cd src/Tools; make check; make depend; make ; make install
setting:relink
- if [ ! -d hostdepend] ; then \
+ if [ ! -d hostdepend ] ; then \
mkdir hostdepend; \
fi
# a script that loads the command.
set auto_index(libraryLoad) [list source [file join $dir ctfDisplay.wish]]
-set auto_index(ctfDisplayDefault) [list source [file join $dir ctfDisplay.wish]]
set auto_index(::CTF2D::Init) [list source [file join $dir ctfDisplay.wish]]
set auto_index(::CTF2D::ctfInfoSync) [list source [file join $dir ctfDisplay.wish]]
set auto_index(::CTF2D::ctfInfoUpload) [list source [file join $dir ctfDisplay.wish]]
set auto_index(::CTF2D::CTFCalculation) [list source [file join $dir ctfDisplay.wish]]
set auto_index(::CTF2D::ScatteringCalc) [list source [file join $dir ctfDisplay.wish]]
set auto_index(::CTF2D::ctfInfoSave) [list source [file join $dir ctfDisplay.wish]]
-set auto_index(::CTF2D::ctfInfoSaveDefaultDir) [list source [file join $dir ctfDisplay.wish]]
-set auto_index(::CTF2D::ctfInfoSaveDefault) [list source [file join $dir ctfDisplay.wish]]
set auto_index(::CTF2D::ctfInfoLoad) [list source [file join $dir ctfDisplay.wish]]
-set auto_index(::CTF2D::dummyFunc) [list source [file join $dir ctfDisplay.wish]]
--- /dev/null
+# Top Level Makefile
+
+all:
+ cd Objects; make
+ cd Tools; make
+
+check: check-objects check-tools
+
+
+check-objects:
+ rm -f Objects/Makefile; cp -f Config/Template/ObjectsHomeTemplate.Dir/Makefile Objects/Makefile
+ cd Objects; dotSourceInMakefileCreate; make check
+
+check-tools:
+ rm -f Tools/Makefile ; cp -f Config/Template/ToolsHomeTemplate.Dir/Makefile Tools/Makefile
+ cd Tools ; dotSourceInMakefileCreate; make check
+
+depend:
+ cd Objects; make depend
+ cd Tools; make depend
+
+install:
+ cd Objects; make install
+ cd Tools; make install
+
+clean:
+ cd Objects; make clean
+ cd Tools; make clean
+
<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/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/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/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/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/stringGet.c:
-
-../src/stringGetFromFile.c:
-
-../src/stringIsSame.c:
-
-../src/stringUtil.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/eosFunc.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">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/eosPointCopy.c:
-
-../src/eosPointProject.c:
-
-../src/eosPointRead.c:
-
-../src/eosPointRotate.c:
-
-../src/eosPointUtil.c:
-
-../src/eosPointWrite.c:
</PRE>
<HR>
<A NAME="include">
--- /dev/null
+all:
+ for dir in ${SOURCE}; \
+ do \
+ ${CD} $${dir}; make all; $(CD) ..; \
+ done
+
+install:
+ for dir in ${SOURCE}; \
+ do \
+ ${CD} $${dir}; make install; ${CD} ..; \
+ done
+
+put:
+ for dir in ${SOURCE}; \
+ do \
+ ${CD} $${dir}; make put; ${CD} ..; \
+ done
+
+clean:
+ for dir in ${SOURCE}; \
+ do \
+ ${CD} $${dir}; make clean; ${CD} ..; \
+ done
+
+check:
+ @for dir in ${SOURCE}; \
+ do \
+ $(CD) $${dir}; \
+ dotSourceInMakefileCreate ./ $$dir $(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
+
+depend: check
+ @for dir in ${SOURCE}; \
+ do \
+ ${CD} $${dir}; make depend; ${CD} ..; \
+ done
+
+backup:
+ cd ../.. ; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/Config ; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/Makefile ; \
+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/.[A-z]*
+ @for dir in ${SOURCE}; \
+ do \
+ ${CD} $${dir}; 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 dir in ${SOURCE}; \
+ do \
+ ${CD} $${dir}; make backup; ${CD} ..; \
+ done
+
+distribute:
+ cd ../.. ; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/Config ; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/Makefile ; \
+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/.[A-z]*
+ @for dir in ${SOURCE}; \
+ do \
+ ${CD} $${dir}; 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 dir in ${SOURCE}; \
+ do \
+ ${CD} $${dir}; make distribute-all; ${CD} ..; \
+ done
+
-/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: dcdCompareCA: 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: dcdDistanceAtomBetweenAtom: No such file or directory
-<HTML>
-<HEAD>
-<TITLE>Display2</TITLE>
-</HEAD>
-<BODY>
-<H1>Display2</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: Display2
-Options:
- [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Optional :Input:mrcImage
- [-t[epmlate] Template (%d.roi ).as(String ) ] :Optional :Template for InputFile
- [-H[ighForThres] ThresHigh (0.0 ).as(Real ) ] :Optional :HighThres
- [-L[owForThres] ThresLow (0.0 ).as(Real ) ] :Optional :LowThres
- [-Zoom Zoom (1.0 ).as(Real ) ] :Optional :Zoom for InputFile
- [-Inverse ] :Optional :Inverse (HighValue(dark)<->LowValue(bright)) for InputFile
- [-o[utput] Out (.EosLog ).as(String ) ] :Optional :OutputLogFile
- [-def[ault] Default (~/.Eos/Display2).as(String ) ] :Optional :OutputLogFile
- [-display geometry (:0.0 ).as(String ) ] :Optional :OutputLogFile
- [-geometry display (1024x1024+0+0).as(String ) ] :Optional :OutputLogFile
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
-New wish commands of Display2
-mrcInfoSet [z|min|max] value
-mrcInfoSet [log|pow]
-mrcInfoGet [Nx|Ny|Nz|Max|Min|Mean|Hist]
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: Display2: 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: Display3: 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: Eos: No such file or directory
-<HTML>
-<HEAD>
-<TITLE>StereoDisplay</TITLE>
-</HEAD>
-<BODY>
-<H1>StereoDisplay</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: StereoDisplay
-Options:
- [-il[nputl] Inl (NULL ).as(inFile ) ] :Optional :Input: Left
- [-ir[nputr] Inr (NULL ).as(inFile ) ] :Optional :Input: Right
- [-I[nputFileList] In (NULL ).as(inFileList ) ] :Optional :Input: Left Right
- [-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 -----
->>> -I for InFileList
-Left1 Right1
-Left2 Right2
-.....
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: StereoDisplay: 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: Visualmake: No such file or directory
-/bin/bash: ctfDisplay: そのようなファイルやディレクトリはありません
+/bin/bash: ctfDisplay: 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: imagesClustering: No such file or directory
-/bin/bash: imagesView: そのようなファイルやディレクトリはありません
+/bin/bash: imagesView: 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: obj3Don2DImageView: 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
+/bin/bash: smolet: No such file or directory
-/bin/bash: mallocCheck: そのようなファイルやディレクトリはありません
+/bin/bash: mallocCheck: 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: ctfDeterminationFromPhaseComparison: No such file or directory
-/bin/bash: ctfFunction: 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>ctfFunction</TITLE>
+</HEAD>
+<BODY>
+<H1>ctfFunction</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: ctfFunction
+Options:
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-Rmax Rmax (0.1 ).as(Real ) ] :Optional :Rmax[/A]
+ [-dR dR (0.0001 ).as(Real ) ] :Optional :dR[/A]
+ [-kV kV (200 ).as(Real ) ] :Optional :AccVol[kV]
+ [-Cs Cs (2.1 ).as(Real ) ] :Optional :Cs[mm]
+ [-df Defocus (27000 ).as(Real ) ] :Essential :Defocus[A]:under(+)
+ [-A AoverP (0.0 ).as(Real ) ] :Optional :AmplitudeContrast/PhaseContrast
+ [-Ain Ain (0.02 ).as(Real ) ] :Optional :IlluminationAperture[mrad]
+ [-ctfMode ctfMode (32 ).as(Integer ) ] :Optional :CTFMode
+ [-pvm pvm (0 ).as(Integer ) ] :Optional :PVM: MultiProcessor
+ [-pvmList pvmList (stdin ).as(inFile ) ] :Optional :PVM Host List: MultiProcessor
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+>>>> ctfMode <<<<
+ 0: Phase CTF
+ 1: PhaseCTF + ratio*AmpCTF
+ 32: EnvFromAillumination*()
+>>>> mode <<<<
+No action
+</PRE>
+</BODY>
+</HTML>
-/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: ctfFunctionServer: No such file or directory
-/bin/bash: ctfInfoSet: 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>ctfInfoSet</TITLE>
+</HEAD>
+<BODY>
+<H1>ctfInfoSet</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: ctfInfoSet
+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: ctfMultiFunction: 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>ctfMultiFunction</TITLE>
+</HEAD>
+<BODY>
+<H1>ctfMultiFunction</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: ctfMultiFunction
+Options:
+ [-I[nput array of file]In (NULL ).as(inFileListNoOpen ) ] :Optional :InputDataFiles
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-Rmax Rmax (0.1 ).as(Real ) ] :Optional :Rmax[/A]
+ [-dR dR (0.0001 ).as(Real ) ] :Optional :dR[/A]
+ [-Ain Ain (0.02 ).as(Real ) ] :Optional :IlluminationAperture[mrad]
+ [-ctfMode ctfMode (33 ).as(Integer ) ] :Optional :CTFMode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+>>>> ctfMode <<<<
+ 0: Phase CTF
+ 1: PhaseCTF + ratio*AmpCTF
+ 32: EnvFromAillumination*()
+>>>> File Format <<<<
+Defocus[A] Cs[mm] AccV[kV] AmplitudeContrast
+Info file was made by llExtractWithLayerSeparationFilamentInfo -oI
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: ctfWeightMapCreation: 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>ctfWeightMapCreation</TITLE>
+</HEAD>
+<BODY>
+<H1>ctfWeightMapCreation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: ctfWeightMapCreation
+Options:
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-kV kV (200 ).as(Real ) ] :Optional :AccVol[kV]
+ [-Cs Cs (1.7 ).as(Real ) ] :Optional :Cs[mm]
+ [-df Defocus (2.7 ).as(Real ) ] :Essential :Defocus[A]:under(+)
+ [-white WhiteNoise (1.0 ).as(Real ) ] :Optional :WhiteNoise(N/S)
+ [-noise Noise (NULL ).as(inFile ) ] :Optional :Noise Power Spectrum
+ [-splusn SplusN (NULL ).as(inFile ) ] :Optional :Signal+Noise Power Spectrum
+ [-dRinv dRinv (1024*5/3 ).as(Real ) ] :Essential :dRinv[A]
+ [-dRmaxInv dRmaxInv (10.0 ).as(Real ) ] :Essential :dRmaxInv[A]
+ [-SinWin SinWinRminInv (20.0 ).as(Real )
+ SinWinRmaxInv (10.0 ).as(Real ) ] :Optional :RminInv[A] RmaxInv[A]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+Mode:
+ 0: No correction : F = G
+ 1: Phase contrast : F = G*(H/abs(H))(Only 1 or -1)
+ 2: Phase contrast : F = G*H (Winer filter (S/N << 1))
+ 3: Phase contrast : F = G/H (Inverse filter)
+ 4: Phase contrast : F = G*(H/(H*H + N*N)) (Winer filter (white noise : Required Option -white))
+ 5: Phase contrast : F = G*(H/abs(H)*abs(G*G-N*N)/(G*G)) (Winer filter: Required Option -noise, -splusn))
+</PRE>
+</BODY>
+</HTML>
-/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: ctfZeroPoint: 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>defocusDeterminationFromThonRing</TITLE>
+</HEAD>
+<BODY>
+<H1>defocusDeterminationFromThonRing</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: defocusDeterminationFromThonRing
+Options:
+ [-i[nput] In (stdin ).as(inFile ) ] :Optional :InputDataFile
+ [-i[nput] N[ame] InN (stdin ).as(String ) ] :Optional :InputNameInInformationFile
+ [-i[nput] R[eference]InR (stdin ).as(String ) ] :Optional :InputReferenceForLength
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-o[utput] I[nformation]OutI (stdout ).as(outFile ) ] :Optional :OutputInformationFile
+ [-o[utput] I[nformation]OutI2 (stdout ).as(outFile ) ] :Optional :OutputInformationFile
+ [-o[utput] I[nformation]OutI3 (stdout ).as(outFile ) ] :Optional :OutputInformationFile
+ [-kV kV (200 ).as(Real ) ] :Optional :kV
+ [-Cs Cs (2.1 ).as(Real ) ] :Optional :Cs[mm]
+ [-A[mplitude contrast]AoverP (0.05 ).as(Real ) ] :Optional :The ratio of amplitude contrast to phase contrast
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-ctfMode ctfMode (0 ).as(Integer ) ] :Optional :CTFMode
+ [-truePitch truePitch (430 ).as(Real ) ] :Optional :True Pitch
+ [-PixelSize PixelSize (5 ).as(Real ) ] :Optional :Pixel Size [A]
+ [-deltadY deltadY (0.5 ).as(Real ) ] :Optional :A range of deltadY to determine dY.
+ [-R[/A] R (NULL ).as(Real ) ... ] :Variable :ThonRing[/A]
+----- Additional Usage -----
+>>>> o[uput] I[nformation] <<<<
+This file is used for [mrcImageMultiCTFCompensation and mrcImageCTFCompensation]
+>>>> o[uput] I[nformation] 2<<<<
+This file is used for [llDataCTFCompensate -I2]
+>>>> o[uput] I[nformation] 3<<<<
+This file is used for [llExtractWithLayerSeparation]
+Options: -truePitch, -PixelSize, -deltadY and -ctfMode
+>>>> ctfMode <<<<
+ 0: Phase CTF
+ 1: PhaseCTF + ratio*AmpCTF
+>>>> mode <<<<
+No action
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: electronWaveLength: 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>electronWaveLength</TITLE>
+</HEAD>
+<BODY>
+<H1>electronWaveLength</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: electronWaveLength
+Options:
+ [-kV kV (200 ).as(Real ) ] :Optional :InputDataFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: molecularEnvelopeResampling: 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>molecularEnvelopeResampling</TITLE>
+</HEAD>
+<BODY>
+<H1>molecularEnvelopeResampling</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: molecularEnvelopeResampling
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-Rmax Rmax (1.0 ).as(Real ) ] :Optional :Rmax: [/A]
+ [-dR dR (0.01 ).as(Real ) ] :Optional :dR: [/A]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</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
+<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: 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: homology2PG: 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: pgDataBaseSelectServer: 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: pgJournalSelect: 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: pgJournalSelectCORBAClient: 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: pgJournalSelectCORBAServer: 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: pgMemoSelectCORBAServer: 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: pgSelect: No such file or directory
-SOURCE_FILE =\
+SOURCE=\
+eosBayesInit \
#LastSource
-/bin/bash: eosBayesInit: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>eosBayesInit</TITLE>
+</HEAD>
+<BODY>
+<H1>eosBayesInit</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: eosBayesInit
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input:Control
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output:Bayes
+ [-n[um] numDistribution (3 ).as(Integer )
+ numLikelihood (3 ).as(Integer ) ] :Essential :Integer
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-<HTML>
-<HEAD>
-<TITLE>eosPointProjector</TITLE>
-</HEAD>
-<BODY>
-<H1>eosPointProjector</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: eosPointProjector
-Options:
- [-i[nput] In (stdin ).as(inFile::ASCII ) ] :Optional :Input: eosPoint
- [-i[nput]t[ype] InType (3 ).as(Integer ) ] :Optional :Input: eosPointType
- [-o[utput] Out (stdout ).as(outFile::ASCII ) ] :Optional :Output: eosPoint
- [-o[utput]t[ype] OutType (3 ).as(Integer ) ] :Optional :Input: eosPointType
- [-E[uler]A[ngle] EAMode (YOYS ).as(String )
- Rot1 (0.0 ).as(Real )
- Rot2 (0.0 ).as(Real )
- Rot3 (0.0 ).as(Real ) ] :Optional :Input: EulerAngleMode Rot1 Rot2 Rot3
- [-I[nput] InList (NULL ).as(inFileList::ASCII ) ] :Optional :Input: eosPointFileList
- [-O[uput] OutList (NULL ).as(outFileList::ASCII ) ] :Optional :Output: eosPointFileList
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Additional Usage -----
->> eosPointFileType
-type-0: x y z
-type-1: x y z sig
-type-2: x y z sigx sigy sigz
-type-3: x y z sig sigx sigy sigz
->> mode
-0: x-projection
-1: y-projection
-2: z-projection
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: eosPointProjector: No such file or directory
[-arrow[Shape] R1 (0.1 ).as(Real )
R2 (0.4 ).as(Real )
Rho (0.75 ).as(Real ) ] :Optional :Arrow
+ [-skip skipX (1 ).as(Integer )
+ skipY (1 ).as(Integer )
+ skipZ (1 ).as(Integer ) ] :Optional :SkipVoxel
[-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
[-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
-<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: 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: mrc2lattice: 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: mrc2pov: 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
+/bin/bash: mrc2viff: No such file or directory
Options:
[-i[nput] inFile (NULL ).as(inFile ) ] :Essential :InputDataFile
[-o[utput] outFile (NULL ).as(outFile ) ] :Essential :OutputDataFile
- [-r[esolution] Resolution (2.5 ).as(Real ) ] :Optional :Resolution[A]
+ [-r[esolution] Resolution (1.0 ).as(Real ) ] :Optional :Resolution[A]
[-t[ime] time (1.0 ).as(Real ) ] :Optional :x OptimalTime
[-d[irnum] dirnum (0 ).as(Integer ) ] :Optional :tiffDirectoryNumber
[-I[nverse] ] :Optional :Black<->White
-/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: hf2000Init: 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: hf2000LenzCurrent: 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: hf2000SpecimenPosition: 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: khorosFilterGenerate: No such file or directory
-/bin/bash: largeIPInfo: 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>largeIPInfo</TITLE>
+</HEAD>
+<BODY>
+<H1>largeIPInfo</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: largeIPInfo
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-start startx (0 ).as(Integer )
+ starty (0 ).as(Integer ) ] :Optional :StartCoord
+ [-step stepx (1 ).as(Integer )
+ stepy (1 ).as(Integer ) ] :Optional :StepCoord
+ [-size width (LARGE_IP_IMAGE_WIDTH).as(Integer )
+ height (LARGE_IP_IMAGE_HEIGHT).as(Integer ) ] :Optional :SizeCoord
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: llDataAverage: 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>llDataAverage</TITLE>
+</HEAD>
+<BODY>
+<H1>llDataAverage</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: llDataAverage
+Options:
+ [-M[odel] Model (NULL ).as(inFile ) ] :Essential :Input: ModelFileName(llData)
+ [-i[nput] In (NULL ).as(inFileList ) ] :Essential :Input: InputDataFile
+ [-l[ayer] llInfo (NULL ).as(inFile ) ] :Essential :Input: Layer Line Information
+ [-A[verage] Ave (NULL ).as(outFile ) ] :Essential :Output: Averaged File Name
+ [-o[utput] OutParam (stdout ).as(appendFile ) ] :Optional :Output: FittedParameter
+ [-o2[utput] OutParam2 (NULL ).as(outFileList ) ] :Optional :Output: FittedParameter(phi, z)
+ [-O[utput] Out (NULL ).as(outFileList ) ] :Optional :Output: FittedData
+ [-P2[plot] P2 (NULL ).as(outFile ) ] :Optional :Output: P2PlotData
+ [-t[ruePitch] truePitch (1.0 ).as(Real ) ] :Optional :True Pitch
+ [-d[eltaR] dR (1.0 ).as(Real ) ] :Optional :deltaR
+ [-r[adial] rmin (1.0 ).as(Real )
+ rmax (1.0 ).as(Real )
+ dr (1.0 ).as(Real ) ] :Optional :Radial[Ratio]
+ [-p[hi] phimin (0.0 ).as(Real )
+ phimax (180.0 ).as(Real )
+ dphi (5.0 ).as(Real ) ] :Optional :Phi [degree]
+ [-z[shift] zmin (0.0 ).as(Real )
+ zmax (60.0 ).as(Real )
+ dz (5.0 ).as(Real ) ] :Optional :z [A]
+ [-withoutAntiPole ] :Optional :Not Allow Antipole
+ [-C[utValue] CutValue (1.0 ).as(Real ) ] :Optional :CutValue
+ [-pvm pvm (0 ).as(Integer ) ] :Optional :PVM:
+ [-pvmList pvmList (stdin ).as(inFile ) ] :Optional :PVM: HostList
+ [-pvmList Log (stdout ).as(appendFile ) ] :Optional :PVM: HostList
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+</PRE>
+</BODY>
+</HTML>
-/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>llDataAxisSearch</TITLE>
+</HEAD>
+<BODY>
+<H1>llDataAxisSearch</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: llDataAxisSearch
+Options:
+ [-i1[nput] In1 (NULL ).as(inFile ) ] :Optional :In: NearSide
+ [-i2[nput] In2 (NULL ).as(inFile ) ] :Optional :In: FarSide
+ [-o1[utput] Out1 (NULL ).as(outFile ) ] :Optional :Out: NearSide
+ [-o2[utput] Out2 (NULL ).as(outFile ) ] :Optional :Out: FarSide
+ [-a[verage] Avg (NULL ).as(outFile ) ] :Optional :Out: Average
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :Out: FitParam
+ [-op2[utput] OutP2 (NULL ).as(outFile ) ] :Optional :OutParam2: FitParam Distribution [mrcImage]
+ [-t[ruePitch] truePitch (0.0 ).as(Real ) ] :Optional :TruePitch[A]
+ [-l[ayer] L (NULL ).as(inFile ) ] :Optional :LayerInfo
+ [-O[mega] Omin (0.0 ).as(Real )
+ Omax (0.0 ).as(Real )
+ Odelta (1.0 ).as(Real ) ] :Optional :Omega[degree]
+ [-x[shift] xmin (-10.0 ).as(Real )
+ xmax (10.0 ).as(Real )
+ xdelta (0.1 ).as(Real ) ] :Optional :shiftx[A]
+ [-R R (10.0 ).as(Real ) ] :Optional :Resolution[A]
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+----- Layer Line Information File -----
+L N Weight
+..........
+
+----- Control File -----
+In1[inFile:NULL] #In: NearSide
+In2[inFile:NULL] #In: FarSide
+Out1[outFile:NULL] #Out: NearSide
+Out2[outFile:NULL] #Out: FarSide
+Avg[outFile:NULL] #Out: Average
+Out[outFile:NULL] #Out: FitParam
+truePitch[Real:NULL] #TruePitch[A]
+L[inFile:NULL] #LayerInfo
+Omin[Real:0.0] Omax[Real:0.0] Odelta[Real:1.0] #Omega[degree]
+xmin[Real:-10.0] xmax[Real:10.0] xdelta[Real:0.1] #shiftx[A]
+R[Real:10.0] #Resolution[A]
+mode[Integer:0] #Mode
+----- Inside Axis Search Parameter File -----
+info.In1, info.In2, paraFit.Para.R*DEGREE, paraFit.Para.x.Value, paraFit.Para.Omega.Value
+</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
+<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: llDataCompare: 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>llDataCompare</TITLE>
+</HEAD>
+<BODY>
+<H1>llDataCompare</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: llDataCompare
+Options:
+ [-i[nput] In (NULL ).as(inFileList ) ] :Essential :InputDataFileList
+ [-r[eference] Ref (NULL ).as(inFile ) ] :Essential :InputReferenceDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+Mode
+0: Integral
+1: Peak
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: llDataContributionCalcDifferentN: 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>llDataContributionCalcDifferentN</TITLE>
+</HEAD>
+<BODY>
+<H1>llDataContributionCalcDifferentN</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: llDataContributionCalcDifferentN
+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: llDataDump: 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>llDataDump</TITLE>
+</HEAD>
+<BODY>
+<H1>llDataDump</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: llDataDump
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-R[max] RMax (0.1 ).as(Real ) ] :Optional :[/A]
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: llDataEquatorAdd: 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>llDataEquatorAdd</TITLE>
+</HEAD>
+<BODY>
+<H1>llDataEquatorAdd</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: llDataEquatorAdd
+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: llDataExtract: 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>llDataExtract</TITLE>
+</HEAD>
+<BODY>
+<H1>llDataExtract</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: llDataExtract
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-n n (0 ).as(Real ) ] :Optional :n
+ [-l l (0 ).as(Real ) ] :Optional :l
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+input n and l
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: llDataFit: 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>llDataFit</TITLE>
+</HEAD>
+<BODY>
+<H1>llDataFit</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: llDataFit
+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: 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: llDataFitServer: No such file or directory
-/bin/bash: llDataInfo: 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>llDataInfo</TITLE>
+</HEAD>
+<BODY>
+<H1>llDataInfo</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: llDataInfo
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-l[ayer] layer (0 ).as(Integer ) ] :Optional :LayerNumber
+ [-L[ayer] NN (0 ).as(Integer )
+ LL (0 ).as(Integer ) ] :Optional :LayerInfo
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+----- mode -----
+1 : Total Layer Line Infomation
+2 : Information of Each Layer Line
+4 : Data of Each Layer Line
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: llDataLowPassFiltering: 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>llDataLowPassFiltering</TITLE>
+</HEAD>
+<BODY>
+<H1>llDataLowPassFiltering</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: llDataLowPassFiltering
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-t[ruePitch] truePitch (760 ).as(Real ) ] :Essential :[A]
+ [-R[max] RMax (0.1 ).as(Real ) ] :Optional :[/A]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+-m 0: SameMemorySize data
+-m 1: SavedMemorySize data
+</PRE>
+</BODY>
+</HTML>
-/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
+<HTML>
+<HEAD>
+<TITLE>llDataMultiCTFCompensation</TITLE>
+</HEAD>
+<BODY>
+<H1>llDataMultiCTFCompensation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: llDataMultiCTFCompensation
+Options:
+ [-i[nput] In (NULL ).as(inFileList ) ] :Essential :Input: FileList
+ [-M[odel] Ref (NULL ).as(inFile ) ] :Essential :Input: Model Data
+ [-l[ayerLine] llInfo (NULL ).as(inFile ) ] :Essential :Input: Layer Line Information
+ [-A[verageFile] Ave (NULL ).as(outFile ) ] :Essential :Output: AverageFile
+ [-o[utput] OutParam (NULL ).as(appendFile ) ] :Optional :Output: FittedParameter
+ [-O[utput] Out (NULL ).as(outFileList ) ] :Optional :Output: FileList: PhaseShift of Each Filament
+ [-o2[utput] OutParam2 (NULL ).as(outFileList ) ] :Optional :Output: [phi, z] map
+ [-P2[output] OutParamP2 (NULL ).as(outFile ) ] :Optional :Output: For P-P'
+ [-N[oise] Noise (0.0 ).as(Real ) ] :Optional :Noise Ratio
+ [-t[ruePitch] truePitch (761.4 ).as(Real ) ] :Essential :truePitch[A]
+ [-d[eltaR] deltaR (1.0 ).as(Real ) ] :Optional :deltaR[A]
+ [-r[adial] rmin (1.0 ).as(Real )
+ rmax (1.0 ).as(Real )
+ dr (1.0 ).as(Real ) ] :Optional :Radial[Ratio]
+ [-p[hi] phimin (0.0 ).as(Real )
+ phimax (180.0 ).as(Real )
+ dphi (1.0 ).as(Real ) ] :Optional :Phi [degree]
+ [-z[shift] zmin (0.0 ).as(Real )
+ zmax (180.0 ).as(Real )
+ dz (1.0 ).as(Real ) ] :Optional :z [A]
+ [-Rmax Rmax (0.1 ).as(Real ) ] :Optional :Rmax [/A]
+ [-MaxIter[ation] MaxIter (1 ).as(Integer ) ] :Optional :MaxIteration
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+---- InputFileFormat ----
+filename weight(NumberOfAveragedFile) deltaF[A] Cs[mm] kV[kV] ratioOfAmpToPhase
+----- Mode -----
+ 0: |CTFi|/Sigma(SQR(CTFi))
+ 1: CTFi /Sigma(SQR(CTFi))
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: llDataNEstimation: 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>llDataNEstimation</TITLE>
+</HEAD>
+<BODY>
+<H1>llDataNEstimation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: llDataNEstimation
+Options:
+ [-r[peak] r (220 ).as(Real ) ] :Essential :Input: rpeak [A]
+ [-R[peak] R (24 ).as(Real ) ] :Essential :Input: Rpeak [pixel]
+ [-xstep xstep (7 ).as(Real ) ] :Essential :Input: xstep [A]
+ [-W[idth] Width (500 ).as(Real ) ] :Essential :Input: Width [pixel]
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: llDataNormalization: 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>llDataNormalization</TITLE>
+</HEAD>
+<BODY>
+<H1>llDataNormalization</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: llDataNormalization
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :llData:InputDataFile
+ [-r[eference] Ref (NULL ).as(inFile ) ] :Essential :llData:Reference
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :llData(Normalized In):OutputDataFile
+ [-dif[ffence] Dif (NULL ).as(outFile ) ] :Optional :llData(Difference):OutputDataFile
+ [-O[utput] OutParam (stdout ).as(outFile ) ] :Optional :FittedParameter
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: llDataPrint: そのようなファイルやディレクトリはありません
+/bin/bash: llDataPrint: No such file or directory
-/bin/bash: llDataRescaling: 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>llDataRescaling</TITLE>
+</HEAD>
+<BODY>
+<H1>llDataRescaling</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: llDataRescaling
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-r[Scale] rScale (1.0 ).as(Real ) ] :Optional :[]
+ [-dR delBR (0.0 /* No Change */).as(Real ) ] :Optional :[/A]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: llDataResolutionCheck: 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>llDataResolutionCheck</TITLE>
+</HEAD>
+<BODY>
+<H1>llDataResolutionCheck</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: llDataResolutionCheck
+Options:
+ [-i[nput] In (NULL ).as(inFileList ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/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: llDataRotation: No such file or directory
-/bin/bash: llDataSelectionEstimation: 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>llDataSelectionEstimation</TITLE>
+</HEAD>
+<BODY>
+<H1>llDataSelectionEstimation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: llDataSelectionEstimation
+Options:
+ [-i1[nput] N1 (0 ).as(Real )
+ L1 (161 ).as(Real ) ] :Essential :Input: N L
+ [-i2[nput] N2 (14 ).as(Real )
+ L2 (12 ).as(Real ) ] :Essential :Input: N L
+ [-tmax tmax (100 ).as(Real ) ] :Optional :Input: tmax
+ [-umax umax (200 ).as(Real ) ] :Optional :Input: umax
+ [-r[accept] r (0.1 ).as(Real ) ] :Optional :Input: acceptable residue
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/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: llDataSeparate: No such file or directory
-/bin/bash: llDataWeightSet: 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>llDataWeightSet</TITLE>
+</HEAD>
+<BODY>
+<H1>llDataWeightSet</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: llDataWeightSet
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-l[ayerInfo] llInfo (NULL ).as(inFile ) ] :Optional :LayerInfomationFile
+ [-w[eight] weight (1.0 ).as(Real ) ] :Optional :DefaultWeight
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: llDatarMaxLimit: 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>llDatarMaxLimit</TITLE>
+</HEAD>
+<BODY>
+<H1>llDatarMaxLimit</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: llDatarMaxLimit
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-r[Max] rMax (100.0 ).as(Real ) ] :Optional :rMax[A]
+ [-rMin[Max] rMaxMin (100.0 ).as(Real ) ] :Optional :rMaxMin[A]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+
+
+----- rMax Limit Algorithm-----
+Default
+ R < (|n|-2)/(2*PI*rMax): Intensity = 0;
+If -rMin option
+ R < RR: (|n|-2)/(2*PI*rMax) : Intensity = 0.0;
+ R < RRMin: (|n|-2)/(2*PI*rMaxMin): Intensity = (R - RR)/(RRMin - RR)*Intensity;
+
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: ltlgDataInfo: 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>ltlgDataInfo</TITLE>
+</HEAD>
+<BODY>
+<H1>ltlgDataInfo</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: ltlgDataInfo
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- mode -----
+ 1: Header Information
+ 2: (N, L) Information
+ 4: (N, L) Data
+</PRE>
+</BODY>
+</HTML>
-/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
+<HTML>
+<HEAD>
+<TITLE>matrix3DEulerAngleTransform</TITLE>
+</HEAD>
+<BODY>
+<H1>matrix3DEulerAngleTransform</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: matrix3DEulerAngleTransform
+Options:
+ [-i[nputlist] In (NULL ).as(inFileListNoOpen ) ] :Essential :InputDataFileList
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-R[otationalMode] RotationalMode (ZONS ).as(String ) ] :Optional :RotationalMode
+ [-M[ultiplyEulerAngle]RotMode (ZONS ).as(String )
+ Rot1 (0.0 ).as(Real )
+ Rot2 (0.0 ).as(Real )
+ Rot3 (0.0 ).as(Real ) ] :Optional :M * input
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+
+----- input file format -----
+ filename rotationalMode phi theta psi
+ . . . . .
+ . . . . .
+ . . . . .
+
+</PRE>
+</BODY>
+</HTML>
-/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
+<HTML>
+<HEAD>
+<TITLE>matrix3DFromEulerAngle</TITLE>
+</HEAD>
+<BODY>
+<H1>matrix3DFromEulerAngle</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: matrix3DFromEulerAngle
+Options:
+ [-i[nput] In (stdin ).as(inFile ) ] :Optional :InputDataFile
+ [-R[ot] EMode (ZONS ).as(String )
+ Rot1 (0.0 ).as(Real )
+ Rot2 (0.0 ).as(Real )
+ Rot3 (0.0 ).as(Real ) ] :Optional :Input: RotAngle[degree]
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output: Matrix
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/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
+<HTML>
+<HEAD>
+<TITLE>matrix3DInverse</TITLE>
+</HEAD>
+<BODY>
+<H1>matrix3DInverse</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: matrix3DInverse
+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: matrix3DToEulerAngle: 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>matrix3DToEulerAngle</TITLE>
+</HEAD>
+<BODY>
+<H1>matrix3DToEulerAngle</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: matrix3DToEulerAngle
+Options:
+ [-i[nput] In (stdin ).as(inFile ) ] :Optional :Input: Matrix3D
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output: File
+ [-E[uler]M[ngle] EulerMode (ZONS ).as(String ) ] :Optional :Input: Mode
+ [-Check Threshold (1e-4 ).as(Real ) ] :Optional :Input: Check Threshold
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
mrcImageHelicalProjection \
mrcImageHighPassFilter \
mrcImageHighlighting \
+mrcImageHoleFilling \
mrcImageHoughTransform \
mrcImageHoughTransformInverse \
mrcImageInfo \
-/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: fft2d: 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: mrc2dsn6: 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: mrc2hdf: No such file or directory
-/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>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: mrcFFTCentralSectionCompare: 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: 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: mrcImage1dCutAverage: 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: mrcImage3DCTFObservation: 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: mrcImage3DPeakGet: No such file or directory
[-l[abel] Label (NULL ).as(outFile::mrcImage ) ] :Optional :Output: mrcImage:labeling
[-O[utput]H[istgram] OutHist (NULL ).as(outFile::ASCII ) ] :Optional :Output: ASCII: area info
[-H[istgram] DelHist (1 ).as(Real ) ] :Optional :Delta
+ [-N[eighbor] Neighbor (0 ).as(Real ) ] :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 -----
-/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: mrcImageAutoRotationCorrelationResultPrint: 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: mrcImageAutoTriming: No such file or directory
<PRE>
Usage: mrcImageCTFObservation
Options:
- [-i[nput] In (stdin ).as(inFile ) ] :Essential :InputFile
- [-o[utput] Out (stdout ).as(outFile ) ] :Essential :OutputDataFile
+ [-i[nput] In (stdin ).as(inFile::mrcImage ) ] :Essential :Input:2D
+ [-o[utput] Out (stdout ).as(outFile::mrcImage ) ] :Essential :Output:2D
+ [-ctf CTF (stdin ).as(inFile::ASCII ) ] :Optional :Input:ctfInfo
[-kV kV (200 ).as(Real ) ] :Optional :AccVol[kV]
[-Cs Cs (2.1 ).as(Real ) ] :Optional :Cs[mm]
[-df Defocus (27000 ).as(Real ) ] :Optional :Defocus [A]:under(+)
-/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: mrcImageColoring: 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: mrcImageCorrelationServer: 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
+/bin/bash: mrcImageCorrelationWithCTFCompensation: 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
+/bin/bash: mrcImageCutAndSetInArray: No such file or directory
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 6.899392e-310ach
+ [-C[ontour] Contour (10 ).as(Real ) ] :Optional :ContourLevel: 10 6.934030e-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: 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: mrcImageEnhancementWithFuzzySets: 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: mrcImageFilamentSearch: 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: mrcImageFractalFrourierShellCorrelation: 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
+/bin/bash: mrcImageHelicalConvolution: No such file or directory
--- /dev/null
+../../../../../hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageHoleFilling/src/X86LINUX64
\ No newline at end of file
-<HTML>
-<HEAD>
-<TITLE>mrcImageHoleFilling</TITLE>
-</HEAD>
-<BODY>
-<H1>mrcImageHoleFilling</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrcImageHoleFilling
-Options:
- [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input(0:black, positive:white)
- [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output(0:black, 1:white
- [-n[eighbor] Neighbor (8 ).as(Integer ) ] :Optional :Neighbor
- [-b[lack]A[rea] BlackArea (NULL ).as(outFile::mrcImage ) ] :Optional :Output:BlackArea
- [-b[lack]L[abel] BlackLabel (NULL ).as(outFile::mrcImage ) ] :Optional :Output:BlackLabel
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrcImageHoleFilling: No such file or directory
[-Y[Section] Y (0.0 ).as(Real ) ] :Optional :Y Section at y=Y(value)
[-x[Projection] ] :Optional :x Projection[OutPut ASCII FILE]
[-y[Projection] ] :Optional :y Projection[OutPut ASCII FILE]
+ [-L[ength] ] :Optional :with Length[A]
[-H[istgram] H (256 ).as(Integer ) ] :Optional :Histgram: Class Number: Normalize
[-H[istgram]2 H2 (1 ).as(Real ) ] :Optional :Histgram2: Class Width: Integer: Normalize
[-H[istgram]3 H3 (256 ).as(Integer ) ] :Optional :Histgram: Class Number: Count
Options:
[-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input:mrcImage
[-o[utput] Out (stdout ).as(outFile::ASCII ) ] :Optional :Output:distribution
+ [-O[utput]w[hite]all OutWhiteAll (NULL ).as(outFile::mrcImage ) ] :Optional :Output: white+whiteEdge
[-O[utput]w[hite] OutWhite (NULL ).as(outFile::mrcImage ) ] :Optional :Output: white
+ [-O[utput]b[lack]all OutBlackAll (NULL ).as(outFile::mrcImage ) ] :Optional :Output: black+blackEdge
[-O[utput]b[lack] OutBlack (NULL ).as(outFile::mrcImage ) ] :Optional :Output: black
[-O[utput]w[hite]e[dge]OutWhiteEdge (NULL ).as(outFile::mrcImage ) ] :Optional :Output: whiteEdge
[-O[utput]b[lack]e[dge]OutBlackEdge (NULL ).as(outFile::mrcImage ) ] :Optional :Output: blackEdge
+ [-O[utput]dir[ection]Direction (direction ).as(String ) ] :Optional :Output: basename.[0|1|2] vector for any
[-l[ine]t[hickness] LineThicknessX (1 ).as(Real )
LineThicknessY (1 ).as(Real ) ] :Optional :[pixel]
[-l[ine]m[ode] LineMode (0 ).as(Integer ) ] :Optional :LineMode
[-l[ine]s[hape] LineShape (0 ).as(Integer ) ] :Optional :LineShape
+ [-deltaPhi deltaPhi (30 ).as(Real ) ] :Optional :deltaPhi
+ [-deltaTheta deltaTheta (30 ).as(Real ) ] :Optional :deltaTheta
[-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
[-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Additional Usage -----
-/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
+/bin/bash: mrcImageNLMeansFilter: No such file or directory
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)
-6: Pad value 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
+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)))
-<HTML>
-<HEAD>
-<TITLE>mrcImagePeakSearch</TITLE>
-</HEAD>
-<BODY>
-<H1>mrcImagePeakSearch</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrcImagePeakSearch
-Options:
- [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: mrcImage
- [-o[utput] Out (NULL ).as(outFile ) ] :Optional :Output: mrcImage
- [-o[utput]B OutB (NULL ).as(outFile ) ] :Optional :Output: mrcImage:Binary
- [-o[utput]L OutL (NULL ).as(outFile ) ] :Optional :Output: mrcImage:Label
- [-o[utput]A OutA (NULL ).as(outFile ) ] :Optional :Output: mrcImage:Aarea
- [-O[utputPeakStatics]OutStatics (stdout ).as(outFile ) ] :Optional :Output as ASCII: Peak statics
- [-t[hreshold] Sigma (3.0 ).as(Real ) ] :Optional :Input: Peak's values are more than t*sigma.
- [-T[hreshold] Threshold (0.0 ).as(Real ) ] :Optional :Input: Peak's values are more than T.
- [-a[rea] Area (6.0 ).as(Real ) ] :Optional :Input[A^2]: Peak's area are more than a.
- [-A[rea] AreaPixel (9 ).as(Real ) ] :Optional :Input[pixel^2]: Peak's area are more than A.
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrcImagePeakSearch: 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
+/bin/bash: mrcImagePut3D: No such file or directory
[-Ly Ly (5.0 ).as(Real ) ] :Optional :Header Length y [A/Pixel]
[-S[hrink] Shrink (1 ).as(Integer ) ] :Optional :When inputfile is shrinked
[-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-M[ode] ROIShapeMode (0 ).as(Integer ) ] :Optional :RoiShapeMode
[-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
---- mode ----
0: Nearest Neighbor Method
-/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
+<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: 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: mrcImageSNEstimate: 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: mrcImageShapeRelaxation: No such file or directory
-<HTML>
-<HEAD>
-<TITLE>mrcImageShapeSearch</TITLE>
-</HEAD>
-<BODY>
-<H1>mrcImageShapeSearch</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrcImageShapeSearch
-Options:
- [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input
- [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output
- [-Shape Shape (NULL ).as(outFile::mrcImage ) ] :Optional :Output
- [-n[Cube] nCube (0 ).as(Integer ) ] :Optional :Mode
- [-r[adius] minR (3 ).as(Integer )
- maxR (5 ).as(Integer )
- delR (1 ).as(Integer ) ] :Optional :Radius[pixel]
- [-l[ength] minL (3 ).as(Integer )
- maxL (5 ).as(Integer )
- delL (1 ).as(Integer ) ] :Optional :Length[pixel]
- [-Phi minPhi (0.0 ).as(Real )
- maxPhi (359.0 ).as(Real )
- delPhi (45.0 ).as(Real ) ] :Optional :around z-axis[degree]
- [-Theta minTheta (0.0 ).as(Real )
- maxTheta (359.0 ).as(Real )
- delTheta (45.0 ).as(Real ) ] :Optional :around x-axis[degree]
- [-Psi minPsi (0.0 ).as(Real )
- maxPsi (350.0 ).as(Real )
- delPsi (45.0 ).as(Real ) ] :Optional :around x-axis[degree]
- [-thres[Zscore] thresZscore (1.0 ).as(Real ) ] :Optional :Zscore
- [-interp[olationMode]interpMode (0 ).as(Integer ) ] :Optional :interpMode
- [-O[utput]V[ector]BILDOutVectorBILD (NULL ).as(outFile::BILD ) ] :Optional :Output:BILD-vector
- [-arrow[Shape] ArrowR1 (0.1 ).as(Real )
- ArrowR2 (0.4 ).as(Real )
- ArrowRho (0.75 ).as(Real ) ] :Optional :ArrowShape
- [-zoom[Vector] ZoomVector (1.0 ).as(Real ) ] :Optional :Zoom
- [-arrowColorDisk ArrowColorDisk0 (0.0 ).as(Real )
- ArrowColorDisk1 (1.0 ).as(Real )
- ArrowColorDisk2 (0.0 ).as(Real ) ] :Optional :ArrowColorDisk
- [-arrowColorSylinder ArrowColorSylinder0 (1.0 ).as(Real )
- ArrowColorSylinder1 (0.0 ).as(Real )
- ArrowColorSylinder2 (0.0 ).as(Real ) ] :Optional :ArrowColorSylinder
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Additional Usage -----
-0: Cylinder with radius and length
-1: Disk with radius and length(thickness)
-2: Sphere with radius
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrcImageShapeSearch: No such file or directory
>>>> centre type mode
0 : Centre is GC (gravity of centre)
1 : Centre is Rotational Symmetry
+ 2 : Centre is at Image Centre
+ 3 : Centre is at Image Origin
>>>> subtrcation type mode
0 : No Subtraction
1 : Mean Subtraction
-/bin/bash: mrcImageSymmetryFind: 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>mrcImageSymmetryFind</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageSymmetryFind</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageSymmetryFind
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :Output: correlation
+ [-O[utput] Out2 (stdout ).as(outFile ) ] :Optional :Output: SymmetryInformation
+ [-A[verage] Avg (NULL ).as(outFile ) ] :Optional :Output: Average
+ [-centreMode centreMode (1 ).as(Integer ) ] :Optional :Input: 0 : Gravity of Centre; 1 : Search n-fold
+ [-t1[threshold1] threshold1 (1.8 ).as(Real ) ] :Optional :Threshold of CheckByAdd
+ [-t2[threshold2] threshold2 (0.9 ).as(Real ) ] :Optional :Threshold in deciding the symmetry number
+ [-m1[mode1] mode1 (3 ).as(Integer ) ] :Optional :Mode of Check
+ [-m2[mode2] mode2 (2 ).as(Integer ) ] :Optional :Mode of Substruction
+ [-dr[delta r] dr (1 ).as(Real ) ] :Optional :Delta r of outputfile.
+ [-dtheta[delta theta]dtheta (1 ).as(Real ) ] :Optional :Delta theta of outputfile.[DEGREE]
+ [-n[umber] n (10 ).as(Integer ) ] :Optional :Check to the number.
+ [-n[umber]Range nmin (2 ).as(Integer )
+ nmax (10 ).as(Integer ) ] :Optional :Check to the number.
+ [-In Image (NULL ).as(inFileList )
+ Back (NULL ).as(inFileList ) ] :Optional :InputDataFile: Image and Back
+ [-rangex minx (-3 ).as(Real )
+ maxx (3 ).as(Real )
+ delx (1 ).as(Real ) ] :Optional :Input:
+ [-rangey miny (-3 ).as(Real )
+ maxy (3 ).as(Real )
+ dely (1 ).as(Real ) ] :Optional :Input:
+ [-rangez minz (0 ).as(Real )
+ maxz (0 ).as(Real )
+ delz (1 ).as(Real ) ] :Optional :Input:
+ [-rrange rmin (0 ).as(Real )
+ rmax (-1 ).as(Real ) ] :Optional :Input: Rrange[A]
+ [-Algorythm ] :Optional :Algorythm
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+----- Additional Usage -----
+>>>> check type mode
+ 1 : Check by Add
+ 2 : Check by Correlation
+ 4 : Check by Fourier
+ 8 : Check by TTest
+ 16 : Check by SRP
+>>>> centre type mode
+ 0 : Centre is GC (gravity of centre)
+ 1 : Centre is Rotational Symmetry
+ 2 : Centre is at Image Centre
+ 3 : Centre is at Image Origin
+>>>> subtrcation type mode
+ 0 : No Subtraction
+ 1 : Mean Subtraction
+ 2 : Min Subtraction
+</PRE>
+</BODY>
+</HTML>
-/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: mrcView: No such file or directory
-<HTML>
-<HEAD>
-<TITLE>gmolvie</TITLE>
-</HEAD>
-<BODY>
-<H1>gmolvie</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: gmolvie
-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: gmolvie: No such file or directory
-<HTML>
-<HEAD>
-<TITLE>molvie</TITLE>
-</HEAD>
-<BODY>
-<H1>molvie</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: molvie
-Options:
- [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
- [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: molvie: No such file or directory
-<HTML>
-<HEAD>
-<TITLE>molvieDock</TITLE>
-</HEAD>
-<BODY>
-<H1>molvieDock</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: molvieDock
-Options:
- [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
- [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: molvieDock: No such file or directory
-<HTML>
-<HEAD>
-<TITLE>molvieFlight</TITLE>
-</HEAD>
-<BODY>
-<H1>molvieFlight</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: molvieFlight
-Options:
- [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
- [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: molvieFlight: 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: molvieMrcViewer: No such file or directory
-<HTML>
-<HEAD>
-<TITLE>molvieProjection</TITLE>
-</HEAD>
-<BODY>
-<H1>molvieProjection</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: molvieProjection
-Options:
- [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
- [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: molvieProjection: No such file or directory
-<HTML>
-<HEAD>
-<TITLE>molvieViewer</TITLE>
-</HEAD>
-<BODY>
-<H1>molvieViewer</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: molvieViewer
-Options:
- [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
- [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: molvieViewer: No such file or directory
ltlg2ps \
maker2Dto3DEstimator \
marker2Dto3DEstimator \
+mrc2DFTto3DFT \
mrc2Dto3D \
mrc2Dto3DforVariation \
mrc3Dto2D \
-/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>
--- /dev/null
+../../../../../hostdepend/X86LINUX64/src/Tools/rec3d/mrc2DFTto3DFT/src/X86LINUX64
\ No newline at end of file
-<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: No such file or directory
--- /dev/null
+../../../../../hostdepend/X86LINUX64/src/Tools/rec3d/mrc3Dto2DFFT/src/X86LINUX64
\ No newline at end of file
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