• R/O
  • HTTP
  • SSH
  • HTTPS

tutorial: Commit

This repository is for tutorials of Eos.


Commit MetaInfo

Revisionddf0bb529ef3958678a963dd00a6139e2c70a4f9 (tree)
Time2014-09-22 09:51:38
Authorkinoshita-eos <kinoshita@yasu...>
Commiterkinoshita-eos

Log Message

Modify: Remove Test Command
modified: CTFCorrection/CTFCorrection2/Makefile.config
Add: CTFCorrection tutorial data.
new file: CTFCorrection/CTFCorrection5/Input.inimrc
new file: CTFCorrection/CTFCorrection5/Makefile
new file: CTFCorrection/CTFCorrection5/Makefile.config
Add: function to create list about extention.
modified: TIPS/LoopCommand/Makefile.config

Change Summary

Incremental Difference

--- a/CTFCorrection/CTFCorrection2/Makefile.config
+++ b/CTFCorrection/CTFCorrection2/Makefile.config
@@ -75,14 +75,6 @@ ProcessForInput::
7575 mrc2tiff -i $(INPUT).$(INPUT_2D_EXT) -o $(INPUT)_org.tiff;
7676 mrc2tiff -i $(INPUT).$(CTF_2D_EXT) -o $(INPUT)_i.tiff -I;
7777 mrc2tiff -i $(INPUT).$(CTF_2D_EXT) -o $(INPUT).tif;
78-
79-
80-Test::
81- mrcInfo -i Input.mrc -o INFO;
82- NX=$$(head -1 INFO | awk '{printf("%d\n", $$4);}'); \
83- NY=$$(head -1 INFO | awk '{printf("%d\n", $$5);}'); \
84- echo $$NX $$NY;
85-
8678
8779 ##### Commands(Input to Output) #####
8880 .$(INI_PDB_EXT).$(FIL_PDB_EXT):
Binary files /dev/null and b/CTFCorrection/CTFCorrection5/Input.inimrc differ
--- /dev/null
+++ b/CTFCorrection/CTFCorrection5/Makefile
@@ -0,0 +1,69 @@
1+#
2+# This is Makefile for CTF Correction Demo(MultiCompensation).
3+#
4+
5+#### Input extention ####
6+# These extensions must all be different.
7+INI_MRC_EXT=inimrc
8+INPUT_2D_EXT=2d
9+CTF_2D_EXT=prectf
10+FFT_2D_EXT=fft
11+CTF_INFO_EXT=ctfinfo
12+OUT_CTF_EXT=ctf
13+OUT_TIFF_EXT=tiff
14+
15+#### Suffixes rule ####
16+
17+#### INCLUDE ####
18+-include Makefile.config
19+
20+#### Definition ####
21+CCD=14.0
22+
23+# Input FileName
24+INPUT=Input
25+
26+### For mrcImageNoiseAdd
27+NSRATIO=0
28+
29+### For mrcImageSiemensStar
30+SSTAR_SHAPE=0
31+
32+## For mrcImageCTFObservation
33+CTF_KV=200
34+CTF_CS=2.1
35+CTF_DEFOCUS=27000
36+CTF_AIN=0.3 #need CTF_MODE +32
37+CTF_MODE=0
38+
39+## For mrcImageCTFObservation 2
40+CTF2_KV=200
41+CTF2_CS=2.1
42+CTF2_DEFOCUS=9000
43+CTF2_AIN=0.3 #need CTF2_MODE +32
44+CTF2_MODE=0
45+
46+#### For Works ####
47+JOP_NUM=-j 3
48+
49+
50+#### Rules of the list created ####
51+
52+
53+##### Commands #####
54+all5::
55+ make InitialCTFDataFromMRC;
56+ make ProcessForInput;
57+ make ProcessForInput2;
58+ make TIF2CTF2;
59+ make MULTICTF;
60+
61+all5S::
62+ make InitialSiemensStar;
63+ make ProcessForInput;
64+ make ProcessForInput2;
65+ make TIF2CTF2;
66+ make MULTICTF;
67+
68+##### Commands(Input to Output) #####
69+
--- /dev/null
+++ b/CTFCorrection/CTFCorrection5/Makefile.config
@@ -0,0 +1,37 @@
1+#
2+# This is Sub Makefile for CTF Correction Demo(MultiCompensation).
3+#
4+
5+#### Input extention ####
6+
7+#### Suffixes rule ####
8+
9+#### INCLUDE ####
10+-include ../CTFCorrection3/Makefile.config
11+-include ../../TIPS/LoopCommand/Makefile.config
12+
13+#### Definition ####
14+
15+#### Rules of the list created ####
16+
17+
18+##### Commands #####
19+MULTICTF::
20+ INPUT_EXT=$(CTF_2D_EXT) \
21+ LIST_EXT=list \
22+ make InputList;
23+ make $(CTF_INFO_EXT)-list;
24+ make CTFAVG;
25+ INPUT_EXT=$(OUT_CTF_EXT) \
26+ OUTPUT_EXT=$(OUT_TIFF_EXT) \
27+ make LoopCommandEachFile;
28+
29+$(CTF_INFO_EXT)-list::
30+ sed -e s/$(CTF_2D_EXT)/$(CTF_INFO_EXT)/ $(CTF_2D_EXT).list > $(CTF_INFO_EXT).list;
31+
32+CTFAVG::
33+ mrcImageMultiCTFCompensation -i $(CTF_2D_EXT).list -info2 $(CTF_INFO_EXT).list -o $(INPUT).avg.$(OUT_CTF_EXT) -f $(INPUT).avg.$(FFT_2D_EXT);
34+
35+##### Commands(Input to Output) #####
36+.$(OUT_CTF_EXT).$(OUT_TIFF_EXT):
37+ mrc2tiff -i $*.$(OUT_CTF_EXT) -o $*.$(OUT_TIFF_EXT);
--- a/TIPS/LoopCommand/Makefile.config
+++ b/TIPS/LoopCommand/Makefile.config
@@ -27,6 +27,10 @@
2727 # INPUT_EXT: Extention of input files
2828 # OUTPUT_EXT: Extention of ouput files
2929
30+## For InputList::
31+# INPUT_EXT: Extention of input files
32+# LIST_EXT: Extention of input list
33+
3034 ## For SubMakefile
3135 VAR=LoopNumber
3236 CALC_SCALE=15.6
@@ -55,6 +59,10 @@ LoopCommandEachFile::
5559 make $(INPUT_EXT)_LIST;
5660 make $(OUTPUT_EXT);
5761
62+InputList::
63+ touch $(INPUT_EXT).$(LIST_EXT)
64+ ls -1 *.$(INPUT_EXT) >> $(INPUT_EXT).$(LIST_EXT)
65+
5866 LoopCommandHelp::
5967 @echo 'Define the following essential data at Main Makefile.'
6068 @echo ' For LoopCommand::'
@@ -69,6 +77,10 @@ LoopCommandHelp::
6977 @echo ' For LoopCommandEachFile::'
7078 @echo ' INPUT_EXT: Extention of input files'
7179 @echo ' OUTPUT_EXT: Extention of ouput files'
80+ @echo
81+ @echo ' For InputList::'
82+ @echo ' INPUT_EXT: Extention of input files'
83+ @echo ' LIST_EXT: Extention of input list'
7284
7385 ##### Commands(Input to Output) #####
7486
Show on old repository browser