modified ctfforbayes.c

diff --git a/include/ctffuncforbayes.h b/include/ctffuncforbayes.h
index 2c35e4f..a38c825 100644 (file)
--- a/include/ctffuncforbayes.h
+++ b/include/ctffuncforbayes.h
@@ -41,6 +41,8 @@ typedef struct intensityforbayes{
   float* logI;
   float* normII;
   float* logII;
+
+  int MTFmode;
   
   intensityforbayesMode mode;
 
@@ -86,18 +88,18 @@ extern "C" {
 /* prototype begin */
 /*ctfforbayes.c*/
 extern void ctfforbayesInit(FILE* fpt, ctfforbayes* ctf, int mode);
-extern void intensityforbayesInit(intensityforbayes* intensity,int Inum, int mode);
+extern void intensityforbayesInit(intensityforbayes* intensity,int Inum, int MTFmode, int mode);
 extern void intensitySet(ctfforbayes* ctf, intensityforbayes* intensity, int mode);
 extern void spatialfrequencyRead(FILE* fpt, ctfforbayes* ctf, float rmax, float rmin, int mode);
 extern void intensityRead(char* filename, intensityforbayes* intensity, int count, int mode);
 
 extern void ctfFunctionforbayes(ctfforbayes* ctf, intensityforbayes* intensity, eosBayes* d, ctfInfo* info, defocuslikelihoodforbayes* l, int count, int mode);
 extern float MTFFunctionforbayes(float R, float m, int mode);
-extern float ctfforbayesIntensityCalculation(float* parameter, float R, ctfInfo* info, int mode);
-extern void ctfforbayesFree(ctfforbayes* ctf, intensityforbayes* intensity, defocuslikelihoodforbayes* likedihood);
+extern float ctfforbayesIntensityCalculation(float* parameter, float R, ctfInfo* info, int MTFmode, int mode);
+  extern void ctfforbayesFree(ctfforbayes* ctf, intensityforbayes* intensity, defocuslikelihoodforbayes* likedihood, int numLikelihood);
 
 
-/*defocuslikelihood.c*/
+  /*defocuslikelihood.c*/
 extern void defocusLikelihoodInit(defocuslikelihoodforbayes* l, eosBayes d, int mode);
 extern void ctfforbayesXofLikelihoodCalculation(defocuslikelihoodforbayes* l, ctfforbayes* ctf, eosBayes* d, int* L, int count, int mode);
 extern void defocusLikelihood(defocuslikelihoodforbayes* l, ctfforbayes* ctf, eosBayes* d, int count, int mode);
@@ -109,7 +111,7 @@ extern void defocusLikelihoodCalculationLorentz(defocuslikelihoodforbayes* l, eo
 extern void ctfforbayescheckRvsValue(char* filename, float R,float value, int count);
 extern void ctfforbayescheckdifference(char* filename, defocuslikelihoodforbayes* l, eosBayesDistribution* d, int numLikelihood, int count, int mode);
 extern void ctfforbayescheckintensity(ctfforbayes ctf, eosBayesDistribution* d, int numLikelihood, int count, int mode);
-extern void ctfforbayescheckIntensityOfMaxPosterior(ctfforbayes ctf, eosBayesDistribution* d, int numDistribution, ctfInfo* info, int mode);
+  extern void ctfforbayescheckIntensityOfMaxPosterior(ctfforbayes ctf, eosBayesDistribution* d, int numDistribution, ctfInfo* info, int MTFmode, int mode);
 
 /* prototype end */
 

diff --git a/src/Objects/DataManip/ctfInfo/src/ctfforbayes.c b/src/Objects/DataManip/ctfInfo/src/ctfforbayes.c
index a238631..f69e931 100644 (file)
--- a/src/Objects/DataManip/ctfInfo/src/ctfforbayes.c
+++ b/src/Objects/DataManip/ctfInfo/src/ctfforbayes.c
@@ -45,8 +45,9 @@ void ctfforbayesInit(FILE* fpt, ctfforbayes* ctf, int mode){
 }
 
 
-void intensityforbayesInit(intensityforbayes* intensity, int Inum, int mode){
+void intensityforbayesInit(intensityforbayes* intensity, int Inum, int MTFmode, int mode){
 
+  intensity->MTFmode = MTFmode;
 
   intensity->normI = (float*)malloc(sizeof(float)*Inum);
   intensity->logI = (float*)malloc(sizeof(float)*Inum);
@@ -57,6 +58,7 @@ void intensityforbayesInit(intensityforbayes* intensity, int Inum, int mode){
   intensity->mode = 0;
 
   DEBUGPRINT1("Intensityinit finitsh! Inum:%d\n",Inum);
+  DEBUGPRINT1("---MTFmode:%d---\n",MTFmode);
 
 }
 
@@ -178,8 +180,8 @@ void ctfFunctionforbayes(ctfforbayes* ctf, intensityforbayes* intensity, eosBaye
          }
          //DEBUGPRINT3("%d:%d:%d\n",L[0],L[1],L[2]);
          for(j=0;j<ctf->n;j++){
-               intensity->normII[j] = ctfforbayesIntensityCalculation(parameter,ctf->R[j],info,mode);
-               intensity->logII[j]  = log(intensity->normII[j]);
+           intensity->normII[j] = ctfforbayesIntensityCalculation(parameter,ctf->R[j],info,intensity->MTFmode,mode);
+           intensity->logII[j]  = log(intensity->normII[j]);
          }
          
          intensitySet(ctf,intensity,0);
@@ -221,7 +223,7 @@ float MTFFunctionforbayes(float R, float m, int mode){
 }
 
 
-float ctfforbayesIntensityCalculation(float* parameter, float R, ctfInfo* info, int mode){
+float ctfforbayesIntensityCalculation(float* parameter, float R, ctfInfo* info, int MTFmode, int mode){
 
        float S;
        float N;
@@ -231,9 +233,8 @@ float ctfforbayesIntensityCalculation(float* parameter, float R, ctfInfo* info,
        float A;
        float B;
        float m;
-       int mode2;
 
-       mode2 = 1;
+       m = 0;
 
        A = 0;
        B = 0;
@@ -243,7 +244,7 @@ float ctfforbayesIntensityCalculation(float* parameter, float R, ctfInfo* info,
        S = parameter[1];
        N = parameter[2];
 
-       switch(mode2){
+       switch(MTFmode){
          
        case 0:
          
@@ -295,10 +296,19 @@ float ctfforbayesIntensityCalculation(float* parameter, float R, ctfInfo* info,
 }
 
 
-void ctfforbayesFree(ctfforbayes* ctf, intensityforbayes* intensity, defocuslikelihoodforbayes* likedihood){
+void ctfforbayesFree(ctfforbayes* ctf, intensityforbayes* intensity, defocuslikelihoodforbayes* likelihood, int numLikelihood){
+  
+  int i;
   
   DEBUGPRINT("In ctfforbayesfree\n");
 
+  for(i=0;i<numLikelihood;i++){
+    free(likelihood->x[i]);
+  }
+  
+  free(likelihood->width);
+  free(likelihood->x);
+
   free(ctf->R);
   
   free(intensity->normI);

diff --git a/src/Objects/DataManip/ctfInfo/src/ctfforbayescheck.c b/src/Objects/DataManip/ctfInfo/src/ctfforbayescheck.c
index b8f3e6a..3ed81e0 100644 (file)
--- a/src/Objects/DataManip/ctfInfo/src/ctfforbayescheck.c
+++ b/src/Objects/DataManip/ctfInfo/src/ctfforbayescheck.c
@@ -145,7 +145,7 @@ void ctfforbayescheckintensity(ctfforbayes ctf, eosBayesDistribution* d, int num
 }
 
 
-void ctfforbayescheckIntensityOfMaxPosterior(ctfforbayes ctf, eosBayesDistribution* d, int numDistribution, ctfInfo* info, int mode){
+void ctfforbayescheckIntensityOfMaxPosterior(ctfforbayes ctf, eosBayesDistribution* d, int numDistribution, ctfInfo* info, int MTFmode, int mode){
 
   FILE* fpt;
   char s[1024];
@@ -168,7 +168,7 @@ void ctfforbayescheckIntensityOfMaxPosterior(ctfforbayes ctf, eosBayesDistributi
   }
 
   for(i=0;i<ctf.n;i++){
-       intensity[i] = ctfforbayesIntensityCalculation(parameter,ctf.R[i],info,mode);
+    intensity[i] = ctfforbayesIntensityCalculation(parameter,ctf.R[i],info,MTFmode,mode);
   }
 
 

diff --git a/src/Objects/DataManip/ctfInfo/src/ctffuncforbayes.h b/src/Objects/DataManip/ctfInfo/src/ctffuncforbayes.h
index 2c35e4f..a38c825 100644 (file)
--- a/src/Objects/DataManip/ctfInfo/src/ctffuncforbayes.h
+++ b/src/Objects/DataManip/ctfInfo/src/ctffuncforbayes.h
@@ -41,6 +41,8 @@ typedef struct intensityforbayes{
   float* logI;
   float* normII;
   float* logII;
+
+  int MTFmode;
   
   intensityforbayesMode mode;
 
@@ -86,18 +88,18 @@ extern "C" {
 /* prototype begin */
 /*ctfforbayes.c*/
 extern void ctfforbayesInit(FILE* fpt, ctfforbayes* ctf, int mode);
-extern void intensityforbayesInit(intensityforbayes* intensity,int Inum, int mode);
+extern void intensityforbayesInit(intensityforbayes* intensity,int Inum, int MTFmode, int mode);
 extern void intensitySet(ctfforbayes* ctf, intensityforbayes* intensity, int mode);
 extern void spatialfrequencyRead(FILE* fpt, ctfforbayes* ctf, float rmax, float rmin, int mode);
 extern void intensityRead(char* filename, intensityforbayes* intensity, int count, int mode);
 
 extern void ctfFunctionforbayes(ctfforbayes* ctf, intensityforbayes* intensity, eosBayes* d, ctfInfo* info, defocuslikelihoodforbayes* l, int count, int mode);
 extern float MTFFunctionforbayes(float R, float m, int mode);
-extern float ctfforbayesIntensityCalculation(float* parameter, float R, ctfInfo* info, int mode);
-extern void ctfforbayesFree(ctfforbayes* ctf, intensityforbayes* intensity, defocuslikelihoodforbayes* likedihood);
+extern float ctfforbayesIntensityCalculation(float* parameter, float R, ctfInfo* info, int MTFmode, int mode);
+  extern void ctfforbayesFree(ctfforbayes* ctf, intensityforbayes* intensity, defocuslikelihoodforbayes* likedihood, int numLikelihood);
 
 
-/*defocuslikelihood.c*/
+  /*defocuslikelihood.c*/
 extern void defocusLikelihoodInit(defocuslikelihoodforbayes* l, eosBayes d, int mode);
 extern void ctfforbayesXofLikelihoodCalculation(defocuslikelihoodforbayes* l, ctfforbayes* ctf, eosBayes* d, int* L, int count, int mode);
 extern void defocusLikelihood(defocuslikelihoodforbayes* l, ctfforbayes* ctf, eosBayes* d, int count, int mode);
@@ -109,7 +111,7 @@ extern void defocusLikelihoodCalculationLorentz(defocuslikelihoodforbayes* l, eo
 extern void ctfforbayescheckRvsValue(char* filename, float R,float value, int count);
 extern void ctfforbayescheckdifference(char* filename, defocuslikelihoodforbayes* l, eosBayesDistribution* d, int numLikelihood, int count, int mode);
 extern void ctfforbayescheckintensity(ctfforbayes ctf, eosBayesDistribution* d, int numLikelihood, int count, int mode);
-extern void ctfforbayescheckIntensityOfMaxPosterior(ctfforbayes ctf, eosBayesDistribution* d, int numDistribution, ctfInfo* info, int mode);
+  extern void ctfforbayescheckIntensityOfMaxPosterior(ctfforbayes ctf, eosBayesDistribution* d, int numDistribution, ctfInfo* info, int MTFmode, int mode);
 
 /* prototype end */
 

diff --git a/src/Tools/Config/Define.inc b/src/Tools/Config/Define.inc
index 9ee2d89..2b24bf8 100755 (executable)
--- a/src/Tools/Config/Define.inc
+++ b/src/Tools/Config/Define.inc
@@ -1 +1,5 @@
 WORLDNAME=Tools
+WORLDNAME=Tools
+WORLDNAME=Tools
+WORLDNAME=Tools
+WORLDNAME=Tools

diff --git a/src/Tools/ctfInfo/ctfDeterminationByBayes/Config/OptionControlFile b/src/Tools/ctfInfo/ctfDeterminationByBayes/Config/OptionControlFile
index 3fdb1fa..aa3afd0 100755 (executable)
--- a/src/Tools/ctfInfo/ctfDeterminationByBayes/Config/OptionControlFile
+++ b/src/Tools/ctfInfo/ctfDeterminationByBayes/Config/OptionControlFile
@@ -11,3 +11,4 @@
 "-rmin","-rmin","rmin[1/A]","Optional","1","1","rmin","Real","0"
 "-c","-c[onfig]","ConfigurationFile","Optional","1","1","configFile","inFile","NULL"
 "-m","-m[ode]","Mode","Optional","1","1","mode","Integer","0"
+"-MTFmode","-MTFmode","MTFmode","Optional","1","1","MTFmode","Integer","0"

diff --git a/src/Tools/ctfInfo/ctfDeterminationByBayes/inc/ctfDeterminationByBayes.h b/src/Tools/ctfInfo/ctfDeterminationByBayes/inc/ctfDeterminationByBayes.h
index 270a861..e04f3e6 100755 (executable)
--- a/src/Tools/ctfInfo/ctfDeterminationByBayes/inc/ctfDeterminationByBayes.h
+++ b/src/Tools/ctfInfo/ctfDeterminationByBayes/inc/ctfDeterminationByBayes.h
@@ -58,6 +58,9 @@ typedef struct ctfDeterminationByBayesInfo {
     long flagmode;
     long mode;
     
+    long flagMTFmode;
+    long MTFmode;
+    
 } ctfDeterminationByBayesInfo;
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/Tools/ctfInfo/ctfDeterminationByBayes/src/argCheck.c b/src/Tools/ctfInfo/ctfDeterminationByBayes/src/argCheck.c
index b78c0af..73b3360 100755 (executable)
--- a/src/Tools/ctfInfo/ctfDeterminationByBayes/src/argCheck.c
+++ b/src/Tools/ctfInfo/ctfDeterminationByBayes/src/argCheck.c
@@ -152,6 +152,17 @@ argCheck(ctfDeterminationByBayesInfo* info, int argc, char* argv[])
                     }
                     SBREAK;
                 }
+                SCASE("MTFmode") {
+                    if(i+1<argc) {
+                        info->MTFmode = stringGetNthIntegerData(argv[i+1], 1, " ,");
+                        i++;
+                        info->flagMTFmode++;
+                    } else {
+                        usage(argv[0]);
+                        exit(EXIT_FAILURE);
+                    }
+                    SBREAK;
+                }
                 SCASE("h") {
                     usage(argv[0]);
                     exit(EXIT_SUCCESS);

diff --git a/src/Tools/ctfInfo/ctfDeterminationByBayes/src/ctfDeterminationByBayes.c b/src/Tools/ctfInfo/ctfDeterminationByBayes/src/ctfDeterminationByBayes.c
index c1c4f0a..9389bf0 100755 (executable)
--- a/src/Tools/ctfInfo/ctfDeterminationByBayes/src/ctfDeterminationByBayes.c
+++ b/src/Tools/ctfInfo/ctfDeterminationByBayes/src/ctfDeterminationByBayes.c
@@ -70,7 +70,7 @@ main(int argc, char* argv[])
 
   /*For CTF and intensity*/
   ctfforbayesInit(info.fptIn2,&ctf,0);
-  intensityforbayesInit(&intensity,ctf.n,0);
+  intensityforbayesInit(&intensity,ctf.n,info.MTFmode,0);
   spatialfrequencyRead(info.fptIn2,&ctf,info.rmax,info.rmin,0);
   ctfInfoRead(info.fptIn3,&ctfinfo,"",0);
   DEBUGPRINT5("kV:%f  Cs:%f  Ain:%f Cc:%f ctfMode:%ld\n",ctfinfo.kV,ctfinfo.Cs,ctfinfo.Ain,ctfinfo.Cc,ctfinfo.mode);
@@ -98,11 +98,12 @@ main(int argc, char* argv[])
   }
   DEBUGPRINT("loop end\n");
 
-  ctfforbayescheckIntensityOfMaxPosterior(ctf,out.posterior,out.numDistribution,&ctfinfo,2);
+  ctfforbayescheckIntensityOfMaxPosterior(ctf,out.posterior,out.numDistribution,&ctfinfo,intensity.MTFmode,2);
   
   eosBayesPriorWrite(info.fptOut,&out,0);
   
-  ctfforbayesFree(&ctf,&intensity,&likelihood);
+  ctfforbayesFree(&ctf,&intensity,&likelihood,out.numLikelihood);
+
   eosBayesFree(&out);
 
   exit(EXIT_SUCCESS);

diff --git a/src/Tools/ctfInfo/ctfDeterminationByBayes/src/ctfDeterminationByBayes.html b/src/Tools/ctfInfo/ctfDeterminationByBayes/src/ctfDeterminationByBayes.html
old mode 100644 (file)
new mode 100755 (executable)
index 7b161f2..34caa88
--- a/src/Tools/ctfInfo/ctfDeterminationByBayes/src/ctfDeterminationByBayes.html
+++ b/src/Tools/ctfInfo/ctfDeterminationByBayes/src/ctfDeterminationByBayes.html
@@ -20,6 +20,7 @@ Options:
     [-rmin               rmin                (0         ).as(Real                ) ] :Optional  :rmin[1/A]
     [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
     [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-MTFmode            MTFmode             (0         ).as(Integer             ) ] :Optional  :MTFmode
 ----- Additional Usage -----
 </PRE>
 </BODY>

diff --git a/src/Tools/ctfInfo/ctfDeterminationByBayes/src/ctfDeterminationByBayes.pane b/src/Tools/ctfInfo/ctfDeterminationByBayes/src/ctfDeterminationByBayes.pane
index fbe2702..d5acc03 100755 (executable)
--- a/src/Tools/ctfInfo/ctfDeterminationByBayes/src/ctfDeterminationByBayes.pane
+++ b/src/Tools/ctfInfo/ctfDeterminationByBayes/src/ctfDeterminationByBayes.pane
@@ -18,6 +18,7 @@
         -f 1 0 1 0 0 -1x1+1+13.500000 0 0 0.000000 0 0 0 'rmin' 'rmin[1/A]' rmin
         -I 1 0 1 0 0 1 -1x1+1+15.000000 ' ' 'configFile' 'ConfigurationFile' c
         -i 1 0 1 0 0 -1x1+1+16.500000 0 0 0 0 0 'mode' 'Mode' m
+        -i 1 0 1 0 0 -1x1+1+18.000000 0 0 0 0 0 'MTFmode' 'MTFmode' MTFmode
     -E
   -E
 -E

diff --git a/src/Tools/ctfInfo/ctfDeterminationByBayes/src/init.c b/src/Tools/ctfInfo/ctfDeterminationByBayes/src/init.c
index d2055f8..e2f03ae 100755 (executable)
--- a/src/Tools/ctfInfo/ctfDeterminationByBayes/src/init.c
+++ b/src/Tools/ctfInfo/ctfDeterminationByBayes/src/init.c
@@ -24,6 +24,7 @@ init0(ctfDeterminationByBayesInfo* info)
     info->rmin = 0;    info->flagrmin = 0;
     info->fptconfigFile = NULL;    info->flagconfigFile = 0;
     info->mode = 0;    info->flagmode = 0;
+    info->MTFmode = 0;    info->flagMTFmode = 0;
 }
 
 void
@@ -128,6 +129,9 @@ init1(ctfDeterminationByBayesInfo* info)
     if(info->flagmode) {
     }
     
+    if(info->flagMTFmode) {
+    }
+    
 }
 #ifdef KHOROS
 #include <stdio.h>

diff --git a/src/Tools/ctfInfo/ctfDeterminationByBayes/src/usage.c b/src/Tools/ctfInfo/ctfDeterminationByBayes/src/usage.c
index aa28f2c..de336d5 100755 (executable)
--- a/src/Tools/ctfInfo/ctfDeterminationByBayes/src/usage.c
+++ b/src/Tools/ctfInfo/ctfDeterminationByBayes/src/usage.c
@@ -18,6 +18,7 @@ usage(char* thisProgram)
     fprintf(stderr, "    [-rmin               rmin                (0         ).as(Real                ) ] :Optional  :rmin[1/A]\n");
     fprintf(stderr, "    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile\n");
     fprintf(stderr, "    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode\n");
+    fprintf(stderr, "    [-MTFmode            MTFmode             (0         ).as(Integer             ) ] :Optional  :MTFmode\n");
     additionalUsage();
 }