This repository is a base of Eos.
Revisión | cc96e80b04e6f374d6c391afeda0575c50e7896f (tree) |
---|---|
Tiempo | 2014-10-12 15:42:34 |
Autor | Takuo Yasunaga <yasunaga@bio....> |
Commiter | Takuo Yasunaga |
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
@@ -11,10 +11,10 @@ unset ANS | ||
11 | 11 | echo "Directory: $EOS_HOME0"; |
12 | 12 | |
13 | 13 | #### 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/ | |
15 | 15 | if [ ! -d $EOS_HOME0 ] ; then |
16 | 16 | mkdir $EOS_HOME0 |
17 | 17 | fi |
18 | 18 | |
19 | -curl -L $ROOT_EOS_SOURCEFORGE/env/Eos_env | |
19 | +curl -L -o Eos_env.env $ROOT_EOS_SOURCEFORGE/env/Eos_env?export=raw | |
20 | 20 |
@@ -56,6 +56,12 @@ typedef struct ctfInfo { | ||
56 | 56 | long flagWhiteNoiseRaising; |
57 | 57 | float WhiteNoiseRaising; /* WhiteNoise Raising depending upon R */ |
58 | 58 | |
59 | + long flagMaxWhiteNoise; | |
60 | + float MaxWhiteNoise; /* max White Noise*/ | |
61 | + | |
62 | + long flagNdependentWhiteNoise; | |
63 | + float NdependentWhiteNoise; /* max White Noise*/ | |
64 | + | |
59 | 65 | float Inoise2; /* Intensity of noise */ |
60 | 66 | long flagWhiteNoise2; |
61 | 67 | float WhiteNoise2; /* Not Affected by MTF(R)*/ |
@@ -78,6 +78,12 @@ typedef struct ctfInfo { | ||
78 | 78 | long flagWhiteNoiseRaising; |
79 | 79 | float WhiteNoiseRaising; /* WhiteNoise Raising depending upon R */ |
80 | 80 | |
81 | + long flagMaxWhiteNoise; | |
82 | + float MaxWhiteNoise; /* max White Noise*/ | |
83 | + | |
84 | + long flagNdependentWhiteNoise; | |
85 | + float NdependentWhiteNoise; /* max White Noise*/ | |
86 | + | |
81 | 87 | float Inoise2; /* Intensity of noise */ |
82 | 88 | long flagWhiteNoise2; |
83 | 89 | float WhiteNoise2; /* Not Affected by MTF(R)*/ |
@@ -56,6 +56,12 @@ typedef struct ctfInfo { | ||
56 | 56 | long flagWhiteNoiseRaising; |
57 | 57 | float WhiteNoiseRaising; /* WhiteNoise Raising depending upon R */ |
58 | 58 | |
59 | + long flagMaxWhiteNoise; | |
60 | + float MaxWhiteNoise; /* max White Noise*/ | |
61 | + | |
62 | + long flagNdependentWhiteNoise; | |
63 | + float NdependentWhiteNoise; /* max White Noise*/ | |
64 | + | |
59 | 65 | float Inoise2; /* Intensity of noise */ |
60 | 66 | long flagWhiteNoise2; |
61 | 67 | float WhiteNoise2; /* Not Affected by MTF(R)*/ |
@@ -24,7 +24,7 @@ void | ||
24 | 24 | lmrcImageMultiCTFCompensation(mrcImage* dst, mrcImage* src, ctfInfo* ctf, long nfile, lmrcImageMultiCTFCompensationInfo info, long mode) |
25 | 25 | { |
26 | 26 | DEBUGPRINT("lmrcImageMultiCTFCompensation Start\n"); |
27 | - fprintf(stderr, "lmrcImageMultiCTFCompensation Start: %d\n", mode);fflush(stderr); | |
27 | + fprintf(stderr, "lmrcImageMultiCTFCompensation Start: %ld\n", mode);fflush(stderr); | |
28 | 28 | switch(mode&0xf) { |
29 | 29 | case 0: { |
30 | 30 | __lmrcImageMultiCTFCompensationMode0(dst, src, ctf, nfile, info, mode); |
@@ -311,6 +311,12 @@ __lmrcImageMultiCTFCompensationMode0(mrcImage* dst, mrcImage* src, ctfInfo* ctf, | ||
311 | 311 | } else if(ctf[i].flagWhiteNoise) { |
312 | 312 | NW = SQR(ctf[i].WhiteNoise); |
313 | 313 | } |
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 | + } | |
314 | 320 | W += NW; |
315 | 321 | |
316 | 322 | DEBUGPRINT3("R: %f Weight %f NW %f\n", R, Weight[i], NW); |
@@ -200,3 +200,5 @@ WORLDNAME=Tools | ||
200 | 200 | WORLDNAME=Tools |
201 | 201 | WORLDNAME=Tools |
202 | 202 | WORLDNAME=Tools |
203 | +WORLDNAME=Tools | |
204 | +WORLDNAME=Tools |
@@ -6,6 +6,8 @@ | ||
6 | 6 | "-f","-f[ft]","OutputDataFile(averaged fft file)","Optional","1","1","fftOut","outFile","stdout" |
7 | 7 | "-W","-W[hiteNoise]","","Optional","1","1","WhiteNoise","Real","1.0" |
8 | 8 | "-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" | |
9 | 11 | "-SinWin","-SinWin","Windowing by sine function from Rmin[/A] to Rmax[/A]","Optional","2","1","SinWinRmin","Real","0.1","2","SinWinRmax","Real","1.0" |
10 | 12 | "-MaxIter","-MaxIter[ation]","Max Iteration","Optional","1","1","MaxIter","Integer","10" |
11 | 13 | "-ctfMode","-ctfMode","CTFMode: refer to mrcImageCTFObservation","Optional","1","1","CTFMode","Integer","1" |
@@ -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 |
@@ -0,0 +1 @@ | ||
1 | +/Users/tacyas/Eos/src/Config/Template/ToolsTemplate.Dir/Makefile | |
\ No newline at end of file |
@@ -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 |
@@ -39,6 +39,12 @@ typedef struct mrcImageMultiCTFCompensationInfo { | ||
39 | 39 | long flagWhiteNoiseRaising; |
40 | 40 | float WhiteNoiseRaising; |
41 | 41 | |
42 | + long flagMaxWhiteNoise; | |
43 | + float MaxWhiteNoise; | |
44 | + | |
45 | + long flagNdependentWhiteNoise; | |
46 | + long NdependentWhiteNoise; | |
47 | + | |
42 | 48 | long flagSinWinRmin; |
43 | 49 | float SinWinRmin; |
44 | 50 |
@@ -12,7 +12,7 @@ | ||
12 | 12 | void |
13 | 13 | argCheck(mrcImageMultiCTFCompensationInfo* info, int argc, char* argv[]) |
14 | 14 | { |
15 | - long i, j, nv; | |
15 | + long i; | |
16 | 16 | char s[1024]; |
17 | 17 | FILE* fpt; |
18 | 18 |
@@ -94,6 +94,28 @@ argCheck(mrcImageMultiCTFCompensationInfo* info, int argc, char* argv[]) | ||
94 | 94 | } |
95 | 95 | SBREAK; |
96 | 96 | } |
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 | + } | |
97 | 119 | SCASE("SinWin") { |
98 | 120 | if(i+2<argc) { |
99 | 121 | info->SinWinRmin = stringGetNthRealData(argv[i+1], 1, " ,"); |
@@ -18,6 +18,8 @@ init0(mrcImageMultiCTFCompensationInfo* info) | ||
18 | 18 | info->fptfftOut = stdout; info->flagfftOut = 0; |
19 | 19 | info->WhiteNoise = 1.0; info->flagWhiteNoise = 0; |
20 | 20 | info->WhiteNoiseRaising = 1.0; info->flagWhiteNoiseRaising = 0; |
21 | + info->MaxWhiteNoise = 1.0; info->flagMaxWhiteNoise = 0; | |
22 | + info->NdependentWhiteNoise = 1; info->flagNdependentWhiteNoise = 0; | |
21 | 23 | info->SinWinRmin = 0.1; info->flagSinWinRmin = 0; |
22 | 24 | info->SinWinRmax = 1.0; info->flagSinWinRmax = 0; |
23 | 25 | info->MaxIter = 10; info->flagMaxIter = 0; |
@@ -96,6 +98,12 @@ init1(mrcImageMultiCTFCompensationInfo* info) | ||
96 | 98 | if(info->flagWhiteNoiseRaising) { |
97 | 99 | } |
98 | 100 | |
101 | + if(info->flagMaxWhiteNoise) { | |
102 | + } | |
103 | + | |
104 | + if(info->flagNdependentWhiteNoise) { | |
105 | + } | |
106 | + | |
99 | 107 | if(info->flagSinWinRmin) { |
100 | 108 | } |
101 | 109 |
@@ -76,12 +76,14 @@ main(int argc, char* argv[]) | ||
76 | 76 | } else { |
77 | 77 | ctf[i].mode = ctfInfoModePhaseAndAmpCTF; |
78 | 78 | } |
79 | + // WhiteNoise | |
79 | 80 | if(info.flagWhiteNoise) { |
80 | 81 | ctf[i].flagWhiteNoise = 1; |
81 | 82 | ctf[i].WhiteNoise = info.WhiteNoise; |
82 | 83 | } else { |
83 | 84 | ctf[i].flagWhiteNoise = 0; |
84 | 85 | } |
86 | + // NoiseRaising | |
85 | 87 | if(info.flagWhiteNoiseRaising) { |
86 | 88 | ctf[i].flagWhiteNoiseRaising = 1; |
87 | 89 | ctf[i].WhiteNoiseRaising = info.WhiteNoiseRaising; |
@@ -90,6 +92,23 @@ main(int argc, char* argv[]) | ||
90 | 92 | ctf[i].flagWhiteNoiseRaising = 0; |
91 | 93 | ctf[i].WhiteNoiseRaising = 0; |
92 | 94 | } |
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 | + } | |
93 | 112 | if(info.flagSinWinRmin && info.flagSinWinRmax) { |
94 | 113 | ctf[i].flagWin = 1; |
95 | 114 | ctf[i].CutLow = info.SinWinRmin; |
@@ -8,20 +8,23 @@ | ||
8 | 8 | <PRE> |
9 | 9 | Usage: mrcImageMultiCTFCompensation |
10 | 10 | 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 | |
25 | 28 | ----- InputFileFormat ----- |
26 | 29 | filename0 deltaF[A] Cs[mm] kV[kV] ratioOfAmpToPhase |
27 | 30 | filename1 deltaF[A] Cs[mm] kV[kV] ratioOfAmpToPhase |
@@ -13,14 +13,16 @@ | ||
13 | 13 | -O 1 0 1 0 0 1 -1x1+1+6.000000 ' ' 'fftOut' 'OutputDataFile(averaged fft file)' f |
14 | 14 | -f 1 0 1 0 0 -1x1+1+7.500000 0 0 1.000000 0 0 0 'WhiteNoise' '' W |
15 | 15 | -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 | |
24 | 26 | -E |
25 | 27 | -E |
26 | 28 | -E |
@@ -11,7 +11,29 @@ help: | ||
11 | 11 | |
12 | 12 | exec: |
13 | 13 | @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 | |
15 | 18 | @echo "----- Calc check -----" |
16 | 19 | |
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 | + | |
17 | 39 | clean: |
@@ -7,20 +7,22 @@ usage(char* thisProgram) | ||
7 | 7 | { |
8 | 8 | fprintf(stderr, "Usage: %s\n", thisProgram); |
9 | 9 | 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"); | |
24 | 26 | additionalUsage(); |
25 | 27 | } |
26 | 28 |