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

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

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

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

deleted:    "\177"
deleted:    "\177\177"

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 X68MAC

Change src/Makefile

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

// 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/...

Add hostdepend/X86MAC64

modify Makefiles to move hostdependent files to EOS_HOME/hostdepend

separate host-dependent binaries.