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tutorial: Commit

This repository is for tutorials of Eos.


Commit MetaInfo

Revision883de32fca9d4779c4fb8fe9915b7781cc45575f (tree)
Time2014-10-23 17:10:14
Authorkinoshita-eos <kinoshita@yasu...>
Commiterkinoshita-eos

Log Message

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

Change Summary

Incremental Difference

Binary files /dev/null and b/SampleData/1VOM.mrc differ
--- a/Small Tools/mrcImage/mrcImageFourierNeighborCorrelation/Makefile/Makefile
+++ b/Small Tools/mrcImage/mrcImageFourierNeighborCorrelation/Makefile/Makefile
@@ -34,7 +34,7 @@ FILE_NAME=Input
3434
3535 ### ForMask
3636 MASK_F_MODE=4
37-MASK_VALUE=0.0125
37+MASK_VALUE=0.05
3838
3939 # MaskSize
4040 MASK_SIZE_X=256
@@ -44,8 +44,8 @@ MASK_SIZE_Z=256
4444 # FNC Graph Image
4545 X_SIZE_GRAPH=360
4646 Y_SIZE_GRAPH=240
47-S_DATA=1
48-E_DATA=1
47+S_DATA=5
48+E_DATA=2
4949
5050 #### Rules of the list created ####
5151 # Defined at Sub
@@ -60,7 +60,7 @@ Initial::
6060 make InputMaskImage;
6161
6262 Exe::
63- make FNC;
63+ make $(FILE_NAME).$(FNC);
6464
6565 all::
6666 make Initial;
@@ -68,6 +68,7 @@ all::
6868 make Final;
6969
7070 Final::
71+ make FNCInputProjection;
7172 make FNCGnudata;
7273 make FNCGnuplot;
7374
@@ -96,7 +97,11 @@ help_mrcImageFourierNeighborCorrelation::
9697
9798 ##### Commands(Input to Output) #####
9899 # Defined at Sub
100+ifdef MASK
101+ifdef FNC
99102 .$(MASK).$(FNC):
100- mrcImageFourierNeighborCorrelation -i $*.$(INI)pad -o $*.$(FNC) -d 0.025 \
103+ mrcImageFourierNeighborCorrelation -i $*.$(INI)pad -o $*.$(FNC) \
101104 -FSC -mask $*.$(MASK) -maskBack $*.$(MASKBACK) \
102105 -NoiseWeighted -100 -FSCfull -Cref;
106+endif #FNC
107+endif #MASK
--- a/Small Tools/mrcImage/mrcImageFourierNeighborCorrelation/Makefile/Makefile-lib
+++ b/Small Tools/mrcImage/mrcImageFourierNeighborCorrelation/Makefile/Makefile-lib
@@ -13,6 +13,7 @@
1313 -include ${EOS_HOME}/tutorial/TIPS/BackImage/Makefile/Makefile-lib
1414 -include ${EOS_HOME}/tutorial/TIPS/ASCII/Makefile/Makefile-lib
1515 -include ${EOS_HOME}/tutorial/TIPS/Gnuplot/Makefile/Makefile-lib
16+-include ${EOS_HOME}/tutorial/TIPS/Projection3DImage/Makefile/Makefile-lib
1617
1718 #### Definition ####
1819 # Defined at Main
@@ -55,10 +56,17 @@ MaskBackImage::
5556 export BACK=$(MASKBACK); \
5657 make IniBackImage; \
5758 make BackImage;
58-
59-FNC::
60- make $(FILE_NAME).$(FNC);
61-
59+
60+FNCInputProjection::
61+ export PRJ_FILE_NAME=$(FILE_NAME); \
62+ for ext in $(INI)pad $(MASK) $(MASKBACK) ; \
63+ do \
64+ export IN_PRJ=$$ext; \
65+ export PRJ=$$ext'2d'; \
66+ export OUT_PRJ=$$ext'.tiff'; \
67+ make Projection3DImage; \
68+ done;
69+
6270 FNCGnudata::
6371 export IN_ASCII_FILE_NAME=$(FILE_NAME); \
6472 export IN_ASCII=$(FNC); \
@@ -71,12 +79,14 @@ FNCGnudata::
7179 export IN_ASCII=cut; \
7280 export OUT_ASCII_FILE_NAME=$(FILE_NAME); \
7381 export OUT_ASCII=FNC; \
82+ echo $$OUT_ASCII; \
7483 export ASCII_CLMN="1 2"; \
7584 make ExtractColumn; \
7685 num=4; \
7786 OUT_ASCII=$$(head -1 $(FILE_NAME).cut | awk -v v=$$num '{printf("%s", $$v)}'); \
7887 while [ ! -z "$$OUT_ASCII" ] ; \
7988 do \
89+ echo $$OUT_ASCII; \
8090 export ASCII_CLMN="1 `expr $$num + 1`"; \
8191 make ExtractColumn; \
8292 num=`expr $$num + 2`; \
@@ -89,6 +99,7 @@ FNCGnuplot::
8999 export GNU_X_SIZE=$(X_SIZE_GRAPH); \
90100 export GNU_Y_SIZE=$(Y_SIZE_GRAPH); \
91101 data=FNC; \
102+ echo $$data; \
92103 export IN_GNU=$$data; \
93104 export OUT_GNU_FILE_NAME="$(FILE_NAME)-$$data"; \
94105 export VIEW_GNU_FILE_NAME=$$data; \
@@ -97,6 +108,7 @@ FNCGnuplot::
97108 data=$$(head -1 $(FILE_NAME).cut | awk -v v=$$num '{printf("%s", $$v)}'); \
98109 while [ ! -z "$$data" ] ; \
99110 do \
111+ echo $$data; \
100112 export IN_GNU=$$data; \
101113 export OUT_GNU_FILE_NAME="$(FILE_NAME)-$$data"; \
102114 export VIEW_GNU_FILE_NAME="$$data"; \
@@ -106,5 +118,7 @@ FNCGnuplot::
106118 done;
107119
108120 ##### Commands(Input to Output) #####
121+ifdef INI
109122 .$(INI).$(INI)info:
110123 mrcInfo -i $*.$(INI) | head -5 > $*.$(INI)info;
124+endif #INI
--- a/TIPS/BackImage/Makefile/Makefile-lib
+++ b/TIPS/BackImage/Makefile/Makefile-lib
@@ -58,6 +58,10 @@ help_BackImage::
5858 @echo " BACK_LENGTH: length of output"
5959
6060 ##### Commands(Input to Output) #####
61+ifdef IN_BACK
62+ifdef BACK
6163 .$(IN_BACK).$(BACK):
6264 $(ENV_SWITCH)mrcImage3DPad -i $*.$(IN_BACK) -o $*.$(BACK) -M 1 -v $(BACK_VALUE) \
6365 -Nx $(BACK_SIZE_X) -Ny $(BACK_SIZE_Y) -Nz $(BACK_SIZE_Z);
66+endif #BACK
67+endif #IN_BACK
--- a/TIPS/CreateGridImage/Makefile/Makefile-lib
+++ b/TIPS/CreateGridImage/Makefile/Makefile-lib
@@ -36,10 +36,18 @@ Grid2Tiff::
3636 mrc2tiff -i $(FILE_NAME).$(GRID) -o $(FILE_NAME).$(TIFF);
3737
3838 ##### Commands(Input to Output) #####
39+ifdef NUL
40+ifdef ONE
3941 .$(NUL).$(ONE):
4042 mrcImageScalarAdd -i $*.$(NUL) -o $*.$(ONE) -m 1 -v $(POINT_VALUE) \
4143 -x $(POINT_X) -y $(POINT_Y) -z $(POINT_Z);
44+endif #ONE
45+endif #NUL
4246
47+ifdef ONE
48+ifdef GRID
4349 .$(ONE).$(GRID):
4450 mrcImageCrystalCreate -i $*.$(ONE) -o $*.$(GRID) \
4551 -nx $(NUM_X) -ny $(NUM_Y) -nz $(NUM_Z);
52+endif #GRID
53+endif #ONE
--- a/TIPS/MaskImage/Makefile/Makefile-lib
+++ b/TIPS/MaskImage/Makefile/Makefile-lib
@@ -37,8 +37,14 @@ help_MaskImage::
3737 @echo " MASK_F_MODE: low pass filter mode"
3838
3939 ##### Commands(Input to Output) #####
40+ifdef IN_MASK
41+ifdef MASK
4042 .$(IN_MASK).$(MASK)tmp:
4143 mrcImageLowPassFilter -i $*.$(IN_MASK) -o $*.$(MASK)tmp -m $(MASK_F_MODE) -hvp $(MASK_VALUE);
44+endif #MASK
45+endif #IN_MASK
4246
47+ifdef MASK
4348 .$(MASK)tmp.$(MASK):
4449 mrcImageBinalization -i $*.$(MASK)tmp -o $*.$(MASK) -m 32;
50+endif #MASK
--- a/TIPS/Projection3DImage/Makefile/Makefile-lib
+++ b/TIPS/Projection3DImage/Makefile/Makefile-lib
@@ -44,5 +44,9 @@ help_Projection3DImage::
4444 @echo
4545
4646 ##### Commands(Input to Output) #####
47+ifdef PRJ
48+ifdef OUT_PRJ
4749 .$(PRJ).$(OUT_PRJ):
4850 mrc2tiff -i $*.$(PRJ) -o $*.$(OUT_PRJ)
51+endif #OUT_PRJ
52+endif #PRJ
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