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Takuo Yasunaga [Wed, 10 Sep 2014 09:14:32 +0000 (11:14 +0200)]
Usage Bugfixed: +8 -> 8
modified: src/Tools/mrcImage/mrcFFTInfo/src/mrcFFTInfo.c
Takuo Yasunaga [Wed, 10 Sep 2014 08:54:47 +0000 (10:54 +0200)]
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
Takuo Yasunaga [Thu, 4 Sep 2014 07:11:20 +0000 (16:11 +0900)]
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
Takuo Yasunaga [Mon, 11 Aug 2014 02:34:40 +0000 (11:34 +0900)]
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
Takuo Yasunaga [Sun, 10 Aug 2014 10:32:08 +0000 (19:32 +0900)]
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
Takuo Yasunaga [Sat, 9 Aug 2014 20:53:07 +0000 (05:53 +0900)]
Bug fixed:
mrcImageShapePCA
When -C was not defined, wrong processing.
Takuo Yasunaga [Tue, 5 Aug 2014 02:23:13 +0000 (11:23 +0900)]
Add gnuplot as util/bin
At present, we are trying to get utilities by wget/curl.
Takuo Yasunaga [Tue, 5 Aug 2014 01:17:25 +0000 (10:17 +0900)]
Modifiyed mrcImagePixelDataGet: -om (output mode)
modified: mrcImagePixelDataGet
modified: src/Tools/mrcImage/mrcImagePixelDataGet/Config/OptionControlFile
modified: src/Tools/mrcImage/mrcImagePixelDataGet/src/mrcImagePixelDataGet.c
Takuo Yasunaga [Mon, 4 Aug 2014 19:43:48 +0000 (04:43 +0900)]
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
Takuo Yasunaga [Fri, 1 Aug 2014 21:06:17 +0000 (06:06 +0900)]
Add a new command:
new file: mrcImageStack
Takuo Yasunaga [Thu, 31 Jul 2014 18:27:55 +0000 (03:27 +0900)]
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
Takuo Yasunaga [Thu, 31 Jul 2014 18:16:17 +0000 (03:16 +0900)]
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
Takuo Yasunaga [Tue, 29 Jul 2014 13:58:42 +0000 (22:58 +0900)]
Merge branch 'master' of git.sourceforge.jp:/gitroot/eos/base
Conflicts:
bin/wish/Display2/tclIndex
src/Tools/mrcImage/Makefile
Takuo Yasunaga [Sat, 12 Jul 2014 13:35:06 +0000 (22:35 +0900)]
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
Takuo Yasunaga [Mon, 7 Jul 2014 10:29:01 +0000 (19:29 +0900)]
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/*
Takuo Yasunaga [Tue, 1 Jul 2014 02:57:36 +0000 (11:57 +0900)]
Bug fixed:
modified: mrcImageInfo
modified: src/Objects/DataManip/mrcImage/src/mrcImageInfo.c
Takuo Yasunaga [Sat, 28 Jun 2014 04:39:24 +0000 (13:39 +0900)]
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/*
Takuo Yasunaga [Wed, 25 Jun 2014 21:48:15 +0000 (06:48 +0900)]
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
Takuo Yasunaga [Wed, 25 Jun 2014 20:48:27 +0000 (05:48 +0900)]
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/*
Takuo Yasunaga [Sun, 22 Jun 2014 22:28:47 +0000 (07:28 +0900)]
Bug fixed:
Takuo Yasunaga [Sun, 22 Jun 2014 15:03:48 +0000 (00:03 +0900)]
Create a new command for edge enhancement before edge detection
new file: mrcImageEdgeEnhancement
modified: lmrcImageEdgeEnhancement.h
modified: src/Objects/DataManip/mrcImage/src/lmrcImageEdgeEnhancement.c
modified: src/Objects/DataManip/mrcImage/src/lmrcImageEdgeEnhancement.h
new file: src/Objects/DataManip/mrcImage/src/lmrcImagePrevitt.c
new file: src/Objects/DataManip/mrcImage/src/lmrcImageRoberts.c
new file: src/Objects/DataManip/mrcImage/src/lmrcImageSobel.c
modified: src/Tools/Config/Define.inc
modified: src/Tools/mrcImage/mrcImageEdgeEnhancement/*
Takuo Yasunaga [Sat, 21 Jun 2014 09:18:51 +0000 (18:18 +0900)]
Create a new command:
new file: bin/mrcImageDividedByFile
new file: hostdepend/X86MAC64/bin/X86MAC64/mrcImageDividedByFile
Bug fixed: Devided -> Divided : Spell-missing
modified: include/mrcImage.h
modified: src/Objects/DataManip/mrcImage/inc/mrcImage.h
modified: src/Objects/DataManip/mrcImage/src/lmrcImageAverage.c
modified: src/Objects/DataManip/mrcImage/src/lmrcImageMontageCreate.c
modified: src/Objects/DataManip/mrcImage/src/mrcImageOperation.c
modified: src/Tools/Config/Define.inc
new file: src/Tools/mrcImage/mrcImageDividedByFile/*
Takuo Yasunaga [Sat, 21 Jun 2014 07:11:26 +0000 (16:11 +0900)]
Create A new tool:
new file: bin/mrcImageLogicalOperation
new file: hostdepend/X86MAC64/bin/X86MAC64/mrcImageLogicalOperation
new file: lmrcImageLogic.h
new file: lmrcImageLogicalOperation.c
modified: src/Tools/Config/Define.inc
new file: src/Tools/mrcImage/mrcImageLogicalOperation/*
Config/Define.inc
Takuo Yasunaga [Sat, 21 Jun 2014 04:06:21 +0000 (13:06 +0900)]
Create New Tools:
new file: mrcImageBottomHatTransform
new file: mrcImageTopHatTransform
new file: include/lmrcImageEdgeEnhancement.h
new file: src/Objects/DataManip/mrcImage/src/lmrcImageBottomHatTransform.c
new file: src/Objects/DataManip/mrcImage/src/lmrcImageTopHatTransform.c
modified: src/Objects/DataManip/mrcImage/src/lmrcImageMorphology.h
modified: src/Tools/Config/Define.inc
modified: src/Tools/Makefile
Under construction
modified: include/lmrcImageMorphology.h
new file: src/Tools/mrcImage/mrcImageEdgeEnhancement/*
Takuo Yasunaga [Fri, 20 Jun 2014 22:37:54 +0000 (07:37 +0900)]
Under construction.
modified: hostdepend/X86MAC64/src/Tools/rec3d/marker2Dto3DEstimator/src/X86MAC64/marker2Dto3DEstimator
modified: src/Tools/rec3d/marker2Dto3DEstimator/Config/OptionControlFile
modified: src/Tools/rec3d/marker2Dto3DEstimator/src/marker2Dto3DEstimator.c
Takuo Yasunaga [Wed, 11 Jun 2014 04:33:47 +0000 (13:33 +0900)]
New tools
new file: bin/mrcImageAsProbability
new file: bin/mrcImageDeconvolution
new file: bin/marker2Dto3DEstimator
Takuo Yasunaga [Sun, 1 Jun 2014 06:38:42 +0000 (15:38 +0900)]
Add weighted Back-projection lmrc2Dto3D: -m 2
modified: src/Objects/DataManip/transform/src/lmrc2Dto3D.c
modified: src/Tools/rec3d/marker2Dto3DEstimator/src/marker2Dto3DEstimator.c
modified: src/Tools/rec3d/mrc2Dto3D/src/mrc2Dto3D.c
Takuo Yasunaga [Fri, 30 May 2014 02:59:29 +0000 (11:59 +0900)]
Bug fixed:
modified: src/Tools/rec3d/mrcImageInverseRadonTransform/src/mrcImageInverseRadonTransform.c
Under construction:
modified: src/Tools/rec3d/marker2Dto3DEstimator/src/marker2Dto3DEstimator.c
Takuo Yasunaga [Mon, 26 May 2014 18:38:46 +0000 (03:38 +0900)]
Bug fixed:
modified: hostdepend/X86MAC64/bin/X86MAC64/mrcImagePad
modified: hostdepend/X86MAC64/lib/X86MAC64/shared/lmrcImageFFT.sharedo
modified: hostdepend/X86MAC64/lib/X86MAC64/shared/lmrcImageTriming.sharedo
new file: hostdepend/X86MAC64/util/X86MAC64/cuda
modified: src/Objects/DataManip/mrcImage/src/lmrcImageTriming.c
Takuo Yasunaga [Mon, 26 May 2014 17:46:56 +0000 (02:46 +0900)]
modified: env/Eos_env
modify util/HOSTDIR/bin
modified: include/Matrix3D.h
modified: include/eosPoint.h
modified: include/genUtil.h
modified: include/lmrcImageMasking.h
modified: src/Objects/General/Matrix3D/inc/Matrix3D.h
modified: src/Objects/General/Memory/inc/Memory.h
modified: src/Objects/General/Memory/src/memoryAllocate.c
modified: src/Objects/General/Memory/src/memoryByteSwap.c
new file: src/Objects/General/eosFunc/*
Add a new object of eosFunc: Sync/Rect
modified: src/Objects/General/eosPoint/*
Add eosPoint for maker
new file: bin/eosPointRotation
new file: src/Tools/rec3d/marker2Dto3DEstimator/*
Not yet completed
Takuo Yasunaga [Sun, 18 May 2014 12:04:15 +0000 (21:04 +0900)]
modified: hostdepend/X86MAC64/*
modified: include/lmrc2Dto3D.h
modified: src/Config/x86Mac64.inc
modified: src/Objects/DataExpress/eosRuby/src/Swig/mkmf.log
modified: src/Objects/DataExpress/eosRuby/src/Swig/molvieRuby_wrap.c
modified: src/Objects/General/eosCuda/src/eosCuda.cu
modified: src/*/*/*/src/Makefile
Takuo Yasunaga [Sun, 11 May 2014 22:36:46 +0000 (07:36 +0900)]
modified: hostdepend/X86MAC64/bin/X86MAC64/tiff2mrc
modified: hostdepend/X86MAC64/src/Tools/filter/tiff2mrc/src/X86MAC64/tiff2mrc
modified: src/Config/x86Mac64.inc
deleted: src/Objects/General/eosCuda/src/eosCuda.c
Takuo Yasunaga [Sun, 11 May 2014 22:22:59 +0000 (07:22 +0900)]
new file: Integration/Tomography/Makefile.recent
modified: Makefile
modified: hostdepend/X86MAC64/bin/X86MAC64/mrc2tiff
modified: hostdepend/X86MAC64/bin/X86MAC64/mrc2gif
modified: hostdepend/X86MAC64/src/Tools/rec3d/mrc2Dto3D/src/X86MAC64/mrc2Dto3D
added: libtiff, libgif
added: cuda
modified: include/eosPThread.h
modified: src/Config/x86Mac64.inc
modified: src/Objects/General/eosPThread/src/eosPThreadInit.c
modified: src/Objects/General/eosPThread/src/eosPThreadMutex.c
modified: src/Tools/rec3d/mrc2Dto3D/Config/Define.inc
new file: util/srcX86MAC64
Takuo Yasunaga [Mon, 28 Apr 2014 23:31:28 +0000 (08:31 +0900)]
deleted: "\177"
deleted: "\177\177"
Takuo Yasunaga [Thu, 27 Feb 2014 20:00:25 +0000 (05:00 +0900)]
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
Takuo Yasunaga [Sat, 15 Jun 2013 05:30:46 +0000 (14:30 +0900)]
Rebuild for X68MAC
Takuo Yasunaga [Fri, 31 May 2013 16:36:54 +0000 (01:36 +0900)]
Change src/Makefile
Takuo Yasunaga [Sat, 25 May 2013 13:18:13 +0000 (22:18 +0900)]
Apply eosPThread to mrc2Dto3D, -pthread
Modify lmrcImageRhoFiltering
Modify x86Mac64.inc
Modify lmrcImageFFT for odd size images
Modify lmrcImageOperation(lmrcImageAdd) for speed up.
Takuo Yasunaga [Sun, 12 May 2013 19:16:15 +0000 (04:16 +0900)]
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
Takuo Yasunaga [Tue, 7 May 2013 20:01:07 +0000 (05:01 +0900)]
// 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/...
Takuo Yasunaga [Sun, 5 May 2013 01:20:45 +0000 (10:20 +0900)]
Add hostdepend/X86MAC64
Takuo Yasunaga [Sun, 3 Feb 2013 00:09:18 +0000 (09:09 +0900)]
modify Makefiles to move hostdependent files to EOS_HOME/hostdepend
Takuo Yasunaga [Wed, 30 Jan 2013 19:32:46 +0000 (04:32 +0900)]
separate host-dependent binaries.