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Commit MetaInfo

Revisión57e35b6bda749e1819221aa08ea51271efd10116 (tree)
Tiempo2016-05-16 15:47:47
Autor久永浩司 <hisanagakouji@hisa...>
Commiter久永浩司

Log Message

change function of ctfDeterminationByBayes

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Diferencia incremental

--- a/include/ctffuncforbayes.h
+++ b/include/ctffuncforbayes.h
@@ -43,11 +43,15 @@ extern "C" {
4343
4444 extern void ctfforbayesInit(FILE* fpt, ctfforbayes* ctf, int mode);
4545 extern void spatialfrequencyRead(FILE* fpt, ctfforbayes* ctf, int mode);
46-extern void IntensityRead(char* filename, ctfforbayes* ctf,int mode, FILE* fpt);
47-extern void ctfFunctionforbayes(ctfforbayes* ctf, eosBayesDistribution* d, ctfInfo* info, int numLikelihood, int mode, FILE* fpt);
46+extern void IntensityRead(char* filename, ctfforbayes* ctf,int mode);
47+extern void ctfFunctionforbayes(ctfforbayes* ctf, eosBayesDistribution* d, ctfInfo* info, int numLikelihood, int count, int mode);
48+extern float MTFFunctionforbayes(float R, float m, int mode);
4849
49-extern void defocuslikelihood(ctfforbayes ctf, eosBayes* d, int mode);
50-extern void defocuslikelihoodcaluculation(ctfforbayes ctf, eosBayesDistribution* d, int numLikelihood, int mode, FILE* fpt, FILE* fpt2);
50+
51+extern void defocuslikelihood(ctfforbayes ctf, eosBayes* d, int count, int mode);
52+extern void defocuslikelihoodcaluculationLorentz(ctfforbayes ctf, eosBayesDistribution* d, int numLikelihood, int count, int mode);
53+
54+extern void ctfforbayescheckRvsValue(char* filename, float R,float value, int count);
5155
5256 /* prototype end */
5357
--- a/include/eosBayes.h
+++ b/include/eosBayes.h
@@ -25,7 +25,7 @@ typedef struct eosBayes {
2525 typedef enum eosBayesDistributionInfoMode {
2626 eosBayesDistributionInfoModeGaussian=0
2727
28-} eosBayesDistributionInfoMode;
28+} eosBayesDistributionInfoMode;
2929
3030 typedef struct eosBayesDistributionInfo {
3131 float min;
@@ -39,12 +39,13 @@ typedef struct eosBayesDistributionInfo {
3939 // For Gaussian
4040 float mean;
4141 float sigma;
42+
4243 } eosBayesDistributionInfo;
4344
4445
4546 /* eosBayesInit.c */
4647 // Initialization of eosBays
47-extern void leosBayesInit(eosBayes* b, int numDistribution, int numLikelihood, int mode);
48+extern void leosBayesInit(eosBayes* d, int numDistribution, int numLikelihood, int mode);
4849
4950 extern void eosBayesCondition(FILE* fptIn, eosBayes* d, eosBayesDistributionInfo* llinfo, int mode);
5051
@@ -55,9 +56,9 @@ extern void eosBayesDistributionInit(eosBayesDistribution* d,eosBayesDistributio
5556 extern void eosBayesDistributionInitialProbabilitySet(eosBayesDistribution* d, eosBayesDistributionInfo* info, int mode);
5657
5758 /* eosBayesEstimation.c */
58-extern void eosBayesEstimation(eosBayes* d, int mode, FILE* fpt);
59+extern void eosBayesEstimation(eosBayes* d, int mode);
5960 extern void eosBayesPosteriortoPrior(eosBayes* d, int mode);
60-
61+extern void eosBayesloop(eosBayesDistribution* d, int* L, int numDist, int length);
6162
6263 /* eosBayesWrite.c */
6364 extern void eosBayesDistribututionWrite(FILE* fpt, eosBayesDistribution* d, int mode);
@@ -70,6 +71,7 @@ extern void eosBayesWrite(FILE* fpt, eosBayes* d, int mode);
7071 // 1 min1 max1 delta1 n1 out.prior[1].prob[0] ...... prob[n-1]
7172
7273 extern void DistributionChangeCheck(eosBayes* d, int mode);
74+extern void LikelihoodChangeCheck(eosBayes* d, int count, int mode);
7375 //FileFoemat
7476 //min max delta n
7577 //value prob
Binary files /dev/null and b/src/Objects/DataManip/ctfInfo/src/.DS_Store differ
--- a/src/Objects/DataManip/ctfInfo/src/ctfforbayes.c
+++ b/src/Objects/DataManip/ctfInfo/src/ctfforbayes.c
@@ -15,6 +15,7 @@ static char __sccs_id[] = "%Z%ctfforbayes ver%I%; Date:%D% %Z%";
1515 #include <stdio.h>
1616 #include <string.h>
1717 #include <stdlib.h>
18+#include <math.h>
1819 #include "eosBayes.h"
1920 #include "../inc/ctfInfo.h"
2021 #include "./ctffuncforbayes.h"
@@ -23,6 +24,7 @@ static char __sccs_id[] = "%Z%ctfforbayes ver%I%; Date:%D% %Z%";
2324
2425
2526 #define DEBUG
27+#undef DEBUG2
2628 #include "genUtil.h"
2729 #include "String.h"
2830
@@ -65,7 +67,7 @@ void spatialfrequencyRead(FILE* fpt, ctfforbayes* ctf, int mode){
6567
6668
6769
68-void IntensityRead(char* filename, ctfforbayes* ctf, int mode, FILE* fpt){
70+void IntensityRead(char* filename, ctfforbayes* ctf, int mode){
6971 FILE* fin;
7072 int i;
7173 char s[1024];
@@ -80,12 +82,10 @@ void IntensityRead(char* filename, ctfforbayes* ctf, int mode, FILE* fpt){
8082 i=0;
8183 while(NULL != __getStringData(s,"In IntensityRead",fin,stdout,3)){
8284 ctf->I[i] = atof(s);
83- fprintf(fpt,"%f %f\n",ctf->R[i],ctf->I[i]);
8485 i++;
8586 }
8687
8788 fclose(fin);
88- fclose(fpt);
8989
9090 DEBUGPRINT("file closed\n");
9191
@@ -94,69 +94,100 @@ void IntensityRead(char* filename, ctfforbayes* ctf, int mode, FILE* fpt){
9494
9595
9696
97-void ctfFunctionforbayes(ctfforbayes* ctf, eosBayesDistribution* d, ctfInfo* info, int numLikelihood, int mode, FILE* fpt){
97+void ctfFunctionforbayes(ctfforbayes* ctf, eosBayesDistribution* d, ctfInfo* info, int numLikelihood, int count, int mode){
9898
99-
100- float A;
101- float B;
99+ float S;
100+ float N;
101+ float k;
102102 float CTF;
103+ float MTF;
103104
104105 int length;
105106
106107 int i;
107108 int j;
108- int k;
109109
110110 int* L;
111- int N1;
112- int N2;
113111
114- DEBUGPRINT("in ctf\n");
112+ DEBUGPRINT("In ctf\n");
115113
116114 length = 1;
117-
118115 for(i=0;i<numLikelihood;i++){
119- length *= d[i].n;
116+ length *= d[i].n;
120117 }
121-
118+
122119 DEBUGPRINT("L malloc\n");
123-
120+
124121 L = (int *)malloc(sizeof(int)*numLikelihood);
125-
122+
126123 DEBUGPRINT("L malloc\n");
127-
124+
128125 for(i=0;i<ctf->n;i++){
126+
127+ ctf->Ii[i] = (float *)malloc(sizeof(float)*length);
128+ //DEBUGPRINT("Ii malloc\n");
129+
130+ for(j=0;j<length;j++){
131+
132+ eosBayesloop(d,L,numLikelihood,j);
133+
134+ //DEBUGPRINT3("%d:%d:%d\n",L[0],L[1],L[2]);
135+
136+ info->defocus = d[0].min+(d[0].delta*L[0]);
137+ S = d[1].min+(d[1].delta*L[1]);
138+ N = d[2].min+(d[2].delta*L[2]);
139+ CTF = ctfFunction(info, ctf->R[i], 0);
140+
141+ /*value check*/
142+#ifdef DEBUG2
143+ ctfforbayescheckRvsValue("./data/CTF", ctf->R[i], CTF, count);
144+#endif
145+
146+ MTF = MTFFunctionforbayes(ctf->R[i], 0, 0);
147+ //DEBUGPRINT1("MTF:%f\n",MTF);
148+
149+ switch(mode){
150+
151+ case 0:
152+ ctf->Ii[i][j] = (CTF*CTF*S+N)*MTF;
153+ break;
154+
155+ case 1:
156+ k = d[3].min+(d[3].delta*L[3]);
157+ ctf->Ii[i][j] = (CTF*CTF*S*exp(-(k*k)*(ctf->R[i]*ctf->R[i]))+N)*MTF;
158+ break;
159+
160+ default:
161+ fprintf(stderr,"\n");
162+ break;
129163
130- ctf->Ii[i] = (float *)malloc(sizeof(float)*length);
131-// DEBUGPRINT("Ii malloc\n");
132-
133- for(j=0;j<length;j++){
134- N1=1;
135- N2=1;
136- for(k=0;k<numLikelihood-1;k++){
137- N2 = d[k].n;
138- L[k] = (j/N1)%N2;
139- N1 *= d[k].n;
140- }
141- L[numLikelihood-1] = j/N1;
142-
143-// DEBUGPRINT3("%d:%d:%d\n",L[0],L[1],L[2]);
144-
145- info->defocus = d[0].min+(d[0].delta*L[0]);
146- A = d[1].min+(d[1].delta*L[1]);
147- B = d[2].min+(d[2].delta*L[2]);
148- CTF = ctfFunction(info,ctf->R[i], 0);
149- ctf->Ii[i][j] = CTF*CTF*A+B;
150164 }
151- fprintf(fpt,"#%f\n",info->defocus);
152- fprintf(fpt,"%f %f\n",ctf->R[i],CTF);
153-
154165
166+ }
167+
155168 }
156-
157- fclose(fpt);
169+
158170 free(L);
159-
171+
160172 }
161173
162174
175+float MTFFunctionforbayes(float R, float m, int mode){
176+
177+ float MTF;
178+
179+ switch(mode){
180+
181+ case 0:
182+ MTF = exp(-(m*R));
183+ break;
184+
185+ default:
186+ fprintf(stderr,"");
187+ break;
188+
189+ }
190+
191+ return MTF;
192+
193+}
--- /dev/null
+++ b/src/Objects/DataManip/ctfInfo/src/ctfforbayescheck.c
@@ -0,0 +1,44 @@
1+/*
2+# %M% %Y% %I%
3+# The latest update : %G% at %U%
4+#
5+#%Z% ctfforbayescheck ver %I%
6+#%Z% Created by
7+#%Z%
8+#%Z% Usage : ctfforbayescheck
9+#%Z% Attention
10+#%Z%
11+*/
12+static char __sccs_id[] = "%Z%ctfforbayescheck ver%I%; Date:%D% %Z%";
13+
14+
15+#include <stdio.h>
16+#include <string.h>
17+#include <stdlib.h>
18+#include "eosBayes.h"
19+#include "../inc/ctfInfo.h"
20+#include "./ctffuncforbayes.h"
21+
22+#define DEBUG
23+#include "genUtil.h"
24+#include "String.h"
25+
26+
27+
28+void ctfforbayescheckRvsValue(char* filename, float R,float value, int count){
29+
30+ FILE* fpt;
31+ char s[1024];
32+
33+ sprintf(s,"%s%d.out",filename,count);
34+
35+ if((fpt=fopen(s,"a"))==NULL){
36+ fprintf(stderr,"fopen error: %s\n",s);
37+ exit(1);
38+ }
39+
40+ fprintf(fpt,"%f %f\n",R,value);
41+
42+ fclose(fpt);
43+
44+}
--- /dev/null
+++ b/src/Objects/DataManip/ctfInfo/src/ctfforbayescheck.c~
@@ -0,0 +1,44 @@
1+/*
2+# %M% %Y% %I%
3+# The latest update : %G% at %U%
4+#
5+#%Z% ctfforbayescheck ver %I%
6+#%Z% Created by
7+#%Z%
8+#%Z% Usage : ctfforbayescheck
9+#%Z% Attention
10+#%Z%
11+*/
12+static char __sccs_id[] = "%Z%ctfforbayescheck ver%I%; Date:%D% %Z%";
13+
14+
15+#include <stdio.h>
16+#include <string.h>
17+#include <stdlib.h>
18+#include "eosBayes.h"
19+#include "../inc/ctfInfo.h"
20+include "./ctffuncforbayes.h"
21+
22+#define DEBUG
23+#include "genUtil.h"
24+#include "String.h"
25+
26+
27+
28+void ctffobayescheckRvsValue(char* filename, float R,float value, int count){
29+
30+ FILE* fpt;
31+ char s[1024];
32+
33+ sprintf(s,"%s%d.out",filename,count);
34+
35+ if((fpt=fopen(s,"a"))==NULL){
36+ fprintf(stderr,"fopen error: %s\n",s);
37+ exit(1);
38+ }
39+
40+ fprintf(fpt,"%f %f\n",R,value);
41+
42+ fclose(fpt);
43+
44+}
--- a/src/Objects/DataManip/ctfInfo/src/ctffuncforbayes.h
+++ b/src/Objects/DataManip/ctfInfo/src/ctffuncforbayes.h
@@ -28,6 +28,12 @@ typedef struct ctfforbayes{
2828 float** Ii;
2929 } ctfforbayes;
3030
31+typedef struct intencityforbayes{
32+
33+
34+
35+}intencityforbayes;
36+
3137 /* struct end */
3238
3339 #ifdef __cplusplus
@@ -43,11 +49,15 @@ extern "C" {
4349
4450 extern void ctfforbayesInit(FILE* fpt, ctfforbayes* ctf, int mode);
4551 extern void spatialfrequencyRead(FILE* fpt, ctfforbayes* ctf, int mode);
46-extern void IntensityRead(char* filename, ctfforbayes* ctf,int mode, FILE* fpt);
47-extern void ctfFunctionforbayes(ctfforbayes* ctf, eosBayesDistribution* d, ctfInfo* info, int numLikelihood, int mode, FILE* fpt);
52+extern void IntensityRead(char* filename, ctfforbayes* ctf,int mode);
53+extern void ctfFunctionforbayes(ctfforbayes* ctf, eosBayesDistribution* d, ctfInfo* info, int numLikelihood, int count, int mode);
54+extern float MTFFunctionforbayes(float R, float m, int mode);
55+
56+
57+extern void defocuslikelihood(ctfforbayes ctf, eosBayes* d, int count, int mode);
58+extern void defocuslikelihoodcaluculationLorentz(ctfforbayes ctf, eosBayesDistribution* d, int numLikelihood, int count, int mode);
4859
49-extern void defocuslikelihood(ctfforbayes ctf, eosBayes* d, int mode);
50-extern void defocuslikelihoodcaluculation(ctfforbayes ctf, eosBayesDistribution* d, int numLikelihood, int mode, FILE* fpt, FILE* fpt2);
60+extern void ctfforbayescheckRvsValue(char* filename, float R,float value, int count);
5161
5262 /* prototype end */
5363
--- a/src/Objects/DataManip/ctfInfo/src/defocuslikelihood.c
+++ b/src/Objects/DataManip/ctfInfo/src/defocuslikelihood.c
@@ -15,11 +15,13 @@ static char __sccs_id[] = "%Z%defocuslikelihood ver%I%; Date:%D% %Z%";
1515 #include <stdio.h>
1616 #include <string.h>
1717 #include <stdlib.h>
18+#include <math.h>
1819 #include "eosBayes.h"
1920 #include "../inc/ctfInfo.h"
2021 #include "./ctffuncforbayes.h"
2122
2223 #define DEBUG
24+#undef DEBUG2
2325 #include "genUtil.h"
2426 #include "String.h"
2527
@@ -27,10 +29,23 @@ static char __sccs_id[] = "%Z%defocuslikelihood ver%I%; Date:%D% %Z%";
2729
2830
2931
30-void defocuslikelihood(ctfforbayes ctf, eosBayes* d, int mode){
32+void defocuslikelihood(ctfforbayes ctf, eosBayes* d, int count, int mode){
33+
34+ switch(mode){
35+
36+ case 0:
37+ defocuslikelihoodcaluculationLorentz(ctf, d->likelihood, d->numLikelihood, count, 0);
38+ break;
39+
40+ default:
41+ fprintf(stderr,"");
42+ break;
43+
44+ }
45+
3146 }
3247
33-void defocuslikelihoodcaluculation(ctfforbayes ctf, eosBayesDistribution* d, int numLikelihood, int mode, FILE* fpt, FILE* fpt2){
48+void defocuslikelihoodcaluculationLorentz(ctfforbayes ctf, eosBayesDistribution* d, int numLikelihood, int count, int mode){
3449 float difference;
3550 float* sum;
3651
@@ -39,14 +54,11 @@ void defocuslikelihoodcaluculation(ctfforbayes ctf, eosBayesDistribution* d, int
3954 int i;
4055 int j;
4156 int k;
42- int l;
4357
4458 int* L;
45- int N1;
46- int N2;
4759
4860 DEBUGPRINT("In defocuslikelihood\n");
49-
61+
5062 length = 1;
5163 for(i=0;i<numLikelihood;i++){
5264 length *= d[i].n;
@@ -74,56 +86,55 @@ void defocuslikelihoodcaluculation(ctfforbayes ctf, eosBayesDistribution* d, int
7486
7587
7688 for(j=0;j<length;j++){
77- N1=1;
78- N2=1;
79- for(k=0;k<numLikelihood-1;k++){
80- N2 = d[k].n;
81- L[k] = (j/N1)%N2;
82- N1 *= d[k].n;
83- }
84- L[numLikelihood-1] = j/N1;
89+
90+ eosBayesloop(d,L,numLikelihood,j);
8591
8692
87- difference = 0;
88- for(l=45;l<101;l++){
89- fprintf(fpt2,"%f %f %f\n",ctf.R[l],ctf.I[l],ctf.Ii[l][L[0]]);
90- difference += (ctf.I[l]-ctf.Ii[l][j])*(ctf.I[l]-ctf.Ii[l][j]);
91- }
93+ difference = 0;
94+ for(k=100;k<201;k++){
95+ difference += (ctf.I[k]-ctf.Ii[k][j])*(ctf.I[k]-ctf.Ii[k][j]);
9296
93- DEBUGPRINT3("L[0]:%d L[1]:%d L[2]:%d\n",L[0],L[1],L[2]);
97+ /*check value*/
98+#ifdef DEBUG2
99+ ctfforbayescheckRvsValue("./data/diffdef",ctf.R[k],(ctf.I[k]-ctf.Ii[k][L[0]])*(ctf.I[k]-ctf.Ii[k][L[0]]),count);
100+ ctfforbayescheckRvsValue("./data/diffA",ctf.R[k],(ctf.I[k]-ctf.Ii[k][L[1]])*(ctf.I[k]-ctf.Ii[k][L[1]]),count);
101+ ctfforbayescheckRvsValue("./data/diffB",ctf.R[k],(ctf.I[k]-ctf.Ii[k][L[2]])*(ctf.I[k]-ctf.Ii[k][L[2]]),count);
102+#endif
94103
95- d[0].prob[L[0]] += 1/(1e-6 + difference);
96- d[1].prob[L[1]] += 1/(1e-6 + difference);
97- d[2].prob[L[2]] += 1/(1e-6 + difference);
98- }
104+ }
99105
100106
107+ //DEBUGPRINT3("L[0]:%d L[1]:%d L[2]:%d\n",L[0],L[1],L[2]);
108+ for(k=0;k<numLikelihood;k++){
109+ d[k].prob[L[k]] += 1/(1e-6 + difference);
110+ }
101111
102- DEBUGPRINT("likelihood culcu\n");
112+ }
103113
114+
115+
116+ DEBUGPRINT("likelihood culcu\n");
117+
118+ /*normalization*/
104119 for(i=0;i<numLikelihood;i++){
105- for(j=0;j<d[i].n;j++){
106- sum[i] += d[i].prob[j];
107- }
120+ for(j=0;j<d[i].n;j++){
121+ sum[i] += d[i].prob[j];
122+ }
108123 }
124+
109125
110-
111-
126+
112127 for(i=0;i<numLikelihood;i++){
113- DEBUGPRINT2("%dlikelihood.n:%d\n",i,d[i].n);
114- for(j=0;j<d[i].n;j++){
115- d[i].prob[j] /= sum[i];
116- DEBUGPRINT2("likelihood%d:%f\n",i,d[i].prob[j]);
117- fprintf(fpt,"%f\n",d[i].prob[j]);
118- }
128+ DEBUGPRINT2("%dlikelihood.n:%d\n",i,d[i].n);
129+ for(j=0;j<d[i].n;j++){
130+ d[i].prob[j] /= sum[i];
131+ DEBUGPRINT2("likelihood%d:%f\n",i,d[i].prob[j]);
132+ }
119133 }
120-
134+
121135 DEBUGPRINT("free\n");
122-
136+
123137 free(L);
124138 free(sum);
125- fclose(fpt);
126- fclose(fpt2);
127-
128-
139+
129140 }
--- a/src/Objects/General/eosBayes/inc/eosBayes.h
+++ b/src/Objects/General/eosBayes/inc/eosBayes.h
@@ -25,7 +25,7 @@ typedef struct eosBayes {
2525 typedef enum eosBayesDistributionInfoMode {
2626 eosBayesDistributionInfoModeGaussian=0
2727
28-} eosBayesDistributionInfoMode;
28+} eosBayesDistributionInfoMode;
2929
3030 typedef struct eosBayesDistributionInfo {
3131 float min;
@@ -39,12 +39,13 @@ typedef struct eosBayesDistributionInfo {
3939 // For Gaussian
4040 float mean;
4141 float sigma;
42+
4243 } eosBayesDistributionInfo;
4344
4445
4546 /* eosBayesInit.c */
4647 // Initialization of eosBays
47-extern void leosBayesInit(eosBayes* b, int numDistribution, int numLikelihood, int mode);
48+extern void leosBayesInit(eosBayes* d, int numDistribution, int numLikelihood, int mode);
4849
4950 extern void eosBayesCondition(FILE* fptIn, eosBayes* d, eosBayesDistributionInfo* llinfo, int mode);
5051
@@ -55,9 +56,9 @@ extern void eosBayesDistributionInit(eosBayesDistribution* d,eosBayesDistributio
5556 extern void eosBayesDistributionInitialProbabilitySet(eosBayesDistribution* d, eosBayesDistributionInfo* info, int mode);
5657
5758 /* eosBayesEstimation.c */
58-extern void eosBayesEstimation(eosBayes* d, int mode, FILE* fpt);
59+extern void eosBayesEstimation(eosBayes* d, int mode);
5960 extern void eosBayesPosteriortoPrior(eosBayes* d, int mode);
60-
61+extern void eosBayesloop(eosBayesDistribution* d, int* L, int numDist, int length);
6162
6263 /* eosBayesWrite.c */
6364 extern void eosBayesDistribututionWrite(FILE* fpt, eosBayesDistribution* d, int mode);
@@ -70,6 +71,7 @@ extern void eosBayesWrite(FILE* fpt, eosBayes* d, int mode);
7071 // 1 min1 max1 delta1 n1 out.prior[1].prob[0] ...... prob[n-1]
7172
7273 extern void DistributionChangeCheck(eosBayes* d, int mode);
74+extern void LikelihoodChangeCheck(eosBayes* d, int count, int mode);
7375 //FileFoemat
7476 //min max delta n
7577 //value prob
--- a/src/Objects/General/eosBayes/src/eosBayesCondition.c
+++ b/src/Objects/General/eosBayes/src/eosBayesCondition.c
@@ -42,7 +42,7 @@ void eosBayesCondition(FILE* fptIn, eosBayes* d, eosBayesDistributionInfo* llinf
4242 llinfo->sigma = stringGetNthRealData(s, 7," \t");
4343
4444 DEBUGPRINT1("%s\n",s);
45- DEBUGPRINT6("%f %f %f %u %f %f\n",llinfo->min,llinfo->max,llinfo->delta,llinfo->mode,llinfo->mean,llinfo->sigma);
45+ DEBUGPRINT6("min:%f max:%f delta:%f mode:%u mean:%f sigma:%f\n",llinfo->min,llinfo->max,llinfo->delta,llinfo->mode,llinfo->mean,llinfo->sigma);
4646 eosBayesDistributionInit(&(d->prior[i]),llinfo,0);
4747 eosBayesDistributionInit(&(d->posterior[i]),llinfo,0);
4848 eosBayesDistributionInit(&(d->likelihood[i]),llinfo,0);
--- a/src/Objects/General/eosBayes/src/eosBayesDistributionInit.c
+++ b/src/Objects/General/eosBayes/src/eosBayesDistributionInit.c
@@ -37,9 +37,9 @@ void eosBayesDistributionInit(eosBayesDistribution* d, eosBayesDistributionInfo*
3737 d->value[i] = d->min+(d->delta*i);
3838 }
3939
40+/*to swich after*/
4041 if(mode==0){
4142 info->mode = eosBayesDistributionInfoModeGaussian;
4243 }
4344
44-
4545 }
--- a/src/Objects/General/eosBayes/src/eosBayesEstimation.c
+++ b/src/Objects/General/eosBayes/src/eosBayesEstimation.c
@@ -20,7 +20,7 @@ static char __sccs_id[] = "%Z%eosBayesEstimation ver%I%; Date:%D% %Z%";
2020 #define DEBUG
2121 #include "genUtil.h"
2222
23-void eosBayesEstimation(eosBayes* d, int mode, FILE* fpt){
23+void eosBayesEstimation(eosBayes* d, int mode){
2424 int i;
2525 int j;
2626 float sum = 0;
@@ -36,15 +36,11 @@ void eosBayesEstimation(eosBayes* d, int mode, FILE* fpt){
3636 for(j=0;j<d->prior[i].n;j++){
3737 d->posterior[i].prob[j] /= sum;
3838 DEBUGPRINT1("post:%f\n",d->posterior[i].prob[j]);
39- fprintf(fpt,"%f\n",d->posterior[i].prob[j]);
4039 }
41- fprintf(fpt,"\n");
4240
43- DEBUGPRINT2("%dDistribution num:%d",i,d->prior[i].n);
41+ DEBUGPRINT2("%dDistribution num:%d\n",i,d->prior[i].n);
4442 }
4543
46- fclose(fpt);
47-
4844 }
4945
5046
@@ -61,3 +57,23 @@ void eosBayesPosteriortoPrior(eosBayes* d,int mode){
6157 }
6258
6359 }
60+
61+void eosBayesloop(eosBayesDistribution* d, int* L, int numDist, int length){
62+
63+ int N1;
64+ int N2;
65+
66+ int i;
67+
68+ N1=1;
69+ N2=1;
70+
71+ for(i=0;i<numDist-1;i++){
72+ N2 = d[i].n;
73+ L[i] = (length/N1)%N2;
74+ N1 *= d[i].n;
75+ }
76+ L[numDist-1] = length/N1;
77+
78+
79+}
--- a/src/Objects/General/eosBayes/src/eosBayesWrite.c
+++ b/src/Objects/General/eosBayes/src/eosBayesWrite.c
@@ -32,9 +32,9 @@ void eosBayesDistributionWrite(FILE* fpt, eosBayesDistribution* d, int mode){
3232 DEBUGPRINT4("#dist: %f\t%f\t%f\t%d\n",d->min,d->max,d->delta,d->n);
3333 for(i=0;i<d->n;i++){
3434 fprintf(fpt,"%f\n",d->prob[i]);
35- DEBUGPRINT1("%f\n",d->prob[i]);
35+ DEBUGPRINT2("%f %f\n",d->value[i],d->prob[i]);
3636 }
37- fprintf(fpt,"#end\n");
37+ fprintf(fpt,"#end\n\n");
3838
3939 break;
4040 case 2:
@@ -90,7 +90,7 @@ void eosBayesWrite(FILE* fpt, eosBayes* d, int mode){
9090 }
9191
9292
93-extern void DistributionChangeCheck(eosBayes* d, int mode){
93+void DistributionChangeCheck(eosBayes* d, int mode){
9494
9595 FILE* fpt;
9696 int i;
@@ -116,7 +116,7 @@ extern void DistributionChangeCheck(eosBayes* d, int mode){
116116 for(j=0;j<d->prior[i].n;j++){
117117 fprintf(fpt,"%f %f\n",d->prior[i].value[j],d->prior[i].prob[j]);
118118 }
119- fprintf(fpt,"\n");
119+ fprintf(fpt,"\n\n");
120120
121121 fclose(fpt);
122122 break;
@@ -131,9 +131,9 @@ extern void DistributionChangeCheck(eosBayes* d, int mode){
131131 for(j=0;j<d->posterior[i].n;j++){
132132 fprintf(fpt,"%f %f\n",d->posterior[i].value[j],d->posterior[i].prob[j]);
133133 }
134- fprintf(fpt,"\n");
135-
134+ fprintf(fpt,"\n\n");
136135
136+ fclose(fpt);
137137 break;
138138
139139
@@ -148,3 +148,51 @@ extern void DistributionChangeCheck(eosBayes* d, int mode){
148148
149149
150150 }
151+
152+
153+void LikelihoodChangeCheck(eosBayes* d, int count, int mode){
154+
155+ FILE* fpt;
156+ int i;
157+ int j;
158+ char s[1024];
159+
160+ for(i=0;i<d->numDistribution;i++){
161+ sprintf(s,"%s%d.out","./data/likelihood",i);
162+
163+
164+ if(count == 0){
165+
166+ if((fpt=fopen(s,"w"))==NULL){
167+ fprintf(stderr,"fopen error: %s\n",s);
168+ exit(1);
169+ }
170+
171+ fprintf(fpt,"#dist: %f\t%f\t%f\t%d\n",d->likelihood[i].min,d->likelihood[i].max,d->likelihood[i].delta,d->likelihood[i].n);
172+ for(j=0;j<d->likelihood[i].n;j++){
173+ fprintf(fpt,"%f %f\n",d->likelihood[i].value[j],d->likelihood[i].prob[j]);
174+ }
175+ fprintf(fpt,"\n\n");
176+
177+ fclose(fpt);
178+
179+ }else if(count > 0){
180+
181+ if((fpt=fopen(s,"a"))==NULL){
182+ fprintf(stderr,"fopen error: %s\n",s);
183+ exit(1);
184+ }
185+
186+ for(j=0;j<d->likelihood[i].n;j++){
187+ fprintf(fpt,"%f %f\n",d->likelihood[i].value[j],d->likelihood[i].prob[j]);
188+ }
189+ fprintf(fpt,"\n\n");
190+
191+ fclose(fpt);
192+
193+ }
194+
195+ }
196+
197+
198+}
--- a/src/Objects/General/eosBayes/src/leosBayesInit.c
+++ b/src/Objects/General/eosBayes/src/leosBayesInit.c
@@ -18,14 +18,14 @@ static char __sccs_id[] = "%Z%leosBayesInit ver%I%; Date:%D% %Z%";
1818 #include "../inc/eosBayes.h"
1919
2020
21-void leosBayesInit(eosBayes* b, int numDistribution, int numLikelihood, int mode){
21+void leosBayesInit(eosBayes* d, int numDistribution, int numLikelihood, int mode){
2222
23- b->numDistribution = numDistribution;
24- b->numLikelihood = numLikelihood;
23+ d->numDistribution = numDistribution;
24+ d->numLikelihood = numLikelihood;
2525
26- b->prior = (eosBayesDistribution*)malloc(sizeof(eosBayesDistribution)*numDistribution);
27- b->posterior = (eosBayesDistribution*)malloc(sizeof(eosBayesDistribution)*numDistribution);
26+ d->prior = (eosBayesDistribution*)malloc(sizeof(eosBayesDistribution)*numDistribution);
27+ d->posterior = (eosBayesDistribution*)malloc(sizeof(eosBayesDistribution)*numDistribution);
2828
29- b->likelihood = (eosBayesDistribution*)malloc(sizeof(eosBayesDistribution)*numLikelihood);
29+ d->likelihood = (eosBayesDistribution*)malloc(sizeof(eosBayesDistribution)*numLikelihood);
3030
3131 }
--- a/src/Tools/Config/Define.inc
+++ b/src/Tools/Config/Define.inc
@@ -8,3 +8,4 @@ WORLDNAME=Tools
88 WORLDNAME=Tools
99 WORLDNAME=Tools
1010 WORLDNAME=Tools
11+WORLDNAME=Tools
--- a/src/Tools/Makefile
+++ /dev/null
@@ -1 +0,0 @@
1-/Users/hisanagakouji/Eos/src/Config/Template/ToolsHomeTemplate.Dir/Makefile
\ No newline at end of file
--- /dev/null
+++ b/src/Tools/Makefile
@@ -0,0 +1,5 @@
1+include ../Config/Define.inc
2+include Config/Define.inc
3+include .Source
4+
5+include Config/Target.inc
--- a/src/Tools/ctfInfo/ctfDeterminationByBayes/src/ctfDeterminationByBayes.c
+++ b/src/Tools/ctfInfo/ctfDeterminationByBayes/src/ctfDeterminationByBayes.c
@@ -40,105 +40,69 @@ typedef enum lctfDeterminationByBayesMode {
4040 int
4141 main(int argc, char* argv[])
4242 {
43+
44+ ctfDeterminationByBayesInfo info;
45+ ctfInfo ctfinfo;
46+ eosBayesDistributionInfo llinfo;
47+
48+ eosBayes out;
49+ ctfforbayes ctf;
50+ int i;
4351
44- ctfDeterminationByBayesInfo info;
45- ctfInfo ctfinfo;
46- eosBayesDistributionInfo llinfo;
52+ init0(&info);
53+ argCheck(&info, argc, argv);
54+ init1(&info);
4755
48- eosBayes out;
49- ctfforbayes ctf;
50- int i;
56+ DEBUGPRINT("Program Start\n");
5157
52- FILE* fout;
53- FILE* fout2;
54- FILE* fout3;
55- FILE* fout4;
56- FILE* fout5;
58+ ctfinfo.mode = 33;
5759
5860
59- char s[1024];
61+ leosBayesInit(&out, info.numDistribution, info.numLikelihood, info.mode);
62+ eosBayesCondition(info.fptIn, &out, &llinfo, 0);
63+ eosBayesPriorWrite(info.fptOut2, &out,0);
64+ DistributionChangeCheck(&out, 0);
6065
61- init0(&info);
62- argCheck(&info, argc, argv);
63- init1(&info);
6466
65- DEBUGPRINT("Program Start\n");
67+ ctfforbayesInit(info.fptIn2,&ctf,0);
68+ spatialfrequencyRead(info.fptIn2,&ctf,0);
69+ ctfInfoRead(info.fptIn3,&ctfinfo,"",0);
70+ DEBUGPRINT4("kV:%f Cs:%f Ain:%f ctfMode:%d\n",ctfinfo.kV,ctfinfo.Cs,ctfinfo.Ain,ctfinfo.mode);
71+ DEBUGPRINT1("flagIn4:%d\n",info.flagIn4);
6672
67- ctfinfo.mode = 32;
68-
69-
70- leosBayesInit(&out, info.numDistribution, info.numLikelihood, info.mode);
71- eosBayesCondition(info.fptIn, &out, &llinfo, 0);
72- eosBayesPriorWrite(info.fptOut2, &out,0);
73- DistributionChangeCheck(&out, 0);
74-
75-
76- ctfforbayesInit(info.fptIn2,&ctf,0);
77- spatialfrequencyRead(info.fptIn2,&ctf,0);
78- ctfInfoRead(info.fptIn3,&ctfinfo,"",0);
79- DEBUGPRINT3("kV:%f Cs:%f Ain:%f\n",ctfinfo.kV,ctfinfo.Cs,ctfinfo.Ain);
80-
81- for(i=0;i<info.flagIn4;i++){
82-
83- sprintf(s,"%s%d.out","./data/intensity",i);
84- if((fout4=fopen(s,"w"))==NULL){
85- fprintf(stderr,"fopen error: %s\n",s);
86- exit(1);
87- }
88- IntensityRead(info.In4[i],&ctf,0,fout4);
89-
90-
91-
92- DEBUGPRINT("ctf start\n");
93- sprintf(s,"%s%d.out","./data/ctf",i);
94- if((fout=fopen(s,"w"))==NULL){
95- fprintf(stderr,"fopen error: %s\n",s);
96- exit(1);
97- }
98- ctfFunctionforbayes(&ctf,out.likelihood,&ctfinfo,out.numLikelihood,0,fout);
99-
100-
101- DEBUGPRINT("likelihood start\n");
102- sprintf(s,"%s%d.out","./data/likelihood",i);
103- if((fout2=fopen(s,"w"))==NULL){
104- fprintf(stderr,"fopen error: %s\n",s);
105- exit(1);
106- }
107-
108- sprintf(s,"%s%d.out","./data/IandII",i);
109- if((fout5=fopen(s,"w"))==NULL){
110- fprintf(stderr,"fopen error: %s\n",s);
111- exit(1);
112- }
113-
114-
115- defocuslikelihoodcaluculation(ctf,out.likelihood,out.numLikelihood,0,fout2,fout5);
11673
74+ /*defocus estimation*/
75+ for(i=0;i<info.flagIn4;i++){
76+
77+ IntensityRead(info.In4[i],&ctf,0);
78+
79+ DEBUGPRINT("ctf start\n");
80+ ctfFunctionforbayes(&ctf,out.likelihood,&ctfinfo,out.numLikelihood,i,0);
11781
118- DEBUGPRINT("estimate start\n");
119- sprintf(s,"%s%d.out","./data/posterior",i);
120- if((fout3=fopen(s,"w"))==NULL){
121- fprintf(stderr,"fopen error: %s\n",s);
122- exit(1);
123- }
124- eosBayesEstimation(&out,0,fout3);
82+ DEBUGPRINT("likelihood start\n");
12583
126- DistributionChangeCheck(&out,1);
84+ defocuslikelihood(ctf,&out,i,0);
85+ LikelihoodChangeCheck(&out,i,0);
12786
128- DEBUGPRINT("change start\n");
129- eosBayesPosteriortoPrior(&out,0);
130- DEBUGPRINT("loop end\n");
87+ DEBUGPRINT("estimate start\n");
88+ eosBayesEstimation(&out,0);
13189
132- }
133-
134- eosBayesPriorWrite(info.fptOut,&out,0);
90+ DistributionChangeCheck(&out,1);
91+
92+ DEBUGPRINT("change start\n");
93+ eosBayesPosteriortoPrior(&out,0);
94+ DEBUGPRINT("loop end\n");
13595
136- exit(EXIT_SUCCESS);
96+ }
97+
98+ eosBayesPriorWrite(info.fptOut,&out,0);
99+
100+ exit(EXIT_SUCCESS);
137101 }
138102
139103 void
140104 additionalUsage()
141105 {
142- fprintf(stderr, "----- Additional Usage -----\n");
106+ fprintf(stderr, "----- Additional Usage -----\n");
143107 }
144108
--- a/src/Tools/ctfInfo/ctfDeterminationByBayes/src/test/Makefile
+++ b/src/Tools/ctfInfo/ctfDeterminationByBayes/src/test/Makefile
@@ -7,11 +7,11 @@ all: help exec
77
88 help:
99 @echo "----- Help Message Check -----"
10- @../$(OSTYPE)/$(OBJECTNAME) -h
10+ @../$(OSTYPE)/$(OBJECTNAME) -h
1111
1212 exec:
1313 @echo "----- Execution Check -----"
14- ../$(OSTYPE)/$(OBJECTNAME) -i ./data/test.in -i2 ./data/121ptest.R.txt -i3 ./data/ctfInfo -i4 ./data/testList.in -o ./data/posterior.out -O ./data/prior.out -n 3 3
15- @echo "----- Calc check -----"
14+ ../$(OSTYPE)/$(OBJECTNAME) -i ./data/test.in -i2 ./data/disc.ctf.fft.spec.R -i3 ./data/ctfInfo -i4 ./data/testList.in -o ./data/posterior.out -O ./data/prior.out -n 3 3
15+ @echo "----- Calc check -----"
1616
1717 clean:
--- a/src/Tools/ctfInfo/ctfDeterminationByBayes/src/test/Makefile~
+++ /dev/null
@@ -1,17 +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: help exec
7-
8-help:
9- @echo "----- Help Message Check -----"
10- @../$(OSTYPE)/$(OBJECTNAME) -h
11-
12-exec:
13- @echo "----- Execution Check -----"
14- ../$(OSTYPE)/$(OBJECTNAME) -i ./data/test.in -i2 ./data/121ptest.R.txt -i3 ./data/ctfInfo -i4 ./data/testList.in -o ./data/posterior.out -O ./data/prior.out -n 3 3
15- @echo "----- Calc check -----"
16-
17-clean:
--- a/src/Tools/mrcImage/mrcImageCTFObservation/Config/OptionControlFile
+++ b/src/Tools/mrcImage/mrcImageCTFObservation/Config/OptionControlFile
@@ -2,7 +2,7 @@
22 # FileFormat
33 "-i","-i[nput]","Input:2D","Essential","1","1","In","inFile::mrcImage","stdin"
44 "-o","-o[utput]","Output:2D","Essential","1","1","Out","outFile::mrcImage","stdout"
5-"-ctf","-ctf","Input:ctfInfo","Essential","1","1","CTF","inFile::ASCII","stdin"
5+"-ctf","-ctf","Input:ctfInfo","Optional","1","1","CTF","inFile::ASCII","stdin"
66 "-kV","-kV","AccVol[kV]","Optional","1","1","kV","Real","200"
77 "-Cs","-Cs","Cs[mm]","Optional","1","1","Cs","Real","2.1"
88 "-df","-df","Defocus [A]:under(+)","Optional","1","1","Defocus","Real","27000"
--- a/src/Tools/mrcImage/mrcImageCTFObservation/src/init.c
+++ b/src/Tools/mrcImage/mrcImageCTFObservation/src/init.c
@@ -54,11 +54,6 @@ init1(mrcImageCTFObservationInfo* info)
5454 info->fptOut = fileOpen(info->Out, "w");
5555 }
5656
57- if(!info->flagCTF) {
58- stringGetFromFile(s, "CTF", stdin, stdout, 0);
59- info->CTF = stringGetNthWord(s, 1, " ,\t");
60- info->flagCTF++;
61- }
6257 if(info->flagCTF) {
6358 info->fptCTF = fileOpen(info->CTF, "r");
6459 }
--- a/src/Tools/mrcImage/mrcImageCTFObservation/src/mrcImageCTFObservation.html
+++ b/src/Tools/mrcImage/mrcImageCTFObservation/src/mrcImageCTFObservation.html
@@ -10,7 +10,7 @@ Usage: mrcImageCTFObservation
1010 Options:
1111 [-i[nput] In (stdin ).as(inFile::mrcImage ) ] :Essential :Input:2D
1212 [-o[utput] Out (stdout ).as(outFile::mrcImage ) ] :Essential :Output:2D
13- [-ctf CTF (stdin ).as(inFile::ASCII ) ] :Essential :Input:ctfInfo
13+ [-ctf CTF (stdin ).as(inFile::ASCII ) ] :Optional :Input:ctfInfo
1414 [-kV kV (200 ).as(Real ) ] :Optional :AccVol[kV]
1515 [-Cs Cs (2.1 ).as(Real ) ] :Optional :Cs[mm]
1616 [-df Defocus (27000 ).as(Real ) ] :Optional :Defocus [A]:under(+)
--- a/src/Tools/mrcImage/mrcImageCTFObservation/src/mrcImageCTFObservation.pane
+++ b/src/Tools/mrcImage/mrcImageCTFObservation/src/mrcImageCTFObservation.pane
@@ -9,7 +9,7 @@
99 -Q 1 0 5.25x1+47+0 'Close'
1010 -I 1 0 1 1 0 1 -1x1+1+1.500000 ' ' 'In' 'Input:2D' i
1111 -O 1 0 1 1 0 1 -1x1+1+3.000000 ' ' 'Out' 'Output:2D' o
12- -I 1 0 1 1 0 1 -1x1+1+4.500000 ' ' 'CTF' 'Input:ctfInfo' ctf
12+ -I 1 0 1 0 0 1 -1x1+1+4.500000 ' ' 'CTF' 'Input:ctfInfo' ctf
1313 -f 1 0 1 0 0 -1x1+1+6.000000 0 0 200.000000 0 0 0 'kV' 'AccVol[kV]' kV
1414 -f 1 0 1 0 0 -1x1+1+7.500000 0 0 2.100000 0 0 0 'Cs' 'Cs[mm]' Cs
1515 -f 1 0 1 0 0 -1x1+1+9.000000 0 0 27000.000000 0 0 0 'Defocus' 'Defocus [A]:under(+)' df
--- a/src/Tools/mrcImage/mrcImageCTFObservation/src/usage.c
+++ b/src/Tools/mrcImage/mrcImageCTFObservation/src/usage.c
@@ -9,7 +9,7 @@ usage(char* thisProgram)
99 fprintf(stderr, "Options:\n");
1010 fprintf(stderr, " [-i[nput] In (stdin ).as(inFile::mrcImage ) ] :Essential :Input:2D\n");
1111 fprintf(stderr, " [-o[utput] Out (stdout ).as(outFile::mrcImage ) ] :Essential :Output:2D\n");
12- fprintf(stderr, " [-ctf CTF (stdin ).as(inFile::ASCII ) ] :Essential :Input:ctfInfo\n");
12+ fprintf(stderr, " [-ctf CTF (stdin ).as(inFile::ASCII ) ] :Optional :Input:ctfInfo\n");
1313 fprintf(stderr, " [-kV kV (200 ).as(Real ) ] :Optional :AccVol[kV]\n");
1414 fprintf(stderr, " [-Cs Cs (2.1 ).as(Real ) ] :Optional :Cs[mm]\n");
1515 fprintf(stderr, " [-df Defocus (27000 ).as(Real ) ] :Optional :Defocus [A]:under(+)\n");
Binary files /dev/null and b/src/Tools/mrcImage/mrcImageGaussDisc/src/disc.fft differ
Binary files /dev/null and b/src/Tools/mrcImage/mrcImageGaussDisc/src/disc.mrc differ
Binary files /dev/null and b/src/Tools/mrcImage/mrcImageGaussDisc/src/disc2.mrc differ
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