Install Cuda
new file:   hostdepend/X86LINUX64/util/X86LINUX64/cuda
Install ICC
new file:   hostdepend/X86LINUX64ICC/include/*.h
modified:   hostdepend/X86LINUX64ICC/lib/X86LINUX64ICC/libEosObjects.a
Modify eosCuda
modified:   include/eosCuda.h
modified:   src/Objects/General/eosCuda/Config/Define.inc
modified:   src/Objects/General/eosCuda/inc/eosCuda.h
new file:   src/Objects/General/eosCuda/src/eosCuda.cu

Modify Configuration Files  for ICC and CUDA
modified:   include/pdbFile.h
modified:   src/Config/DefineObject.inc
modified:   src/Config/Template/ObjectsTemplate.Dir/src/ARCH/Makefile
modified:   src/Config/x86Linux64icc.inc
modified:   src/Objects/DataManip/Config/Define.inc
modified:   src/Tools/Config/Define.inc

Examples for CUDA Applications:
modified:   src/Tools/mrcImage/mrcImageAddValue/*
modified:   src/Tools/pdbUtil/pdbRotation/*
modified:   src/Objects/DataManip/pdbFile/src/pdbTrans.c
new file:   src/Objects/DataManip/pdbFile/src/pdbTransCuda.cu

We expanded a format of OptionControlFile and added the attribultes of option types
    Ex. inFile ->> inFile::mrcImage or inFile::ASCII

new file:   sbin/awk/ctrl2Function.awk
modified:   sbin/awk/ctrl2argCheck.awk
modified:   sbin/awk/ctrl2configFileRead.awk
modified:   sbin/awk/ctrl2configFileUsage.awk
modified:   sbin/awk/ctrl2controlFile.awk
modified:   sbin/awk/ctrl2header.awk
modified:   sbin/awk/ctrl2init0.awk
modified:   sbin/awk/ctrl2init1.awk
modified:   sbin/awk/ctrl2khorospane.awk
modified:   sbin/awk/ctrl2usage.awk
modified:   sbin/awk/ctrlShow.awk
modified:   sbin/ctrl2argCheck
modified:   sbin/ctrl2configFileRead
modified:   sbin/ctrl2header
modified:   sbin/ctrl2init
modified:   sbin/ctrl2usage
modified:   sbin/ctrl2util

Modifiid Tools by new OptionControlFile

modified:   hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageInfo
modified:   hostdepend/X86LINUX64/bin/X86LINUX64/llExtract
modified:   hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageROI
modified:   hostdepend/X86LINUX64/bin/X86LINUX64/mrcInfo

modified:   mrcSinogramFETcalcSDforNormalize

deleted:    some files

modified:   mrcMeanYlinePos

deleted:    Some files

modified:   mrcImage1dShiftByCorrelation

deleted:   some files

modified:   src/Objects/DataManip/emData/src/emDataRead.c
modified:   src/Tools/filter/emData2mrc/src/emData2mrc

mv:    src/Tools/Test/angleMatchTest_k -> src/Tools/utils
mv:    src/Tools/Test/angleMatchTest_k/src/util.c -> src/Tools/utils

modified:   angleMatchTest_k
modified:   anglediffchk

modified:   mrc2fld
modified:   llDataResolutionCheck.c

Ticket
modified:   mrcImageCoreImageCalc
modified:   pdbChargeFit

modified:   mrcImageMultiCTFDetermination

modified:   ctfMultiFunction

modified:   src/Tools/mrcImage/mrcImageFOMCalc/src/mrcImageFOMCalc.c
deleted:    src/Tools/mrcImage/mrcImageAverage/src/.mrcImageAverage.c.swp

modified:   pdbListRMSDCalc.c

modified:   mrcImageFractalFourierShellCorrelation.c
modified:   pdbListRMSDCalc.c

Bug fixed: Spell miss
modified:   hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAutoFilamentExtract
modified:   hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAutoFilamentExtract/src/X86LINUX64/mrcImageAutoFilamentExtract
modified:   src/Tools/mrcImage/mrcImageAutoFilamentExtract/src/mrcImageAutoFilamentExtract.c

modified:   hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAutoFilamentExtract
modified:   hostdepend/X86LINUX64/bin/X86LINUX64/pdbShapeFit
modified:   hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAutoFilamentExtract/src/X86LINUX64/mrcImageAutoFilamentExtract
modified:   hostdepend/X86LINUX64/src/Tools/pdbUtil/pdbShapeFit/src/X86LINUX64/pdbShapeFit
modified:   src/Tools/mrcImage/mrcImageAutoFilamentExtract/src/mrcImageAutoFilamentExtract.c
modified:   src/Tools/pdbUtil/pdbShapeFit/src/pdbShapeFit.c

Fixed: ticket #33385
modified:   hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageFTest
modified:   hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageFTest/src/X86LINUX64/Makefile
modified:   hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageFTest/src/X86LINUX64/mrcImageFTest
modified:   src/Tools/mrcImage/mrcImageFTest/src/mrcImageFTest.c

modified:   Makefile
modified:   bin/wish/ctfDisplay/ctfDisplay.wish
recompiled for X86MAC64:   hostdepend/X86MAC64/bin/X86MAC64/*
recompiled for X86MAC64:   hostdepend/X86MAC64/lib/X86MAC64/shared/lmrcImageSummationCalculate.sharedo

Rebuild for new versions of OS

Bug fixed:
mrcImageHighlighting

Bug fixed:#
matrix3DInverse
vectorImageNearestNeighborMethod

DensityMode:Bug fixed
modified:   src/Objects/DataManip/pdbFile/src/lpdbSurface.c
modified:   src/Objects/DataManip/pdbFile/src/lpdbSurface.h
modified:   src/Tools/pdbUtil/pdbSurface/Config/OptionControlFile

modified:   Makefile
new file:   bin/X86LINUX64ICC
new file:   bin/mrcImagePanoramaCreate
modified:   hostdepend/X86LINUX64/bin/X86LINUX64/*
modified:   hostdepend/X86LINUX64/lib/X86LINUX64/*
modified:   hostdepend/X86LINUX64/util/X86LINUX64/lib/libgif.la
modified:   hostdepend/X86LINUX64/util/X86LINUX64/lib/libjpeg.a
modified:   hostdepend/X86LINUX64/util/X86LINUX64/lib/libtiff.a
new file:   hostdepend/X86LINUX64ICC/bin/X86LINUX64ICC/*
new file:   hostdepend/X86LINUX64ICC/lib/X86LINUX64ICC/*
modified:   include/lmrcImageROI2D.h
modified:   sbin/MachineIndependent
modified:   src/Makefile
modified:   src/Tools/mrcImage/mrcImageROIs/inc/mrcImageROIs.h
modified:   util/X86LINUX64ICC

For showing step by step
modified:   Makefile

For >2GB: int -> size_t
modified:   src/Objects/DataManip/mrcImage/inc/mrcImage.h
modified:   src/Objects/DataManip/mrcImage/src/mrcImageWrite.c

A new tool to detect Object orientations.
new file:   src/Tools/mrcImage/mrcImageShapeOrientation/*

modified:   hostdepend/X86LINUX64ICC/*
modified:   include/eosPThread.h
modified:   src/Tools/*/*/src/Makefile

Makefile Modification for GPGPU
modified:   src/Config/Template/ToolsTemplate.Dir/src/ARCH/Makefile
modified:   src/Config/Template/ToolsTemplate.Dir/src/Makefile

Makefile modifiction for GPGPU
modified:   src/Config/x86Linux64.inc

pthread bug fix
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageFFT.c
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageRhoFiltering.c
modified:   src/Objects/DataManip/transform/src/lmrc2Dto3D.c
modified:   src/Objects/DataManip/transform/src/lmrc2Dto3D.h
modified:   src/Objects/General/eosPThread/doc/eosPThread.html
modified:   src/Objects/General/eosPThread/inc/eosPThread.h
modified:   src/Objects/General/eosPThread/src/eosPThreadMutex.c
modified:   src/Tools/rec3d/mrc2Dto3D/ Config/OptionControlFile

Crystal.h modified
modified:   src/Objects/General/Crystal/inc/Crystal.h

new file:   bin/mrc2mrc
mrcfile transform
modified:   env/Eos_env
for CUDA
new file:   eosCuda
new file:   include/eosCuda.h
for CUDA
modified:   hostdepend/X86LINUX64/*/X86LINUX64/*
new file:   hostdepend/X86LINUX64ICC/*/X86LINUX64ICC
for icc
modified:   include/Matrix3D.h
modified:   include/mrcImage.h
for mrc2mrc

Modeify compile options for -Wall
modified:   src/Config/x86Linux64.inc

Create a new object : eosCuda for CUDA setting
new file:   src/Objects/General/eosCuda/
new file:   src/Objects/General/eosCuda/inc/eosCuda.h
new file:   src/Objects/General/eosCuda/src/eosCuda.c

Add Shepp and Logan models into mrcImageModelCreate
modified:   src/Tools/mrcImage/mrcImageModelCreate/src/mrcImageModelCreate.c
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageModelCreate.c
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageModelCreate.h

Add usage
modified:   src/Tools/mrcImage/mrcImageSiemensStar/src/mrcImageSiemensStar.c

Modefy arrayPCA
modified:   src/Objects/General/Array/src/arrayPCA.c

Recompiling ctfDisplay and Display2

modified:   bin/wish/Display2/tclIndex
modified:   hostdepend/X86LINUX64/bin/X86LINUX64/*

modified:   src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/
Add the function of range restriction
related: modified:   src/Objects/DataManip/mrcImage/inc/mrcImage.h
related: modified:   src/Objects/DataManip/mrcImage/src/mrcImageInfo.c
modified:   src/Objects/DataManip/mrcImage/src/lmrcSinogramFET.h
modified:   src/Objects/DataManip/mrcImage/src/lmrcSinogramFETPCA.c
related: previous modification for arrayPCA(add average argument);

Merge branch 'master' of git.sourceforge.jp:/gitroot/eos/base

Conflicts:
.gitignore
src/Objects/*/*/doc/*.html

modified:   .gitignore
modified:   bin/wish/ctfDisplay/ctfDisplay.wish
modified:   hostdepend/I386LINUX/*
modified:   hostdepend/X86LINUX64/*
modified:   hostdepend/X86MAC64/*
modified:   include/mrcImage.h
modified:   lib/pdbFile.rb
modified:   sbin/makegeneral
modified:   src/Config/Template/ToolsTemplate.Dir/src/Makefile
deleted:    */.../.EosLog
deleted:    */.../*.html.orig
modified:   src/Tools/*/*/src/Makefile

make rebuild for X86LINUX64
modified:   .gitignore
modified:   bin/wish/Display2/tclIndex

Merge branch 'master' of git.sourceforge.jp:/gitroot/eos/base

Conflicts:
sbin/dotSourceInMakefileCreate
src/Makefile
src/Objects/DataExpress/Contour/doc/Contour.html
src/Objects/DataExpress/alsa/doc/alsa.html
src/Objects/DataExpress/avsFile/doc/avsFile.html
src/Objects/DataExpress/gifFile/doc/gifFile.html
src/Objects/General/.Source
src/Tools/Config/Define.inc
src/Tools/Integration/ctfDisplay/Makefile
src/Tools/Makefile
src/Tools/mrcImage/.Source
src/Tools/mrcImage/Makefile
src/Tools/mrcImage/mrcImage3DPad/src/.EosLog
src/Tools/rec3d/.Source

new file:   bin/mrcImageRandomParticlesImageCreate
new file:   bin/pointsSetToPDB
modified:   bin/wish/Display2/tclIndex
modified:   bin/wish/ctfDisplay/ctfDisplay.wish
modified:   hostdepend/I386LINUX/bin/I386LINUX/*
modified:   hostdepend/I386LINUX/lib/I386LINUX/*

modified:   env/Eos_env
modified:   mrcImage3DPad
add:        gsl as a free numerical analysis
modified:   sbin/dotSourceInMakefileCreate
modified:   src/Makefile
typechange: src/Tools/Makefile
modified:   src/Tools/*/*/src/Makefile

Merge branch 'master' of git.sourceforge.jp:/gitroot/eos/base

Rebuild for X68MAC

Merge branch 'master' of git.sourceforge.jp:/gitroot/eos/base

Conflicts:
src/Tools/mrcImage/mrcImage3DPad/src/.EosLog

For consistency

deleted:    hostdepend/X86LINUX64/src/Objects/DataExpress/openGL/src/X86LINUX64/lmolviePDBRead.c

modified:   src/Tools/mrcImage/mrcImage3DPad/src/.EosLog

Delete needless files

make rebuild for I386LINUX

new file:   mrcImageRandomParticlesImageCreate
modified:   bin/wish/ctfDisplay/ctfDisplay.wish
modified:   hostdepend/I386LINUX/bin/I386LINUX/*
modified:   hostdepend/I386LINUX/src/*/*/*/src/I386LINUX/*
modified:   src/Tools/Config/Define.inc
typechange: src/Tools/Integration/Makefile

modified:   hostdepend/I386LINUX/bin/I386LINUX/*
new file:   hostdepend/I386LINUX/lib/I386LINUX/*
new file:   hostdepend/I386LINUX/src/Objects/*
modified:   hostdepend/I386LINUX/src/Tools/*
new file:   hostdepend/I386LINUX/util/I386LINUX/lib/*
modified:   src/Config/i386Linux.inc

new file:   bin/pointsSetToPDB
new file:   hostdepend/I386LINUX/bin/I386LINUX/*
new file:   hostdepend/I386LINUX/lib/*
modified:   hostdepend/I386LINUX/src/Objects/*/I386LINUX/.Source
modified:   hostdepend/I386LINUX/src/Tools/*/I386LINUX/.Source
new file:   hostdepend/I386LINUX/util/I386LINUX/lib/libglut.so.3
modified:   sbin/dotSourceInMakefileCreate
modified:   src/Makefile

modified:   .gitignore

Change src/Makefile

Merge branch 'master' of git.sourceforge.jp:/gitroot/eos/base into HEAD

Conflicts:
src/Objects/DataManip/transform/doc/transform.html
src/Objects/DataManip/transform/src/lmrc2Dto3D.c
src/Objects/DataManip/transform/src/lmrc3Dto2D.c
src/Objects/General/eosPThread/Makefile
src/Tools/rec3d/mrc2Dto3D/src/.EosLog
src/Tools/rec3d/mrc2Dto3D/src/test/Makefile
src/Tools/rec3d/mrc3Dto2D/src/.EosLog
src/Tools/rec3d/mrc3Dto2D/src/Makefile

Bug fixed : mrc2Dto3D
Apply eosPThread to mrc2Dto3D
thread-possible code separation related fftw

modified:   src/Objects/DataManip/mrcImage/src/lmrcImageFFT.c
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageRhoFiltering.c
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageRhoFiltering.h
modified:   src/Objects/DataManip/mrcImage/src/mrcImageOperation.c
modified:   src/Objects/DataManip/mrcImage/src/mrcImageSectionGet.c
modified:   src/Objects/DataManip/transform/src/lmrc2Dto3D.c
modified:   src/Objects/DataManip/transform/src/lmrc2Dto3D.h
modified:   src/Objects/DataManip/transform/src/lmrc3Dto2D.c
modified:   src/Tools/rec3d/mrc2Dto3D/Config/OptionControlFile
modified:   src/Tools/rec3d/mrc2Dto3D/src/Makefile
modified:   src/Tools/rec3d/mrc2Dto3D/src/mrc2Dto3D.c
modified:   src/Tools/rec3d/mrc2Dto3D/src/test/Makefile

deleted:    src/Tools/rec3d/mrc3Dto2D/src/.co.
deleted:    src/Tools/rec3d/mrc3Dto2D/src/:

modified:   src/Config/Template/ToolsTemplate.Dir/src/Makefile
modified:   src/Objects/DataManip/mrcImage/src/mrcImageGet.c
modified:   src/Objects/DataManip/transform/src/lmrc3Dto2D.c

Create eosPThread for parallel computing
new file:   include/eosPThread.h
new file:   src/Objects/General/eosPThread/inc/eosPThread.h
new file:   src/Objects/General/eosPThread/src/eosPThreadCreate.c
new file:   src/Objects/General/eosPThread/src/eosPThreadInit.c
new file:   src/Objects/General/eosPThread/src/eosPThreadJoin.c
new file:   src/Objects/General/eosPThread/src/eosPThreadMutex.c

Apply eosPThread to mrc3Dto2D
modified:   include/lmrc3Dto2D.h
modified:   src/Objects/DataManip/transform/src/lmrc3Dto2D.c
modified:   src/Objects/DataManip/transform/src/lmrc3Dto2D.h
modified:   src/Tools/rec3d/mrc3Dto2D/Config/OptionControlFile
modified:   src/Tools/rec3d/mrc3Dto2D/src/mrc3Dto2D.c

Modified
modified:   src/Objects/DataManip/mrcImage/src/mrcImageWrite.c
    ** Append mode -> Write mode
modified:   src/Objects/DataManip/transform/src/lFETOrientationSearchByFeatureAlignmentInitSet.c
** Apply arrayPCA version up

Apply eosPThread to mrc2Dto3D, -pthread
Modify lmrcImageRhoFiltering
Modify x86Mac64.inc
Modify lmrcImageFFT for odd size images
Modify lmrcImageOperation(lmrcImageAdd) for speed up.

Create eosPThread for parallel computing
new file:   include/eosPThread.h
new file:   src/Objects/General/eosPThread/inc/eosPThread.h
new file:   src/Objects/General/eosPThread/src/eosPThreadCreate.c
new file:   src/Objects/General/eosPThread/src/eosPThreadInit.c
new file:   src/Objects/General/eosPThread/src/eosPThreadJoin.c
new file:   src/Objects/General/eosPThread/src/eosPThreadMutex.c

Apply eosPThread to mrc3Dto2D
modified:   include/lmrc3Dto2D.h
modified:   src/Objects/DataManip/transform/src/lmrc3Dto2D.c
modified:   src/Objects/DataManip/transform/src/lmrc3Dto2D.h
modified:   src/Tools/rec3d/mrc3Dto2D/Config/OptionControlFile
modified:   src/Tools/rec3d/mrc3Dto2D/src/mrc3Dto2D.c

Modified
modified:   src/Objects/DataManip/mrcImage/src/mrcImageWrite.c
    ** Append mode -> Write mode
modified:   src/Objects/DataManip/transform/src/lFETOrientationSearchByFeatureAlignmentInitSet.c
** Apply arrayPCA version up

compilineg : eosPoint and eosList
new file:   include/eosList.h
modified:   include/eosPoint.h
modified:   src/Objects/DataManip/transform/src/lmrc3Dto2D.c

Merge branch 'master' of git.sourceforge.jp:/gitroot/eos/base

// Modify git command
    modified:   Makefile

    // Create a new command for fitting between two 2D/3D objects using PCA
    new file:   mrcImageShapePCAFit
    new file:   src/Objects/DataManip/mrcImage/src/lmrcImageShapePCA.c
    new file:   src/Objects/DataManip/mrcImage/src/lmrcImageShapePCA.h
    modified:   src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.c

    // Modify Array for PCA. Add average information of each xi
    modified:   src/Objects/General/Array/inc/Array.h
    modified:   src/Objects/General/Array/src/arrayPCA.c
    modified:   src/Objects/General/Array/src/larray2mrc.c

    // Modify Matrix3D for PCA. Add matrix3DfromArray
    modified:   src/Objects/General/Matrix3D/inc/Matrix3D.h
    modified:   src/Objects/General/Matrix3D/src/matrix3DEulerAngleGet.c
    modified:   src/Objects/General/Matrix3D/src/matrix3DUtil.c

    // Modify pdbPCA for changing arrayPCA
    modified:   src/Tools/pdbUtil/pdbPCA/src/pdbPCA.c

    // Bebuilding
    modified:   hostdepend/X86MAC64/...

Merge branch 'master' of git.sourceforge.jp:/gitroot/eos/base

modified:   .gitignore
modified:   Makefile
new file:   examples

Merge branch 'master' of git://git.sourceforge.jp/gitroot/eos/base

Conflicts:
util/X86MAC64

new file:   .gitignore
new file:   doc
new file:   objects
new file:   pione

Add util/XXXX , doc , objects as links

Delete wrong files

modified:   sbin/modifyutil

Add hostdepend/X86MAC64

modified:   Makefile

modified:   Makefile
modified:   mrcImageNoiseReductionByRelaxation
modified:   src/Tools/Config/Define.inc

Modified:   Makefile
Add --tags for git-push

Develope a new tool: mrcImageBilateralFilter
                     lmrcImageBilateralFilter()
in lmrcImageBilateralFilter.c
   lmrcImageBilateralFilter.h

Add mrcImageConvolution
Modify array2mrc
modified:   Makefile
new file:   bin/mrcImageConvolution
modified:   env/Eos_env
new file:   hostdepend/X86LINUX64/src/Objects/General/Array/src/X86LINUX64/larray2mrc.c
modified:   include/Array.h
new file:   include/larray2mrc.h
modified:   include/lmrcImageMorphology.h
modified:   include/mrcImage.h
new file:   src/Objects/General/Array/src/larray2mrc.c
modified:   src/Tools/filter/array2mrc/src/array2mrc.c

Modified Eos/Makefile
modified:   Makefile

Add new tools for mathematical morphology
new file:   mrcImageClosing
new file:   mrcImageDilation
new file:   mrcImageErosion
new file:   mrcImageOpening

Add new object methods
new file:   lmrcImageDilation.c
new file:   lmrcImageErosion.c
new file:   lmrcImageMorphology.c
new file:   lmrcImageOpening.c
new file:   lmrcImageDilation.c
new file:   lmrcImageErosion.c
new file:   lmrcImageMorphology.c
new file:   lmrcImageOpening.c
new file:   lmrcImageMorphology.h

Add Lee-sigma filter in mrcImageSmoothing
modified:   mrcImageSmoothing

Add examples of Makefile in the directory of Integration/
new file:   Integration/CTF/Makefile-CTF
new file:   Integration/Compare/MakefileCompare
new file:   Integration/MultiCTF/Makefile.ForFukunaga
new file:   Integration/MultiCTF/Makefile.ForFukunaga2
new file:   Integration/RandomConical/Makefile.RandomConical
new file:   Integration/RandomConical/Makefile.To.RandomConical
new file:   Integration/SingleParticle/Makefile-fromKanae
new file:   Integration/Tomography/Makefile.Tomo
new file:   Integration/Tomography/Makefile.Tomo2
new file:   Integration/Tomography/Makefile.Tomo2-TakazakiVersion
new file:   Integration/Tomography/Makefile.Tomo2-TakazakiVersion2
new file:   Integration/Tomography/Makefile.fromMingyue20090502
new file:   Integration/Tomography/Makefile.fromMingyue20090519
new file:   Integration/Tomography/Makefile.fromMingyue2009059
new file:   Integration/Tomography/Makefile.fromMingyue20110507

modified:   Makefile

Modified  Eos/Makefile

Eos_env

update pdbMove. Add -toOrigin -originTo -GCtoOrigin

Change util directories

Update pdbPCA, -oU -oM -oPDB

mrcInfoSet has been updated and renewed to set FixedValues as default values.

Add mrcImageToPointsSet and Add a function of rmsd calculcation using mrcImageSubtraction and mrcImageNormalizedSubtraction. Modify mrcImageInit.

modify Makefiles to move hostdependent files to EOS_HOME/hostdepend

separate host-dependent binaries.

mrcImageSymetryFind and mrcImage3DWindowing modified

Delete .EosLog

Fixed conflict

Add Tools/Makefile

mrcImageAverage: add -w and -oW options

merge

merge

Newly updated. mrc2000

mrcImageTransformSign

add mrcImageParticleCandidateExtract

test

Fixed

Add util