Add: SampleData to be added noise

	new file:   SampleData/1VOM.mrc

Modify: Create image files for -i -mask -maskBack
	modified:   Small Tools/mrcImage/mrcImageFourierNeighborCorrelation/Makefile/Makefile
	modified:   Small Tools/mrcImage/mrcImageFourierNeighborCorrelation/Makefile/Makefile-lib

Modify: Bug fixed: make for undefined suffix
	modified:   TIPS/BackImage/Makefile/Makefile-lib
	modified:   TIPS/CreateGridImage/Makefile/Makefile-lib
	modified:   TIPS/MaskImage/Makefile/Makefile-lib
	modified:   TIPS/Projection3DImage/Makefile/Makefile-lib

diff --git a/SampleData/1VOM.mrc b/SampleData/1VOM.mrc
new file mode 100644 (file)
index 0000000..5c6a965
Binary files /dev/null and b/SampleData/1VOM.mrc differ

diff --git a/Small Tools/mrcImage/mrcImageFourierNeighborCorrelation/Makefile/Makefile b/Small Tools/mrcImage/mrcImageFourierNeighborCorrelation/Makefile/Makefile
index 6e8fe82..e5af7c9 100644 (file)
--- a/Small Tools/mrcImage/mrcImageFourierNeighborCorrelation/Makefile/Makefile
+++ b/Small Tools/mrcImage/mrcImageFourierNeighborCorrelation/Makefile/Makefile
@@ -34,7 +34,7 @@ FILE_NAME=Input
 
 ### ForMask
 MASK_F_MODE=4
-MASK_VALUE=0.0125
+MASK_VALUE=0.05
 
 # MaskSize
 MASK_SIZE_X=256
@@ -44,8 +44,8 @@ MASK_SIZE_Z=256
 # FNC Graph Image
 X_SIZE_GRAPH=360
 Y_SIZE_GRAPH=240
-S_DATA=1
-E_DATA=1
+S_DATA=5
+E_DATA=2
 
 #### Rules of the list created ####
 # Defined at Sub
@@ -60,7 +60,7 @@ Initial::
        make InputMaskImage;
 
 Exe::
-       make FNC;
+       make $(FILE_NAME).$(FNC);
 
 all::
        make Initial;
@@ -68,6 +68,7 @@ all::
        make Final;
 
 Final::
+       make FNCInputProjection;
        make FNCGnudata;
        make FNCGnuplot;
 
@@ -96,7 +97,11 @@ help_mrcImageFourierNeighborCorrelation::
 
 ##### Commands(Input to Output) #####
 # Defined at Sub
+ifdef MASK
+ifdef FNC
 .$(MASK).$(FNC):
-       mrcImageFourierNeighborCorrelation -i $*.$(INI)pad -o $*.$(FNC) -d 0.025 \
+       mrcImageFourierNeighborCorrelation -i $*.$(INI)pad -o $*.$(FNC) \
                                                                                -FSC -mask $*.$(MASK) -maskBack $*.$(MASKBACK) \
                                                                                -NoiseWeighted -100 -FSCfull -Cref;
+endif #FNC
+endif #MASK

diff --git a/Small Tools/mrcImage/mrcImageFourierNeighborCorrelation/Makefile/Makefile-lib b/Small Tools/mrcImage/mrcImageFourierNeighborCorrelation/Makefile/Makefile-lib
index 01a3f1d..0d6277e 100644 (file)
--- a/Small Tools/mrcImage/mrcImageFourierNeighborCorrelation/Makefile/Makefile-lib
+++ b/Small Tools/mrcImage/mrcImageFourierNeighborCorrelation/Makefile/Makefile-lib
@@ -13,6 +13,7 @@
 -include ${EOS_HOME}/tutorial/TIPS/BackImage/Makefile/Makefile-lib
 -include ${EOS_HOME}/tutorial/TIPS/ASCII/Makefile/Makefile-lib
 -include ${EOS_HOME}/tutorial/TIPS/Gnuplot/Makefile/Makefile-lib
+-include ${EOS_HOME}/tutorial/TIPS/Projection3DImage/Makefile/Makefile-lib
 
 #### Definition ####
 # Defined at Main
@@ -55,10 +56,17 @@ MaskBackImage::
        export BACK=$(MASKBACK); \
        make IniBackImage; \
        make BackImage;
-       
-FNC::
-       make $(FILE_NAME).$(FNC);
-       
+
+FNCInputProjection::
+       export PRJ_FILE_NAME=$(FILE_NAME); \
+       for ext in $(INI)pad $(MASK) $(MASKBACK) ; \
+       do \
+               export IN_PRJ=$$ext; \
+               export PRJ=$$ext'2d'; \
+               export OUT_PRJ=$$ext'.tiff'; \
+               make Projection3DImage; \
+       done;
+
 FNCGnudata::
        export IN_ASCII_FILE_NAME=$(FILE_NAME); \
        export IN_ASCII=$(FNC); \
@@ -71,12 +79,14 @@ FNCGnudata::
        export IN_ASCII=cut; \
        export OUT_ASCII_FILE_NAME=$(FILE_NAME); \
        export OUT_ASCII=FNC; \
+       echo $$OUT_ASCII; \
        export ASCII_CLMN="1 2"; \
        make ExtractColumn; \
        num=4; \
        OUT_ASCII=$$(head -1 $(FILE_NAME).cut | awk -v v=$$num '{printf("%s", $$v)}'); \
        while [ ! -z "$$OUT_ASCII" ] ; \
        do \
+               echo $$OUT_ASCII; \
                export ASCII_CLMN="1 `expr $$num + 1`"; \
                make ExtractColumn; \
                num=`expr $$num + 2`; \
@@ -89,6 +99,7 @@ FNCGnuplot::
        export GNU_X_SIZE=$(X_SIZE_GRAPH); \
        export GNU_Y_SIZE=$(Y_SIZE_GRAPH); \
        data=FNC; \
+       echo $$data; \
        export IN_GNU=$$data; \
        export OUT_GNU_FILE_NAME="$(FILE_NAME)-$$data"; \
        export VIEW_GNU_FILE_NAME=$$data; \
@@ -97,6 +108,7 @@ FNCGnuplot::
        data=$$(head -1 $(FILE_NAME).cut | awk -v v=$$num '{printf("%s", $$v)}'); \
        while [ ! -z "$$data" ] ; \
        do \
+               echo $$data; \
                export IN_GNU=$$data; \
                export OUT_GNU_FILE_NAME="$(FILE_NAME)-$$data"; \
                export VIEW_GNU_FILE_NAME="$$data"; \
@@ -106,5 +118,7 @@ FNCGnuplot::
        done;
 
 ##### Commands(Input to Output) #####
+ifdef INI
 .$(INI).$(INI)info:
        mrcInfo -i $*.$(INI) | head -5 > $*.$(INI)info;
+endif #INI

diff --git a/TIPS/BackImage/Makefile/Makefile-lib b/TIPS/BackImage/Makefile/Makefile-lib
index 96ecef2..d958dd4 100644 (file)
--- a/TIPS/BackImage/Makefile/Makefile-lib
+++ b/TIPS/BackImage/Makefile/Makefile-lib
@@ -58,6 +58,10 @@ help_BackImage::
        @echo "         BACK_LENGTH:            length of output"
 
 ##### Commands(Input to Output) #####
+ifdef IN_BACK
+ifdef BACK
 .$(IN_BACK).$(BACK):
        $(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);
+endif #BACK
+endif #IN_BACK

diff --git a/TIPS/CreateGridImage/Makefile/Makefile-lib b/TIPS/CreateGridImage/Makefile/Makefile-lib
index 9e251e5..6287362 100644 (file)
--- a/TIPS/CreateGridImage/Makefile/Makefile-lib
+++ b/TIPS/CreateGridImage/Makefile/Makefile-lib
@@ -36,10 +36,18 @@ Grid2Tiff::
        mrc2tiff -i $(FILE_NAME).$(GRID) -o $(FILE_NAME).$(TIFF);
 
 ##### Commands(Input to Output) #####
+ifdef NUL
+ifdef ONE
 .$(NUL).$(ONE):
        mrcImageScalarAdd -i $*.$(NUL) -o $*.$(ONE) -m 1 -v $(POINT_VALUE) \
                                                -x $(POINT_X) -y $(POINT_Y) -z $(POINT_Z);
+endif #ONE
+endif #NUL
 
+ifdef ONE
+ifdef GRID
 .$(ONE).$(GRID):
        mrcImageCrystalCreate -i $*.$(ONE) -o $*.$(GRID) \
                                                        -nx $(NUM_X) -ny $(NUM_Y) -nz $(NUM_Z);
+endif #GRID
+endif #ONE

diff --git a/TIPS/MaskImage/Makefile/Makefile-lib b/TIPS/MaskImage/Makefile/Makefile-lib
index 34a801c..8806af5 100644 (file)
--- a/TIPS/MaskImage/Makefile/Makefile-lib
+++ b/TIPS/MaskImage/Makefile/Makefile-lib
@@ -37,8 +37,14 @@ help_MaskImage::
        @echo "         MASK_F_MODE:            low pass filter mode"
 
 ##### Commands(Input to Output) #####
+ifdef IN_MASK
+ifdef MASK
 .$(IN_MASK).$(MASK)tmp:
        mrcImageLowPassFilter -i $*.$(IN_MASK) -o $*.$(MASK)tmp -m $(MASK_F_MODE) -hvp $(MASK_VALUE);
+endif #MASK
+endif #IN_MASK
 
+ifdef MASK
 .$(MASK)tmp.$(MASK):
        mrcImageBinalization -i $*.$(MASK)tmp -o $*.$(MASK) -m 32;
+endif #MASK

diff --git a/TIPS/Projection3DImage/Makefile/Makefile-lib b/TIPS/Projection3DImage/Makefile/Makefile-lib
index 97e7dee..5658124 100644 (file)
--- a/TIPS/Projection3DImage/Makefile/Makefile-lib
+++ b/TIPS/Projection3DImage/Makefile/Makefile-lib
@@ -44,5 +44,9 @@ help_Projection3DImage::
        @echo
 
 ##### Commands(Input to Output) #####
+ifdef PRJ
+ifdef OUT_PRJ
 .$(PRJ).$(OUT_PRJ):
        mrc2tiff -i $*.$(PRJ) -o $*.$(OUT_PRJ)
+endif #OUT_PRJ
+endif #PRJ