From: kinoshita-eos Date: Wed, 15 Oct 2014 08:48:01 +0000 (+0900) Subject: Add: tutorial of mrcImageFourierNeighborCorrelation X-Git-Tag: v2.0.2p0033 X-Git-Url: http://git.osdn.net/view?p=eos%2Ftutorial.git;a=commitdiff_plain;h=refs%2Ftags%2Fv2.0.2p0033 Add: tutorial of mrcImageFourierNeighborCorrelation new file: SampleData/1VOM-N.mrc new file: Small Tools/mrcImageFourierNeighborCorrelation/Makefile new file: Small Tools/mrcImageFourierNeighborCorrelation/Makefile.config renamed: TIPS/BackData/Makefile -> TIPS/BackImage/Makefile renamed: TIPS/BackData/Makefile.config -> TIPS/BackImage/Makefile.config deleted: TIPS/BinShape/Makefile.config modified: TIPS/CreateGridImage/Makefile.config new file: TIPS/MaskImage/.EosLog renamed: TIPS/BinShape/Makefile -> TIPS/MaskImage/Makefile new file: TIPS/MaskImage/Makefile.config --- diff --git a/SampleData/1VOM-N.mrc b/SampleData/1VOM-N.mrc new file mode 100644 index 0000000..6e2c367 Binary files /dev/null and b/SampleData/1VOM-N.mrc differ diff --git a/Small Tools/mrcImageFourierNeighborCorrelation/Makefile b/Small Tools/mrcImageFourierNeighborCorrelation/Makefile new file mode 100644 index 0000000..f998f3f --- /dev/null +++ b/Small Tools/mrcImageFourierNeighborCorrelation/Makefile @@ -0,0 +1,50 @@ +# +# This is Main Makefile for mrcImageFourierNeighborCorrelation. +# + +#### Input extention #### +INI=mrc +MASK=mask +MASKBACK=maskback +FSC=fsc + +#### Suffixes rule #### +# Defined at Sub + +#### INCLUDE #### +-include Makefile.config + +#### Definition #### +# Path of Input File +INPUT_PATH=../../SampleData/1VOM-N.mrc + +### FileData +FILE_NAME=Input + +### ForMask +MASK_F_MODE=4 +MASK_VALUE=0.0125 + +# MaskSize +MASK_SIZE_X=256 +MASK_SIZE_Y=256 +MASK_SIZE_Z=256 + +#### Rules of the list created #### +# Defined at Sub + +##### Commands ##### +# Defined at Sub basically +all:: + make InitialData; + make InputInfo; + make MaskBackImage; + make InputBackImage; + make InputMaskImage; + make FSC; + +##### Commands(Input to Output) ##### +# Defined at Sub +.$(MASK).$(FSC): + mrcImageFourierNeighborCorrelation -i $*.$(INI)pad -o $*.$(FSC) -d 0.025 \ + -FSC -mask $*.$(MASK) -maskBack $*.$(MASKBACK); diff --git a/Small Tools/mrcImageFourierNeighborCorrelation/Makefile.config b/Small Tools/mrcImageFourierNeighborCorrelation/Makefile.config new file mode 100644 index 0000000..c92d54c --- /dev/null +++ b/Small Tools/mrcImageFourierNeighborCorrelation/Makefile.config @@ -0,0 +1,63 @@ +# +# This is Sub Makefile for mrcImageFourierNeighborCorrelation. +# + +#### Input extention #### +# Defined at Main + +#### Suffixes rule #### +.SUFFIXES: .$(INI) .$(INI)info .$(FSC) + +#### INCLUDE #### +-include ${EOS_HOME}/tutorial/TIPS/MaskImage/Makefile.config +-include ${EOS_HOME}/tutorial/TIPS/BackImage/Makefile.config + +#### Definition #### +# Defined at Main + +# For ../NulImage/Makefile.config +MASK_FILE_NAME=$(FILE_NAME) +BACK_FILE_NAME=$(FILE_NAME) +BACK_SIZE_X=$(MASK_SIZE_X) +BACK_SIZE_Y=$(MASK_SIZE_Y) +BACK_SIZE_Z=$(MASK_SIZE_Z) +BACK_IN_VALUE=1 +BACK_VALUE=0 + +#### Rules of the list created #### + + +##### Commands ##### +InitialData:: + touch $(FILE_NAME).$(INI); + rm $(FILE_NAME).$(INI); + ln -s $(INPUT_PATH) $(FILE_NAME).$(INI) + +InputInfo:: + make $(FILE_NAME).$(INI)info; + +InputBackImage:: + export IN_BACK=$(INI); \ + export BACK=$(INI)pad; \ + make BackImage; + +InputMaskImage:: + export IN_MASK=$(INI)pad; \ + make MaskImage; + +MaskBackImage:: + export BACK_IN_SIZE_X=$$(head -1 $(FILE_NAME).$(INI)info | awk '{printf("%d", $$4)}'); \ + export BACK_IN_SIZE_Y=$$(head -1 $(FILE_NAME).$(INI)info | awk '{printf("%d", $$5)}'); \ + export BACK_IN_SIZE_Z=$$(head -1 $(FILE_NAME).$(INI)info | awk '{printf("%d", $$6)}'); \ + export BACK_LENGTH=$$(tail -1 $(FILE_NAME).$(INI)info | awk '{printf("%f", $$4)}'); \ + export IN_BACK=$(MASKBACK)ini; \ + export BACK=$(MASKBACK); \ + make IniBackImage; \ + make BackImage; + +FSC:: + make $(FILE_NAME).$(FSC); + +##### Commands(Input to Output) ##### +.$(INI).$(INI)info: + mrcInfo -i $*.$(INI) | head -5 > $*.$(INI)info diff --git a/TIPS/BackData/Makefile b/TIPS/BackImage/Makefile similarity index 100% rename from TIPS/BackData/Makefile rename to TIPS/BackImage/Makefile diff --git a/TIPS/BackData/Makefile.config b/TIPS/BackImage/Makefile.config similarity index 76% rename from TIPS/BackData/Makefile.config rename to TIPS/BackImage/Makefile.config index abbe30d..76803de 100644 --- a/TIPS/BackData/Makefile.config +++ b/TIPS/BackImage/Makefile.config @@ -9,12 +9,12 @@ .SUFFIXES: .$(NUL) .$(IN_BACK) .$(BACK) #### INCLUDE #### --include ../NulImage/Makefile.config +-include ${EOS_HOME}/tutorial/TIPS/NulImage/Makefile.config #### Definition #### # Defined at Main -# For ../NulImage/Makefile.config +# For TIPS/NulImage/Makefile.config NUL_FILE_NAME=$(BACK_FILE_NAME) NUL_SIZE_X=$(BACK_IN_SIZE_X) NUL_SIZE_Y=$(BACK_IN_SIZE_Y) @@ -28,6 +28,7 @@ NUL_LENGTH=$(BACK_LENGTH) ##### Commands ##### IniBackImage:: + export NUL=$(IN_BACK); \ make NulImage; BackImage:: @@ -35,9 +36,6 @@ BackImage:: ##### Commands(Input to Output) ##### -.$(NUL).$(IN_BACK): - ln -s $*.$(NUL) $*.$(IN_BACK); - .$(IN_BACK).$(BACK): - mrcImage3DPad -i $*.$(IN_BACK) -o $*.$(BACK) -M 1 -v $(BACK_VALUE) \ + $(ENV_SWITCH)mrcImage3DPad -i $*.$(IN_BACK) -o $*.$(BACK) -M 1 -v $(BACK_VALUE) \ -Nx $(BACK_SIZE_X) -Ny $(BACK_SIZE_Y) -Nz $(BACK_SIZE_Z); diff --git a/TIPS/BinShape/Makefile.config b/TIPS/BinShape/Makefile.config deleted file mode 100644 index 9f7618e..0000000 --- a/TIPS/BinShape/Makefile.config +++ /dev/null @@ -1,28 +0,0 @@ -# -# This is Sub Makefile for Create Bin Image that has same shape as Input. -# - -#### Input extention #### -# Defined at Main - -#### Suffixes rule #### -.SUFFIXES: .$(IN_SBIN) .$(SBIN) - -#### INCLUDE #### - -#### Definition #### -# Defined at Main - - -#### Rules of the list created #### - - -##### Commands ##### -ShapeBinImage:: - make $(SBIN_FILE_NAME).$(SBIN); - - -##### Commands(Input to Output) ##### -.$(IN_SBIN).$(SBIN): - mrcImageLowPassFilter -i $*.$(IN_SBIN) -o $*.$(SBIN)tmp -m $(SBIN_F_MODE) -hvp $(SBIN_VALUE); - mrcImageBinalization -i $*.$(SBIN)tmp -o $*.$(SBIN) -m 32; diff --git a/TIPS/CreateGridImage/Makefile.config b/TIPS/CreateGridImage/Makefile.config index 0234888..e93d860 100644 --- a/TIPS/CreateGridImage/Makefile.config +++ b/TIPS/CreateGridImage/Makefile.config @@ -9,7 +9,7 @@ .SUFFIXES: .$(NUL) .$(ONE) .$(GRID) #### INCLUDE #### --include ../NulImage/Makefile.config +-include ${EOS_HOME}/tutorial/TIPS/NulImage/Makefile.config #### Definition #### # Defined at Main diff --git a/TIPS/MaskImage/.EosLog b/TIPS/MaskImage/.EosLog new file mode 100644 index 0000000..f5c549b --- /dev/null +++ b/TIPS/MaskImage/.EosLog @@ -0,0 +1 @@ +/Users/teppeikinoshita/Eos/bin/X86MAC64/mrcInfo -i /Users/teppeikinoshita/Desktop/work/img/Input-1VOM-N.mrc diff --git a/TIPS/BinShape/Makefile b/TIPS/MaskImage/Makefile similarity index 80% rename from TIPS/BinShape/Makefile rename to TIPS/MaskImage/Makefile index 2584d3e..74a23c9 100644 --- a/TIPS/BinShape/Makefile +++ b/TIPS/MaskImage/Makefile @@ -3,8 +3,8 @@ # #### Input extention #### -IN_SBIN=inimrc -SBIN=sbin +IN_MASK=inimrc +MASK=mask #### Suffixes rule #### # Defined at Sub @@ -14,10 +14,10 @@ SBIN=sbin #### Definition #### ### FileData -SBIN_FILE_NAME=Input +MASK_FILE_NAME=Input # ImageSize -SBIN_F_MODE=4 -SBIN_VALUE=0.0125 +MASK_F_MODE=4 +MASK_VALUE=0.0125 #### Rules of the list created #### @@ -26,7 +26,7 @@ SBIN_VALUE=0.0125 ##### Commands ##### # Defined at Sub basically all:: - make ShapeBinImage + make MaskImage ##### Commands(Input to Output) ##### # Defined at Sub diff --git a/TIPS/MaskImage/Makefile.config b/TIPS/MaskImage/Makefile.config new file mode 100644 index 0000000..329e6d7 --- /dev/null +++ b/TIPS/MaskImage/Makefile.config @@ -0,0 +1,30 @@ +# +# This is Sub Makefile for Create Mask Image that has same shape as Input. +# + +#### Input extention #### +# Defined at Main + +#### Suffixes rule #### +.SUFFIXES: .$(IN_MASK) .$(MASK) .$(MASK)tmp + +#### INCLUDE #### + +#### Definition #### +# Defined at Main + + +#### Rules of the list created #### + + +##### Commands ##### +MaskImage:: + make $(MASK_FILE_NAME).$(MASK); + + +##### Commands(Input to Output) ##### +.$(IN_MASK).$(MASK)tmp: + mrcImageLowPassFilter -i $*.$(IN_MASK) -o $*.$(MASK)tmp -m $(MASK_F_MODE) -hvp $(MASK_VALUE); + +.$(MASK)tmp.$(MASK): + mrcImageBinalization -i $*.$(MASK)tmp -o $*.$(MASK) -m 32;