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tutorial: Commit

This repository is for tutorials of Eos.


Commit MetaInfo

Revision5713907742f401c5bd4e518e1bcabf7779484433 (tree)
Time2014-11-25 12:09:25
Authorkinoshita-eos <kinoshita@yasu...>
Commiterkinoshita-eos

Log Message

Modify: tutorial for PIONE
new file: SampleCode/PIONE/Package5/Initial2.pione
new file: SampleCode/PIONE/Package6/Annotation3.0.pione
new file: SampleCode/PIONE/Package6/Final3.pione

Modify: Add Help Message for lib.
modified: Small Tools/Template/Makefile/Makefile

Add: tutorial for mrcImageRandomParticlesImageCreate
new file: Small Tools/mrcImage/mrcImageRandomParticlesImageCreate/Makefile/Makefile
new file: Small Tools/mrcImage/mrcImageRandomParticlesImageCreate/Makefile/Makefile-lib

Change Summary

Incremental Difference

--- /dev/null
+++ b/SampleCode/PIONE/Package5/Initial2.pione
@@ -0,0 +1,12 @@
1+Rule Initial
2+ input '*.mrc'
3+ output '{$I[1][1]}.parameters'
4+Action
5+ mrcInfo -i {$I[1]} \
6+ | head -1 \
7+ | awk '{printf("%s %s %s", $4, $5, $6)}' \
8+ | tr -c '[0-9]' ' ' \
9+ > TMP
10+ awk '{printf("%d %d %d", $1*4/5, $2*4/5, $3*4/5)}' TMP \
11+ > {$O[1]}
12+End
--- /dev/null
+++ b/SampleCode/PIONE/Package6/Annotation3.0.pione
@@ -0,0 +1,4 @@
1+.@ PackageName :: "CenterGet"
2+.@ Editor :: "Kinoshita"
3+.@ Tag :: "v0.3.0"
4+.@ Parent :: &CenterGet.editor("Kinoshita").tag("v0.2.0")
--- /dev/null
+++ b/SampleCode/PIONE/Package6/Final3.pione
@@ -0,0 +1,13 @@
1+Rule Final
2+ input '*.mrc'
3+ input '{$I[1][1]}.roi'
4+ output '*.tiff'.all
5+Action
6+ for (( num = 0; num <= 2; num++ )) ; \
7+ do \
8+ mrcImageProjection -i {$I[1]} -o {$I[1]}.2d -m ${num}; \
9+ mrc2tiff -i {$I[1]}.2d -o {$I[1]}-${num}.tiff; \
10+ mrcImageProjection -i {$I[2]} -o {$I[2]}.2d -m ${num}; \
11+ mrc2tiff -i {$I[2]}.2d -o {$I[2]}-${num}.tiff; \
12+ done;
13+End
--- a/Small Tools/Template/Makefile/Makefile
+++ b/Small Tools/Template/Makefile/Makefile
@@ -70,6 +70,9 @@ help_!!Command!!::
7070 @echo
7171 @echo " all: Initial -> Exe -> Final."
7272 @echo
73+ @echo " help: Show this help."
74+ @echo " help_XXXX: Show XXXX help."
75+ @echo
7376 @echo " (Setting Data):"
7477 @echo " FILE_NAME: filename of input"
7578
--- /dev/null
+++ b/Small Tools/mrcImage/mrcImageRandomParticlesImageCreate/Makefile/Makefile
@@ -0,0 +1,97 @@
1+#
2+# This is Main Makefile for mrcImageRandomParticlesImageCreate.
3+#
4+# Created by template v2.0.2p0065
5+#
6+
7+#### Root Makefile ####
8+MAKE_ROOT=mrcImageRandomParticlesImageCreate
9+TOOLS_CLASS=mrcImage
10+TOOLS_COMMAND=$(MAKE_ROOT)
11+OBJECTS_GROUP=DataManip
12+OBJECTS_CLASS=mrcImage
13+OBJECTS_COMMAND=l$(MAKE_ROOT)
14+
15+#### Input extention ####
16+INI=ini
17+IN=list
18+OUT=mrc
19+
20+#### Suffixes rule ####
21+# Defined at Sub
22+
23+#### INCLUDE ####
24+# Help-include-file must always be put on top.
25+-include ${EOS_HOME}/tutorial/TIPS/Help/Makefile/Makefile-lib
26+-include ${EOS_HOME}/tutorial/TIPS/Debugger/Makefile/Makefile-lib
27+-include Makefile-lib
28+
29+#### Definition ####
30+# Path of Input File
31+# Basically, use a linked data from /SampleData.
32+INPUT_PATH=${EOS_HOME}/tutorial/SampleData/1VOM.mrc
33+
34+### FileData
35+FILE_NAME=Input
36+
37+### OPTIONS
38+NX=512
39+NY=512
40+RND_SEED=54321
41+
42+#### Rules of the list created ####
43+# Defined at Sub
44+
45+##### Commands #####
46+# Defined at Sub basically
47+# By make Initial, Create input data for this command.
48+Initial::
49+ make InitialData;
50+
51+# By make Exe, Execute the sample of this command.
52+Exe::
53+ if [ ! -z "$(RND_SEED)" ] ; then \
54+ OPTION="$${OPTION} -seed $(RND_SEED)"; \
55+ fi; \
56+ if [ ! -z "$(NX)" -a ! -z "$(NY)" ] ; then \
57+ OPTION="$${OPTION} -N $(NX) $(NY)"; \
58+ fi; \
59+ mrcImageRandomParticlesImageCreate -i $(FILE_NAME).$(IN) -o $(FILE_NAME).$(OUT) $${OPTION};
60+
61+# By make Final, Make visualize Output for this command.
62+Final::
63+ mrc2tiff -i $(FILE_NAME).$(OUT) -o $(FILE_NAME).tiff;
64+
65+# By make all, Initial -> Exe -> Final.
66+all::
67+ make Initial;
68+ make Exe;
69+ make Final;
70+
71+help_mrcImageRandomParticlesImageCreate::
72+ @echo
73+ @echo "Makefile for mrcImageRandomParticlesImageCreate"
74+ @echo "This is Main Makefile for mrcImageRandomParticlesImageCreate."
75+ @echo
76+ @echo " (Command):"
77+ @echo " Initial: Create input data for this command."
78+ @echo " (Setting Data):"
79+ @echo " INI: input extention for Initial"
80+ @echo
81+ @echo " Exe: Execute the sample of this command."
82+ @echo " (Setting Data):"
83+ @echo " IN: input list extention"
84+ @echo " OUT: output extention"
85+ @echo " NX: output size x"
86+ @echo " NY: output size y"
87+ @echo " RND_SEED: seed of random number"
88+ @echo
89+ @echo " Final: Make visualize Output for this command."
90+ @echo
91+ @echo " all: Initial -> Exe -> Final."
92+ @echo
93+ @echo " (Setting Data):"
94+ @echo " FILE_NAME: filename of input"
95+
96+##### Commands(Input to Output) #####
97+# Defined at Sub
--- /dev/null
+++ b/Small Tools/mrcImage/mrcImageRandomParticlesImageCreate/Makefile/Makefile-lib
@@ -0,0 +1,31 @@
1+#
2+# This is Sub Makefile for mrcImageRandomParticlesImageCreate.
3+#
4+# Created by template v2.0.2p0065
5+#
6+
7+#### Input extention ####
8+# Defined at Main
9+
10+#### Suffixes rule ####
11+.SUFFIXES: .$(INI)
12+
13+#### INCLUDE ####
14+# Use TIPS File.
15+# -include ${EOS_HOME}/tutorial/TIPS/XXXX/Makefile/Makefile-lib
16+
17+#### Definition ####
18+# Defined at Main
19+
20+#### Rules of the list created ####
21+
22+
23+##### Commands #####
24+InitialData::
25+ $(RM) $(FILE_NAME).$(INI);
26+ $(RM) $(FILE_NAME).$(IN);
27+ mrcImageProjection -i $(INPUT_PATH) -o $(FILE_NAME).$(INI);
28+ echo "$(FILE_NAME).$(INI)" >> $(FILE_NAME).$(IN);
29+
30+##### Commands(Input to Output) #####
31+
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