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 (file)
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 (file)
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 (file)
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 (file)
--- 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 (file)
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 (file)
--- 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 (file)
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 (file)
--- 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 (file)
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;