASE("delta") {
+ if(i+1<argc) {
+ info->OutDelta = stringGetNthWord(argv[i+1], 1, " ,");
+ i++;
+ info->flagOutDelta++;
+ } else {
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ }
+ SBREAK;
+ }
+ SCASE("c") {
+ if(i+1<argc) {
+ info->configFile = stringGetNthWord(argv[i+1], 1, " ,");
+ i++;
+ info->flagconfigFile++;
+ } else {
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ }
+ SBREAK;
+ }
+ SCASE("m") {
+ if(i+1<argc) {
+ info->mode = stringGetNthIntegerData(argv[i+1], 1, " ,");
+ i++;
+ info->flagmode++;
+ } else {
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ }
+ SBREAK;
+ }
+ SCASE("h") {
+ usage(argv[0]);
+ exit(EXIT_SUCCESS);
+ break;
+ }
+ SCASE("html") {
+ htmlBeforeUsage(argv[0]);
+ usage(argv[0]);
+ htmlAfterUsage(argv[0]);
+ exit(EXIT_SUCCESS);
+ break;
+ }
+ SDEFAULT {
+ fprintf(stderr, "Not Supported Options: :%s\n", argv[i]);
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ break;
+ }
+ SSWITCHEND;
+ }
+ }
+}
--- /dev/null
+/*
+# eosPointPositionCorrection : $Revision$
+# $Date$
+# Created by $Author$
+# Usage : eosPointPositionCorrection
+# Attention
+# $Loccker$
+# $State$
+#
+*/
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#define GLOBAL_DECLARATION
+#include "../inc/config.h"
+
+#undef DEBUG
+#include "genUtil.h"
+#include "eosPoint.h"
+
+#include "leosPointPositionCorrection.h"
+
+int
+main(int argc, char* argv[])
+{
+ eosPointPositionCorrectionInfo info;
+ leosPointPositionCorrectionInfo linfo;
+ eosPoint inP;
+ eosPoint outP;
+
+ init0(&info);
+ argCheck(&info, argc, argv);
+ init1(&info);
+
+ DEBUGPRINT("Program Start\n");
+ eosPointRead(info.fptIn, &inP, info.InType);
+
+ linfo.n = info.N;
+ leosPointPositionCorrection(&outP, &inP, &linfo, info.mode);
+
+ eosPointWrite(info.fptOut, &outP, info.OutType);
+ if(info.flagOutDelta) {
+ eosPointWrite(info.fptOutDelta, &(linfo.db), 0);
+ }
+ exit(EXIT_SUCCESS);
+}
+
+void
+additionalUsage()
+{
+ fprintf(stderr, "----- Additional Usage -----\n");
+ eosPointFileFormatUsage(stderr);
+}
+
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>eosPointPositionCorrection</TITLE>
+</HEAD>
+<BODY>
+<H1>eosPointPositionCorrection</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: eosPointPositionCorrection
+Options:
+ [-i[nput] In (NULL ).as(inFile::eosPoint ) ] :Essential :Input:eosPoint
+ [-i[nput]t[ype] InType (0 ).as(Integer ) ] :Optional :Input:eosPointMode
+ [-n[umber] N (-1 ).as(Integer ) ] :Optional :Input:number of Point, n, dependent upon m=n/(n-1)/2, a point number in In
+ [-o[utput] Out (stdout ).as(outFile::eosPoint ) ] :Optional :Output:eosPoint
+ [-o[utput]t[ype] OutType (0 ).as(Integer ) ] :Optional :Output:eosPoint
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+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
+-F 4.3 1 0 52x1+0+0 +0+0 'Cantata' cantata
+ -M 1 1 52x1+0+0 +1+0 ' ' subform
+ -P 1 0 52x1+0+1 +0+0 ' ' eosPointPositionCorrection
+ -D 1 0 9x1+0+0 'Options' _gui_options
+ -H 1 6x1+0+0 'License' 'license' $BOOTSTRAP/repos/license/License license
+ -E
+ -R 1 0 1 5x1+35+0 'Run' 'execute operation' $EOS/bin/eosPointPositionCorrection
+ -H 1 5x1+41+0 'Help' 'help page' $EOS/src/Tools/eosPoint/eosPointPositionCorrection/doc/eosPointPositionCorrection.doc help
+ -Q 1 0 5.25x1+47+0 'Close'
+ -I 1 0 1 1 0 1 -1x1+1+1.500000 ' ' 'In' 'Input:eosPoint' i
+ -i 1 0 1 0 0 -1x1+1+3.000000 0 0 0 0 0 'InType' 'Input:eosPointMode' it
+ -i 1 0 1 0 0 -1x1+1+4.500000 0 0 -1 0 0 'N' 'Input:number of Point, n, dependent upon m=n/(n-1)/2, a point number in In' n
+ -O 1 0 1 0 0 1 -1x1+1+6.000000 ' ' 'Out' 'Output:eosPoint' o
+ -i 1 0 1 0 0 -1x1+1+7.500000 0 0 0 0 0 'OutType' 'Output:eosPoint' ot
+ -O 1 0 1 0 0 1 -1x1+1+9.000000 ' ' 'OutDelta' 'Output:eosPoint' delta
+ -I 1 0 1 0 0 1 -1x1+1+10.500000 ' ' 'configFile' 'ConfigurationFile' c
+ -i 1 0 1 0 0 -1x1+1+12.000000 0 0 0 0 0 'mode' 'Mode' m
+ -E
+ -E
+-E
--- /dev/null
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#include "../inc/config.h"
+#include "genUtil.h"
+#include "eosString.h"
+#include "File.h"
+#include "Memory.h"
+
+
+void
+init0(eosPointPositionCorrectionInfo* info)
+{
+ info->fptIn = NULL; info->flagIn = 0;
+ info->InType = 0; info->flagInType = 0;
+ info->N = -1; info->flagN = 0;
+ info->fptOut = stdout; info->flagOut = 0;
+ info->OutType = 0; info->flagOutType = 0;
+ info->fptOutDelta = stdout; info->flagOutDelta = 0;
+ info->fptconfigFile = NULL; info->flagconfigFile = 0;
+ info->mode = 0; info->flagmode = 0;
+}
+
+void
+init1(eosPointPositionCorrectionInfo* info)
+{
+ char s[1024];
+ int i;
+ if(!info->flagIn) {
+ stringGetFromFile(s, "In", stdin, stdout, 0);
+ info->In = stringGetNthWord(s, 1, " ,\t");
+ info->flagIn++;
+ }
+ if(info->flagIn) {
+ info->fptIn = fileOpen(info->In, "r");
+ }
+
+ if(info->flagInType) {
+ }
+
+ if(info->flagN) {
+ }
+
+ if(info->flagOut) {
+ info->fptOut = fileOpen(info->Out, "w");
+ }
+
+ if(info->flagOutType) {
+ }
+
+ if(info->flagOutDelta) {
+ info->fptOutDelta = fileOpen(info->OutDelta, "w");
+ }
+
+ if(info->flagconfigFile) {
+ info->fptconfigFile = fileOpen(info->configFile, "r");
+ }
+
+ if(info->flagmode) {
+ }
+
+}
+#ifdef KHOROS
+#include <stdio.h>
+#include "bootstrap.h"
+#include "dataserv.h"
+#include "datamanip.h"
+extern void func_usage_additions(void);
+extern void func_free_args(kexit_status status, kaddr client_data);
+extern void func_get_args(kform* pane);
+
+void
+func_usage_additions(void)
+{
+}
+void
+func_free_args(kexit_status status, kaddr client_data)
+{
+}
+void
+func_get_args(kform* pane)
+{
+}
+void
+khorosInit(int argc, char* argv[])
+{
+ char* eospath;
+ char panepath[1024];
+ FILE* fpt;
+
+ eospath = getenv("EOS_HOME");
+ sprintf(panepath, "%s/src/Tools/eosPoint/eosPointPositionCorrection/src/eosPointPositionCorrection.pane", eospath);
+ khoros_initialize(argc, argv, "EOS");
+ fpt = fopen(panepath, "r"); if(NULL!=fpt) {
+ fclose(fpt);
+ kclui_initialize(panepath, KGEN_NONE, "EOS", "eosPointPositionCorrection",
+ func_usage_additions,
+ func_get_args,
+ func_free_args);
+ }
+}
+#endif /* KHOROS */
--- /dev/null
+include ../../Config/Define.inc
+include ../../../Config/Define.inc
+include ../../../../Config/Define.inc
+include ../../../../../Config/Define.inc
+
+all: help exec
+
+help:
+ @echo "----- Help Message Check -----"
+ @../$(OSTYPE)/$(OBJECTNAME) -h
+
+exec:
+ @echo "----- Execution Check -----"
+ ../$(OSTYPE)/$(OBJECTNAME) -i data/test.in -n 3 -o data/test.out -m 0; cat data/test.out
+ ../$(OSTYPE)/$(OBJECTNAME) -i data/test1.in -n 3 -o data/test1.out -m 0; cat data/test1.out
+ ../$(OSTYPE)/$(OBJECTNAME) -i data/test2.in -n 4 -o data/test2.out -m 0; cat data/test2.out
+ ../$(OSTYPE)/$(OBJECTNAME) -i data/test.in -n 3 -o data/test-2.out -ot 2 -delta data/test.delta -m 0; cat data/test-2.out
+ ../$(OSTYPE)/$(OBJECTNAME) -i data/test1.in -n 3 -o data/test1-2.out -ot 2 -delta data/test-1.delta -m 0; cat data/test1-2.out
+ ../$(OSTYPE)/$(OBJECTNAME) -i data/test2.in -n 4 -o data/test2-2.out -ot 2 -delta data/test-2.delta -m 0; cat data/test2-2.out
+ ../$(OSTYPE)/$(OBJECTNAME) -i data/test.in -n 3 -o data/test-3.out -ot 3 -delta data/test.delta -m 0; cat data/test-3.out
+ ../$(OSTYPE)/$(OBJECTNAME) -i data/test1.in -n 3 -o data/test1-3.out -ot 3 -delta data/test-1.delta -m 0; cat data/test1-3.out
+ ../$(OSTYPE)/$(OBJECTNAME) -i data/test2.in -n 4 -o data/test2-3.out -ot 3 -delta data/test-2.delta -m 0; cat data/test2-3.out
+ @echo "----- Calc check -----"
+
+clean:
--- /dev/null
+../../../../../..//data/eosPointPositionCorrection
\ No newline at end of file
--- /dev/null
+#include <stdio.h>
+#include <stdlib.h>
+#include "../inc/config.h"
+
+void
+usage(char* thisProgram)
+{
+ fprintf(stderr, "Usage: %s\n", thisProgram);
+ fprintf(stderr, "Options:\n");
+ fprintf(stderr, " [-i[nput] In (NULL ).as(inFile::eosPoint ) ] :Essential :Input:eosPoint\n");
+ fprintf(stderr, " [-i[nput]t[ype] InType (0 ).as(Integer ) ] :Optional :Input:eosPointMode\n");
+ fprintf(stderr, " [-n[umber] N (-1 ).as(Integer ) ] :Optional :Input:number of Point, n, dependent upon m=n/(n-1)/2, a point number in In\n");
+ fprintf(stderr, " [-o[utput] Out (stdout ).as(outFile::eosPoint ) ] :Optional :Output:eosPoint\n");
+ fprintf(stderr, " [-o[utput]t[ype] OutType (0 ).as(Integer ) ] :Optional :Output:eosPoint\n");
+ fprintf(stderr, " [-delta OutDelta (stdout ).as(outFile::eosPoint ) ] :Optional :Output:eosPoint\n");
+ fprintf(stderr, " [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile\n");
+ fprintf(stderr, " [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode\n");
+ additionalUsage();
+}
+
+void
+htmlBeforeUsage(char* thisProgram)
+{
+ fprintf(stderr, "<HTML>\n");
+ fprintf(stderr, "<HEAD>\n");
+ fprintf(stderr, "<TITLE>%s</TITLE>\n", thisProgram);
+ fprintf(stderr, "</HEAD>\n");
+ fprintf(stderr, "<BODY>\n");
+ fprintf(stderr, "<H1>%s</H1>\n", thisProgram);
+ fprintf(stderr, "<H2>Usage</H2>\n");
+ fprintf(stderr, "<PRE>\n");
+}
+
+void
+htmlAfterUsage(char* thisProgram)
+{
+ fprintf(stderr, "</PRE>\n");
+ fprintf(stderr, "</BODY>\n");
+ fprintf(stderr, "</HTML>\n");
+}
--- /dev/null
+#include <stdio.h>
+#include <stdlib.h>
+#include "../inc/config.h"
+
-/bin/bash: eosPointProjector: No such file or directory
+/bin/bash: eosPointProjector: そのようなファイルやディレクトリはありません
-/bin/bash: eosPointRotation: No such file or directory
+/bin/bash: eosPointRotation: そのようなファイルやディレクトリはありません
mrc2bild \
mrc2fld \
mrc2gif \
+mrc2hdf \
mrc2lattice \
mrc2mrc \
mrc2png \
--- /dev/null
+include ../../Config/Define.inc
+include ../../../Config/Define.inc
+include ../../../../Config/Define.inc
+include ../../../../../Config/Define.inc
+
+all: help exec
+
+help:
+ @echo "----- Help Message Check -----"
+ @../$(OSTYPE)/$(OBJECTNAME) -h
+
+exec:
+ @echo "----- Execution Check -----"
+ ../$(OSTYPE)/$(OBJECTNAME)
+ @echo "----- Calc check -----"
+
+clean:
--- /dev/null
+../../../../../..//data/bin2mrc
\ No newline at end of file
-/bin/bash: moi2mrc: No such file or directory
+/bin/bash: moi2mrc: そのようなファイルやディレクトリはありません
-<HTML>
-<HEAD>
-<TITLE>mrc2gif</TITLE>
-</HEAD>
-<BODY>
-<H1>mrc2gif</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrc2gif
-Options:
- [-i[nput] inFile (NULL ).as(inFile ) ] :Essential :InputDataFile
- [-o[utput] outFile (NULL ).as(outFile ) ] :Essential :OutputDataFile
- [-H[igh] High (0 ).as(Real ) ] :Optional :HighThreshold
- [-L[ow] Low (0 ).as(Real ) ] :Optional :LowThreshold
- [-I[nverse] ] :Optional :Inverse(Black is white)
- [-z[Section] Z (0 ).as(Integer ) ] :Optional :z-section
- [-e[xtention] format (%s.%04d ).as(String ) ] :Optional :SerialSection Format
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode:
- 0 (8bits), 1(16bits)
-
--z
- -1: Serial Files
- z(>0): Section at z
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrc2gif: そのようなファイルやディレクトリはありません
OBJECTNAME = mrc2hdf
-EXTRA_LIB =
+EXTRA_LIB = -lhdf5
EXTRA_CCOPTS =
EXTRA_INC =
# OptionControlFile
# FileFormat
-"-i","-i[nput]","InputDataFile","Essential","1","1","In","inFile","NULL"
+"-i","-i[nput]","Input","Optional","1","1","In","inFile::mrcInfo","NULL"
+"-I","-I[nput]","Input:FileList","Optional","1","1","InList","inFileList::mrcInfo","NULL"
"-o","-o[utput]","OutputDataFile","Essential","1","1","Out","outFile","NULL"
"-c","-c[onfig]","ConfigurationFile","Optional","1","1","configFile","inFile","NULL"
+"-nres","-nres[olution]","Pyramidal Resolution","Optional","1","1","nResolution","Integer","1"
+"-M","-M[ode]","Mode:0 hdf5 1 imaris","Optional","1","1","hdf5mode","Integer","1"
"-m","-m[ode]","Mode","Optional","1","1","mode","Integer","0"
char* In;
FILE* fptIn;
+ long flagInList;
+ char** InList;
+ char* InListList;
+ FILE** fptInList;
+ FILE* fptInListList;
+
long flagOut;
char* Out;
FILE* fptOut;
char* configFile;
FILE* fptconfigFile;
+ long flagnResolution;
+ long nResolution;
+
+ long flaghdf5mode;
+ long hdf5mode;
+
long flagmode;
long mode;
--- /dev/null
+../../../../../hostdepend/X86LINUX64/src/Tools/filter/mrc2hdf/src/X86LINUX64
\ No newline at end of file
}
SBREAK;
}
+ SCASE("I") {
+ if(i+1<argc) {
+ info->InListList = stringGetNthWord(argv[i+1], 1, " ,");
+ i++;
+ info->flagInList++;
+ } else {
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ }
+ SBREAK;
+ }
SCASE("o") {
if(i+1<argc) {
info->Out = stringGetNthWord(argv[i+1], 1, " ,");
}
SBREAK;
}
+ SCASE("nres") {
+ if(i+1<argc) {
+ info->nResolution = stringGetNthIntegerData(argv[i+1], 1, " ,");
+ i++;
+ info->flagnResolution++;
+ } else {
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ }
+ SBREAK;
+ }
+ SCASE("M") {
+ if(i+1<argc) {
+ info->hdf5mode = stringGetNthIntegerData(argv[i+1], 1, " ,");
+ i++;
+ info->flaghdf5mode++;
+ } else {
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ }
+ SBREAK;
+ }
SCASE("m") {
if(i+1<argc) {
info->mode = stringGetNthIntegerData(argv[i+1], 1, " ,");
init0(mrc2hdfInfo* info)
{
info->fptIn = NULL; info->flagIn = 0;
+ info->fptInList = NULL; info->fptInListList = NULL; info->flagInList = 0;
info->fptOut = NULL; info->flagOut = 0;
info->fptconfigFile = NULL; info->flagconfigFile = 0;
+ info->nResolution = 1; info->flagnResolution = 0;
+ info->hdf5mode = 1; info->flaghdf5mode = 0;
info->mode = 0; info->flagmode = 0;
}
{
char s[1024];
int i;
- if(!info->flagIn) {
- stringGetFromFile(s, "In", stdin, stdout, 0);
- info->In = stringGetNthWord(s, 1, " ,\t");
- info->flagIn++;
- }
if(info->flagIn) {
info->fptIn = fileOpen(info->In, "r");
}
+ if(info->flagInList) {
+ info->fptInListList = fileOpen(info->InListList, "r");
+ fseek(info->fptInListList, 0L, SEEK_SET);
+ i=0;
+ while(NULL!=stringGetFromFile(s, "", info->fptInListList, stdout, 1)) {
+ i++;
+ }
+ info->fptInList = (FILE**)memoryAllocate(i*sizeof(FILE*), "in init1");
+ info->InList = (char**)memoryAllocate(i*sizeof(char*), "in init1");
+ info->flagInList = i;
+ fseek(info->fptInListList, 0L, SEEK_SET);
+ i=0;
+ while(NULL!=stringGetFromFile(s, "", info->fptInListList, stdout, 1)) {
+ info->InList[i] = stringGetNthWord(s, 1, " ,\t");
+ info->fptInList[i] = fileOpen(info->InList[i],"r");
+ i++;
+ }
+ }
+
if(!info->flagOut) {
stringGetFromFile(s, "Out", stdin, stdout, 0);
info->Out = stringGetNthWord(s, 1, " ,\t");
info->fptconfigFile = fileOpen(info->configFile, "r");
}
+ if(info->flagnResolution) {
+ }
+
+ if(info->flaghdf5mode) {
+ }
+
if(info->flagmode) {
}
#include <stdlib.h>
#include <string.h>
#include <math.h>
+#include <float.h>
#define GLOBAL_DECLARATION
#include "../inc/config.h"
#define DEBUG
#include "genUtil.h"
+#include "Memory.h"
#include "mrcImage.h"
-#include "hdf5.h"
+#include "lmrcImageProjection.h"
+#include <hdf5.h>
-/*
-Example:
typedef struct lmrc2hdfInfo {
- float a;
- int b;
+ int numFile;
+ int nResolution;
} lmrc2hdfInfo;
typedef enum lmrc2hdfMode {
a=0,
b=1
} lmrc2hdfMode;
-*/
+
+extern int lmrc2hdfimaris(hid_t* out, mrcImage* in, lmrc2hdfInfo* linfo, int mode);
+extern int lmrc2hdf(hid_t* out, mrcImage* in, lmrc2hdfInfo* linfo, int mode);
int
main(int argc, char* argv[])
{
mrc2hdfInfo info;
+ lmrc2hdfInfo linfo;
+ mrcImage* in;
+
+ hid_t out;
+ herr_t status;
+
+ int i;
init0(&info);
argCheck(&info, argc, argv);
init1(&info);
DEBUGPRINT("Program Start\n");
+ if(info.flagIn) {
+ linfo.numFile = 1;
+ in = (mrcImage*)memoryAllocate(sizeof(mrcImage), "in main");
+ mrcFileRead(in, info.In, "in main", 0);
+ } else if(info.flagInList) {
+ linfo.numFile = info.flagInList;
+ in = (mrcImage*)memoryAllocate(sizeof(mrcImage)*linfo.numFile, "in main");
+ for(i=0; i<linfo.numFile; i++) {
+ mrcFileRead(&(in[i]), info.InList[i], "in main", 0);
+ }
+ } else {
+ fprintf(stderr, "-i or -I is necessary\n");
+ usage(argv[0]);
+ }
+ linfo.nResolution = info.nResolution;
+ //out = H5Fopen(info.Out, H5F_ACC_TRUNC, H5P_DEFAULT);
+ out = H5Fcreate(info.Out, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+ if(out<0) {
+ fprintf(stderr, "Not openend:%s\n", info.Out);
+ exit(EXIT_FAILURE);
+ }
+
+ switch(info.hdf5mode) {
+ case 0: {
+ lmrc2hdf(&out, in, &linfo, info.mode);
+ break;
+ }
+ case 1: {
+ lmrc2hdfimaris(&out, in, &linfo, info.mode);
+ break;
+ }
+ default: {
+ fprintf(stderr, "not supported hdf5mode: %ld\n", info.hdf5mode);
+ usage(argv[0]);
+ exit(EXIT_FAILURE);
+ }
+ }
+ status = H5Fclose(out);
exit(EXIT_SUCCESS);
}
{
fprintf(stderr, "----- Additional Usage -----\n");
}
+
+
+int
+lhdfAttributeString(hid_t gIDChannel, char tag[], char* stmp)
+{
+ hsize_t sdim;
+ hid_t attrspaceID, attrID;
+ hid_t stringType;
+ herr_t status;
+
+ sdim = strlen(stmp);
+ attrspaceID = H5Screate_simple(1, &sdim, NULL);
+ stringType = H5Tcopy(H5T_C_S1);
+ status = H5Tset_size(stringType, 1);
+ status = H5Tset_strpad(stringType, H5T_STR_NULLTERM);
+ DEBUGPRINT3("space: %lld type: %lld status: %d \n", attrspaceID, stringType, status);
+ attrID = H5Acreate(gIDChannel, tag, stringType, attrspaceID, H5P_DEFAULT, H5P_DEFAULT);
+ DEBUGPRINT1("attrID: %lld\n", attrID);
+ status = H5Awrite(attrID, stringType, stmp);
+ status = H5Aclose(attrID);
+ status = H5Sclose(attrspaceID);
+
+ return status;
+}
+
+int
+lhdfAttributeUInt32(hid_t gIDChannel, char tag[], uint32_t* i, hsize_t num)
+{
+ hid_t attrspaceID, attrID;
+ herr_t status;
+
+ attrspaceID = H5Screate_simple(1, &num, NULL);
+ attrID = H5Acreate(gIDChannel, tag, H5T_STD_U32LE, attrspaceID, H5P_DEFAULT, H5P_DEFAULT);
+ status = H5Awrite(attrID, H5T_STD_U32LE, i);
+ status = H5Aclose(attrID);
+ status = H5Sclose(attrspaceID);
+
+ return status;
+}
+
+int
+lhdfAttributeInt2String(hid_t gIDChannel, char tag[], hsize_t i)
+{
+ char stmp[1024];
+ hsize_t sdim;
+ hid_t attrspaceID, attrID;
+ hid_t stringType;
+ herr_t status;
+
+ sprintf(stmp, "%lld", i);
+ sdim = strlen(stmp);
+ attrspaceID = H5Screate_simple(1, &sdim, NULL);
+ stringType = H5Tcopy(H5T_C_S1);
+ status = H5Tset_size(stringType, 1);
+ status = H5Tset_strpad(stringType, H5T_STR_NULLTERM);
+ DEBUGPRINT3("space: %lld type: %lld status: %d \n", attrspaceID, stringType, status);
+ attrID = H5Acreate(gIDChannel, tag, stringType, attrspaceID, H5P_DEFAULT, H5P_DEFAULT);
+ DEBUGPRINT1("attrID: %lld\n", attrID);
+ status = H5Awrite(attrID, stringType, stmp);
+ status = H5Aclose(attrID);
+ status = H5Sclose(attrspaceID);
+
+ return status;
+}
+
+int
+lhdfAttributeReal2String(hid_t gIDChannel, char tag[], double f)
+{
+ char stmp[1024];
+ hsize_t sdim;
+ hid_t attrspaceID, attrID;
+ hid_t stringType;
+ herr_t status;
+
+ sprintf(stmp, "%lf", f);
+ sdim = strlen(stmp);
+ attrspaceID = H5Screate_simple(1, &sdim, NULL);
+ stringType = H5Tcopy(H5T_C_S1);
+ status = H5Tset_size(stringType, 1);
+ status = H5Tset_strpad(stringType, H5T_STR_NULLTERM);
+ DEBUGPRINT3("space: %lld type: %lld status: %d \n", attrspaceID, stringType, status);
+ attrID = H5Acreate(gIDChannel, tag, stringType, attrspaceID, H5P_DEFAULT, H5P_DEFAULT);
+ DEBUGPRINT1("attrID: %lld\n", attrID);
+ status = H5Awrite(attrID, stringType, stmp);
+ status = H5Aclose(attrID);
+ status = H5Sclose(attrspaceID);
+
+ return status;
+}
+
+int
+lmrc2hdfimaris(hid_t* out, mrcImage* in, lmrc2hdfInfo* linfo, int mode)
+{
+ // String for tags
+ static hsize_t sdim=1024;
+ char tmp[sdim];
+ char stmp[sdim];
+ // Histogram
+ static hsize_t nHist1024=1024;
+ static hsize_t nHist=256;
+ hsize_t iLevel;
+ uint64_t hist1024[nHist1024];
+ uint64_t hist[nHist];
+
+ // image
+ double data;
+ float* image;
+
+ hsize_t dims[4];
+ hsize_t chunk[4];
+
+ // for hdf5
+ herr_t status;
+ hid_t datasetID;
+ hid_t datasetID2;
+ hid_t dataspaceID;
+ hid_t dataspaceID2;
+ hid_t datasetPropertyID;
+ hid_t dset;
+ static uint32_t numOfDataSets = 1;
+
+ int nGroup=4;
+ hid_t groupID[4];
+ char* groupName[] = {"/DataSet", "/DataSetInfo", "/DataSetTimes", "/Thumbnail"};
+ int val;
+ int i, ires, itime, ichannel;
+ uint64_t i64;
+ int nres, ntime, nchannel;
+ hid_t dsetID, dspaceID, gIDRes, gIDTime, gIDChannel, attrID, attrspaceID, stringType;
+ mrcImageParaTypeReal x, y, z;
+ mrcImageParaTypeReal xorg, yorg, zorg;
+ int irange, numrange;
+ unsigned char* thumbImage;
+ double sum, min, max;
+ mrcImage tmpImage;
+ lmrcImageProjectionInfo lpro;
+
+ DEBUGPRINT("Start lmrc2hdfimaris\n");
+ // Top Level Attribute
+ lhdfAttributeString(*out, "DataSetDirectoryName", "DataSet");
+ lhdfAttributeString(*out, "DataSetInfoDirectoryName", "DataSetInfo");
+ lhdfAttributeString(*out, "ImarisDataSet", "ImarisDataSet");
+ lhdfAttributeString(*out, "ImarisVersion", "5.5.0");
+ lhdfAttributeUInt32(*out, "NumberOfDataSets", &numOfDataSets, 1);
+ lhdfAttributeString(*out, "ThumbnailDirectoryName", "Thumbnail");
+
+ // Top Level Groups
+ for(i=0; i<nGroup; i++) {
+ DEBUGPRINT2("Group: %s %d\n", groupName[i], i);
+ groupID[i] = H5Gcreate2(*out, groupName[i], H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ if(groupID[i]<0) {
+ fprintf(stderr, "Not create Group: %s\n", groupName[i]);
+ exit(EXIT_FAILURE);
+ } else {
+ DEBUGPRINT1("Success: %d\n", i);
+ }
+ }
+
+ // DataSet/.../Data
+ dims[0] = in[0].HeaderN.z;
+ dims[1] = in[0].HeaderN.y;
+ dims[2] = in[0].HeaderN.x;
+
+ chunk[0] = dims[0];
+ chunk[1] = dims[1];
+ chunk[2] = dims[2];
+
+ datasetPropertyID = H5Pcreate(H5P_DATASET_CREATE);
+ status = H5Pset_chunk(datasetPropertyID, 3, chunk);
+
+ val = 3;
+ status = H5Pset_fill_value(datasetPropertyID, H5T_NATIVE_INT, &val);
+ status = H5Pset_alloc_time(datasetPropertyID, H5D_ALLOC_TIME_EARLY);
+ status = H5Pclose(datasetPropertyID);
+
+ // DataSet
+ nres = linfo->nResolution;
+ ntime = linfo->numFile;
+ nchannel = 1;
+ // ResolutionLevel
+ for(ires=0; ires<nres; ires++) {
+ sprintf(tmp, "%s/%s %d", groupName[0], "ResolutionLevel", ires);
+ gIDRes = H5Gcreate2(groupID[0], tmp, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ DEBUGPRINT1("%s\n", tmp);
+ for(itime=0; itime<ntime; itime++) {
+ sprintf(tmp, "%s/%s %d/%s %d", groupName[0], "ResolutionLevel", ires, "TimePoint", itime);
+ gIDTime = H5Gcreate2(gIDRes, tmp, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ DEBUGPRINT1("%s\n", tmp);
+ for(ichannel=0; ichannel<nchannel; ichannel++) {
+ sprintf(tmp, "%s/%s %d/%s %d/%s %d", groupName[0], "ResolutionLevel", ires, "TimePoint", itime, "Channel", ichannel);
+ gIDChannel = H5Gcreate2(gIDTime, tmp, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ DEBUGPRINT1("%s\n", tmp);
+ // Channel Attribute
+ lhdfAttributeInt2String(gIDChannel, "ImageSizeX", dims[2]);
+ lhdfAttributeInt2String(gIDChannel, "ImageSizeY", dims[1]);
+ lhdfAttributeInt2String(gIDChannel, "ImageSizeZ", dims[0]);
+
+ // TimePoint
+ dspaceID = H5Screate_simple(3, dims, NULL);
+ sprintf(tmp, "%s/%s %d/%s %d/%s %d/%s", groupName[0], "ResolutionLevel", ires, "TimePoint", itime, "Channel", ichannel, "Data");
+ DEBUGPRINT1("%s\n", tmp);
+ DEBUGPRINT1("mode: %d\n", in[ichannel].HeaderMode);
+ image = (float*)memoryAllocate(sizeof(float)*dims[0]*dims[1]*dims[2], "in lmrc2hdfimars");
+
+ for(i=0; i<256; i++) hist[i] = 0;
+ for(i=0; i<1024; i++) hist1024[i] = 0;
+ DEBUGPRINT("image\n");
+ if(in[itime].HeaderAMax<=in[itime].HeaderAMin) {
+ fprintf(stderr, "Image data is flat\n");
+ for(i=0; i<dims[0]*dims[1]*dims[2]; i++) {
+ image[i] = in[itime].HeaderAMin;
+ hist[0]++;
+ hist1024[0]++;
+ }
+ } else {
+ irange=1<<ires;
+ DEBUGPRINT2("res: %d irange %d\n", ires, irange);
+ for(z=0; z<dims[0]; z++) {
+ if(0==(((int)(z/dims[0]*100))%10)) {
+ DEBUGPRINT2("%d/%llu\n", (int)z, dims[0]);
+ }
+ for(y=0; y<dims[1]; y++) {
+ for(x=0; x<dims[2]; x++) {
+ i64 = (double)x + (double)y*(double)dims[2] + (double)z*(double)dims[2]*(double)dims[1];
+ if(dims[0]*dims[1]*dims[2]<=i64) {
+ DEBUGPRINT1("%f \n", x + (double)y*(double)dims[2] + (double)z*(double)dims[2]*(double)dims[1]);
+ DEBUGPRINT4("%lld %f %f %f\n", i64, x, y, z);
+ DEBUGPRINT4("%lld %lld %lld %lld\n", dims[0]*dims[1]*dims[2], dims[2], dims[1], dims[0]);
+ }
+ sum = numrange = 0;
+ for(zorg=z*irange;zorg<(z+1)*irange; zorg++) {
+ for(yorg=y*irange;yorg<(y+1)*irange; yorg++) {
+ for(xorg=x*irange;xorg<(x+1)*irange; xorg++) {
+ numrange++;
+ mrcPixelDataGet(&(in[itime]), xorg, yorg, zorg, &data, mrcPixelRePart, mrcPixelHowNearest);
+ sum+=data;
+ }
+ }
+ }
+ if(0<numrange) {
+ data = sum/numrange;
+#undef DEBUG2
+#ifdef DEBUG2
+ if(0<data) {
+ DEBUGPRINT4("%llu %f = %f / %d\n", i64, data, sum, numrange);
+ }
+#endif
+#undef DEBUG2
+ } else {
+ //DEBUGPRINT("numrange is zero: Something wrong\n");
+ data = 0;
+ }
+ image[i64] = (float)data;
+ }
+ }
+ }
+
+ DEBUGPRINT("MIN/MAX\n");
+ min= max = image[0];
+ for(i64=1; i64<dims[2]*dims[1]*dims[0]; i64++) {
+ if(image[i64]<min) min = image[i64];
+ if(max<image[i64]) max = image[i64];
+ }
+ DEBUGPRINT2("%f/%f\n", min, max);
+ DEBUGPRINT("HISTGRAM\n");
+ for(i64=1; i64<dims[2]*dims[1]*dims[0]; i64++) {
+ data = image[i64];
+ iLevel = MAX(0,MIN(1023,(int)((data-min)/(max-min)*1023+0.5)));
+ hist1024[iLevel]++;
+ iLevel = MAX(0,MIN( 255,(int)((data-min)/(max-min)* 255+0.5)));
+ hist[iLevel]++;
+ }
+ }
+ DEBUGPRINT("H5Dcreate");
+ dsetID = H5Dcreate(gIDChannel, tmp, H5T_IEEE_F32LE, dspaceID, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ status = H5Dwrite(dsetID, H5T_IEEE_F32LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, image);
+ DEBUGPRINT3("%s End: dataset %lld status %d\n", tmp, dsetID, status);
+ status = H5Dclose(dsetID);
+ status = H5Sclose(dspaceID);
+ // Histogram
+ lhdfAttributeInt2String(gIDChannel, "HistogramMax", max);
+ lhdfAttributeInt2String(gIDChannel, "HistogramMin", min);
+ lhdfAttributeInt2String(gIDChannel, "HistogramMax1024", max);
+ lhdfAttributeInt2String(gIDChannel, "HistogramMin1024", min);
+
+ // Histogram
+ dspaceID = H5Screate_simple(1, &nHist, NULL);
+ sprintf(tmp, "%s/%s %d/%s %d/%s %d/%s", groupName[0], "ResolutionLevel", ires, "TimePoint", itime, "Channel", ichannel, "Histogram");
+ dsetID = H5Dcreate(gIDChannel, tmp, H5T_STD_U64LE, dspaceID, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ status = H5Dwrite(dsetID, H5T_STD_U64LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, hist);
+ status = H5Dclose(dsetID);
+ status = H5Sclose(dspaceID);
+
+ // Histogram1024
+ dspaceID = H5Screate_simple(1, &nHist1024, NULL);
+ sprintf(tmp, "%s/%s %d/%s %d/%s %d/%s", groupName[0], "ResolutionLevel", ires, "TimePoint", itime, "Channel", ichannel, "Histogram1024");
+ dsetID = H5Dcreate(gIDChannel, tmp, H5T_STD_U64LE, dspaceID, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ status = H5Dwrite(dsetID, H5T_STD_U64LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, hist1024);
+ status = H5Dclose(dsetID);
+ status = H5Sclose(dspaceID);
+
+ // Group Close
+ status = H5Gclose(gIDChannel);
+ }
+ status = H5Gclose(gIDTime);
+ }
+ //memoryFree(image);
+ dims[0]/=2;
+ dims[1]/=2;
+ dims[2]/=2;
+ status = H5Gclose(gIDRes);
+ }
+ DEBUGPRINT("DataSetInfo\n");
+ {
+ char* dsiGroupName[] = {"Channel 0", "Image", "Imaris", "ImarisDataSet", "Log", "TImeInfo"};
+ int dsiNGroup = 6;
+ hid_t dsiGroupID[dsiNGroup];
+
+ for(i=0; i<dsiNGroup; i++) {
+ sprintf(stmp, "%s/%s", groupName[1], dsiGroupName[i]);
+ dsiGroupID[i] = H5Gcreate2(*out, stmp, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ }
+ // Channel 0
+ lhdfAttributeString(dsiGroupID[0], "Name", "No");
+ lhdfAttributeString(dsiGroupID[0], "Color", "1 0 0");
+ lhdfAttributeString(dsiGroupID[0], "ColorMode", "BaseColor");
+ lhdfAttributeReal2String(dsiGroupID[0], "ColorOpacity", 1.00);
+ lhdfAttributeReal2String(dsiGroupID[0], "Min", in[0].HeaderAMax);
+ lhdfAttributeReal2String(dsiGroupID[0], "Max", in[0].HeaderAMin);
+ // Image
+ lhdfAttributeString(dsiGroupID[1], "Description", "No");
+ lhdfAttributeString(dsiGroupID[1], "Name", "No");
+ lhdfAttributeInt2String(dsiGroupID[1], "Noc", 1);
+ lhdfAttributeReal2String(dsiGroupID[1], "ExtMin0", in[0].HeaderStartN.x*in[0].HeaderLength.x);
+ lhdfAttributeReal2String(dsiGroupID[1], "ExtMin1", in[0].HeaderStartN.y*in[0].HeaderLength.y);
+ lhdfAttributeReal2String(dsiGroupID[1], "ExtMin2", in[0].HeaderStartN.z*in[0].HeaderLength.z);
+ lhdfAttributeReal2String(dsiGroupID[1], "ExtMax0", (in[0].HeaderStartN.x+dims[2]-1)*in[0].HeaderLength.x);
+ lhdfAttributeReal2String(dsiGroupID[1], "ExtMax1", (in[0].HeaderStartN.y+dims[1]-1)*in[0].HeaderLength.y);
+ lhdfAttributeReal2String(dsiGroupID[1], "ExtMax2", (in[0].HeaderStartN.z+dims[0]-1)*in[0].HeaderLength.z);
+ lhdfAttributeString(dsiGroupID[1], "Unit", "um");
+ lhdfAttributeInt2String(dsiGroupID[1], "X", dims[2]);
+ lhdfAttributeInt2String(dsiGroupID[1], "Y", dims[1]);
+ lhdfAttributeInt2String(dsiGroupID[1], "Z", dims[0]);
+ // Imaris
+ lhdfAttributeString(dsiGroupID[2], "Version", "5,5");
+ // ImarisDataSet
+ lhdfAttributeString(dsiGroupID[3], "Creator", "lmrc2hdf5imaris");
+ lhdfAttributeString(dsiGroupID[3], "NumberOfImages", "1");
+ lhdfAttributeString(dsiGroupID[3], "Version", "1.0");
+
+ for(i=dsiNGroup-1; i>=0; i--) {
+ status = H5Gclose(dsiGroupID[i]);
+ }
+
+ }
+ DEBUGPRINT("DataSetTimes\n");
+ DEBUGPRINT("Thumbnail\n");
+ // Thumbnail
+ sprintf(tmp, "%s/%s", groupName[3], "Data");
+ thumbImage = (unsigned char*) memoryAllocate(sizeof(unsigned char)*dims[0]*dims[1], "in imaris");
+ lpro.mode = 0;
+ lmrcImageProjection(&tmpImage, &in[0], &lpro);
+
+ min = FLT_MAX;
+ max = FLT_MIN;
+ for(x=0; x<dims[2]; x++) {
+ for(y=0; y<dims[1]; y++) {
+ mrcPixelDataGet(&tmpImage, x, y, 0, &data, mrcPixelRePart, mrcPixelHowNearest);
+ if(data<min) min = data;
+ if(max<data) max = data;
+ }
+ }
+ DEBUGPRINT1("min: %f\n", min);
+ DEBUGPRINT1("max: %f\n", max);
+ for(x=0; x<dims[2]; x++) {
+ for(y=0; y<dims[1]; y++) {
+ mrcPixelDataGet(&tmpImage, x, y, 0, &data, mrcPixelRePart, mrcPixelHowNearest);
+ if(max<=min) {
+ thumbImage[(int)(x+y*dims[2])] = 0;
+ } else {
+ thumbImage[(int)(x+y*dims[2])] = (int)(255*((data-min)/(max-min)-0.5));
+ }
+ }
+ }
+
+ dspaceID = H5Screate_simple(2, &(dims[1]), NULL);
+ sprintf(tmp, "%s/%s", groupName[3], "Data");
+ dsetID = H5Dcreate2(groupID[3], tmp, H5T_STD_U8LE, dspaceID, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ status = H5Dwrite(dsetID, H5T_NATIVE_CHAR, H5S_ALL, H5S_ALL, H5P_DEFAULT, thumbImage);
+ mrcImageFree(&tmpImage, "in lmrc2hdfimaris");
+
+ status = H5Dclose(dsetID);
+ status = H5Sclose(dspaceID);
+
+ for(i=nGroup-1; i>=0; i--) {
+ status = H5Gclose(groupID[i]);
+ }
+
+ return 0;
+}
+int
+lmrc2hdf(hid_t* out, mrcImage* in, lmrc2hdfInfo* linfo, int mode)
+{
+ char tmp[1024];
+ hsize_t dims[4];
+ hsize_t chunk[4];
+ herr_t status;
+ hid_t datasetID;
+ hid_t datasetID2;
+ hid_t dataspaceID;
+ hid_t dataspaceID2;
+ hid_t datasetPropertyID;
+ hid_t dset;
+ hid_t nGroup=4;
+ hid_t groupID[4];
+ char* groupName[] = {"/DataSet", "/DataSet/ResolutionLevel 0", "/DataSet/ResolutionLevel 0/TimePoint 0", "/DataSet/ResolutionLevel 0/TimePoint 0/Channel 0"};
+ //char* groupName[] = {"/DataSet"};
+ int val;
+ int i;
+
+ nGroup = 1;
+ for(i=0; i<nGroup; i++) {
+ DEBUGPRINT1("Group: %s\n", groupName[i]);
+ groupID[i] = H5Gcreate2(*out, groupName[i], H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ if(groupID[i]<0) {
+ fprintf(stderr, "Not create Group: %s\n", groupName[i]);
+ exit(EXIT_FAILURE);
+ } else {
+ DEBUGPRINT("Success\n");
+ }
+ }
+
+ dims[0] = in->HeaderN.x;
+ dims[1] = in->HeaderN.y;
+ dims[2] = in->HeaderN.z;
+ dims[3] = linfo->numFile;
+
+ chunk[0] = dims[0];
+ chunk[1] = dims[1];
+ chunk[2] = dims[2];
+ chunk[3] = dims[3];
+
+ datasetPropertyID = H5Pcreate(H5P_DATASET_CREATE);
+ status = H5Pset_chunk(datasetPropertyID, 4, chunk);
+
+ val = 4;
+ status = H5Pset_fill_value(datasetPropertyID, H5T_NATIVE_INT, &val);
+ status = H5Pset_alloc_time(datasetPropertyID, H5D_ALLOC_TIME_EARLY);
+
+ dataspaceID2 = H5Screate_simple(4, dims, NULL);
+ //datasetID2 = H5Dcreate(*out, "/prop", H5T_STD_I32LE, dataspaceID2, H5P_DEFAULT, datasetPropertyID, H5P_DEFAULT);
+ i=0;
+ sprintf(tmp, "%s/%s", groupName[i], "Data");
+ datasetID2 = H5Dcreate2(groupID[i], tmp, H5T_STD_I32LE, dataspaceID2, H5P_DEFAULT, datasetPropertyID, H5P_DEFAULT);
+ status = H5Pclose(datasetPropertyID);
+ status = H5Dclose(datasetID2);
+ status = H5Sclose(dataspaceID2);
+
+
+ dataspaceID = H5Screate_simple(4, dims, NULL);
+ switch(in->HeaderMode) {
+ case mrcCharImage:
+ datasetID = H5Dcreate(*out, "/mrc", H5T_STD_U8LE, dataspaceID, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ status = H5Dwrite(datasetID, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, in->Image);
+ break;
+ case mrcShortImage:
+ datasetID = H5Dcreate(*out, "/mrc", H5T_STD_I16LE, dataspaceID, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ status = H5Dwrite(datasetID, H5T_NATIVE_SHORT, H5S_ALL, H5S_ALL, H5P_DEFAULT, in->Image);
+ break;
+ case mrcUShortImage:
+ datasetID = H5Dcreate(*out, "/mrc", H5T_STD_U16LE, dataspaceID, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ status = H5Dwrite(datasetID, H5T_NATIVE_USHORT, H5S_ALL, H5S_ALL, H5P_DEFAULT, in->Image);
+ break;
+ case mrcFloatImage:
+ datasetID = H5Dcreate(*out, "/mrc", H5T_IEEE_F32LE, dataspaceID, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ status = H5Dwrite(datasetID, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT, in->Image);
+ break;
+ default:
+ fprintf(stderr, "Not supported: %d\n", in->HeaderMode);
+ exit(EXIT_FAILURE);
+ break;
+ }
+
+ status = H5Dclose(datasetID);
+ status = H5Sclose(dataspaceID);
+
+ for(i=nGroup-1; i>=0; i--) {
+ status = H5Gclose(groupID[i]);
+ }
+
+ return 0;
+}
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>mrc2hdf</TITLE>
+</HEAD>
+<BODY>
+<H1>mrc2hdf</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrc2hdf
+Options:
+ [-i[nput] In (NULL ).as(inFile::mrcInfo ) ] :Optional :Input
+ [-I[nput] InList (NULL ).as(inFileList::mrcInfo ) ] :Optional :Input:FileList
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-nres[olution] nResolution (1 ).as(Integer ) ] :Optional :Pyramidal Resolution
+ [-M[ode] hdf5mode (1 ).as(Integer ) ] :Optional :Mode:0 hdf5 1 imaris
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-R 1 0 1 5x1+35+0 'Run' 'execute operation' $EOS/bin/mrc2hdf
-H 1 5x1+41+0 'Help' 'help page' $EOS/src/Tools/filter/mrc2hdf/doc/mrc2hdf.doc help
-Q 1 0 5.25x1+47+0 'Close'
- -I 1 0 1 1 0 1 -1x1+1+1.500000 ' ' 'In' 'InputDataFile' i
- -O 1 0 1 1 0 1 -1x1+1+3.000000 ' ' 'Out' 'OutputDataFile' o
- -I 1 0 1 0 0 1 -1x1+1+4.500000 ' ' 'configFile' 'ConfigurationFile' c
- -i 1 0 1 0 0 -1x1+1+6.000000 0 0 0 0 0 'mode' 'Mode' m
+ -I 1 0 1 0 0 1 -1x1+1+1.500000 ' ' 'In' 'Input' i
+ -I 1 0 1 0 0 1 -1x1+1+3.000000 ' ' 'InList' 'Input:FileList' I
+ -O 1 0 1 1 0 1 -1x1+1+4.500000 ' ' 'Out' 'OutputDataFile' o
+ -I 1 0 1 0 0 1 -1x1+1+6.000000 ' ' 'configFile' 'ConfigurationFile' c
+ -i 1 0 1 0 0 -1x1+1+7.500000 0 0 1 0 0 'nResolution' 'Pyramidal Resolution' nres
+ -i 1 0 1 0 0 -1x1+1+9.000000 0 0 1 0 0 'hdf5mode' 'Mode:0 hdf5 1 imaris' M
+ -i 1 0 1 0 0 -1x1+1+10.500000 0 0 0 0 0 'mode' 'Mode' m
-E
-E
-E
--- /dev/null
+include ../../Config/Define.inc
+include ../../../Config/Define.inc
+include ../../../../Config/Define.inc
+include ../../../../../Config/Define.inc
+
+all: help exec
+
+help:
+ @echo "----- Help Message Check -----"
+ @../$(OSTYPE)/$(OBJECTNAME) -h
+
+exec:
+ @echo "----- Execution Check -----"
+ rm -rf data/test.ims data/test2.ims
+ ../$(OSTYPE)/$(OBJECTNAME) -i data/test.mrc -o data/test.ims
+ ../$(OSTYPE)/$(OBJECTNAME) -i data/test.mrc -o data/test-4.ims -nres 4
+ ../$(OSTYPE)/$(OBJECTNAME) -I data/test.lst -o data/test2.ims
+ @echo "----- Calc check -----"
+
+clean:
--- /dev/null
+../../../../../..//data/mrc2hdf
\ No newline at end of file
{
fprintf(stderr, "Usage: %s\n", thisProgram);
fprintf(stderr, "Options:\n");
- fprintf(stderr, " [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile\n");
+ fprintf(stderr, " [-i[nput] In (NULL ).as(inFile::mrcInfo ) ] :Optional :Input\n");
+ fprintf(stderr, " [-I[nput] InList (NULL ).as(inFileList::mrcInfo ) ] :Optional :Input:FileList\n");
fprintf(stderr, " [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile\n");
fprintf(stderr, " [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile\n");
+ fprintf(stderr, " [-nres[olution] nResolution (1 ).as(Integer ) ] :Optional :Pyramidal Resolution\n");
+ fprintf(stderr, " [-M[ode] hdf5mode (1 ).as(Integer ) ] :Optional :Mode:0 hdf5 1 imaris\n");
fprintf(stderr, " [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode\n");
additionalUsage();
}
-/bin/bash: mrc2lattice: No such file or directory
+/bin/bash: mrc2lattice: そのようなファイルやディレクトリはありません
-/bin/bash: mrc2pov: No such file or directory
+/bin/bash: mrc2pov: そのようなファイルやディレクトリはありません
-/bin/bash: mrc2viff: No such file or directory
+/bin/bash: mrc2viff: そのようなファイルやディレクトリはありません
switch(unit) {
case RESUNIT_NONE: {
//strUnit = stringGetDefinedValue(s, "unit", "="));
- if(strUnit[0]!=NULL) {
+ if(strUnit[0]!='\0') {
if(strncmp(strUnit,"micron",6)==0) {
unitAng= 1e4;
} else {
if(linfo->flagOffset) {
data += linfo->Offset;
}
- mrcPixelDataSet(mrc, col, (float)(h - 1 - row), linfo->currentz, data, mrcPixelMag);
+ mrcPixelDataSet(mrc, col, (float)(h - 1 - row), linfo->currentz, data, mrcPixelRePart);
}
}
break;
#else
data = (double)*((unsigned char*)(tiffBufferLong+col+w*row) + 0);
#endif
- mrcPixelDataSet(mrc, col, row, linfo->currentz, data, mrcPixelMag);
+ mrcPixelDataSet(mrc, col, row, linfo->currentz, data, mrcPixelRePart);
break;
}
case 0x10: {
#else
data = (double)*((unsigned char*)(tiffBufferLong+col+w*row) + 1);
#endif
- mrcPixelDataSet(mrc, col, row, linfo->currentz, data, mrcPixelMag);
+ mrcPixelDataSet(mrc, col, row, linfo->currentz, data, mrcPixelRePart);
break;
}
case 0x20: {
#else
data = (double)*((unsigned char*)(tiffBufferLong+col+w*row) + 2);
#endif
- mrcPixelDataSet(mrc, col, row, linfo->currentz, data, mrcPixelMag);
+ mrcPixelDataSet(mrc, col, row, linfo->currentz, data, mrcPixelRePart);
break;
}
case 0x40: {
#else
data = (double)*((unsigned char*)(tiffBufferLong+col+w*row) + 3);
#endif
- mrcPixelDataSet(mrc, col, row, linfo->currentz, data, mrcPixelMag);
+ mrcPixelDataSet(mrc, col, row, linfo->currentz, data, mrcPixelRePart);
break;
}
default: {
#else
data = (double)*((unsigned short*)(tiffBufferLong+(col+w*row)) + 0);
#endif
- mrcPixelDataSet(mrc, col, row, linfo->currentz, data, mrcPixelMag);
+ mrcPixelDataSet(mrc, col, row, linfo->currentz, data, mrcPixelRePart);
break;
}
case 0x10: {
#else
data = (double)*((unsigned short*)(tiffBufferLong+(col+w*row)) + 1);
#endif
- mrcPixelDataSet(mrc, col, row, linfo->currentz, data, mrcPixelMag);
+ mrcPixelDataSet(mrc, col, row, linfo->currentz, data, mrcPixelRePart);
break;
}
case 0x20: {
#else
data = (double)*((unsigned short*)(tiffBufferLong+(col+w*row)) + 2);
#endif
- mrcPixelDataSet(mrc, col, row, linfo->currentz, data, mrcPixelMag);
+ mrcPixelDataSet(mrc, col, row, linfo->currentz, data, mrcPixelRePart);
break;
}
case 0x40: {
#else
data = (double)*((unsigned short*)(tiffBufferLong+(col+w*row)) + 3);
#endif
- mrcPixelDataSet(mrc, col, row, linfo->currentz, data, mrcPixelMag);
+ mrcPixelDataSet(mrc, col, row, linfo->currentz, data, mrcPixelRePart);
break;
}
default: {
-/bin/bash: hf2000Init: No such file or directory
+/bin/bash: hf2000Init: そのようなファイルやディレクトリはありません
-/bin/bash: hf2000LenzCurrent: No such file or directory
+/bin/bash: hf2000LenzCurrent: そのようなファイルやディレクトリはありません
-/bin/bash: hf2000SpecimenPosition: No such file or directory
+/bin/bash: hf2000SpecimenPosition: そのようなファイルやディレクトリはありません
-/bin/bash: khorosFilterGenerate: No such file or directory
+/bin/bash: khorosFilterGenerate: そのようなファイルやディレクトリはありません
-/bin/bash: llDataAxisSearch: No such file or directory
+/bin/bash: llDataAxisSearch: そのようなファイルやディレクトリはありません
-<HTML>
-<HEAD>
-<TITLE>llDataCTFCompensate</TITLE>
-</HEAD>
-<BODY>
-<H1>llDataCTFCompensate</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: llDataCTFCompensate
-Options:
- [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
- [-I[nput] In1 (NULL ).as(inFile ) ] :Optional :InputCTFInformation
- [-I2[nput] In2 (NULL ).as(inFile ) ] :Optional :InputCTFInformation2
- [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
- [-t[ruePitch] truePitch (430.0 ).as(Real ) ] :Essential :truePitch[A]
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
------ CTFInformation file 1 -----
-RR0 F0 PHI0 : If R.lt.RR0, F0=0; If RR0.le.R.lt.RR1, Linear Interpolation F0, F1
-RR1 F1 PHI1 : If RR1.le.R <RR2,
-.................................................
-RRn Fn PHIn : If RRn<= R , F*0 PHI = 0
------ Control File -----
-In[inFile:NULL] #InputDataFile
-In1[inFile:NULL] #InputCTFInformation
-Out[outFile:NULL] #OutputDataFile
-truePitch[Real:100.0] #truePitch[A]
-mode[Integer:0] #Mode
------ CTFInformation file 2 -----
-dF[A] Cs[mm] Acc[kV] ratioOfAmpToPhase
------ How to make file 1 or file 2 -----
-llExtractCtfinfFileCreate make these files.
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: llDataCTFCompensate: そのようなファイルやディレクトリはありません
-/bin/bash: llDataFitServer: No such file or directory
+/bin/bash: llDataFitServer: そのようなファイルやディレクトリはありません
-/bin/bash: llDataMultiCTFCompensation: No such file or directory
+/bin/bash: llDataMultiCTFCompensation: そのようなファイルやディレクトリはありません
-<<<<<<< HEAD
-/bin/bash: llDataPrint: No such file or directory
-=======
<HTML>
<HEAD>
<TITLE>llDataPrint</TITLE>
</PRE>
</BODY>
</HTML>
->>>>>>> 05144f7ae9b3e43a94f011609484b025af01d7ae
-/bin/bash: llDataRotation: No such file or directory
+/bin/bash: llDataRotation: そのようなファイルやディレクトリはありません
-/bin/bash: llDataSeparate: No such file or directory
+/bin/bash: llDataSeparate: そのようなファイルやディレクトリはありません
-/bin/bash: matrix3DEulerAngleTransform: No such file or directory
+/bin/bash: matrix3DEulerAngleTransform: そのようなファイルやディレクトリはありません
-/bin/bash: matrix3DFromEulerAngle: No such file or directory
+/bin/bash: matrix3DFromEulerAngle: そのようなファイルやディレクトリはありません
-/bin/bash: matrix3DInverse: No such file or directory
+/bin/bash: matrix3DInverse: そのようなファイルやディレクトリはありません
-/bin/bash: fft2d: No such file or directory
+/bin/bash: fft2d: そのようなファイルやディレクトリはありません
-/bin/bash: mrc2dsn6: No such file or directory
+/bin/bash: mrc2dsn6: そのようなファイルやディレクトリはありません
-/bin/bash: mrc2hdf: No such file or directory
+/bin/bash: mrc2hdf: そのようなファイルやディレクトリはありません
-/bin/bash: mrcFFTCTFCompensation: No such file or directory
+/bin/bash: mrcFFTCTFCompensation: そのようなファイルやディレクトリはありません
-<HTML>
-<HEAD>
-<TITLE>mrcFFTCentralSection</TITLE>
-</HEAD>
-<BODY>
-<H1>mrcFFTCentralSection</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrcFFTCentralSection
-Options:
- [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input: mrc(3D)
- [-t[emplate] Template (NULL ).as(inFile::mrcImage ) ] :Optional :Input: mrcFFT(2D)
- [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output: mrcFFT(2D)
- [-o[utput]I[mage] OutImage (NULL ).as(outFile::mrcImage ) ] :Optional :Output: mrcImage(2D)
- [-E[uler]A[ngle] EAMode (YOYS ).as(String )
- Rot1 (0.0 ).as(Real )
- Rot2 (0.0 ).as(Real )
- Rot3 (0.0 ).as(Real ) ] :Optional :EulerAngle
- [-trans[late] TransX (0.0 ).as(Real )
- TransY (0.0 ).as(Real ) ] :Optional :Traslation(2D)
- [-InterpMode InterpMode (0 ).as(Integer ) ] :Optional :Interpolation Mode
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Additional Usage -----
--t[emplate] : If not set, the size of out (Nx, Ny) is set as the size of in (Nx, Ny).</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrcFFTCentralSection: そのようなファイルやディレクトリはありません
-<HTML>
-<HEAD>
-<TITLE>mrcFFTCentralSectionCompare</TITLE>
-</HEAD>
-<BODY>
-<H1>mrcFFTCentralSectionCompare</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrcFFTCentralSectionCompare
-Options:
- [-i[nput] In2D (NULL ).as(inFile::mrcImage ) ] :Essential :Input: 2D(FFT)
- [-i[nput]3d In3D (NULL ).as(inFile::mrcImage ) ] :Essential :Input: 3D(FFT)
- [-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: EulerAngle
- [-trans[late] TransX (0.0 ).as(Real )
- TransY (0.0 ).as(Real ) ] :Optional :Input: Translation
- [-InterpMode InterpMode (0 ).as(Integer ) ] :Optional :Interpolation Mode
- [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output:Likelihood
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrcFFTCentralSectionCompare: そのようなファイルやディレクトリはありません
-/bin/bash: mrcFFTIQEstimation: No such file or directory
+/bin/bash: mrcFFTIQEstimation: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImage1dCutAverage: No such file or directory
+/bin/bash: mrcImage1dCutAverage: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImage3DCTFObservation: No such file or directory
+/bin/bash: mrcImage3DCTFObservation: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImage3DPeakGet: No such file or directory
+/bin/bash: mrcImage3DPeakGet: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageAutoFilamentExtract: No such file or directory
+/bin/bash: mrcImageAutoFilamentExtract: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageAutoRotationCorrelationResultPrint: No such file or directory
+/bin/bash: mrcImageAutoRotationCorrelationResultPrint: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageAutoTriming: No such file or directory
+/bin/bash: mrcImageAutoTriming: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageBilateralFilter: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>mrcImageBilateralFilter</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageBilateralFilter</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageBilateralFilter
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-s[igma]D[ensity] SigmaDensity (2.0 ).as(Real ) ] :Optional :SigmaDensity
+ [-k[ernal]T[type]D[ensity]KernelTypeDensity (0 ).as(Integer ) ] :Optional :KernelTypeForDensity
+ [-s[igma]S[pace] SigmaSpace (1.0 ).as(Real ) ] :Optional :SigmaSpace
+ [-s[igma]S[pace]3 SigmaSpaceX (1.0 ).as(Real )
+ SigmaSpaceY (1.0 ).as(Real )
+ SigmaSpaceZ (1.0 ).as(Real ) ] :Optional :SigmaSpace(3D)
+ [-k[ernel]T[ype]S[pace]KernelTypeSpace (0 ).as(Integer ) ] :Optional :KernelTypeForSpace
+ [-k[ernel]S[ize] KernelSize (5 ).as(Integer ) ] :Optional :KernelSize
+ [-k[ernel]S[ize]3 KernelSizeX (5 ).as(Integer )
+ KernelSizeY (5 ).as(Integer )
+ KernelSizeZ (5 ).as(Real ) ] :Optional :KernelSize(3D)
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+Bilateral Filter
+ by Tomashi and Manduchi
+ 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>
-/bin/bash: mrcImageCTFCompensation: No such file or directory
+/bin/bash: mrcImageCTFCompensation: そのようなファイルやディレクトリはありません
-<HTML>
-<HEAD>
-<TITLE>mrcImageCTFCompensationForTiltImage</TITLE>
-</HEAD>
-<BODY>
-<H1>mrcImageCTFCompensationForTiltImage</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrcImageCTFCompensationForTiltImage
-Options:
- [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
- [-I[nformation] Info (NULL ).as(inFile ) ] :Essential :Infomation
- [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [cut[Back] cut (6 ).as(Integer ) ] :Optional :Cut
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrcImageCTFCompensationForTiltImage: そのようなファイルやディレクトリはありません
-<<<<<<< HEAD
-/bin/bash: mrcImageChainCodeCalc: No such file or directory
-=======
/bin/bash: mrcImageChainCodeCalc: そのようなファイルやディレクトリはありません
->>>>>>> 05144f7ae9b3e43a94f011609484b025af01d7ae
-<HTML>
-<HEAD>
-<TITLE>mrcImageColoring</TITLE>
-</HEAD>
-<BODY>
-<H1>mrcImageColoring</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrcImageColoring
-Options:
- [-r[ed] rIn (NULL ).as(inFile ) ] :Optional :Red:InputDataFile
- [-g[reen] gIn (NULL ).as(inFile ) ] :Optional :Green:InputDataFile
- [-b[lue] bIn (NULL ).as(inFile ) ] :Optional :Blue:InputDataFile
- [-rH[ight] rHigh (1 ).as(Real ) ] :Optional :Red:HighThres
- [-rL[ow] rLow (0 ).as(Real ) ] :Optional :Red:LowThres
- [-gH[ight] gHigh (1 ).as(Real ) ] :Optional :Green:HighThres
- [-gL[ow] gLow (0 ).as(Real ) ] :Optional :Green:LowThres
- [-bH[ibht] bHigh (1 ).as(Real ) ] :Optional :Blue:HibhThres
- [-bL[ow] bLow (0 ).as(Real ) ] :Optional :BLue:LowThres
- [-o[utput] Out (NULL ).as(outFile ) ] :Optional :gif:OutputDataFile
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrcImageColoring: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageConvolution: No such file or directory
+/bin/bash: mrcImageConvolution: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageCoreImageCalc: No such file or directory
+/bin/bash: mrcImageCoreImageCalc: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageCorrelationServer: No such file or directory
+/bin/bash: mrcImageCorrelationServer: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageCorrelationWithCTFCompensation: No such file or directory
+/bin/bash: mrcImageCorrelationWithCTFCompensation: そのようなファイルやディレクトリはありません
-<<<<<<< HEAD
-/bin/bash: mrcImageCrystalDeform: No such file or directory
-=======
/bin/bash: mrcImageCrystalDeform: そのようなファイルやディレクトリはありません
->>>>>>> 05144f7ae9b3e43a94f011609484b025af01d7ae
-/bin/bash: mrcImageCutAndSetInArray: No such file or directory
+/bin/bash: mrcImageCutAndSetInArray: そのようなファイルやディレクトリはありません
Options:
[-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
[-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
- [-C[ontour] Contour (10 ).as(Real ) ] :Optional :ContourLevel: 10 9.881313e-324ach
+ [-C[ontour] Contour (10 ).as(Real ) ] :Optional :ContourLevel: 10 5.533535e-322ach
[-log Log (NULL ).as(appendFile ) ] :Optional :OutputDataFile
[-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
[-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
-/bin/bash: mrcImageEdgeImageGet: No such file or directory
+/bin/bash: mrcImageEdgeImageGet: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageEnhancementWithFuzzySets: No such file or directory
+/bin/bash: mrcImageEnhancementWithFuzzySets: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageFFTLayerLineExtraction: No such file or directory
+/bin/bash: mrcImageFFTLayerLineExtraction: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageFOMCalc: No such file or directory
+/bin/bash: mrcImageFOMCalc: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageFOMCalc: No such file or directory
+/bin/bash: mrcImageFOMCalc: そのようなファイルやディレクトリはありません
-<<<<<<< HEAD
-<HTML>
-<HEAD>
-<TITLE>mrcImageFeatureCalc</TITLE>
-</HEAD>
-<BODY>
-<H1>mrcImageFeatureCalc</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrcImageFeatureCalc
-Options:
- [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input:binary(BandW)
- [-r[erencence] Ref (NULL ).as(inFile::mrcImage ) ] :Optional :Input:reference(density)
- [-o[utput] Out (stdout ).as(outFile::ASCII ) ] :Optional :Output:
- [-o[utput]GC OutGC (NULL ).as(outFile::mrcImage ) ] :Optional :Output:gc
- [-o[utput]L[abel] OutLabel (NULL ).as(outFile::mrcImage ) ] :Optional :Output:Label
- [-o[utput]P[eprimeter]OutPerimeter (NULL ).as(outFile::mrcImage ) ] :Optional :Output:Label
- [-o[utput]S[urfaceArea]OutSurfaceArea (NULL ).as(outFile::mrcImage ) ] :Optional :Output:SurfaceArea
- [-n[eighbor] neighbor (0 ).as(Integer ) ] :Optional :Neighbor: [4(0)|8 or 6(0)|18|26]
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Additional Usage -----
-Mode
-</PRE>
-</BODY>
-</HTML>
-=======
/bin/bash: mrcImageFeatureCalc: そのようなファイルやディレクトリはありません
->>>>>>> 05144f7ae9b3e43a94f011609484b025af01d7ae
-/bin/bash: mrcImageFilamentSearch: No such file or directory
+/bin/bash: mrcImageFilamentSearch: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageFractalFrourierShellCorrelation: No such file or directory
+/bin/bash: mrcImageFractalFrourierShellCorrelation: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageGaussSphere: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>mrcImageGaussSphere</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageGaussSphere</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageGaussSphere
+Options:
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-E[uler]A[ngle] EA (YOYS ).as(String )
+ Rot1 (0.0 ).as(Real )
+ Rot2 (0.0 ).as(Real )
+ Rot3 (0.0 ).as(Real ) ] :Optional :Input: Gauss Sphere: Rotation
+ [-centre ShiftX (0.0 ).as(Real )
+ ShiftY (0.0 ).as(Real )
+ ShiftZ (0.0 ).as(Real ) ] :Optional :Input: Gauss Sphere: Centre
+ [-sigmax sigmax (10 ).as(Real ) ] :Optional :sigmax[A]
+ [-sigmay sigmay (20 ).as(Real ) ] :Optional :sigmay[A]
+ [-sigmaz sigmaz (30 ).as(Real ) ] :Optional :sigmaz[A]
+ [-sigma_range sigma_range (3 ).as(Real ) ] :Optional :x times
+ [-weight weight (10 ).as(Real ) ] :Optional :weight
+ [-size size (5 ).as(Real ) ] :Optional :Pixel Size[A]
+ [-W[idth] Width (0 ).as(Real ) ] :Optional :Width[A]
+ [-H[ight] Height (0 ).as(Real ) ] :Optional :Height[A]
+ [-S[ection] Section (0 ).as(Real ) ] :Optional :Section[A]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (2 ).as(Integer ) ] :Optional :Mode
+Gauss Sphere is cutted at sigma_range*sigma
+Gauss Sphere = weight * exp ( - ((x^2 / sigmax^2)+(y^2 / sigmay^2)+(z^2 / sigmaz^2))
+mrcImageFileSize is (sigma_range*sigmax*2) x (sigma_range*sigmay*2) x (sigma_range*sigmaz*2)
+-----------------------------------------------------------------------------------
+-EA: for rotation
+-----------------------------------------------------------------------------------
+mode 0 char
+mode 2 float
+</PRE>
+</BODY>
+</HTML>
--- /dev/null
+../../../../../hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageGradient/src/X86LINUX64
\ No newline at end of file
-/bin/bash: mrcImageHelicalConvolution: No such file or directory
+/bin/bash: mrcImageHelicalConvolution: そのようなファイルやディレクトリはありません
--- /dev/null
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+
+#include "../inc/config.h"
+#undef DEBUG
+#include "genUtil.h"
+#include "mrcImage.h"
+
+typedef struct infoDataList {
+ mrcImage datXSection;
+ mrcImage datYSection;
+ mrcImage datXProj;
+ mrcImage datYProj;
+ double* datHistgram;
+ mrcImageInformation info;
+ int flagLength;
+} infoDataList;
+
+extern void lmrcImageInfo(infoDataList* data, mrcImage* img, mrcImageInfoInfo* info);
+extern void outputMrcImageInfo(FILE* fpt, infoDataList* data, mrcImage* img, mrcImageInfoInfo* info);
+
+int
+main(int argc, char* argv[])
+{
+ mrcImage img;
+ mrcImageInfoInfo info;
+ infoDataList data;
+
+ init0(&info);
+ argCheck(&info, argc, argv);
+ init1(&info);
+
+ data.flagLength = info.Length;
+#ifdef DEBUG
+ mrcFileRead(&img, info.In, "from Main Routine", 1);
+#else
+ mrcFileRead(&img, info.In, "from Main Routine", 0);
+#endif
+
+ lmrcImageInfo(&data, &img, &info);
+ outputMrcImageInfo(info.fptOut, &data, &img, &info);
+ exit(EXIT_SUCCESS);
+}
+
+void
+additionalUsage()
+{
+ fprintf(stderr, "----- Additional Usage -----\n");
+ fprintf(stderr, "The -I option uses -rmax or -m options\n");
+ fprintf(stderr, "-m 0: mean of all density\n");
+ fprintf(stderr, " 1: mean of sphere surface density at rmax\n");
+ fprintf(stderr, " 2: mean of cylinder surface density at rmax\n");
+ fprintf(stderr, " 3: mean of edge pixels \n");
+ fprintf(stderr, " 4: mean of Centre\n");
+ fprintf(stderr, " 5: mean of Sparse \n");
+ fprintf(stderr, " 6: mean of 2DEdge\n");
+ fprintf(stderr, " 7: RMS of all pixels \n");
+ fprintf(stderr, " 8: sd of all axes\n");
+}
+
+void
+lmrcImageInfo(infoDataList* data, mrcImage* img, mrcImageInfoInfo* info)
+{
+ if(info->flagX) {
+ lmrcImageXSection(&(data->datXSection), img, info->X);
+ }
+ if(info->flagY) {
+ lmrcImageYSection(&(data->datYSection), img, info->Y);
+ }
+ if(info->xProjection) {
+ lmrcImageXProjection(&(data->datXProj), img);
+ }
+ if(info->yProjection) {
+ lmrcImageYProjection(&(data->datYProj), img);
+ }
+ if(info->flagH) {
+ lmrcImageHistgram(&(data->datHistgram), info->H, img);
+ }
+ if(info->flagH2) {
+ lmrcImageHistgram2(&(data->datHistgram), info->H2, img);
+ }
+ if(info->flagH3) {
+ lmrcImageHistgram3(&(data->datHistgram), info->H3, img);
+ }
+ if(info->flagH4) {
+ lmrcImageHistgram4(&(data->datHistgram), info->H4, img);
+ }
+ if(info->flagH5) {
+ lmrcImageHistgram5(&(data->datHistgram), info->H5, info->Low, info->High, img);
+ }
+ if(info->flagH6) {
+ lmrcImageHistgram6(&(data->datHistgram), info->H6, info->Low, info->High, img);
+ }
+ if(info->Info) {
+ data->info.rmax = info->rmax;
+ data->info.flagrmax = info->flagrmax;
+ data->info.mode = info->mode;
+ lmrcImageInformation(&(data->info), img);
+ }
+}
+
+void
+outputMrcImageInfo(FILE* fpt, infoDataList* dat, mrcImage* img, mrcImageInfoInfo* info)
+{
+ int i, ix, iy, j;
+ double data;
+ double dens;
+
+ if(info->flagX) {
+ for(iy=0; iy<img->HeaderN.y; iy++) {
+ fprintf(fpt, "%5d %15.6g", iy, mrcPixelDataGet(&(dat->datXSection),
+ 0.0,
+ (mrcImageParaTypeReal)iy,
+ 0.0,
+ &data,
+ mrcPixelRePart,
+ mrcPixelHowNearest));
+ if(dat->flagLength) {
+ fprintf(fpt, " %15.6g", iy*img->HeaderLength.y);
+ }
+ fprintf(fpt, "\n");
+ }
+ }
+
+ if(info->flagY) {
+ for(ix=0; ix<img->HeaderN.x; ix++) {
+ fprintf(fpt, "%5d %15.6g", ix, mrcPixelDataGet(&(dat->datYSection),
+ (mrcImageParaTypeReal)ix,
+ 0.0,
+ 0.0,
+ &data,
+ mrcPixelRePart,
+ mrcPixelHowNearest));
+
+ if(dat->flagLength) {
+ fprintf(fpt, " %15.6g", iy*img->HeaderLength.x);
+ }
+ fprintf(fpt, "\n");
+ }
+ }
+
+ if(info->xProjection) {
+ for(ix=0; ix<img->HeaderN.x; ix++) {
+ fprintf(fpt, "%5d %15.6g", ix, mrcPixelDataGet(&(dat->datXProj),
+ (mrcImageParaTypeReal)ix,
+ 0.0,
+ 0.0,
+ &data,
+ mrcPixelRePart,
+ mrcPixelHowNearest));
+
+ if(dat->flagLength) {
+ fprintf(fpt, " %15.6g", iy*img->HeaderLength.x);
+ }
+ fprintf(fpt, "\n");
+ }
+ }
+
+ if(info->yProjection) {
+ for(iy=0; iy<img->HeaderN.y; iy++) {
+ fprintf(fpt, "%5d %15.6g", iy, mrcPixelDataGet(&(dat->datYProj),
+ 0.0,
+ (mrcImageParaTypeReal)iy,
+ 0.0,
+ &data,
+ mrcPixelRePart,
+ mrcPixelHowNearest));
+ if(dat->flagLength) {
+ fprintf(fpt, " %15.6g", iy*img->HeaderLength.y);
+ }
+ fprintf(fpt, "\n");
+ }
+ }
+ if(info->flagH) {
+ for(i=0; i<info->H; i++) {
+ DEBUGPRINT2("MAX: %g, MIN: %g\n", img->HeaderAMax, img->HeaderAMin);
+ dens = (img->HeaderAMax-img->HeaderAMin)/(info->H-1)*i+img->HeaderAMin,
+ fprintf(fpt, "%15.6g %15.6g |",
+ dens,
+ dat->datHistgram[i]);
+ for(j=0; j<dat->datHistgram[i]*16; j++) {
+ fprintf(fpt, " ");
+ }
+ fprintf(fpt, "*\n");
+ }
+ }
+ if(info->flagH5) {
+ for(i=0; i<info->H5; i++) {
+ DEBUGPRINT2("MAX: %g, MIN: %g\n", img->HeaderAMax, img->HeaderAMin);
+ dens = (info->High-info->Low)/(info->H5-1)*i+info->Low,
+ fprintf(fpt, "%15.6g %15.6g |",
+ dens,
+ dat->datHistgram[i]);
+ for(j=0; j<dat->datHistgram[i]*16; j++) {
+ fprintf(fpt, " ");
+ }
+ fprintf(fpt, "*\n");
+ }
+ }
+ if(info->flagH2) {
+ unsigned long n;
+
+ n = (unsigned long)((img->HeaderAMax - img->HeaderAMin)/info->H2 + 1);
+ for(i=0; i<n; i++) {
+ dens = img->HeaderAMin + i*info->H2;
+ fprintf(fpt, "%15.6g %15.6g |",
+ dens,
+ dat->datHistgram[i]);
+
+ for(j=0; j<dat->datHistgram[i]*16; j++) {
+ fprintf(fpt, " ");
+ }
+ fprintf(fpt, "*\n");
+ }
+ }
+ if(info->flagH6) {
+ unsigned long n;
+
+ n = (unsigned long)((info->High - info->Low)/info->H6 + 1);
+ for(i=0; i<n; i++) {
+ dens = info->Low + i*info->H6;
+ fprintf(fpt, "%15.6g %15.6g \n",
+ dens,
+ dat->datHistgram[i]);
+
+ }
+ }
+ if(info->flagH3) {
+ for(i=0; i<info->H; i++) {
+ DEBUGPRINT2("MAX: %g, MIN: %g\n", img->HeaderAMax, img->HeaderAMin);
+ dens = (img->HeaderAMax-img->HeaderAMin)/(info->H3-1)*i+img->HeaderAMin,
+ fprintf(fpt, "%15.6g %15.6g \n",
+ dens,
+ dat->datHistgram[i]);
+ }
+ }
+ if(info->flagH4) {
+ unsigned long n;
+
+ n = (unsigned long)((img->HeaderAMax - img->HeaderAMin)/info->H4 + 1);
+ for(i=0; i<n; i++) {
+ dens = img->HeaderAMin + i*info->H4;
+ fprintf(fpt, "%15.6g %15.6g \n",
+ dens,
+ dat->datHistgram[i]);
+
+ }
+ }
+ if(info->Info) {
+ switch(info->mode){
+ case meanOfAll:{
+ DEBUGPRINT3("SizeCheck: int %d: mrcImageParaTypeIntegerCoord: %d = 3x%d \n",
+ sizeof(int), sizeof(mrcImageParaTypeIntegerCoord), sizeof(mrcImageParaTypeInteger));
+ DEBUGPRINT3("SizeCheck: info:%d Coord%d Coord.x:%d\n",
+ sizeof(dat->info), sizeof(dat->info.minCoord), sizeof(dat->info.minCoord.x));
+ fprintf(fpt, "Min: %15.6g (%d, %d, %d)\n", dat->info.min,
+ (int)dat->info.minCoord.x, (int)dat->info.minCoord.y, (int)dat->info.minCoord.z);
+ fprintf(fpt, "Max: %15.6g (%d, %d, %d)\n", dat->info.max,
+ (int)dat->info.maxCoord.x, (int)dat->info.maxCoord.y, (int)dat->info.maxCoord.z);
+ fprintf(fpt, "Mean: %15.6g\n", dat->info.mean);
+ fprintf(fpt, "SD: %15.6g\n", dat->info.sd);
+ fprintf(fpt, "SE: %15.6g\n", dat->info.se);
+ fprintf(fpt, "Sum: %15.6g\n", dat->info.mean*img->HeaderN.x*img->HeaderN.y*img->HeaderN.z);
+ break;
+ }
+ case meanOfCylinderSurface:{
+ fprintf(fpt, "Mean:%15.6g\n", dat->info.meanOfCylinderSurface);
+ fprintf(fpt, "SD:%15.6g\n", dat->info.sdOfCylinderSurface);
+ fprintf(fpt, "SE:%15.6g\n", dat->info.seOfCylinderSurface);
+ break;
+ }
+ case meanOfSphereSurface:{
+ fprintf(fpt, "Mean:%15.6g\n", dat->info.meanOfSphereSurface);
+ fprintf(fpt, "SD:%15.6g\n", dat->info.sdOfSphereSurface);
+ fprintf(fpt, "SE:%15.6g\n", dat->info.seOfSphereSurface);
+ break;
+ }
+ case meanOfEdge:{
+ fprintf(fpt, "Mean: %15.6g\n", dat->info.meanOfEdge);
+ fprintf(fpt, "SD: %15.6g\n", dat->info.sdOfEdge);
+ fprintf(fpt, "SE: %15.6g\n", dat->info.seOfEdge);
+ break;
+ }
+ case RMSofAllPixels:{
+ fprintf(fpt, "RMS: %15.6g\n", dat->info.RMS);
+ break;
+ }
+ case sdOfAllAxis:{
+ fprintf(fpt, "aveOfAllAxis: %15.6g %15.6g %15.6g\n", dat->info.aveOfAllAxis.x , dat->info.aveOfAllAxis.y, dat->info.aveOfAllAxis.z);
+ fprintf(fpt, "sdOfAllAxis: %15.6g %15.6g %15.6g\n", dat->info.sdOfAllAxis.x , dat->info.sdOfAllAxis.y, dat->info.sdOfAllAxis.z);
+ break;
+ }
+ default:{
+ fprintf(stderr, "Not supported mode :%ld", info->mode);
+ exit(EXIT_FAILURE);
+ }
+
+ }
+ }
+}
lmrcImageHistgram5(&(data->datHistgram), info->H5, info->Low, info->High, img);
}
if(info->flagH6) {
- lmrcImageHistgram5(&(data->datHistgram), info->H6, info->Low, info->High, img);
+ lmrcImageHistgram6(&(data->datHistgram), info->H6, info->Low, info->High, img);
}
if(info->Info) {
data->info.rmax = info->rmax;
../$(OSTYPE)/$(OBJECTNAME) -i data/test.roi -I -m 5
../$(OSTYPE)/$(OBJECTNAME) -i data/test.roi -I -m 6
../$(OSTYPE)/$(OBJECTNAME) -i data/test.roi -I -m 7
+ ../$(OSTYPE)/$(OBJECTNAME) -i data/test.roi -H6 1 -High 256 -L 0
@echo "----- Calc check -----"
exec2:
-/bin/bash: mrcImageMergeFFT: No such file or directory
+/bin/bash: mrcImageMergeFFT: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageMultiCTFCompensation: No such file or directory
+/bin/bash: mrcImageMultiCTFCompensation: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageMultiCTFDetermination: No such file or directory
+/bin/bash: mrcImageMultiCTFDetermination: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageNLMeansFilter: No such file or directory
+/bin/bash: mrcImageNLMeansFilter: そのようなファイルやディレクトリはありません
-<HTML>
-<HEAD>
-<TITLE>mrcImagePad</TITLE>
-</HEAD>
-<BODY>
-<H1>mrcImagePad</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrcImagePad
-Options:
- [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input DataFile
- [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output DataFile
- [-W[idth] Width (0 ).as(Integer ) ] :Optional :Width[pixel]
- [-H[eight] Height (0 ).as(Integer ) ] :Optional :Height[pixel]
- [-V[alue] Value (0.0 ).as(Real ) ] :Optional :Padding Value(float on avgrage density)
- [-E[xpected]V[alue] ExpectedValue (0.0 ).as(Real ) ] :Optional :Expected Value for Background
- [-AW AvgWnd (2000.0 ).as(Real ) ] :Optional :Averaging Window Size [A]
- [-AWMin AWMin (20 ).as(Real ) ] :Optional :Averaging Window Size[pixel]
- [-AWMax AWMax (22 ).as(Real ) ] :Optional :Averaging Window Size[pixel]
- [-Tilt TiltAxisAngle (0 ).as(Real )
- TiltAngle (0 ).as(Real ) ] :Optional :TiltImage: TiltAxisAngle TiltAngle
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :Configuration File
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Mode -----
-0: Pad average density(Image Center)
-1: Pad average density of x=0 and x=MAX(x)(Image Center)
-2: Pad dynamic average density of x=0 and x=MAX(x)(Image Center)
-3: Pad average density of x=0,MAX(x) and y=0,MAX(y), (Image Center)
-4: Pad average density of bottom left
-5: Pad value (Image Center):Image Value(No Change)
-6: Pad value of bottom left:Image Value(No Change)
-7: Pad value estimated from outside circle
-8: Pad value estimated from outside ring: -AWMin -AMax
-9: Pad value is Value (Currently the same as 5)
-10: Periphery Masking Using ExpectedValue
-11: Normalized Padding using (I(x,y)-avg(bg))/avg(bg))
-12: Normalized Padding using (I(x,y)-avg(I))/sqrt(var(I)))
-13: Normalized Padding using (I(x,y)-avg(bg))/sqrt(var(bg)))
-14: Normalized Padding using (I(x,y)-avg(bg))/(avg(I)-avg(bg))
-15: Tilted Image Circle Average: Need two values of TiltAxisAngle TiltAngle
-16: Pad dynamic average density of x=0,MAX(x) and y=0,Max(y)(Image Center)
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrcImagePad: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImagePanoramaCreate: No such file or directory
+/bin/bash: mrcImagePanoramaCreate: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImagePeakSearch: No such file or directory
+/bin/bash: mrcImagePeakSearch: そのようなファイルやディレクトリはありません
-<<<<<<< HEAD
-/bin/bash: mrcImagePerimeterCalc: No such file or directory
-=======
/bin/bash: mrcImagePerimeterCalc: そのようなファイルやディレクトリはありません
->>>>>>> 05144f7ae9b3e43a94f011609484b025af01d7ae
-/bin/bash: mrcImagePrint: No such file or directory
+/bin/bash: mrcImagePrint: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImagePrint3D: No such file or directory
+/bin/bash: mrcImagePrint3D: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImagePut3D: No such file or directory
+/bin/bash: mrcImagePut3D: そのようなファイルやディレクトリはありません
-<HTML>
-<HEAD>
-<TITLE>mrcImageROIs</TITLE>
-</HEAD>
-<BODY>
-<H1>mrcImageROIs</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrcImageROIs
-Options:
- [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
- [-I[nformation] Info (NULL ).as(inFile ) ] :Essential :Information
- [-o[utput] Out (NULL ).as(outFile ) ] :Optional :MontageFile
- [-S[hrink] Shrink (NULL ).as(Integer ) ] :Optional :When inputimage was shrunk
- [-width Width (0.0 ).as(Real ) ] :Optional :Width
- [-height Height (0.0 ).as(Real ) ] :Optional :Height
- [-NonPeriodic ] :Optional :Zero Outof Range
- [-PadMode PadMode (0 ).as(Integer ) ] :Optional :PadMode(refer to mrcImagePad)
- [-M[ode] Mode (2 ).as(Integer ) ] :Optional :ImageType:0 byte 1 short 2 float
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Additional Usage -----
------ Mode -----
-0: Nearest
-1: Bilinear
-2: CubicConvolution
------ Information File Format -----
-Shape ShapeInfo1 ... [Additional AdditionalInfo1 ...]
-...............
-Shape: OutFileName Rect blx bly brx bry trx try tlx tly
-Shape: OutFileName TiltRect blx bly brx bry trx try tlx tly
-Shape: OutFileName Rect2 centerx centery width height
-Shape: OutFileName Circle centerx centery radius
-Shape: OutFileName Line startx starty endx endy
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrcImageROIs: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageRadialDistribution: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>mrcImageRadialDistribution</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageRadialDistribution</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageRadialDistribution
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output: ASCII
+ [-O[utputMRC] Out2 (NULL ).as(outFile ) ] :Optional :Output: MRC
+ [-centre Cx (0.0 ).as(Real )
+ Cy (0.0 ).as(Real ) ] :Optional :[pixel]
+ [-Cs[phere] Csx (0.0 ).as(Real )
+ Csy (0.0 ).as(Real )
+ Csz (0.0 ).as(Real ) ] :Optional :[pixel]
+ [-Avg ] :Optional :flagAvg: Averaged Intensity
+ [-Inv ] :Optional :flagInv: Inversed Intensity
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+>> Mode
+ 0: 2D or 3D(Cylindrical Coordinates)
+ 1: 2D or 3D(Spherical Coordinates)
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: mrcImageSNEstimate: No such file or directory
+/bin/bash: mrcImageSNEstimate: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageShapePCA: No such file or directory
+/bin/bash: mrcImageShapePCA: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageShapePCAFit: No such file or directory
+/bin/bash: mrcImageShapePCAFit: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageShapeRelaxation: No such file or directory
+/bin/bash: mrcImageShapeRelaxation: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageShapeSearch: No such file or directory
+/bin/bash: mrcImageShapeSearch: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageSimilarityEstimate: No such file or directory
+/bin/bash: mrcImageSimilarityEstimate: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageSpatialFrequencyFilter: No such file or directory
+/bin/bash: mrcImageSpatialFrequencyFilter: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageSphereCheck: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>mrcImageSphereCheck</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageSphereCheck</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageSphereCheck
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output:
+ [-n[ormalized] OutNOr (NULL ).as(outFile ) ] :Optional :Output: NormalizedImage
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
--- /dev/null
+../../../../../hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageStreamLine/src/X86LINUX64
\ No newline at end of file
[-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
[-m[ode] mode (0 ).as(Integer ) ] :Essential :RealSpaceCalculating
[-LabelingMode labelingmode (0 ).as(Integer ) ] :Optional :LabelingMode
- [-max[value] max (800 ).as(Integer ) ] :Optional :Density Max value:Support Constraint()
- [-min[value] min (200 ).as(Integer ) ] :Optional :Density Min value:Support Constraint()
+ [-max[value] max (800 ).as(Integer ) ] :Optional :Density Max value:Support Constraint(%)
+ [-min[value] min (200 ).as(Integer ) ] :Optional :Density Min value:Support Constraint(%)
[-sh[ape] shape (0 ).as(Integer ) ] :Optional :Shape:0(Rectangule),1(Globe)
[-h[alf]v[alue]p[oint]hvp (0.0 ).as(Real ) ] :Optional :Half value point(/[A])
[-Inverse ] :Optional :Inverse
-<<<<<<< HEAD
-/bin/bash: mrcImageSurfaceAreaCalc: No such file or directory
-=======
/bin/bash: mrcImageSurfaceAreaCalc: そのようなファイルやディレクトリはありません
->>>>>>> 05144f7ae9b3e43a94f011609484b025af01d7ae
-/bin/bash: mrcImageTiltAxisSearchHelp: No such file or directory
+/bin/bash: mrcImageTiltAxisSearchHelp: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageUnbentROI: No such file or directory
+/bin/bash: mrcImageUnbentROI: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageUnsharpening: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>mrcImageUnsharpening</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageUnsharpening</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageUnsharpening
+Options:
+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input: mrcImage
+ [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output: mrcImage
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+--UnsharpeningMode--
+0: 0 -1 0
+ -1 5 -1
+ 0 -1 0
+1:-1 -1 -1
+ -1 9 -1
+ -1 -1 -1
+2: 1 -2 1
+ -2 5 -2
+ 1 -2 1
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: mrcImageVarianceAnalysis: No such file or directory
+/bin/bash: mrcImageVarianceAnalysis: そのようなファイルやディレクトリはありません
[-D[elta] Delta (5.0 ).as(Real ) ] :Optional :Delta[A]
[-R[ange] MinVol (0.0 ).as(Real )
MaxVol (200.0 ).as(Real )
- DeltaVol (10.0 ).as(Real ) ] :Optional :vol
+ DeltaVol (10.0 ).as(Real ) ] :Optional :vol%
[-I[nverse] ] :Optional :Inverse
[-format Format (ContourLevel(%3g): %g %lu).as(StringAll ) ] :Optional :Format
[-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
-/bin/bash: mrcMultiFFTCentralSectionsSigmaCalc: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>mrcMultiFFTCentralSectionsSigmaCalc</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcMultiFFTCentralSectionsSigmaCalc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcMultiFFTCentralSectionsSigmaCalc
+Options:
+ [-i[nput] In (NULL ).as(inFileNoOpen::mrcImage)
+ PathIn (./ ).as(String ) ] :Essential :Input:2DFT
+ [-i[nput]L[ikelihood]InLikelihood (NULL ).as(inFileListNoOpen )
+ PathL (./ ).as(String ) ] :Essential :Input: LikelihoodList
+ [-i[nput]3d[SectionList]In3D (NULL ).as(inFileListNoOpen )
+ Path3D (./ ).as(String ) ] :Essential :Input: CentralSectionList
+ [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output: 2DSigma
+ [-EulerMode EulerMode (YOYS ).as(String ) ] :Optional :Input: EulerMode
+ [-Rot1 Rot1Start (0.0 ).as(Real )
+ Rot1End (360.0 ).as(Real )
+ Rot1Delta (10 ).as(Real ) ] :Optional :OutputDataFile
+ [-Rot2 Rot2Start (0.0 ).as(Real )
+ Rot2End (360.0 ).as(Real )
+ Rot2Delta (10 ).as(Real ) ] :Optional :OutputDataFile
+ [-Rot3 Rot3Start (0.0 ).as(Real )
+ Rot3End (360.0 ).as(Real )
+ Rot3Delta (10 ).as(Real ) ] :Optional :OutputDataFile
+ [-trans[late] TransX (0.0 ).as(Real )
+ TransY (0.0 ).as(Real ) ] :Optional :Input: Translation
+ [-InterpMode InterpMode (0 ).as(Integer ) ] :Optional :Interpolation Mode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: mrcRefNormalizing: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>mrcRefNormalizing</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcRefNormalizing</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcRefNormalizing
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: mrcView: No such file or directory
+/bin/bash: mrcView: そのようなファイルやディレクトリはありません
-/bin/bash: molvieMrcViewer: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>molvieMrcViewer</TITLE>
+</HEAD>
+<BODY>
+<H1>molvieMrcViewer</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: molvieMrcViewer
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: pdbAtomSection: No such file or directory
+/bin/bash: pdbAtomSection: そのようなファイルやディレクトリはありません
-/bin/bash: pdbHomologySearch: No such file or directory
+/bin/bash: pdbHomologySearch: そのようなファイルやディレクトリはありません
-/bin/bash: pdbRhoFit: No such file or directory
+/bin/bash: pdbRhoFit: そのようなファイルやディレクトリはありません
-/bin/bash: pdbRhoFitTm: No such file or directory
+/bin/bash: pdbRhoFitTm: そのようなファイルやディレクトリはありません
-/bin/bash: pdbTempFactorSet: No such file or directory
+/bin/bash: pdbTempFactorSet: そのようなファイルやディレクトリはありません
-<HTML>
-<HEAD>
-<TITLE>pdbTrans</TITLE>
-</HEAD>
-<BODY>
-<H1>pdbTrans</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: pdbTrans
-Options:
- [-i[nput] inFile (NULL ).as(inFile ) ] :Essential :Input: DataFile
- [-o[utput] outFile (NULL ).as(outFile ) ] :Essential :Output: DataFile
- [-M[atrix] matFile (NULL ).as(inFile ) ] :Optional :Input: MatrixFile[4][4]
- [-E[uler]A[ngle] RotMode (YOYS ).as(String )
- Rot1 (0.0 ).as(Real )
- Rot2 (0.0 ).as(Real )
- Rot3 (0.0 ).as(Real ) ] :Optional :Input:
- [-cuda cudaDeviceID (0 ).as(Integer ) ] :Optional :cuda
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
->>> Matrix3D File Format y = Ax + b<<<
-a11 a21 a31 : Rotation Array : y=Ax
-a12 a22 a32
-a13 a23 a33
-b1 b2 b3 : Translation Array : y = x + b
---- Attention ---
-If both options of -M and -EA are set,
- first, translation and rotation by -M will be performed
- then, rotation by -EA will be done.
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: pdbTrans: そのようなファイルやディレクトリはありません
-/bin/bash: pdbView: No such file or directory
+/bin/bash: pdbView: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageNeuralNetParticleExtraction: No such file or directory
+/bin/bash: mrcImageNeuralNetParticleExtraction: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageNeuralNetParticleLearning: No such file or directory
+/bin/bash: mrcImageNeuralNetParticleLearning: そのようなファイルやディレクトリはありません
-/bin/bash: CheckCommonLineData: No such file or directory
+/bin/bash: CheckCommonLineData: そのようなファイルやディレクトリはありません
-/bin/bash: CheckOfOrientation: No such file or directory
+/bin/bash: CheckOfOrientation: そのようなファイルやディレクトリはありません
-/bin/bash: CheckOrientationByDegree: No such file or directory
+/bin/bash: CheckOrientationByDegree: そのようなファイルやディレクトリはありません
-/bin/bash: CommonLineCalculation: No such file or directory
+/bin/bash: CommonLineCalculation: そのようなファイルやディレクトリはありません
-/bin/bash: LCalculationForOrientationSearch: No such file or directory
+/bin/bash: LCalculationForOrientationSearch: そのようなファイルやディレクトリはありません
-/bin/bash: ProjectionDirectionMapCreate: No such file or directory
+/bin/bash: ProjectionDirectionMapCreate: そのようなファイルやディレクトリはありません
-<HTML>
-<HEAD>
-<TITLE>WeightCalculationOfCommonLineSearch</TITLE>
-</HEAD>
-<BODY>
-<H1>WeightCalculationOfCommonLineSearch</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: WeightCalculationOfCommonLineSearch
-Options:
- [-I[nput] In (NULL ).as(inFileList ) ] :Essential :InputDataFileList
- [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
- [-L[ength]T[hreshold]M[ode]LengthThresholdMode (0 ).as(Integer ) ] :Essential :Length threshold mode in LengthCorrelation
- [-L[ength]T[hreshold]R[atio]LengthThresholdRatio(0.25 ).as(Real ) ] :Optional :Length threshold ratio in LengthCorrelation : -LTM=0
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
-
------ Mode -----
--m :
- 0 : Addition weight
- 1 : Multiplication weight
-
------ input file format -----
-filename(sin) rotationalmode angle angle angle
- . . . . .
- . . . . .
- . . . . .
- . . . . .
-
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: WeightCalculationOfCommonLineSearch: そのようなファイルやディレクトリはありません
-/bin/bash: WeightCalculationOfCommonLineSearchByAllSinogram: No such file or directory
+/bin/bash: WeightCalculationOfCommonLineSearchByAllSinogram: そのようなファイルやディレクトリはありません
-/bin/bash: calcCommonLine: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>calcCommonLine</TITLE>
+</HEAD>
+<BODY>
+<H1>calcCommonLine</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: calcCommonLine
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Optional :InputEulerAnglesList
+ [-R[ot]1 EMode1 (YOYS ).as(String )
+ Rot1_1 (0.0 ).as(Real )
+ Rot1_2 (0.0 ).as(Real )
+ Rot1_3 (0.0 ).as(Real ) ] :Optional :Input: RotAngle1[degree]
+ [-R[ot]2 EMode2 (YOYS ).as(String )
+ Rot2_1 (0.0 ).as(Real )
+ Rot2_2 (0.0 ).as(Real )
+ Rot2_3 (0.0 ).as(Real ) ] :Optional :Input: RotAngle2[degree]
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output:Degrees
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: commonLinesSearchByVoting: 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 ).as(inFile ) ] :Optional :InputCorrelationMapList
+ [-i[nput]c[ommonLines]InC (NULL ).as(inFile ) ] :Optional :InputCommonLinesList
+ [-i[nput]c[orrect]c[ommonLines]InCC (NULL ).as(inFile ) ] :Optional :InputCorrectCommonLinesList
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputFilteredCommonLinesList
+ [-o[utput]a[ll] OutA (NULL ).as(outFile ) ] :Optional :OutputAllCommonLinesList
+ [-o[utput]d[etecting]r[ate]OutDR (NULL ).as(outFile ) ] :Optional :OutputDetectingRate
+ [-o[utput]d[etecting]r[ate]a[ll]OutDRA (NULL ).as(outFile ) ] :Optional :OutputDetectingRateALL
+ [-o[utput]p[eaks]h[istgram]OutPH (NULL ).as(outFile ) ] :Optional :OutputPeaksHistgram
+ [-e[stimation]n[umber]en (1 ).as(Integer ) ] :Optional :EstimationNumber
+ [-th[resholdLevel] th (1 ).as(Integer ) ] :Optional :ThresholdLevel
+ [-histgramCreate[Flag] ] :Optional :HistgramCreateFlag
+ [-extend[VotingFlag] ] :Optional :ExtendVotingFlag
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :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>
-<HTML>
-<HEAD>
-<TITLE>ll2ltlg</TITLE>
-</HEAD>
-<BODY>
-<H1>ll2ltlg</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: ll2ltlg
-Options:
- [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
- [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-t[itle] Title (NULL ).as(String ) ] :Optional :Title
- [-l[lMax] llMax (1 ).as(Integer ) ] :Optional :llMax
- [-D[elRInv] delRInv (1.0 ).as(Real ) ] :Optional :delRInv[A]
- [-R[MaxInv] RMaxInv (1.0 ).as(Real ) ] :Optional :RMaxInv[A]
- [-d[elr] delr (1.0 ).as(Real ) ] :Optional :delr[A]
- [-r[Max] rMax (1.0 ).as(Real ) ] :Optional :rMax[A]
- [-f[lagOutputInfo] flagOutputInfo (0 ).as(Integer ) ] :Optional :flagOutputInfo
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
->> controlFile Format : replaced by other options which are definitely shown.
-
-Title [char*80]
-InFile [char*80]
-OutFile[char*80]
-InveseOfllDataSamplingSize[Angstrom] llMax llDataMuxiumResolution[Angstrom]
-ltlgDataSamplingSize[Angstrom] ltlgDataMaximumRadius[Angstrom]
-IList(mode)
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: ll2ltlg: そのようなファイルやディレクトリはありません
-/bin/bash: llExtract: No such file or directory
+/bin/bash: llExtract: そのようなファイルやディレクトリはありません
-/bin/bash: llExtractWithLayerSeparation: No such file or directory
+/bin/bash: llExtractWithLayerSeparation: そのようなファイルやディレクトリはありません
-/bin/bash: llExtractWithLayerSeparationServer: No such file or directory
+/bin/bash: llExtractWithLayerSeparationServer: そのようなファイルやディレクトリはありません
-/bin/bash: llExtractWithLayerSeparationSingle: No such file or directory
+/bin/bash: llExtractWithLayerSeparationSingle: そのようなファイルやディレクトリはありません
-/bin/bash: ltlg2mrc: No such file or directory
+/bin/bash: ltlg2mrc: そのようなファイルやディレクトリはありません
-/bin/bash: ltlg2ps: No such file or directory
+/bin/bash: ltlg2ps: そのようなファイルやディレクトリはありません
-/bin/bash: marker2Dto3DEstimator: No such file or directory
+/bin/bash: marker2Dto3DEstimator: そのようなファイルやディレクトリはありません
-<HTML>
-<HEAD>
-<TITLE>mrc2Dto3D</TITLE>
-</HEAD>
-<BODY>
-<H1>mrc2Dto3D</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrc2Dto3D
-Options:
- [-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(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
- 1 : RealSpace: Circle(same density)
- 2 : RealSpace: Circle(weighted density)
- 3 : RealSpace: Square(weighted density)
- 4 : Fourier Space : Plane(same density) -CounterThreshold 0.5
- 5 : Fourier Space : Plane(Linear Gradient)-CounterThreshold 0.5
- 6 : Fourier Space : Plane(Cosine Gradient) Current Recommende using -CounterThreshold 0.5
--------------------------------
--I Option file format
-filename0 RotationOrder0 rot1 rot2 rot3
-filename1 RotationOrder1 rot1 rot2 rot3
-.......................................
->>> RotationOrder : Eular Angle Expression <<<
-Example: YOYS : RotY(rot3)RotX(rot2)RotY(rot1)*v
-First Rotation : y-axis : Y: Y : [X|Y|Z] Axis used initially
-Second Rotation : x-axis : O: Odd : [O|E] Parity of axis permutation
-Last Rotation : z-axis : Y: Yes : [Y|N] Repetition of initial axis as last
-v1 = A v0 : S: Staic : [S|R] Frame from which axes are taken
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrc2Dto3D: そのようなファイルやディレクトリはありません
-/bin/bash: mrc2Dto3DforVariation: No such file or directory
+/bin/bash: mrc2Dto3DforVariation: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageOrientationSearch: No such file or directory
+/bin/bash: mrcImageOrientationSearch: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageOrientationSearchByHigherSelection: No such file or directory
+/bin/bash: mrcImageOrientationSearchByHigherSelection: そのようなファイルやディレクトリはありません
-/bin/bash: mrcImageOrientationSearchByHybridization: No such file or directory
+/bin/bash: mrcImageOrientationSearchByHybridization: そのようなファイルやディレクトリはありません
-<HTML>
-<HEAD>
-<TITLE>mrcImageOrientationSearchBySimultaneousMinimization</TITLE>
-</HEAD>
-<BODY>
-<H1>mrcImageOrientationSearchBySimultaneousMinimization</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrcImageOrientationSearchBySimultaneousMinimization
-Options:
- [-I[nputFileList] In (NULL ).as(inFileListNoOpen ) ] :Essential :InputDataFileList
- [-o[utput] Out (NULL ).as(outFileNoOpen ) ] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
- [-dt[heta] dtheta (1 ).as(Real ) ] :Optional :dtheta
- [-dp[si] dpsi (1 ).as(Real ) ] :Optional :dpsi
- [-m[odeof]s[election]ms (0 ).as(Integer ) ] :Optional :modeofselection
- [-i[nitial]r[andom]d[ata]ird (1 ).as(Integer ) ] :Optional :InitialRandomData
- [-M[ax]C[ount] MC (100 ).as(Integer ) ] :Optional :MaxCount
- [-F[ileName]H[eader] FileNameHeader (EulerAngle).as(String ) ] :Optional :FileNameHeader
- [-m[odeof]i[nitial]d[ada]mid (0 ).as(Integer ) ] :Optional :modeofinitialdata
- [-i[nputFile]i[nitial]d[ata]InInitial (NULL ).as(inFile ) ] :Optional :InputDataFileOfInitialData
- [-m[odeof]s[tart]p[oint]msp (0 ).as(Integer ) ] :Optional :mode of start point
- [-m[odeof]a[ngular]a[rea]maa (0 ).as(Integer ) ] :Optional :mode of angular area
- [-p[revious]dt[heta] pdtheta (0 ).as(Integer ) ] :Optional :previous dtheta
- [-p[revious]dp[si] pdpsi (0 ).as(Integer ) ] :Optional :previous dpsi
- [-m[ode]L[calculation]modeL (0 ).as(Integer ) ] :Optional :Mode of L calculation
- [-m[ode]T[hreshold]A[ngularweight]modeTA (0 ).as(Integer ) ] :Optional :Mode of Threshold of AngularWeight
- [-m[ode]c[alculation]a[rea]modeCA (0 ).as(Integer ) ] :Optional :mode of Lvalue of calculation area
- [-t[hreshold]c[alculation]a[rea]TCA (0 ).as(Real ) ] :Optional :Threshold of Lvalue of calculation area
- [-m[ode]f[ix] modeF (0 ).as(Integer ) ] :Optional :mode of fix
-
------ ModeSelection -----
--ms : 0 : random
- : 1 : myself (-ird)
-
------ Mode --------------
--m : 0 : input data --> sinogram
- : 1 : --> sinogramFT
-
------ Angle -------------
--dt : DEGREE
--dp : DEGREE
--pdt : DEGREE
--pdp : DEGREE
-
------ ModeOfInitialData -------------
--mid : 0 : There is not initial data
- 1 : There is initial data (-iid)
-
------ ModeOfLcalculation -------------
--mL : 0 : differential of length
- 1 : differential of phase
- 2 : addition to derivation1D (multiply)
- 3 : addition to derivation1D (difference)
-
------ ModeOfThresholdAngularWeight -------------
--mTA : 0 : 1.0e-4
- 1 : 1 degree
- 2 : dpsi
-
------ ModeOfStartPoint -------------
--msp : 0 : origin
- 1 : initial data (-iid)
-
------ ModeOfAngularArea -------------
--maa : 0 : all area
- 1 : aroud previous delta (-pdt -pdp)
-
------ ModeOfCalculationArea -------------
--mca : 0 : all area
- 1 : cut under -tca(1/angstrom)
-
------ ModeOfFix -------------
--mf : 0 : don't fix one plane
- 1 : fix one plane (first file is fixed)
-
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrcImageOrientationSearchBySimultaneousMinimization: そのようなファイルやディレクトリはありません
-/bin/bash: mrcRadon2Dto3D: No such file or directory
+/bin/bash: mrcRadon2Dto3D: そのようなファイルやディレクトリはありません
-/bin/bash: energyTransferModelCheck: No such file or directory
+/bin/bash: energyTransferModelCheck: そのようなファイルやディレクトリはありません
-/bin/bash: muscleSimulation: No such file or directory
+/bin/bash: muscleSimulation: そのようなファイルやディレクトリはありません
TARGET=hdf5
-HDF5-VERSION=1.12.0
-HDF5-VERSION2=1-12-0
+HDF5-VERSION=1.13.0
+HDF5-VERSION2=1-13-0
init:: init-hdf5
config:: config-hdf5
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