git add -v --all .
git-add-hostdepend::
- #echo tacyas@git.sourceforge.jp:/gitroot/eos/hostdependX86MAC64.git
- #echo $${EOS_GITUSER}@$(EOS_GIT_REPOSITRY_HOSTDEPEND)$${EOS_HOSTDIR}.git
cd hostdepend/$${EOS_HOSTDIR}/ ; git remote add hostdepend$${EOS_HOSTDIR} $${EOS_GITUSER}@$(EOS_GIT_REPOSITRY_HOSTDEPEND)$${EOS_HOSTDIR}.git | echo "Already exist"
- #git subtree add --prefix=hostdepend/$${EOS_HOSTDIR}/ --squash hostdepend$${EOS_HOSTDIR} master
- cd hostdepend/$${EOS_HOSTDIR}/ ; git add -v --all . ; git commit
+ cd hostdepend/$${EOS_HOSTDIR}/ ; git add -v --all .
git-add-optional::
cd optional; git add -v --all .
git-commit-all:: git-commit git-commit-data git-commit-optional git-commit-tutorial git-commit-others
-git-commit::
+git-commit:: git-commit-hostdepend
git commit
+git-commit-hostdepend::
+ cd hostdepend/$${EOS_HOSTDIR}/ ; git commit
+
git-commit-optional::
cd optional; git commit
--- /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(roiAreaRotateStart) [list source [file join $dir RoiAreaRotate.wish]]
-set auto_index(roiAreaRotateMotion) [list source [file join $dir RoiAreaRotate.wish]]
-set auto_index(roiAreaRotateEnd) [list source [file join $dir RoiAreaRotate.wish]]
-set auto_index(rectangleRotate) [list source [file join $dir RoiAreaRotate.wish]]
-set auto_index(rectangleRotateCalc) [list source [file join $dir RoiAreaRotate.wish]]
-set auto_index(lineRotate) [list source [file join $dir RoiAreaRotate.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(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(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(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(mrcImageInformationWinCreate) [list source [file join $dir Display2Info.wish]]
+set auto_index(imageInformationWinCreate) [list source [file join $dir Display2Info.wish]]
+set auto_index(layerLineInformationWinCreate) [list source [file join $dir Display2Info.wish]]
+set auto_index(projectionInformationWinCreate) [list source [file join $dir Display2Info.wish]]
+set auto_index(sectionInformationWinCreate) [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(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(display2MenuSet2) [list source [file join $dir Display2Menu2.wish]]
-set auto_index(fft2dCmd) [list source [file join $dir fft2dCmd.wish]]
-set auto_index(display2BindingSet) [list source [file join $dir Display2Binding.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(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(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(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]]
-<<<<<<< HEAD
-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(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(rectangleResize) [list source [file join $dir RoiAreaResize.wish]]
-set auto_index(rectangleResizeCalc) [list source [file join $dir RoiAreaResize.wish]]
-set auto_index(lineResize) [list source [file join $dir RoiAreaResize.wish]]
-set auto_index(splineResize) [list source [file join $dir RoiAreaResize.wish]]
-=======
-set auto_index(fft2dCmd) [list source [file join $dir fft2dCmd.wish]]
->>>>>>> FETCH_HEAD
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(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(mrcImageInformationWinCreate) [list source [file join $dir Display2Info.wish]]
-set auto_index(imageInformationWinCreate) [list source [file join $dir Display2Info.wish]]
-set auto_index(layerLineInformationWinCreate) [list source [file join $dir Display2Info.wish]]
-set auto_index(projectionInformationWinCreate) [list source [file join $dir Display2Info.wish]]
-set auto_index(sectionInformationWinCreate) [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(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(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(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(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(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(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(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(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(rectangleResize) [list source [file join $dir RoiAreaResize.wish]]
+set auto_index(rectangleResizeCalc) [list source [file join $dir RoiAreaResize.wish]]
+set auto_index(lineResize) [list source [file join $dir RoiAreaResize.wish]]
+set auto_index(splineResize) [list source [file join $dir RoiAreaResize.wish]]
+set auto_index(roiAreaRotateStart) [list source [file join $dir RoiAreaRotate.wish]]
+set auto_index(roiAreaRotateMotion) [list source [file join $dir RoiAreaRotate.wish]]
+set auto_index(roiAreaRotateEnd) [list source [file join $dir RoiAreaRotate.wish]]
+set auto_index(rectangleRotate) [list source [file join $dir RoiAreaRotate.wish]]
+set auto_index(rectangleRotateCalc) [list source [file join $dir RoiAreaRotate.wish]]
+set auto_index(lineRotate) [list source [file join $dir RoiAreaRotate.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(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]]
-<<<<<<< HEAD
-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(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(unitCellRecreate) [list source [file join $dir UnitCell.wish]]
->>>>>>> FETCH_HEAD
+set auto_index(fft2dCmd) [list source [file join $dir fft2dCmd.wish]]
--- /dev/null
+all:
+ for i in $(SOURCE); \
+ do \
+ echo $$i; \
+ $(CD) $$i; \
+ $(MAKE) all; \
+ $(CD) ..; \
+ done
+
+install:
+ for i in $(SOURCE);\
+ do \
+ $(CD) $$i; $(MAKE) install; $(CD) ..; \
+ done
+
+debug:
+ for i in $(SOURCE); \
+ do \
+ echo $$i; \
+ $(CD) $$i; \
+ $(MAKE) debug; \
+ $(CD) ..; \
+ done
+
+install-debug:
+ for i in $(SOURCE);\
+ do \
+ $(CD) $$i; $(MAKE) install-debug; $(CD) ..; \
+ done
+
+clean:
+ for i in $(SOURCE);\
+ do \
+ $(CD) $$i; $(MAKE) clean; $(CD) ..; \
+ done
+
+put:
+ for i in $(SOURCE);\
+ do \
+ $(CD) $$i; $(MAKE) put; $(CD) ..; \
+ done
+
+depend: check
+ for i in $(SOURCE);\
+ do \
+ $(CD) $$i; $(MAKE) depend; $(CD) ..; \
+ done
+
+check::
+ @if [ ! -d $(EOS_HOME)/lib ] ; then \
+ mkdir $(EOS_HOME)/lib ; \
+ fi
+ @if [ ! -d $(EOS_HOME)/include ] ; then \
+ mkdir $(EOS_HOME)/include ; \
+ fi
+ @for i in $(SOURCE);\
+ do \
+ $(CD) $$i; \
+ dotSourceInMakefileCreate ./ $$i $(WORLDNAME); \
+ $(RM) -f Makefile; \
+ $(CP) ../../Config/Template/$(WORLDNAME)ClassTemplate.Dir/Makefile Makefile; \
+ $(CD) Config; \
+ $(RM) -f Target.inc; \
+ $(CP) ../../../Config/Template/$(WORLDNAME)ClassTemplate.Dir/Config/Target.inc Target.inc; \
+ $(CD) ..; \
+ $(MAKE) check; \
+ $(CD) ..; \
+ done
+
+backup::
+ @cd ../..; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/Config ; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/Makefile ; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/.[A-z]*
+ @for i in $(SOURCE);\
+ do \
+ $(CD) $$i; $(MAKE) backup; $(CD) ..; \
+ done
+
+backup-all::
+ @cd ../..; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/Config ; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/Makefile ; \
+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/.[A-z]*
+ @for i in $(SOURCE);\
+ do \
+ $(CD) $$i; $(MAKE) backup-all; $(CD) ..; \
+ done
+
+distribute::
+ @cd ../..; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/Config ; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/Makefile ; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/.[A-z]*
+ @for i in $(SOURCE);\
+ do \
+ $(CD) $$i; $(MAKE) distribute; $(CD) ..; \
+ done
+
+distribute-all::
+ @cd ../..; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/Config ; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/Makefile ; \
+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/.[A-z]*
+ @for i in $(SOURCE);\
+ do \
+ $(CD) $$i; $(MAKE) distribute-all; $(CD) ..; \
+ done
+
+<HTML>
+<HEAD>
+<TITLE>
+ctfInfo
+</TITLE>
+</HEAD>
+<BODY bgcolor="#ffffcc">
+<H1> ctfInfo Object </H1>
+
+<H2> <A HREF="#information"> information from souce codes</A></H2>
+<H2> <A HREF="#include"> include file </A></H2>
+<HR>
+<A NAME="Information">
+<H2>Information from source codes</H2>
+</A>
+<PRE>
+../src/ctfDeterminationFromPhaseComparison.c:
+
+../src/ctfFunction.c:
+
+../src/ctfInfoPVM.c:
+
+../src/ctfInfoRead.c:
+
+../src/ctfInfoWrite.c:
+
+../src/ctfInfoWrite2.c:
+
+../src/ctfWeight.c:
+
+../src/ctfZeroPoint.c:
+
+../src/lastigmatismDetection.c:
+
+../src/lctfDetermination.c:
+
+../src/lctfDetermine.c:
+
+../src/lmolecularEnvelope.c:
+
+../src/lmrcFSInfoScatteringAngularDistributionAverageSection.c:
+
+../src/powerspectraTangentLine.c:
+
+../src/thonRing.c:
+</PRE>
+<HR>
+<A NAME="include">
+<H2>ctfInfo.h</H2>
+</A>
+<PRE>
+#ifndef CTF_INFO_H
+#define CTF_INFO_H
+#include <stdio.h>
+
+/* constant begin */
+#define ctfInfoModeWithAmplitudeContrast 0x0f
+#define ctfInfoModeWithMTF 0x10
+#define ctfInfoModeWithIlluminationAngle 0x20
+#define ctfInfoModeWithEnergySpread 0x40
+#define ctfInfoModeAbsoluteValue 0x100
+
+typedef enum ctfInfoMode {
+ ctfInfoModePhaseCTFOnly = 0,
+ ctfInfoModePhaseAndAmpCTF = 1
+} ctfInfoMode;
+
+typedef enum ctfInfoMTFMode {
+ ctfInfoMTFModeSingleExp = 0,
+ ctfInfoMTFModeSingleLorentzian = 1,
+ ctfInfoMTFModeBoth = 2,
+ ctfInfoMTFModeLinear = 3,
+ ctfInfoMTFModeBothSum = 4,
+ ctfInfoMTFModePolynomial = 5
+} ctfInfoMTFMode;
+/* constant end */
+
+/* struct begin */
+typedef struct moleculrEnvelope {
+ char* filename;
+ int nR;
+ float* R;
+ float* Envelope;
+ int mode;
+} molecularEnvelope;
+
+typedef struct ctfInfo {
+ float kV; /* kV */
+ float defocus; /* A : Underfocus is plus, while overfocus is minus*/
+ float Cc; /* mm */
+ float dE;
+ float Cs; /* mm */
+ float Ain; /* mrad : Illumination Angle */
+ long flagWin; /* Windowing */
+ float CutLow; /* Windowing: CutLow A-1 */
+ float CutHigh; /* Windowing: CutHigh A-1 */
+
+ float I0; /* Intensity */
+ float Isignal; /* Intensity of signal */
+
+ float ratioOfAmpToPhase; /* The ratio of amp to phase */
+
+ float Inoise; /* Intensity of noise : Isignal*/
+ long flagWhiteNoise;
+ float WhiteNoise; /* Affected by MTF(R) */
+
+ long flagWhiteNoiseRaising;
+ float WhiteNoiseRaising; /* WhiteNoise Raising depending upon R */
+
+ long flagMaxWhiteNoise;
+ float MaxWhiteNoise; /* max White Noise*/
+
+ long flagNdependentWhiteNoise;
+ float NdependentWhiteNoise; /* max White Noise*/
+
+ float Inoise2; /* Intensity of noise */
+ long flagWhiteNoise2;
+ float WhiteNoise2; /* Not Affected by MTF(R)*/
+
+ int flagAstigmatism;
+ float defocus2D[2]; /* A : Normally [0]: Max [1]: Min */
+ float defocus0axis; /* radian : angle of the defocus2D[0]-axis */
+
+ long mode;
+
+ long flagMagnification;
+ float Magnification;
+
+ /* MTF(R): Modulation Transfer Function */
+ ctfInfoMTFMode MTFMode;
+ float BofMTF; /* Exponential: exp(-B R) */
+ float BofMTF2; /* Lorentzian : 1/(B*B+R*R) */
+ float WeightOfSecondTermForMTF; /* 0 <-> 1 */
+ /*for PolynomialExpNoise*//*d = degree*/
+ float BofMTFd2;
+ float BofMTFd3;
+ float BofMTFd4;
+ float BofMTFd5;
+ float BofMTFd6;
+
+ /* Molecular Envelope: Scattering Factor */
+ /* For Gaussian */
+ float MolecEnv; /* A : */
+ /* For Table */
+ long flagMolecEnvTable;
+ molecularEnvelope MolecEnvTable;
+ /* For Lorentzian */
+ float flagElastic;
+ float Elastic;
+ float ElasticShift;
+ float ElasticWidth;
+ float ElasticRing;
+ float ElasticRingPosition;
+ float ElasticRingWidth;
+
+ /* Stage Vibration */
+ long flagVibration;
+ long VibrationMode;
+ float BofVibration;
+
+ /* Aliasing and Sampling */
+ long flagAliasing;
+ float NyquistFrequency;
+ long flagSampling;
+
+ /* Inelastic Signal */
+ /* For Gaussian */
+ long flagWithInElastic;
+ float InElasticGaussian;
+ /* For Table */
+ long flagWithInElasticTable;
+ molecularEnvelope InElasticEnvTable;
+ /* Lorentzian */
+ long flagInElastic;
+ float InElastic;
+ float InElasticShift;
+ float InElasticWidth;
+ float InElasticRing;
+ float InElasticRingPosition;
+ float InElasticRingWidth;
+} ctfInfo;
+/* struct end */
+
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* prototype begin */
+
+extern void ctfInfoSendByPVM(ctfInfo* info, int tid, long mode);
+extern void ctfInfoRecieveByPVM(ctfInfo* info, int tid, long mode);
+extern float ctfSignalFunction(ctfInfo* info, float R, long mode);
+extern float ctfNoiseFunction(ctfInfo* info, float R, long mode);
+extern float ctfNoise2Function(ctfInfo* info, float R, long mode);
+extern float ctfSignalPowerFunction(ctfInfo* info, float R, long mode);
+extern float ctfNoisePowerFunction(ctfInfo* info, float R, long mode);
+extern float ctfNoise2PowerFunction(ctfInfo* info, float R, long mode);
+extern float ctfScatteringFunction(ctfInfo* info, float R, long mode);
+extern float ctfMolecularEnvelopeFunction(ctfInfo* info, float R, long mode);
+extern float ctfMolecularEnvelopeInElasticFunction(ctfInfo* info, float R, long mode);
+extern float ctfVibrationFunction(ctfInfo* info, float R, long mode);
+extern float ctfFunction(ctfInfo* info, float R, long mode);
+extern float ctfFunctionSampling(float R, float Nyquist, long mode);
+extern void ctfFunctionPVMStart(ctfInfo* info, float R, int tid, long mode);
+extern float ctfFunctionPVMEnd(ctfInfo* info, float R, int tid, long mode);
+extern void ctfFunctionPVMServer();
+extern float ctfEnvelopFunction(ctfInfo* info, float R, long mode);
+extern float ctfMTFFunction(ctfInfo* info, float R, long mode);
+extern float ctfFunction2D(ctfInfo* info, float X, float Y, long mode);
+extern float wavelengthOfElectron(float E);
+extern float defocusDeterminationFromThonRing(ctfInfo* info, float R, long n, long mode);
+extern void ctfWeightForCorrectionUsage(FILE* fpt);
+extern float ctfWeightForCorrection2D(ctfInfo* info, float X, float Y, long mode);
+extern float ctfWeightForCorrection(ctfInfo* info, float R, long mode);
+extern void lmolecularEnvelopeFileRead(FILE* fpt, molecularEnvelope* mol, int mode);
+extern void lmolecularEnvelopeFileWrite(FILE* fpt, molecularEnvelope* mol, int mode);
+extern void lmolecularEnvelopeResampling(molecularEnvelope* dst, molecularEnvelope* src, float dR, float RMax, int mode);
+extern float lmolecularEnvelopeDataGet(molecularEnvelope* src, float R, int mode);
+extern void ctfInfoRead(FILE* fpt, ctfInfo* ctf, char* pre, int mode);
+extern void ctfInfoWrite(FILE* fpt, ctfInfo ctf, char* pre, int mode);
+/* prototype end */
+
+#ifdef __cplusplus
+};
+#endif
+
+#endif
+</PRE>
+</BODY>
+</HTML>
<H2>Information from source codes</H2>
</A>
<PRE>
+../src/fftn.c:
+
+../src/lmrcFETnormalizeBySD.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/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/lmrcImageHoughTransform.c:
+
+../src/lmrcImageLabeling.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/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/lmrcImageSolventFlattening.c:
+
+../src/lmrcImageSpatialFrequencyFilter.c:
+
+../src/lmrcImageSphere.c:
+
+../src/lmrcImageSplit.c:
+
+../src/lmrcImageStack.c:
+
+../src/lmrcImageStudentCalculate.c:
+
+../src/lmrcImageSubtractionCalc.c:
+
+../src/lmrcImageSummationCalculate.c:
+
+../src/lmrcImageSymmetryFind.c:
+
+../src/lmrcImageTfunction.c:
+
+../src/lmrcImageToneReversal.c:
+
+../src/lmrcImageTopHatTransform.c:
+
+../src/lmrcImageTrans.c:
+
+../src/lmrcImageTransformDescartesIntoPolar.c:
+
+../src/lmrcImageTriming.c:
+
+../src/lmrcImageVolumeCalc.c:
+
+../src/lmrcImageWindowing.c:
+
+../src/lmrcImagesFTest.c:
+
+../src/lmrcImagesStatDataGet.c:
+
+../src/lmrcImagesTTest.c:
+
+../src/lmrcImagesVarianceAnalysis.c:
+
+../src/lmrcImagesVarianceMap.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">
SpecialNumber \
String \
Vector \
-X86MAC64 \
dummy \
eosCuda \
eosFunc \
<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">
--- /dev/null
+include ../../../../Config/Define.inc
+include ../../../Config/Define.inc
+include ../../Config/Define.inc
+include ../Config/Define.inc
+
+SOURCEDOC = $(OBJECTNAME).html
+DOCDSTDIR = $(EOS_HOME)/doc/Objects
+TARGETDOC = $(DOCDSTDIR)/$(SOURCEDOC)
+
+all: $(SOURCEDOC)
+
+install : $(TARGETDOC)
+
+$(TARGETDOC):$(SOURCEDOC)
+ $(INSTALL) -m 444 *.html $(DOCDSTDIR)
+ @cd $(DOCDSTDIR); make
+
+$(SOURCEDOC) : .$(SOURCEDOC) .header .footer ../inc/$(OBJECTNAME).h Makefile ../src/*.c
+ @echo Creating $(OBJECTNAME).html
+ @cat .header > $(SOURCEDOC)
+ @#htmlUpdateTime >> $(SOURCEDOC)
+ @cat .$(SOURCEDOC) >> $(SOURCEDOC)
+ @echo \<HR\> >> $(SOURCEDOC)
+ @echo "<A NAME=\"Information\">" >> $(SOURCEDOC)
+ @echo "<H2>Information from source codes</H2>" >> $(SOURCEDOC)
+ @echo "</A>" >> $(SOURCEDOC)
+ @echo "<PRE>" >> $(SOURCEDOC)
+ -@ident ../src/*.c >> $(SOURCEDOC)
+ @echo "</PRE>" >> $(SOURCEDOC)
+ @echo \<HR\> >> $(SOURCEDOC)
+ @echo \<A NAME=\"include\"\>>> $(SOURCEDOC)
+ @echo "<H2>$(OBJECTNAME).h</H2>">> $(SOURCEDOC)
+ @echo \</A\> >>$(SOURCEDOC)
+ @echo \<PRE\> >> $(SOURCEDOC)
+ @cat ../inc/$(OBJECTNAME).h >> $(SOURCEDOC)
+ @echo \</PRE\> >> $(SOURCEDOC)
+ @cat .footer >> $(SOURCEDOC)
+
+clean:
+
+depend:
-/bin/bash: dcdAtomChangeDistanceFromAtom: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>dcdAtomChangeDistanceFromAtom</TITLE>
+</HEAD>
+<BODY>
+<H1>dcdAtomChangeDistanceFromAtom</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: dcdAtomChangeDistanceFromAtom
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: dcdAtomDistanceDistribution: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>dcdAtomDistanceDistribution</TITLE>
+</HEAD>
+<BODY>
+<H1>dcdAtomDistanceDistribution</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: dcdAtomDistanceDistribution
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-o[utput]mrc OutMRC (NULL ).as(outFile ) ] :Optional :Output: MRCFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: dcdFilePrint: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>dcdFilePrint</TITLE>
+</HEAD>
+<BODY>
+<H1>dcdFilePrint</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: dcdFilePrint
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: DCD
+ [-i[nput]p[db] InPDB (NULL ).as(inFile ) ] :Optional :Input: PDB
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: ASCII
+ [-o[utput]p[db] OutPDB (NULL ).as(outFile ) ] :Optional :Output: PDB
+ [-r[ange] rStart (10 ).as(Integer )
+ rEnd (100 ).as(Integer )
+ rDelta (10 ).as(Integer ) ] :Optional :Input: Start End Delta
+ [-s[tart] Start (10 ).as(Integer ) ] :Optional :Input: Start
+ [-e[nd] End (100 ).as(Integer ) ] :Optional :Input: End
+ [-d[elta] Delta (10 ).as(Integer ) ] :Optional :Input: Delta(Interval)
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: dcdInfo: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>dcdInfo</TITLE>
+</HEAD>
+<BODY>
+<H1>dcdInfo</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: dcdInfo
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: DCD
+ [-i[nput]p[db] InPDB (NULL ).as(inFile ) ] :Optional :Input: PDB
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: ASCII
+ [-o[utput]p[db] OutPDB (NULL ).as(outFile ) ] :Optional :Output: PDB
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: dcdSelectAtoms: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>dcdSelectAtoms</TITLE>
+</HEAD>
+<BODY>
+<H1>dcdSelectAtoms</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: dcdSelectAtoms
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: dcdSerectAtom: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>dcdSerectAtom</TITLE>
+</HEAD>
+<BODY>
+<H1>dcdSerectAtom</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: dcdSerectAtom
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: dcdTimeSeriesBehavior: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>dcdTimeSeriesBehavior</TITLE>
+</HEAD>
+<BODY>
+<H1>dcdTimeSeriesBehavior</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: dcdTimeSeriesBehavior
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/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
+++ /dev/null
-/Users/tacyas/Eos/src/Config/Template/ToolsHomeTemplate.Dir/Makefile
\ No newline at end of file
--- /dev/null
+include ../Config/Define.inc
+include Config/Define.inc
+include .Source
+
+include Config/Target.inc
-/bin/bash: ctfEnvelopFunctionEstimate: 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>ctfEnvelopFunctionEstimate</TITLE>
+</HEAD>
+<BODY>
+<H1>ctfEnvelopFunctionEstimate</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: ctfEnvelopFunctionEstimate
+Options:
+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input:
+ [-o[utput] Out (stdout ).as(outFile::ASCII ) ] :Optional :Output:
+ [-degree degree (6 ).as(Integer ) ] :Optional :[dim]
+ [-Range CutLow (0.01 ).as(Real )
+ CutHigh (0.2 ).as(Real ) ] :Optional :[/A]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: mrc2gif: No such file or directory
+/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
-/bin/bash: mrcImageColoring: No such file or directory
+/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
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 5.533535e-322ach
+ [-C[ontour] Contour (10 ).as(Real ) ] :Optional :ContourLevel: 10 6.899440e-310ach
[-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: 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>
[-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
[-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: molvieDock: No such file or directory
+/bin/bash: molvieDock: そのようなファイルやディレクトリはありません
-/bin/bash: molvieProjection: No such file or directory
+/bin/bash: molvieProjection: そのようなファイルやディレクトリはありません
-/bin/bash: molvieViewer: No such file or directory
+/bin/bash: molvieViewer: 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>
energyTransferModelCheck \
energyTransferModelResultCheck \
muscleSimulation \
+probabilityDensityFunction \
#LastSource
--- /dev/null
+../../../../../hostdepend/X86LINUX64/src/Tools/simulation/probabilityDensityFunction/src/X86LINUX64
\ No newline at end of file
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>probabilityDensityFunction</TITLE>
+</HEAD>
+<BODY>
+<H1>probabilityDensityFunction</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: probabilityDensityFunction
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
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