Bug fixed:
Eos_env
install-eos.sh

recompiled for cuda:

Move test data from src/bin directories to data/.

Rebuld:
modified:   hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAutoCorrelationWithWindowing
modified:   hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCTFCompensationForTiltImage
copied:     hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/X86LINUX64/mrcImageNormalizedSubtraction -> hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageNormalizedSubtraction
modified:   hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageSpatialFrequencyFilter
modified:   hostdepend/X86LINUX64/lib/X86LINUX64/libArray.a
modified:   hostdepend/X86LINUX64/lib/X86LINUX64/libEosObjects.a
modified:   hostdepend/X86LINUX64/lib/X86LINUX64/libTclTk.a
modified:   hostdepend/X86LINUX64/lib/X86LINUX64/libctfInfo.a
modified:   hostdepend/X86LINUX64/lib/X86LINUX64/libgifFile.a
modified:   hostdepend/X86LINUX64/lib/X86LINUX64/libllData.a
modified:   hostdepend/X86LINUX64/lib/X86LINUX64/libmrcImage.a
modified:   hostdepend/X86LINUX64/lib/X86LINUX64/libpdbFile.a
modified:   hostdepend/X86LINUX64/lib/X86LINUX64/libtransform.a
modified:   hostdepend/X86LINUX64/lib/X86LINUX64/shared/lmrcImageSpatialFrequencyFilter.sharedo
modified:   hostdepend/X86LINUX64/src/Objects/DataExpress/TclTk/src/X86LINUX64/libTclTk.a
modified:   hostdepend/X86LINUX64/src/Objects/DataExpress/gifFile/src/X86LINUX64/libgifFile.a
modified:   hostdepend/X86LINUX64/src/Objects/DataManip/ctfInfo/src/X86LINUX64/libctfInfo.a
modified:   hostdepend/X86LINUX64/src/Objects/DataManip/llData/src/X86LINUX64/libllData.a
modified:   hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/libmrcImage.a
modified:   hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/libmrcImage.debug.a
modified:   hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageSpatialFrequencyFilter.sharedo
modified:   hostdepend/X86LINUX64/src/Objects/DataManip/pdbFile/src/X86LINUX64/libpdbFile.a
modified:   hostdepend/X86LINUX64/src/Objects/DataManip/transform/src/X86LINUX64/libtransform.a
modified:   hostdepend/X86LINUX64/src/Objects/General/Array/src/X86LINUX64/libArray.a
new file:   hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/X86LINUX64/mrcImageAutoCorrelationWithWindowing
modified:   hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCTFCompensationForTiltImage/src/X86LINUX64/mrcImageCTFCompensationForTiltImage
modified:   hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageNormalizedSubtraction/src/X86LINUX64/mrcImageNormalizedSubtraction
modified:   hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageSpatialFrequencyFilter/src/X86LINUX64/mrcImageSpatialFrequencyFilter
modified:   src/Objects/DataExpress/eosRuby/src/Swig/molvieRuby_wrap.c
modified:   src/Tools/Integration/Display2/src/Display2.html
modified:   src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/mrcImageAutoCorrelationWithWindowing.html
modified:   src/Tools/mrcImage/mrcImageDensityInfo/src/mrcImageDensityInfo.html
typechange: src/Tools/mrcImage/mrcImageNormalizedSubtraction/Makefile
modified:   src/Tools/mrcImage/mrcImageSplit/src/mrcImageSplit.html

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

Conflicts:
bin/wish/Display2/tclIndex
env/install-eos.sh

modified:   Makefile
modified:   bin/wish/Display2/tclIndex
modified:   env/Eos_env
modified:   env/install-eos.sh
deleted:    examples
deleted:    hostdepend/X86LINUX64/util/X86LINUX64/share/ri/1.9.1/system/REXML/Parsers/XPathParser/Predicate-i.ri
deleted:    hostdepend/X86LINUX64/util/X86LINUX64/share/ri/1.9.1/system/REXML/Parsers/XPathParser/predicate-i.ri

To Merge:
modified:   bin/wish/Display2/tclIndex
modified:   env/install-eos.sh

Modified dotSourceInMakefileCreate:
modified:   sbin/dotSourceInMakefileCreate
modified:   src/Config/Template/Makefile
modified:   src/Makefile
modified:   src/Objects/.Source.org

Recompiled:
deleted:    hostdepend/X86LINUX64/util/X86LINUX64/share/ri/1.9.1/system/REXML/Parsers/XPathParser/Predicate-i.ri
deleted:    hostdepend/X86LINUX64/util/X86LINUX64/share/ri/1.9.1/system/REXML/Parsers/XPathParser/predicate-i.ri
modified:   hostdepend/X86MAC64/bin/X86MAC64/mrcImageCTFCompensationForTiltImage
modified:   hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageCTFCompensationForTiltImage/src/X86MAC64/mrcImageCTFCompensationForTiltImage
modified:   src/Objects/DataExpress/eosRuby/src/Swig/molvieRuby_wrap.c
modified:   src/Tools/mrcImage/mrcImageCTFCompensationForTiltImage/src/mrcImageCTFCompensationForTiltImage.c

pione-dir: deleted
deleted:    pione

Bug fixed: No.34544: -o help meesage in mrcImageSpatialFrequencyFilter
modified:   hostdepend/X86MAC64/bin/X86MAC64/mrcImageSpatialFrequencyFilter
modified:   src/Tools/mrcImage/mrcImageSpatialFrequencyFilter/Config/OptionControlFile
typechange: src/Tools/mrcImage/mrcImageSpatialFrequencyFilter/doc/Makefile
modified:   src/Tools/mrcImage/mrcImageSpatialFrequencyFilter/src/mrcImageSpatialFrequencyFilter.html
modified:   src/Tools/mrcImage/mrcImageSpatialFrequencyFilter/src/usage.c

Bug fixed:
modified:   Makefile
modified:   sbin/makegeneral
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageSpatialFrequencyFilter.c
typechange: src/Tools/mrcImage/mrcImageFourierNeighborCorrelation/Makefile

Conflicts:
src/Tools/Makefile
src/Tools/mrcImage/Makefile

install command
env/install-eos.sh

modified:   env/Eos_env
modified:   env/install-eos.sh

modified:   hostdepend/X86LINUX64/lib/X86LINUX64/libEosObjects.a

Bug fixed: for -NoiseWeighted Brestore
modified:   hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageFourierNeighborCorrelation

rebuild: mrcImageWindowing

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

Conflicts:
src/Tools/mrcImage/mrcImageWindowing/src/mrcImageWindowing.html

Add exp/gauss window: lmrcImageWindowing
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageWindowing.c

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

Conflicts:
src/Tools/Integration/Display2/src/Display2.html
src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/mrcImageAutoCorrelationWithWindowing.html
src/Tools/mrcImage/mrcImageDensityInfo/src/mrcImageDensityInfo.html
src/Tools/mrcImage/mrcImageSplit/src/mrcImageSplit.html
src/Tools/mrcImage/mrcImageWindowing/src/mrcImageWindowing.html

recompiled:
modified:   hostdepend/X86LINUX64/*
bin/X86LINUX64/CheckCommonLineData

rebuild: for X86MAC64

modified:   hostdepend/X86MAC64/*

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

Modified tools: mrcImageFourierNeighborCorrelation / mrcImageFourierShellCorrelation
Weighted Noise for mrcImageSpatialFrequencyFilter (Smoothing considering FSC)

modified:   src/Objects/DataManip/mrcImage/src/lmrcImageFourierNeighborCorrelation.c
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageFourierNeighborCorrelation.h
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageFourierShellCorrelation.c
modified:   src/Tools/Config/Define.inc
modified:   src/Tools/mrcImage/mrcImageFourierNeighborCorrelation/Config/OptionControlFile
typechange: src/Tools/mrcImage/mrcImageFourierNeighborCorrelation/Makefile
modified:   src/Tools/mrcImage/mrcImageFourierNeighborCorrelation/inc/mrcImageFourierNeighborCorrelation.h
modified:   src/Tools/mrcImage/mrcImageFourierNeighborCorrelation/src/mrcImageFourierNeighborCorrelation.c
modified:   src/Tools/mrcImage/mrcImageFourierNeighborCorrelation/src/test/Makefile
for testing:
modified:   src/Tools/mrcImage/mrcImageSpatialFrequencyFilter/src/test/Makefile

Modified Tools: mrcInfo %ld -> %d
modified:   src/Objects/DataManip/mrcImage/src/mrcImagePrint.c

Under construction:
modified:   env/Eos_env
modified:   env/install-eos.sh
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageWindowing.c
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageWindowing.h

Modify: Eos_env: First AID for case of no CUDA.
modified:   env/Eos_env

Recompiled:
modified:   hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageNullImageCreate
modified:   hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageNullImageCreate/src/X86LINUX64/mrcImageNullImageCreate

Modified: mrcImageNullImageCreate
modified:   hostdepend/X86MAC64/bin/X86MAC64/mrcImageNullImageCreate
modified:   src/Tools/Config/Define.inc
typechange: src/Tools/mrcImage/Makefile
modified:   src/Tools/mrcImage/mrcImageNullImageCreate/Config/OptionControlFile
modified:   src/Tools/mrcImage/mrcImageNullImageCreate/src/mrcImageNullImageCreate.c

Bug fixed:
modified:   env/Eos_env

Under construction:
modified:   env/install-eos.sh

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

Conflicts:
src/Objects/DataManip/mrcImage/src/mrcImagePrint.c

Recompiled:
modified:   src/Tools/mrcImage/mrcImageFourierNeighborCorrelation/src/mrcImageFourierNeighborCorrelation.html

Bug fixed:
modified:   src/Objects/DataManip/mrcImage/src/mrcImagePrint.c
modified:   src/Tools/mrcImage/mrcImageFourierNeighborCorrelation/src/mrcImageFourierNeighborCorrelation.c

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

Conflicts:
src/Tools/mrcImage/mrcImageFourierNeighborCorrelation/src/mrcImageFourierNeighborCorrelation.html

modified:   Integration/FSC/Makefile
modified:   hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageFourierNeighborCorrelation
modified:   hostdepend/X86LINUX64/bin/X86LINUX64/mrcInfo
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageFourierNeighborCorrelation.c
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageFourierNeighborCorrelation.h
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageMultiplying.c
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageMultiplying.h
new file:   src/Objects/DataManip/mrcImage/src/lmrcImageNoiseCreate.c
new file:   src/Objects/DataManip/mrcImage/src/lmrcImageNoiseCreate.h
modified:   src/Objects/DataManip/mrcImage/src/mrcImagePrint.c
modified:   src/Tools/mrcImage/mrcImageFourierNeighborCorrelation/Config/OptionControlFile
modified:   src/Tools/mrcImage/mrcImageFourierNeighborCorrelation/src/mrcImageFourierNeighborCorrelation.c
modified:   src/Tools/mrcImage/mrcImageMultiplyingbyFile/src/mrcImageMultiplyingbyFile.c
modified:   src/Tools/mrcImage/mrcImageNoiseCreate/src/mrcImageNoiseCreate.c

recompiled:
modified:   hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageFourierNeighborCorrelation
modified:   hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageMultiplyingbyFile
modified:   hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageNoiseCreate
modified:   hostdepend/X86LINUX64/lib/X86LINUX64/libEosObjects.a
modified:   hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageFourierNeighborCorrelation/src/X86LINUX64/mrcImageFourierNeighborCorrelation
modified:   hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageMultiplyingbyFile/src/X86LINUX64/mrcImageMultiplyingbyFile
modified:   hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageNoiseCreate/src/X86LINUX64/mrcImageNoiseCreate
modified:   src/Tools/mrcImage/mrcImageFourierNeighborCorrelation/src/mrcImageFourierNeighborCorrelation.html

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

Modified Tools:
modified:   hostdepend/X86MAC64/bin/X86MAC64/mrcImageFourierNeighborCorrelation
modified:   hostdepend/X86MAC64/bin/X86MAC64/mrcImageMultiplyingbyFile
modified:   hostdepend/X86MAC64/bin/X86MAC64/mrcImageNoiseCreate
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageFourierNeighborCorrelation.c
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageFourierNeighborCorrelation.h
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageMultiplying.c
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageMultiplying.h
new file:   src/Objects/DataManip/mrcImage/src/lmrcImageNoiseCreate.c
new file:   src/Objects/DataManip/mrcImage/src/lmrcImageNoiseCreate.h
modified:   src/Tools/mrcImage/mrcImageFourierNeighborCorrelation/Config/OptionControlFile
modified:   src/Tools/mrcImage/mrcImageFourierNeighborCorrelation/src/mrcImageFourierNeighborCorrelation.c
modified:   src/Tools/mrcImage/mrcImageMultiplyingbyFile/src/mrcImageMultiplyingbyFile.c
modified:   src/Tools/mrcImage/mrcImageNoiseCreate/src/mrcImageNoiseCreate.c

Recompiled:
modified:   hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageFourierShellCorrelation
new file:   hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageSpatialFrequencyFilter

Bug fixed: mrcImageSpatialFrequencyFilter

Create a new tool: mrcImageSpatialFrequencyFilter
new file:   bin/mrcImageSpatialFrequencyFilter

Modified tools: mrcImageFourierNeighborCorrelation, mrcImageFourierShellCorrelation
modified:   include/lmrcImageFourierNeighborCorrelation.h
modified:   include/lmrcImageFourierShellCorrelation.h
new file:   include/lmrcImageSpatialFrequencyFilter.h

Rebuild: for X86LINUX64
modified:   hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageMultiCTFCompensation
modified:   hostdepend/X86LINUX64/lib/X86LINUX64/libEosObjects.a
modified:   hostdepend/X86LINUX64/lib/X86LINUX64/libctfInfo.a
modified:   hostdepend/X86LINUX64/lib/X86LINUX64/libmrcImage.a
modified:   hostdepend/X86LINUX64/lib/X86LINUX64/shared/lmrcImageMultiCTFCompensation.sharedo
copied:     hostdepend/X86LINUX64/lib/X86LINUX64/libctfInfo.a -> hostdepend/X86LINUX64/src/Objects/DataManip/ctfInfo/src/X86LINUX64/libctfInfo.a
modified:   hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/libmrcImage.a
modified:   hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/libmrcImage.debug.a
new file:   hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageFourierNeighborCorrelation.c
modified:   hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageMultiCTFCompensation.sharedo
modified:   hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/X86LINUX64/mrcImageMultiCTFCompensation

Modified Tools: mrcImageMultiCTFCompensation
modified:   src/Objects/DataManip/ctfInfo/inc/ctfInfo.h
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageMultiCTFCompensation.c
modified:   src/Tools/mrcImage/mrcImageMultiCTFCompensation/Config/OptionControlFile
modified:   src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/mrcImageMultiCTFCompensation.c

Modified for X86LINUX65:
new file:   hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageFourierNeighborCorrelation
modified:   hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageFourierShellCorrelation

New Tools:
new file:   bin/mrcImageFourierNeighborCorrelation

Modified Toos:
modified file:   bin/mrcImageFourierShellCorrelation

Incomplete, under construction:
new file:   bin/dmInfo

modified:   bin/wish/Display2/tclIndex
modified:   hostdepend/X86MAC64/bin/X86MAC64/*
modified:   hostdepend/X86MAC64/lib/X86MAC64/libEosObjects.a
modified:   hostdepend/X86MAC64/lib/X86MAC64/*

Bug fixed: Axis
modified:   mrcImageHighPassFilter
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageHighPassFilter.c

modified:   Integration/FSC/Makefile
modified:   bin/wish/Display2/tclIndex
modified:   hostdepend/X86LINUX64/bin/X86LINUX64/*
modified:   hostdepend/X86LINUX64/lib/X86LINUX64/*

Modified mrcImageNormalizing: Add AssumeAsGaussian
modified:   mrcImageNormalizing
modified:   include/lmrcImageNormalizing.h
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageNormalizing.c
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageNormalizing.h

Add Integeration/FSC
new file:   Integration/FSC/Makefile

Modified: Add usage related to -M
modified:   src/Objects/DataManip/bmpFile/inc/bmpFile.h
modified:   src/Objects/DataManip/bmpFile/src/lbmp2mrc.c

Modified: bmp2mrc supported Y/R/G/B to mono of mrcImage, respecitively.
modified:   src/Objects/DataManip/bmpFile/src/lbmp2mrc.c
modified:   src/Tools/filter/bmp2mrc/src/bmp2mrc.c

Add -thres for mrcImageAutoRotationAverage
modified:   mrcImageAutoRotationAverage
Add lmrcImageAverageOverThreshold
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageAverage.c
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageAverage.h

Create a new tool of mrcImageAutoRotationAverage:
new file:   mrcImageAutoRotationAverage
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageCorrelation.h
Input/Output separation of struct

Modifiy mrcImage3DPad: Filament/Sphere/Elliposiod/Rectangle
modified:   include/lmrcImage3DPad.h
modified:   src/Objects/DataManip/mrcImage/src/lmrcImage3DPad.c
modified:   src/Objects/DataManip/mrcImage/src/lmrcImage3DPad.h
modified:   src/Tools/mrcImage/mrcImage3DPad/src/mrcImage3DPad.c

Modify genUtil.h

name change eosPointTracker

Function Added
new file:   eosPointProjector
Completed
modified:   marker2Dto3DEstimator
Not yet completed
modified:   src/Objects/General/eosPoint/inc/eosPoint.h
new file:   src/Objects/General/eosPoint/src/eosPointProject.c
modified:   src/Objects/General/eosPoint/src/eosPointRead.c
modified:   src/Tools/rec3d/marker2Dto3DEstimator/src/marker2Dto3DEstimator.c

Bug fixed: ctrl2init0
modified:   sbin/awk/ctrl2init0.awk

Bug Fixed: ID 34305: git-fetch-tag in Makefile
modified:   Makefile

Bug Fixed: help message of option -Shape
modified:   src/Tools/mrcImage/mrcImageSiemensStar/src/mrcImageSiemensStar.c

Modify: ID 34305: git-tag-fetch
modified:   Makefile

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

Modify: ID 34304: Initialize of Option -N
modified:   src/Tools/mrcImage/mrcImageSiemensStar/src/init.c

Bug-fixed:
lmrcImageCTFCompensation
-flagWin : Sine window

modified:   src/Objects/DataManip/mrcImage/src/lmrcImageCTFCompensation.c

Usage Bugfixed: +8 -> 8
modified:   src/Tools/mrcImage/mrcFFTInfo/src/mrcFFTInfo.c

mrcFFTInfo: Function Added
with nDivision and angle: mode 7
with SD : +32
with Log : +64

modified:   include/mrcImage.h
modified:   src/Objects/DataManip/mrcImage/src/lmrcFFTInfo.c
modified:   src/Tools/mrcImage/mrcFFTInfo/Config/OptionControlFile
modified:   src/Tools/mrcImage/mrcFFTInfo/src/mrcFFTInfo.c

Ticke: #34276

modified:   src/Tools/mrcImage/mrcImageSiemensStar/Config/OptionControlFile
typechange: src/Tools/mrcImage/mrcImageSiemensStar/Makefile
modified:   src/Tools/mrcImage/mrcImageSiemensStar/doc/Makefile
modified:   src/Tools/mrcImage/mrcImageSiemensStar/inc/mrcImageSiemensStar.h
modified:   src/Tools/mrcImage/mrcImageSiemensStar/src/mrcImageSiemensStar.c
modified:   src/Tools/mrcImage/mrcImageSiemensStar/src/test/Makefile

Not yet:
new file:   env/install-eos.sh
modified:   hostdepend/X86MAC64/src/Tools/Test/cufft/src/X86MAC64/.Depend
modified:   hostdepend/X86MAC64/src/Tools/Test/cufft/src/X86MAC64/Makefile

Add: 34213
make git-tag(-XXX) in Makefile.
modified:   Makefile

Ticket 34171
Add message at make git-push in Makefile.

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

Add: 34169
Makefile
make git-add -v for optional, data, tutorial, others

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

Window Functions were added.
src/Objects/DataManip/mrcImage/src/lmrcImageWindowing.c
src/Objects/DataManip/mrcImage/src/lmrcImageWindowing.h
modified:   src/Tools/mrcImage/mrcImageWindowing/Config/OptionControlFile

Bug fixed:34157
modified: Makefile
for miss of merge.

Bug fixed:
modified: Makefile
For the case of not working remote rm, when init.

lmrcImageMasking: Tools to Objects
modified:   mrcImageMasking
modified:   include/lmrcImageMasking.h
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageMasking.c
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageMasking.h
modified:   src/Tools/mrcImage/mrcImageMasking/src/mrcImageMasking.c

Bug fixed:
modified:   Makefile
When GITUSER was not defined, we could not clone GITs.

Bug fixed:
  mrcImageShapePCA
  When -C was not defined, wrong processing.

Add Zephyr

Bug fixed:
EOS_GIT_USER -> EOS_GITUSER

Add gnuplot as util/bin
At present, we are trying to get utilities by wget/curl.

Modifiyed mrcImagePixelDataGet: -om (output mode)
modified:   mrcImagePixelDataGet
modified:   src/Tools/mrcImage/mrcImagePixelDataGet/Config/OptionControlFile
modified:   src/Tools/mrcImage/mrcImagePixelDataGet/src/mrcImagePixelDataGet.c

Add new filters for mrcImageSmoothing
Edge and Line Weights Smoothing
Contrast sensitve weights smoothing
Gradient inverse weighted smoothing

modified:   mrcImageSmoothing
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageSmoothing.c
modified:   src/Tools/mrcImage/mrcImageSmoothing/src/test/Makefile

Add new utils:
cmake
gdb
boost

Update for X86LINUX64ICC
modified:   hostdepend/X86LINUX64ICC/*

Add a new command:
new file:   mrcImageStack

Merged Version for X86LINUX64
modified:   env/Eos_env
modified:   hostdepend/X86LINUX64/*
new file:   hostdepend/X86LINUX64ICC/*

Bug fixed:
Change lmrcImageDevidedByReal to lmrcImageDividedByReal.

modified:   src/Objects/DataManip/transform/src/lmrc2Dto3D.c
modified:   src/Tools/mrcImage/mrcImage3DSymmetryFind/src/mrcImage3DSymmetryFind.c
modified:   src/Tools/mrcImage/mrcImageCorrelation/src/mrcImageCorrelation.c
modified:   src/Tools/mrcImage/mrcImageUnbentROI/src/mrcImageUnbentROI.c

Filename Changed
deleted:    src/Objects/DataManip/mrcImage/src/1
deleted:    src/Objects/DataManip/mrcImage/src/lmrcImagePrevitt.c

Add new functions
modified:   hostdepend/X86MAC64/bin/X86MAC64/mrcImageEdgeEnhancement
modified:   hostdepend/X86MAC64/bin/X86MAC64/mrcImageSmoothing

modified:   include/lmrcImageEdgeEnhancement.h

  Add Negative Laplacian
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageEdgeEnhancement.c
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageEdgeEnhancement.h
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageNegativeLaplacian.c

  Add Weighted Mean Filter
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageSmoothing.c

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

Conflicts:
bin/wish/Display2/tclIndex
src/Tools/mrcImage/Makefile

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

Conflicts:
hostdepend/X86LINUX64/lib/X86LINUX64/libEosObjects.a
hostdepend/X86LINUX64/lib/X86LINUX64/libEosObjects.so
lib/tclIndex

Bug fixed: mrc2map
modified:   src/Objects/DataManip/mapFile/src/mapFileRead.c
modified:   src/Tools/mrcImage/mrc2dsn6/src/mrc2dsn6.c
modified:   src/Tools/mrcImage/mrc2map/src/mrc2map.c
modified:   src/Tools/mrcImage/mrcImagePixelDataGet/src/test/Makefile

Rebuild for Tools:

lmrcImageFFT: for CUDA
Bug fixed: fo cufftw

modified:   bin/wish/Display2/tclIndex
modified:   env/Eos_env
modified:   lib/tclIndex
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageFFT.c
modified:   src/Tools/Config/Define.inc
typechange: src/Tools/Makefile
typechange: src/Tools/mrcImage/Makefile
modified:   src/Tools/mrcImage/mrcImageFFT/Config/Define.inc
modified:   src/Tools/mrcImage/mrcImageFFT/doc/Makefile
modified:   src/Tools/mrcImage/mrcImageFFT/src/mrcImageFFT.c

Change ln to cp
typechange: src/Tools/Makefile

Add a new funciton and fixed bugs : mrcImageEdgeEnhancement
modified:   include/lmrcImageEdgeEnhancement.h
new file:   src/Objects/DataManip/mrcImage/src/lmrcImageDifferential.c
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageEdgeEnhancement.c
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageEdgeEnhancement.h
modified:   src/Objects/DataManip/mrcImage/src/lmrcImagePrevitt.c
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageRoberts.c
modified:   src/Objects/DataManip/mrcImage/src/lmrcImageSobel.c
modified:   src/Tools/Config/Define.inc

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

modified:   .gitignore

Modified:
Makefile for CUDA/nvcc

Modified:
modified:   .gitignore
modified:   bin/wish/Display2/tclIndex

rebuild:
modified:   hostdepend/X86LINUX64/bin/X86LINUX64/*
modified:   hostdepend/X86LINUX64/lib/X86LINUX64/*

mrcImageGetPixels for CUDA/No Cuda

modified:   include/mrcImage.h
new file:   include/mrcImageGetPixelsCUDA.h
modified:   src/Config/x86Mac64.inc
modified:   src/Objects/DataManip/mrcImage/inc/mrcImage.h
new file:   src/Objects/DataManip/mrcImage/src/mrcImageGetPixels.c
new file:   src/Objects/DataManip/mrcImage/src/mrcImageGetPixelsCUDA.cu
new file:   src/Objects/DataManip/mrcImage/src/mrcImageGetPixelsCUDA.h
modified:   src/Tools/Config/Define.inc

mrcImagePixelDataGet for CUDA:
modified:   src/Tools/mrcImage/mrcImagePixelDataGet/*

Bug fixed:
modified:   mrcImageInfo
modified:   src/Objects/DataManip/mrcImage/src/mrcImageInfo.c

A new command : for floating. Previously, we have used mrcImagePad for floating
new file:   bin/mrcImageFloating
new file:   src/Objects/DataManip/mrcImage/src/lmrcImageFloating.c
new file:   src/Objects/DataManip/mrcImage/src/lmrcImageFloating.h
new file:   src/Tools/mrcImage/mrcImageFloating/*

Bug fixed for Color Images:
modified:   src/Objects/DataManip/bmpFile/src/bmpFileRead.c
modified:   src/Objects/DataManip/bmpFile/src/lbmp2mrc.c
modified:   src/Tools/filter/bmp2mrc/src/test/Makefile

Add a new function:
BMP File Format:
new file:   bin/bmp2mrc
new file:   bin/bmpFileInfo
new file:   include/bmpFile.h
new file:   src/Objects/DataManip/bmpFile/*
new file:   src/Objects/DataManip/bmpFile/inc/bmpFile.h
new file:   src/Objects/DataManip/bmpFile/src/bmpFileInfo.c
new file:   src/Objects/DataManip/bmpFile/src/bmpFileRead.c
new file:   src/Objects/DataManip/bmpFile/src/lbmp2mrc.c

new file:   src/Tools/bmpFile/
new file:   src/Tools/bmpFile/bmpFileInfo/*
new file:   src/Tools/filter/bmp2mrc/*

Modify Makefile to see gcc commands
modified:   src/Config/Template/ObjectsTemplate.Dir/src/ARCH/Makefile
modified:   src/Config/x86Mac64.inc
modified:   src/Objects/DataManip/Makefile

Install ruby1.9.1
new file:   hostdepend/X86MAC64/util/X86MAC64/lib/ruby/1.9.1/*
new file:   hostdepend/X86MAC64/util/X86MAC64/share/ri/1.9.1/*

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

Rebuild for X86LINUX:
modified:   hostdepend/X86LINUX64/bin/X86LINUX64/*

Bug fixed: