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base: Commit

This repository is a base of Eos.


Commit MetaInfo

Revisióncc96e80b04e6f374d6c391afeda0575c50e7896f (tree)
Tiempo2014-10-12 15:42:34
AutorTakuo Yasunaga <yasunaga@bio....>
CommiterTakuo Yasunaga

Log Message

Modified Tools: mrcImageMultiCTFCompensation
modified: src/Objects/DataManip/ctfInfo/inc/ctfInfo.h
modified: src/Objects/DataManip/mrcImage/src/lmrcImageMultiCTFCompensation.c
modified: src/Tools/mrcImage/mrcImageMultiCTFCompensation/Config/OptionControlFile
modified: src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/mrcImageMultiCTFCompensation.c

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Diferencia incremental

--- a/env/install-eos.sh
+++ b/env/install-eos.sh
@@ -11,10 +11,10 @@ unset ANS
1111 echo "Directory: $EOS_HOME0";
1212
1313 #### No Change
14-ROOT_EOS_SOURCEFORGE=https://sourceforge.jp/projects/eos/scm/git/base/blobs/master/env/Eos_env
14+ROOT_EOS_SOURCEFORGE=https://sourceforge.jp/projects/eos/scm/git/base/blobs/master/
1515 if [ ! -d $EOS_HOME0 ] ; then
1616 mkdir $EOS_HOME0
1717 fi
1818
19-curl -L $ROOT_EOS_SOURCEFORGE/env/Eos_env
19+curl -L -o Eos_env.env $ROOT_EOS_SOURCEFORGE/env/Eos_env?export=raw
2020
Binary files a/hostdepend/X86MAC64/bin/X86MAC64/mrcImageMultiCTFCompensation and b/hostdepend/X86MAC64/bin/X86MAC64/mrcImageMultiCTFCompensation differ
Binary files a/hostdepend/X86MAC64/lib/X86MAC64/libEosObjects.a and b/hostdepend/X86MAC64/lib/X86MAC64/libEosObjects.a differ
Binary files a/hostdepend/X86MAC64/lib/X86MAC64/libmrcImage.a and b/hostdepend/X86MAC64/lib/X86MAC64/libmrcImage.a differ
Binary files a/hostdepend/X86MAC64/lib/X86MAC64/shared/lmrcImageMultiCTFCompensation.sharedo and b/hostdepend/X86MAC64/lib/X86MAC64/shared/lmrcImageMultiCTFCompensation.sharedo differ
Binary files a/hostdepend/X86MAC64/src/Objects/DataManip/mrcImage/src/X86MAC64/libmrcImage.a and b/hostdepend/X86MAC64/src/Objects/DataManip/mrcImage/src/X86MAC64/libmrcImage.a differ
Binary files a/hostdepend/X86MAC64/src/Objects/DataManip/mrcImage/src/X86MAC64/libmrcImage.debug.a and b/hostdepend/X86MAC64/src/Objects/DataManip/mrcImage/src/X86MAC64/libmrcImage.debug.a differ
Binary files a/hostdepend/X86MAC64/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageMultiCTFCompensation.sharedo and b/hostdepend/X86MAC64/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageMultiCTFCompensation.sharedo differ
Binary files a/hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/X86MAC64/mrcImageMultiCTFCompensation and b/hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/X86MAC64/mrcImageMultiCTFCompensation differ
--- a/include/ctfInfo.h
+++ b/include/ctfInfo.h
@@ -56,6 +56,12 @@ typedef struct ctfInfo {
5656 long flagWhiteNoiseRaising;
5757 float WhiteNoiseRaising; /* WhiteNoise Raising depending upon R */
5858
59+ long flagMaxWhiteNoise;
60+ float MaxWhiteNoise; /* max White Noise*/
61+
62+ long flagNdependentWhiteNoise;
63+ float NdependentWhiteNoise; /* max White Noise*/
64+
5965 float Inoise2; /* Intensity of noise */
6066 long flagWhiteNoise2;
6167 float WhiteNoise2; /* Not Affected by MTF(R)*/
--- a/src/Objects/DataManip/ctfInfo/doc/ctfInfo.html
+++ b/src/Objects/DataManip/ctfInfo/doc/ctfInfo.html
@@ -78,6 +78,12 @@ typedef struct ctfInfo {
7878 long flagWhiteNoiseRaising;
7979 float WhiteNoiseRaising; /* WhiteNoise Raising depending upon R */
8080
81+ long flagMaxWhiteNoise;
82+ float MaxWhiteNoise; /* max White Noise*/
83+
84+ long flagNdependentWhiteNoise;
85+ float NdependentWhiteNoise; /* max White Noise*/
86+
8187 float Inoise2; /* Intensity of noise */
8288 long flagWhiteNoise2;
8389 float WhiteNoise2; /* Not Affected by MTF(R)*/
--- a/src/Objects/DataManip/ctfInfo/inc/ctfInfo.h
+++ b/src/Objects/DataManip/ctfInfo/inc/ctfInfo.h
@@ -56,6 +56,12 @@ typedef struct ctfInfo {
5656 long flagWhiteNoiseRaising;
5757 float WhiteNoiseRaising; /* WhiteNoise Raising depending upon R */
5858
59+ long flagMaxWhiteNoise;
60+ float MaxWhiteNoise; /* max White Noise*/
61+
62+ long flagNdependentWhiteNoise;
63+ float NdependentWhiteNoise; /* max White Noise*/
64+
5965 float Inoise2; /* Intensity of noise */
6066 long flagWhiteNoise2;
6167 float WhiteNoise2; /* Not Affected by MTF(R)*/
--- a/src/Objects/DataManip/mrcImage/src/lmrcImageMultiCTFCompensation.c
+++ b/src/Objects/DataManip/mrcImage/src/lmrcImageMultiCTFCompensation.c
@@ -24,7 +24,7 @@ void
2424 lmrcImageMultiCTFCompensation(mrcImage* dst, mrcImage* src, ctfInfo* ctf, long nfile, lmrcImageMultiCTFCompensationInfo info, long mode)
2525 {
2626 DEBUGPRINT("lmrcImageMultiCTFCompensation Start\n");
27- fprintf(stderr, "lmrcImageMultiCTFCompensation Start: %d\n", mode);fflush(stderr);
27+ fprintf(stderr, "lmrcImageMultiCTFCompensation Start: %ld\n", mode);fflush(stderr);
2828 switch(mode&0xf) {
2929 case 0: {
3030 __lmrcImageMultiCTFCompensationMode0(dst, src, ctf, nfile, info, mode);
@@ -311,6 +311,12 @@ __lmrcImageMultiCTFCompensationMode0(mrcImage* dst, mrcImage* src, ctfInfo* ctf,
311311 } else if(ctf[i].flagWhiteNoise) {
312312 NW = SQR(ctf[i].WhiteNoise);
313313 }
314+ if(ctf[i].flagNdependentWhiteNoise) {
315+ NW = NW/sqrt(ctf[i].NdependentWhiteNoise);
316+ }
317+ if(ctf[i].flagMaxWhiteNoise) {
318+ NW = MIN(NW, ctf[i].MaxWhiteNoise);
319+ }
314320 W += NW;
315321
316322 DEBUGPRINT3("R: %f Weight %f NW %f\n", R, Weight[i], NW);
--- a/src/Tools/Config/Define.inc
+++ b/src/Tools/Config/Define.inc
@@ -200,3 +200,5 @@ WORLDNAME=Tools
200200 WORLDNAME=Tools
201201 WORLDNAME=Tools
202202 WORLDNAME=Tools
203+WORLDNAME=Tools
204+WORLDNAME=Tools
--- a/src/Tools/mrcImage/mrcImageMultiCTFCompensation/Config/OptionControlFile
+++ b/src/Tools/mrcImage/mrcImageMultiCTFCompensation/Config/OptionControlFile
@@ -6,6 +6,8 @@
66 "-f","-f[ft]","OutputDataFile(averaged fft file)","Optional","1","1","fftOut","outFile","stdout"
77 "-W","-W[hiteNoise]","","Optional","1","1","WhiteNoise","Real","1.0"
88 "-WR","-W[hiteNoise]R[aising]","Weight:W*exp(WR*R)","Optional","1","1","WhiteNoiseRaising","Real","1.0"
9+"-maxWR","-maxW[hiteNoise]R[aising]","max(W*exp(WR*R),maxWhiteNoise)","Optional","1","1","MaxWhiteNoise","Real","1.0"
10+"-NdepWR","-Ndep[endent]W[hiteNoise]R[aising]","W*exp(WR*R)/sqrt(N)","Optional","1","1","NdependentWhiteNoise","Integer","1"
911 "-SinWin","-SinWin","Windowing by sine function from Rmin[/A] to Rmax[/A]","Optional","2","1","SinWinRmin","Real","0.1","2","SinWinRmax","Real","1.0"
1012 "-MaxIter","-MaxIter[ation]","Max Iteration","Optional","1","1","MaxIter","Integer","10"
1113 "-ctfMode","-ctfMode","CTFMode: refer to mrcImageCTFObservation","Optional","1","1","CTFMode","Integer","1"
--- a/src/Tools/mrcImage/mrcImageMultiCTFCompensation/Makefile
+++ /dev/null
@@ -1,104 +0,0 @@
1-include ../../../Config/Define.inc
2-include ../../Config/Define.inc
3-include ../Config/Define.inc
4-include Config/Define.inc
5-
6-all:
7- cd src; make all; cd ..
8-
9-install:
10- cd src; make install; cd ..
11-
12-
13-putSF:
14- if [ -f private ] ; \
15- then \
16- echo "$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME) is private"; \
17- else \
18- cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE commit || cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE import src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME); \
19- fi
20-
21-put:
22- cd src; make put; cd ..
23-
24-clean:
25- cd src; make clean; cd ..
26-
27-depend:
28- cd src; make depend; cd ..
29-
30-check:
31- @if [ ! -d $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) ] ; then \
32- echo making directory; \
33- mkdir -p $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE); \
34- fi
35- ln -sf ../../../../../hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) src/$(OSTYPE);
36- @$(RM) src/Makefile
37- @echo "New src/Makefile"
38- @$(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/src/Makefile src/Makefile
39- @cd src; touch $(OSTYPE)/.Depend; make depend
40-
41-cvsupdate::
42- cvs -d $(EOS_CVSROOT) update -d
43-
44-cvscommit::
45- cvs -d $(EOS_CVSROOT) commit
46-
47-backup:
48- @cd ../../../..; \
49- echo $(OBJECTNAME) ; \
50- tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \
51- tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
52- tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
53- tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
54- tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
55- tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
56- tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
57- tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
58- tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile
59-
60-backup-all:
61- @cd ../../../..; \
62- echo $(OBJECTNAME) ; \
63- tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \
64- tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
65- tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
66- tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
67- tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
68- tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
69- tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
70- tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
71- tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile
72-
73-distribute:
74- cd ../../../..; \
75- echo $(OBJECTNAME) ; \
76- tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \
77- tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
78- tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
79- tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
80- tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
81- tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
82- tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
83- tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
84- tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \
85- tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
86-
87-distribute-all:
88- @cd ../../../..; \
89- echo $(OBJECTNAME) ; \
90- tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \
91- tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
92- tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
93- tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
94- tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
95- tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
96- tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
97- tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
98- tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \
99- tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
100-
101-eosintroduce:
102- ${EOS_HOME}/sbin/eosintroduce ${WORLDNAME} ${CLASSNAME} ${OBJECTNAME} ./
103-
104-include Config/Target.inc
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageMultiCTFCompensation/Makefile
@@ -0,0 +1 @@
1+/Users/tacyas/Eos/src/Config/Template/ToolsTemplate.Dir/Makefile
\ No newline at end of file
--- a/src/Tools/mrcImage/mrcImageMultiCTFCompensation/doc/Makefile
+++ b/src/Tools/mrcImage/mrcImageMultiCTFCompensation/doc/Makefile
@@ -1 +1 @@
1-/home/people/tacyas/Eos/src/Config/Template/ToolsTemplate.Dir/doc/Makefile
\ No newline at end of file
1+/Users/tacyas/Eos/src/Config/Template/ToolsTemplate.Dir/doc/Makefile
\ No newline at end of file
--- a/src/Tools/mrcImage/mrcImageMultiCTFCompensation/inc/mrcImageMultiCTFCompensation.h
+++ b/src/Tools/mrcImage/mrcImageMultiCTFCompensation/inc/mrcImageMultiCTFCompensation.h
@@ -39,6 +39,12 @@ typedef struct mrcImageMultiCTFCompensationInfo {
3939 long flagWhiteNoiseRaising;
4040 float WhiteNoiseRaising;
4141
42+ long flagMaxWhiteNoise;
43+ float MaxWhiteNoise;
44+
45+ long flagNdependentWhiteNoise;
46+ long NdependentWhiteNoise;
47+
4248 long flagSinWinRmin;
4349 float SinWinRmin;
4450
--- a/src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/argCheck.c
+++ b/src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/argCheck.c
@@ -12,7 +12,7 @@
1212 void
1313 argCheck(mrcImageMultiCTFCompensationInfo* info, int argc, char* argv[])
1414 {
15- long i, j, nv;
15+ long i;
1616 char s[1024];
1717 FILE* fpt;
1818
@@ -94,6 +94,28 @@ argCheck(mrcImageMultiCTFCompensationInfo* info, int argc, char* argv[])
9494 }
9595 SBREAK;
9696 }
97+ SCASE("maxWR") {
98+ if(i+1<argc) {
99+ info->MaxWhiteNoise = stringGetNthRealData(argv[i+1], 1, " ,");
100+ i++;
101+ info->flagMaxWhiteNoise++;
102+ } else {
103+ usage(argv[0]);
104+ exit(EXIT_FAILURE);
105+ }
106+ SBREAK;
107+ }
108+ SCASE("NdepWR") {
109+ if(i+1<argc) {
110+ info->NdependentWhiteNoise = stringGetNthIntegerData(argv[i+1], 1, " ,");
111+ i++;
112+ info->flagNdependentWhiteNoise++;
113+ } else {
114+ usage(argv[0]);
115+ exit(EXIT_FAILURE);
116+ }
117+ SBREAK;
118+ }
97119 SCASE("SinWin") {
98120 if(i+2<argc) {
99121 info->SinWinRmin = stringGetNthRealData(argv[i+1], 1, " ,");
--- a/src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/init.c
+++ b/src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/init.c
@@ -18,6 +18,8 @@ init0(mrcImageMultiCTFCompensationInfo* info)
1818 info->fptfftOut = stdout; info->flagfftOut = 0;
1919 info->WhiteNoise = 1.0; info->flagWhiteNoise = 0;
2020 info->WhiteNoiseRaising = 1.0; info->flagWhiteNoiseRaising = 0;
21+ info->MaxWhiteNoise = 1.0; info->flagMaxWhiteNoise = 0;
22+ info->NdependentWhiteNoise = 1; info->flagNdependentWhiteNoise = 0;
2123 info->SinWinRmin = 0.1; info->flagSinWinRmin = 0;
2224 info->SinWinRmax = 1.0; info->flagSinWinRmax = 0;
2325 info->MaxIter = 10; info->flagMaxIter = 0;
@@ -96,6 +98,12 @@ init1(mrcImageMultiCTFCompensationInfo* info)
9698 if(info->flagWhiteNoiseRaising) {
9799 }
98100
101+ if(info->flagMaxWhiteNoise) {
102+ }
103+
104+ if(info->flagNdependentWhiteNoise) {
105+ }
106+
99107 if(info->flagSinWinRmin) {
100108 }
101109
--- a/src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/mrcImageMultiCTFCompensation.c
+++ b/src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/mrcImageMultiCTFCompensation.c
@@ -76,12 +76,14 @@ main(int argc, char* argv[])
7676 } else {
7777 ctf[i].mode = ctfInfoModePhaseAndAmpCTF;
7878 }
79+ // WhiteNoise
7980 if(info.flagWhiteNoise) {
8081 ctf[i].flagWhiteNoise = 1;
8182 ctf[i].WhiteNoise = info.WhiteNoise;
8283 } else {
8384 ctf[i].flagWhiteNoise = 0;
8485 }
86+ // NoiseRaising
8587 if(info.flagWhiteNoiseRaising) {
8688 ctf[i].flagWhiteNoiseRaising = 1;
8789 ctf[i].WhiteNoiseRaising = info.WhiteNoiseRaising;
@@ -90,6 +92,23 @@ main(int argc, char* argv[])
9092 ctf[i].flagWhiteNoiseRaising = 0;
9193 ctf[i].WhiteNoiseRaising = 0;
9294 }
95+ // <axWhiteNoise
96+ if(info.flagMaxWhiteNoise) {
97+ ctf[i].flagMaxWhiteNoise = 1;
98+ ctf[i].MaxWhiteNoise = info.MaxWhiteNoise;
99+ DEBUGPRINT2("maxWhiteNoise: %d %f\n", 1, info.MaxWhiteNoise);
100+ } else {
101+ ctf[i].flagMaxWhiteNoise = 0;
102+ ctf[i].MaxWhiteNoise = info.MaxWhiteNoise;
103+ }
104+ // N-dependent
105+ if(info.flagNdependentWhiteNoise) {
106+ ctf[i].flagNdependentWhiteNoise = 1;
107+ ctf[i].NdependentWhiteNoise = info.NdependentWhiteNoise;
108+ } else {
109+ ctf[i].flagNdependentWhiteNoise = 0;
110+ ctf[i].NdependentWhiteNoise = info.NdependentWhiteNoise;
111+ }
93112 if(info.flagSinWinRmin && info.flagSinWinRmax) {
94113 ctf[i].flagWin = 1;
95114 ctf[i].CutLow = info.SinWinRmin;
--- a/src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/mrcImageMultiCTFCompensation.html
+++ b/src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/mrcImageMultiCTFCompensation.html
@@ -8,20 +8,23 @@
88 <PRE>
99 Usage: mrcImageMultiCTFCompensation
1010 Options:
11- [-i[nput] In (stdin )] :Essential :Input: filename ...
12- [-info2 CTF (stdin )] :Optional :InputFileList: the same order as the input: ctfinfo from Display2/ctfDisplay
13- [-o[utput] Out (stdout )] :Essential :OutputDataFile(average file)
14- [-f[ft] fftOut (stdout )] :Optional :OutputDataFile(averaged fft file)
15- [-W[hiteNoise] WhiteNoise (1.0 )] :Optional :
16- [-W[hiteNoise]R[aising]WhiteNoiseRaising (1.0 )] :Optional :Weight:W*exp(WR*R)
17- [-SinWin SinWinRmin (0.1 )SinWinRmax (1.0 )] :Optional :Windowing by sine function from Rmin[/A] to Rmax[/A]
18- [-MaxIter[ation] MaxIter (10 )] :Optional :Max Iteration
19- [-ctfMode CTFMode (1 )] :Optional :CTFMode: refer to mrcImageCTFObservation
20- [-solventMode solventMode (0 )] :Optional :If solvent flatterning is used, NEED
21- [-solventSTD solventSTD (-1.0 )] :Optional :If solvent flatterning is used as mode=1, NEED
22- [-log[file] Log (stderr )] :Optional :Log File Name
23- [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
24- [-m[ode] mode (0 )] :Optional :Mode
11+ [-i[nput] In (stdin ).as(inFileList ) ] :Essential :Input: filename ...
12+ [-info2 CTF (stdin ).as(inFileList ) ] :Optional :InputFileList: the same order as the input: ctfinfo from Display2/ctfDisplay
13+ [-o[utput] Out (stdout ).as(outFile ) ] :Essential :OutputDataFile(average file)
14+ [-f[ft] fftOut (stdout ).as(outFile ) ] :Optional :OutputDataFile(averaged fft file)
15+ [-W[hiteNoise] WhiteNoise (1.0 ).as(Real ) ] :Optional :
16+ [-W[hiteNoise]R[aising]WhiteNoiseRaising (1.0 ).as(Real ) ] :Optional :Weight:W*exp(WR*R)
17+ [-maxW[hiteNoise]R[aising]MaxWhiteNoise (1.0 ).as(Real ) ] :Optional :max(W*exp(WR*R),maxWhiteNoise)
18+ [-Ndep[endent]W[hiteNoise]R[aising]NdependentWhiteNoise(1 ).as(Integer ) ] :Optional :W*exp(WR*R)/sqrt(N)
19+ [-SinWin SinWinRmin (0.1 ).as(Real )
20+ SinWinRmax (1.0 ).as(Real ) ] :Optional :Windowing by sine function from Rmin[/A] to Rmax[/A]
21+ [-MaxIter[ation] MaxIter (10 ).as(Integer ) ] :Optional :Max Iteration
22+ [-ctfMode CTFMode (1 ).as(Integer ) ] :Optional :CTFMode: refer to mrcImageCTFObservation
23+ [-solventMode solventMode (0 ).as(Real ) ] :Optional :If solvent flatterning is used, NEED
24+ [-solventSTD solventSTD (-1.0 ).as(Real ) ] :Optional :If solvent flatterning is used as mode=1, NEED
25+ [-log[file] Log (stderr ).as(outFile ) ] :Optional :Log File Name
26+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
27+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
2528 ----- InputFileFormat -----
2629 filename0 deltaF[A] Cs[mm] kV[kV] ratioOfAmpToPhase
2730 filename1 deltaF[A] Cs[mm] kV[kV] ratioOfAmpToPhase
--- a/src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/mrcImageMultiCTFCompensation.pane
+++ b/src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/mrcImageMultiCTFCompensation.pane
@@ -13,14 +13,16 @@
1313 -O 1 0 1 0 0 1 -1x1+1+6.000000 ' ' 'fftOut' 'OutputDataFile(averaged fft file)' f
1414 -f 1 0 1 0 0 -1x1+1+7.500000 0 0 1.000000 0 0 0 'WhiteNoise' '' W
1515 -f 1 0 1 0 0 -1x1+1+9.000000 0 0 1.000000 0 0 0 'WhiteNoiseRaising' 'Weight:W*exp(WR*R)' WR
16- -I 1 0 0 1 0 1 -1x1+1+10 ' ' '0.1' 'SinWinRmin' Windowing by sine function from Rmin[/A] to Rmax[/A]
17- -i 1 0 1 0 0 -1x1+1+12.000000 0 0 10 0 0 'MaxIter' 'Max Iteration' MaxIter
18- -i 1 0 1 0 0 -1x1+1+13.500000 0 0 1 0 0 'CTFMode' 'CTFMode: refer to mrcImageCTFObservation' ctfMode
19- -f 1 0 1 0 0 -1x1+1+15.000000 0 0 0.000000 0 0 0 'solventMode' 'If solvent flatterning is used, NEED' solventMode
20- -f 1 0 1 0 0 -1x1+1+16.500000 0 0 -1.000000 0 0 0 'solventSTD' 'If solvent flatterning is used as mode=1, NEED ' solventSTD
21- -O 1 0 1 0 0 1 -1x1+1+18.000000 ' ' 'Log' 'Log File Name' log
22- -I 1 0 1 0 0 1 -1x1+1+19.500000 ' ' 'configFile' 'ConfigurationFile' c
23- -i 1 0 1 0 0 -1x1+1+21.000000 0 0 0 0 0 'mode' 'Mode' m
16+ -f 1 0 1 0 0 -1x1+1+10.500000 0 0 1.000000 0 0 0 'MaxWhiteNoise' 'max(W*exp(WR*R),maxWhiteNoise)' maxWR
17+ -i 1 0 1 0 0 -1x1+1+12.000000 0 0 1 0 0 'NdependentWhiteNoise' 'W*exp(WR*R)/sqrt(N)' NdepWR
18+ -I 1 0 0 1 0 1 -1x1+1+13 ' ' '0.1' 'SinWinRmin' Windowing by sine function from Rmin[/A] to Rmax[/A]
19+ -i 1 0 1 0 0 -1x1+1+15.000000 0 0 10 0 0 'MaxIter' 'Max Iteration' MaxIter
20+ -i 1 0 1 0 0 -1x1+1+16.500000 0 0 1 0 0 'CTFMode' 'CTFMode: refer to mrcImageCTFObservation' ctfMode
21+ -f 1 0 1 0 0 -1x1+1+18.000000 0 0 0.000000 0 0 0 'solventMode' 'If solvent flatterning is used, NEED' solventMode
22+ -f 1 0 1 0 0 -1x1+1+19.500000 0 0 -1.000000 0 0 0 'solventSTD' 'If solvent flatterning is used as mode=1, NEED ' solventSTD
23+ -O 1 0 1 0 0 1 -1x1+1+21.000000 ' ' 'Log' 'Log File Name' log
24+ -I 1 0 1 0 0 1 -1x1+1+22.500000 ' ' 'configFile' 'ConfigurationFile' c
25+ -i 1 0 1 0 0 -1x1+1+24.000000 0 0 0 0 0 'mode' 'Mode' m
2426 -E
2527 -E
2628 -E
--- a/src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/test/Makefile
+++ b/src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/test/Makefile
@@ -11,7 +11,29 @@ help:
1111
1212 exec:
1313 @echo "----- Execution Check -----"
14- ../$(OSTYPE)/$(OBJECTNAME)
14+ ../$(OSTYPE)/$(OBJECTNAME) -i data/in.lst -o data/out.W -info2 data/in.ctflst -ctfMode 33 -W 1.0
15+ ../$(OSTYPE)/$(OBJECTNAME) -i data/in.lst -o data/out.WR -info2 data/in.ctflst -ctfMode 33 -W 0.06 -WR 10
16+ ../$(OSTYPE)/$(OBJECTNAME) -i data/in.lst -o data/out.WR -info2 data/in.ctflst -ctfMode 33 -W 0.06 -WR 10
17+ ../$(OSTYPE)/$(OBJECTNAME) -i data/in.lst -o data/out.WRmaxNdep -info2 data/in.ctflst -ctfMode 33 -W 0.06 -WR 10 -maxWR 0.1 -NdepWR 100
1518 @echo "----- Calc check -----"
1619
20+init:
21+ pdb2mrc2d -i data/121p-GC.pdb -o data/test.mrc2d -n 128 128 -d 2 2 -S -128 -128 -sig 1.6 -w 1.0
22+ mrcImageCTFObservation -i data/test.mrc2d -o data/test.mrc2d.def2 -kV 200 -df 20000 -Cs 1.7 -Ain 0.04 -A 0.1 -ctfMode 33 -white 1.0
23+ mrcImageNoiseAdd -i data/test.mrc2d.def2 -o data/test.mrc2d.def2.tst -SN 1.0
24+ mrcImageCTFObservation -i data/test.mrc2d -o data/test.mrc2d.def5 -kV 200 -df 50000 -Cs 1.7 -Ain 0.04 -A 0.1 -ctfMode 33 -white 1.0
25+ mrcImageNoiseAdd -i data/test.mrc2d.def5 -o data/test.mrc2d.def5.tst -SN 1.0
26+ echo "data/test.mrc2d.def2.tst" > data/in.lst
27+ echo "data/test.mrc2d.def5.tst" >> data/in.lst
28+ echo "data/test.mrc2d.def2.ctfinfo" > data/in.ctflst
29+ echo "data/test.mrc2d.def5.ctfinfo" >> data/in.ctflst
30+ echo "kV: 200" > data/def.ctfinfo
31+ echo "Cs: 1.7" >> data/def.ctfinfo
32+ echo "Ai: 0.04" >> data/def.ctfinfo
33+ echo "AoverP: 0.1" >> data/def.ctfinfo
34+ cp data/def.ctfinfo data/test.mrc2d.def2.ctfinfo
35+ cp data/def.ctfinfo data/test.mrc2d.def5.ctfinfo
36+ echo "defocus: 20000" >> data/test.mrc2d.def2.ctfinfo
37+ echo "defocus: 50000" >> data/test.mrc2d.def5.ctfinfo
38+
1739 clean:
--- a/src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/usage.c
+++ b/src/Tools/mrcImage/mrcImageMultiCTFCompensation/src/usage.c
@@ -7,20 +7,22 @@ usage(char* thisProgram)
77 {
88 fprintf(stderr, "Usage: %s\n", thisProgram);
99 fprintf(stderr, "Options:\n");
10- fprintf(stderr, " [-i[nput] In (stdin )] :Essential :Input: filename ...\n");
11- fprintf(stderr, " [-info2 CTF (stdin )] :Optional :InputFileList: the same order as the input: ctfinfo from Display2/ctfDisplay\n");
12- fprintf(stderr, " [-o[utput] Out (stdout )] :Essential :OutputDataFile(average file)\n");
13- fprintf(stderr, " [-f[ft] fftOut (stdout )] :Optional :OutputDataFile(averaged fft file)\n");
14- fprintf(stderr, " [-W[hiteNoise] WhiteNoise (1.0 )] :Optional :\n");
15- fprintf(stderr, " [-W[hiteNoise]R[aising]WhiteNoiseRaising (1.0 )] :Optional :Weight:W*exp(WR*R)\n");
16- fprintf(stderr, " [-SinWin SinWinRmin (0.1 )SinWinRmax (1.0 )] :Optional :Windowing by sine function from Rmin[/A] to Rmax[/A]\n");
17- fprintf(stderr, " [-MaxIter[ation] MaxIter (10 )] :Optional :Max Iteration\n");
18- fprintf(stderr, " [-ctfMode CTFMode (1 )] :Optional :CTFMode: refer to mrcImageCTFObservation\n");
19- fprintf(stderr, " [-solventMode solventMode (0 )] :Optional :If solvent flatterning is used, NEED\n");
20- fprintf(stderr, " [-solventSTD solventSTD (-1.0 )] :Optional :If solvent flatterning is used as mode=1, NEED \n");
21- fprintf(stderr, " [-log[file] Log (stderr )] :Optional :Log File Name\n");
22- fprintf(stderr, " [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile\n");
23- fprintf(stderr, " [-m[ode] mode (0 )] :Optional :Mode\n");
10+ fprintf(stderr, " [-i[nput] In (stdin ).as(inFileList ) ] :Essential :Input: filename ...\n");
11+ fprintf(stderr, " [-info2 CTF (stdin ).as(inFileList ) ] :Optional :InputFileList: the same order as the input: ctfinfo from Display2/ctfDisplay\n");
12+ fprintf(stderr, " [-o[utput] Out (stdout ).as(outFile ) ] :Essential :OutputDataFile(average file)\n");
13+ fprintf(stderr, " [-f[ft] fftOut (stdout ).as(outFile ) ] :Optional :OutputDataFile(averaged fft file)\n");
14+ fprintf(stderr, " [-W[hiteNoise] WhiteNoise (1.0 ).as(Real ) ] :Optional :\n");
15+ fprintf(stderr, " [-W[hiteNoise]R[aising]WhiteNoiseRaising (1.0 ).as(Real ) ] :Optional :Weight:W*exp(WR*R)\n");
16+ fprintf(stderr, " [-maxW[hiteNoise]R[aising]MaxWhiteNoise (1.0 ).as(Real ) ] :Optional :max(W*exp(WR*R),maxWhiteNoise)\n");
17+ fprintf(stderr, " [-Ndep[endent]W[hiteNoise]R[aising]NdependentWhiteNoise(1 ).as(Integer ) ] :Optional :W*exp(WR*R)/sqrt(N)\n");
18+ fprintf(stderr, " [-SinWin SinWinRmin (0.1 ).as(Real ) \n SinWinRmax (1.0 ).as(Real ) ] :Optional :Windowing by sine function from Rmin[/A] to Rmax[/A]\n");
19+ fprintf(stderr, " [-MaxIter[ation] MaxIter (10 ).as(Integer ) ] :Optional :Max Iteration\n");
20+ fprintf(stderr, " [-ctfMode CTFMode (1 ).as(Integer ) ] :Optional :CTFMode: refer to mrcImageCTFObservation\n");
21+ fprintf(stderr, " [-solventMode solventMode (0 ).as(Real ) ] :Optional :If solvent flatterning is used, NEED\n");
22+ fprintf(stderr, " [-solventSTD solventSTD (-1.0 ).as(Real ) ] :Optional :If solvent flatterning is used as mode=1, NEED \n");
23+ fprintf(stderr, " [-log[file] Log (stderr ).as(outFile ) ] :Optional :Log File Name\n");
24+ fprintf(stderr, " [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile\n");
25+ fprintf(stderr, " [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode\n");
2426 additionalUsage();
2527 }
2628
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