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tutorial: Commit

This repository is for tutorials of Eos.


Commit MetaInfo

Revision5451499f8bec11727c31b8125864777b72dbb3d5 (tree)
Time2014-10-15 17:48:01
Authorkinoshita-eos <kinoshita@yasu...>
Commiterkinoshita-eos

Log Message

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

Change Summary

Incremental Difference

Binary files /dev/null and b/SampleData/1VOM-N.mrc differ
--- /dev/null
+++ b/Small Tools/mrcImageFourierNeighborCorrelation/Makefile
@@ -0,0 +1,50 @@
1+#
2+# This is Main Makefile for mrcImageFourierNeighborCorrelation.
3+#
4+
5+#### Input extention ####
6+INI=mrc
7+MASK=mask
8+MASKBACK=maskback
9+FSC=fsc
10+
11+#### Suffixes rule ####
12+# Defined at Sub
13+
14+#### INCLUDE ####
15+-include Makefile.config
16+
17+#### Definition ####
18+# Path of Input File
19+INPUT_PATH=../../SampleData/1VOM-N.mrc
20+
21+### FileData
22+FILE_NAME=Input
23+
24+### ForMask
25+MASK_F_MODE=4
26+MASK_VALUE=0.0125
27+
28+# MaskSize
29+MASK_SIZE_X=256
30+MASK_SIZE_Y=256
31+MASK_SIZE_Z=256
32+
33+#### Rules of the list created ####
34+# Defined at Sub
35+
36+##### Commands #####
37+# Defined at Sub basically
38+all::
39+ make InitialData;
40+ make InputInfo;
41+ make MaskBackImage;
42+ make InputBackImage;
43+ make InputMaskImage;
44+ make FSC;
45+
46+##### Commands(Input to Output) #####
47+# Defined at Sub
48+.$(MASK).$(FSC):
49+ mrcImageFourierNeighborCorrelation -i $*.$(INI)pad -o $*.$(FSC) -d 0.025 \
50+ -FSC -mask $*.$(MASK) -maskBack $*.$(MASKBACK);
--- /dev/null
+++ b/Small Tools/mrcImageFourierNeighborCorrelation/Makefile.config
@@ -0,0 +1,63 @@
1+#
2+# This is Sub Makefile for mrcImageFourierNeighborCorrelation.
3+#
4+
5+#### Input extention ####
6+# Defined at Main
7+
8+#### Suffixes rule ####
9+.SUFFIXES: .$(INI) .$(INI)info .$(FSC)
10+
11+#### INCLUDE ####
12+-include ${EOS_HOME}/tutorial/TIPS/MaskImage/Makefile.config
13+-include ${EOS_HOME}/tutorial/TIPS/BackImage/Makefile.config
14+
15+#### Definition ####
16+# Defined at Main
17+
18+# For ../NulImage/Makefile.config
19+MASK_FILE_NAME=$(FILE_NAME)
20+BACK_FILE_NAME=$(FILE_NAME)
21+BACK_SIZE_X=$(MASK_SIZE_X)
22+BACK_SIZE_Y=$(MASK_SIZE_Y)
23+BACK_SIZE_Z=$(MASK_SIZE_Z)
24+BACK_IN_VALUE=1
25+BACK_VALUE=0
26+
27+#### Rules of the list created ####
28+
29+
30+##### Commands #####
31+InitialData::
32+ touch $(FILE_NAME).$(INI);
33+ rm $(FILE_NAME).$(INI);
34+ ln -s $(INPUT_PATH) $(FILE_NAME).$(INI)
35+
36+InputInfo::
37+ make $(FILE_NAME).$(INI)info;
38+
39+InputBackImage::
40+ export IN_BACK=$(INI); \
41+ export BACK=$(INI)pad; \
42+ make BackImage;
43+
44+InputMaskImage::
45+ export IN_MASK=$(INI)pad; \
46+ make MaskImage;
47+
48+MaskBackImage::
49+ export BACK_IN_SIZE_X=$$(head -1 $(FILE_NAME).$(INI)info | awk '{printf("%d", $$4)}'); \
50+ export BACK_IN_SIZE_Y=$$(head -1 $(FILE_NAME).$(INI)info | awk '{printf("%d", $$5)}'); \
51+ export BACK_IN_SIZE_Z=$$(head -1 $(FILE_NAME).$(INI)info | awk '{printf("%d", $$6)}'); \
52+ export BACK_LENGTH=$$(tail -1 $(FILE_NAME).$(INI)info | awk '{printf("%f", $$4)}'); \
53+ export IN_BACK=$(MASKBACK)ini; \
54+ export BACK=$(MASKBACK); \
55+ make IniBackImage; \
56+ make BackImage;
57+
58+FSC::
59+ make $(FILE_NAME).$(FSC);
60+
61+##### Commands(Input to Output) #####
62+.$(INI).$(INI)info:
63+ mrcInfo -i $*.$(INI) | head -5 > $*.$(INI)info
--- a/TIPS/BackData/Makefile.config
+++ b/TIPS/BackImage/Makefile.config
@@ -9,12 +9,12 @@
99 .SUFFIXES: .$(NUL) .$(IN_BACK) .$(BACK)
1010
1111 #### INCLUDE ####
12--include ../NulImage/Makefile.config
12+-include ${EOS_HOME}/tutorial/TIPS/NulImage/Makefile.config
1313
1414 #### Definition ####
1515 # Defined at Main
1616
17-# For ../NulImage/Makefile.config
17+# For TIPS/NulImage/Makefile.config
1818 NUL_FILE_NAME=$(BACK_FILE_NAME)
1919 NUL_SIZE_X=$(BACK_IN_SIZE_X)
2020 NUL_SIZE_Y=$(BACK_IN_SIZE_Y)
@@ -28,6 +28,7 @@ NUL_LENGTH=$(BACK_LENGTH)
2828
2929 ##### Commands #####
3030 IniBackImage::
31+ export NUL=$(IN_BACK); \
3132 make NulImage;
3233
3334 BackImage::
@@ -35,9 +36,6 @@ BackImage::
3536
3637
3738 ##### Commands(Input to Output) #####
38-.$(NUL).$(IN_BACK):
39- ln -s $*.$(NUL) $*.$(IN_BACK);
40-
4139 .$(IN_BACK).$(BACK):
42- mrcImage3DPad -i $*.$(IN_BACK) -o $*.$(BACK) -M 1 -v $(BACK_VALUE) \
40+ $(ENV_SWITCH)mrcImage3DPad -i $*.$(IN_BACK) -o $*.$(BACK) -M 1 -v $(BACK_VALUE) \
4341 -Nx $(BACK_SIZE_X) -Ny $(BACK_SIZE_Y) -Nz $(BACK_SIZE_Z);
--- a/TIPS/BinShape/Makefile.config
+++ /dev/null
@@ -1,28 +0,0 @@
1-#
2-# This is Sub Makefile for Create Bin Image that has same shape as Input.
3-#
4-
5-#### Input extention ####
6-# Defined at Main
7-
8-#### Suffixes rule ####
9-.SUFFIXES: .$(IN_SBIN) .$(SBIN)
10-
11-#### INCLUDE ####
12-
13-#### Definition ####
14-# Defined at Main
15-
16-
17-#### Rules of the list created ####
18-
19-
20-##### Commands #####
21-ShapeBinImage::
22- make $(SBIN_FILE_NAME).$(SBIN);
23-
24-
25-##### Commands(Input to Output) #####
26-.$(IN_SBIN).$(SBIN):
27- mrcImageLowPassFilter -i $*.$(IN_SBIN) -o $*.$(SBIN)tmp -m $(SBIN_F_MODE) -hvp $(SBIN_VALUE);
28- mrcImageBinalization -i $*.$(SBIN)tmp -o $*.$(SBIN) -m 32;
--- a/TIPS/CreateGridImage/Makefile.config
+++ b/TIPS/CreateGridImage/Makefile.config
@@ -9,7 +9,7 @@
99 .SUFFIXES: .$(NUL) .$(ONE) .$(GRID)
1010
1111 #### INCLUDE ####
12--include ../NulImage/Makefile.config
12+-include ${EOS_HOME}/tutorial/TIPS/NulImage/Makefile.config
1313
1414 #### Definition ####
1515 # Defined at Main
--- /dev/null
+++ b/TIPS/MaskImage/.EosLog
@@ -0,0 +1 @@
1+/Users/teppeikinoshita/Eos/bin/X86MAC64/mrcInfo -i /Users/teppeikinoshita/Desktop/work/img/Input-1VOM-N.mrc
--- a/TIPS/BinShape/Makefile
+++ b/TIPS/MaskImage/Makefile
@@ -3,8 +3,8 @@
33 #
44
55 #### Input extention ####
6-IN_SBIN=inimrc
7-SBIN=sbin
6+IN_MASK=inimrc
7+MASK=mask
88
99 #### Suffixes rule ####
1010 # Defined at Sub
@@ -14,10 +14,10 @@ SBIN=sbin
1414
1515 #### Definition ####
1616 ### FileData
17-SBIN_FILE_NAME=Input
17+MASK_FILE_NAME=Input
1818 # ImageSize
19-SBIN_F_MODE=4
20-SBIN_VALUE=0.0125
19+MASK_F_MODE=4
20+MASK_VALUE=0.0125
2121
2222
2323 #### Rules of the list created ####
@@ -26,7 +26,7 @@ SBIN_VALUE=0.0125
2626 ##### Commands #####
2727 # Defined at Sub basically
2828 all::
29- make ShapeBinImage
29+ make MaskImage
3030
3131 ##### Commands(Input to Output) #####
3232 # Defined at Sub
--- /dev/null
+++ b/TIPS/MaskImage/Makefile.config
@@ -0,0 +1,30 @@
1+#
2+# This is Sub Makefile for Create Mask Image that has same shape as Input.
3+#
4+
5+#### Input extention ####
6+# Defined at Main
7+
8+#### Suffixes rule ####
9+.SUFFIXES: .$(IN_MASK) .$(MASK) .$(MASK)tmp
10+
11+#### INCLUDE ####
12+
13+#### Definition ####
14+# Defined at Main
15+
16+
17+#### Rules of the list created ####
18+
19+
20+##### Commands #####
21+MaskImage::
22+ make $(MASK_FILE_NAME).$(MASK);
23+
24+
25+##### Commands(Input to Output) #####
26+.$(IN_MASK).$(MASK)tmp:
27+ mrcImageLowPassFilter -i $*.$(IN_MASK) -o $*.$(MASK)tmp -m $(MASK_F_MODE) -hvp $(MASK_VALUE);
28+
29+.$(MASK)tmp.$(MASK):
30+ mrcImageBinalization -i $*.$(MASK)tmp -o $*.$(MASK) -m 32;
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