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tutorial: Commit

This repository is for tutorials of Eos.


Commit MetaInfo

Revisiond1a575e1a1abcf6972cd0b064423fa80cbcc189c (tree)
Time2014-09-16 18:06:59
Authorkinoshita-eos <kinoshita@yasu...>
Commiterkinoshita-eos

Log Message

Modify: support of Noise Data for CTFCorrection
modified: CTFCorrection/CTFCorrection2/Makefile
Modify: add variable for defocus
modified: CTFCorrection/CTFCorrection3/Makefile

Change Summary

Incremental Difference

--- a/CTFCorrection/CTFCorrection2/Makefile
+++ b/CTFCorrection/CTFCorrection2/Makefile
@@ -62,7 +62,11 @@ PROJECTION_START_Y=-`expr $(PROJECTION_PIXEL_Y) / 4`
6262 #PROJECTION_START_Y=0
6363
6464 ### For mrcImageNoiseAdd
65-SNRATIO=10000
65+SNRATIO=1
66+NSRATIO=0
67+
68+### For mrcImageSiemensStar
69+SSTAR_SHAPE=0
6670
6771 #### For Works ####
6872 JOP_NUM=-j 3
@@ -75,8 +79,8 @@ $(CTF_2D_EXT):$(INPUT_2D_LIST:.$(INPUT_2D_EXT)=.$(CTF_2D_EXT))
7579 ##### Commands #####
7680 all::
7781 # make InitialCTFDataFromPDB;
78-# make InitialSiemensStar;
79- make InitialCTFDataFromMRC;
82+ make InitialSiemensStar;
83+# make InitialCTFDataFromMRC;
8084 make ProcessForInput;
8185 make TIF2CTF;
8286 make $(INPUT).tiff
@@ -89,7 +93,9 @@ InitialCTFDataFromMRC::
8993 cp $(INPUT).$(INI_MRC_EXT) $(INPUT).$(INPUT_2D_EXT);
9094
9195 InitialSiemensStar::
92- mrcImageSiemensStar -o $(INPUT).$(INPUT_2D_EXT);
96+ mrcImageSiemensStar -o $(INPUT).$(INPUT_2D_EXT)tmp -m 2 -Shape $(SSTAR_SHAPE);
97+ mrcImageNoiseAdd -i $(INPUT).$(INPUT_2D_EXT)tmp -o $(INPUT).$(INPUT_2D_EXT) -NS $(NSRATIO) -SD 1;
98+ rm $(INPUT).$(INPUT_2D_EXT)tmp;
9399
94100 ProcessForInput::
95101 make $(INPUT).$(CTF_2D_EXT);
--- a/CTFCorrection/CTFCorrection3/Makefile
+++ b/CTFCorrection/CTFCorrection3/Makefile
@@ -16,7 +16,8 @@
1616 -include CTFInfo1List
1717
1818 #### Definition ####
19-
19+## For mrcImageCTFObservation
20+CTF_DEFOCUS=9000
2021
2122 #### Rules of the list created ####
2223 ctfinfoauto2: $(FFTS:.fft=.ctfinfoauto2)
@@ -45,7 +46,7 @@ all1::
4546 make ImageAverage;
4647
4748 ProcessForInput2::
48- mrcImageCTFObservation -i $(INPUT).$(INPUT_2D_EXT) -o $(INPUT)-2.$(CTF_2D_EXT) -df 9000;
49+ mrcImageCTFObservation -i $(INPUT).$(INPUT_2D_EXT) -o $(INPUT)-2.$(CTF_2D_EXT) -df $(CTF_DEFOCUS);
4950 ln -s $(INPUT)-2.$(CTF_2D_EXT) $(INPUT)-2.mrc;
5051 mrc2tiff -i $(INPUT)-2.$(INPUT_2D_EXT) -o $(INPUT)-2_org.tiff;
5152 mrc2tiff -i $(INPUT)-2.$(CTF_2D_EXT) -o $(INPUT)-2_i.tiff -I;
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