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Stirng.h -> eosString.h
[eos/base.git] / src / Tools / ctfInfo / ctfDeterminationByBayes / src / ctfDeterminationByBayes.c
diff --git a/src/Tools/ctfInfo/ctfDeterminationByBayes/src/ctfDeterminationByBayes.c b/src/Tools/ctfInfo/ctfDeterminationByBayes/src/ctfDeterminationByBayes.c
index ddb69d9..2328ce9 100755 (executable)
--- a/src/Tools/ctfInfo/ctfDeterminationByBayes/src/ctfDeterminationByBayes.c
+++ b/src/Tools/ctfInfo/ctfDeterminationByBayes/src/ctfDeterminationByBayes.c
@@ -22,7 +22,7 @@
 #define DEBUG
 #include "genUtil.h"
 #include "ctfDeterminationByBayes.h"
-#include "String.h"
+#include "eosString.h"
 
 /*
 Example:
@@ -37,14 +37,13 @@ typedef enum lctfDeterminationByBayesMode {
 } lctfDeterminationByBayesMode;
 */
 
-void DefocusEstimationLoop(ctfDeterminationByBayesInfo info, eosBayes* out, ctfInfo* ctfinfo, ctfforbayes* ctf, intensityforbayes* intensity, defocuslikelihoodforbayes* likelihood, int mode);
+void DefocusEstimationLoop(ctfDeterminationByBayesInfo info, eosBayes* out, ctfInfo* ctfinfo, ctfforbayes* ctf, intensityforbayes* intensity, defocuslikelihoodforbayes* likelihood, int count, int mode);
 
 int
 main(int argc, char* argv[]) 
 {
   
   int i;
-  int j;
 
   ctfDeterminationByBayesInfo info;
   ctfInfo ctfinfo;
@@ -59,12 +58,15 @@ main(int argc, char* argv[])
   float Rmax;
   float Rmin;
   float Rintermediate;
+  float Rfirstpeak;
+
 
   init0(&info);
   argCheck(&info, argc, argv);
   init1(&info);
 
   DEBUGPRINT("Program Start\n");
+  DEBUGPRINT("local binary:MTF plus\n");
 
   ctfinfo.mode = 33;
 
@@ -72,7 +74,7 @@ main(int argc, char* argv[])
   leosBayesInit(&out, info.numDistribution, info.numLikelihood, info.mode);
   eosBayesCondition(info.fptIn, &out, &llinfo, 0);
   eosBayesPriorWrite(&out,0);
-  DistributionChangeCheck(&out, 0);
+  DistributionChangeCheck(&out, 0, 0);
 
 
   /*For CTF and intensity*/
@@ -81,30 +83,56 @@ main(int argc, char* argv[])
   spatialfrequencyRead(info.fptIn2,&ctf,info.rmax,info.rmin,0);
   ctfInfoRead(info.fptIn3,&ctfinfo,"",0);
   DEBUGPRINT6("kV:%f  Cs:%f  Ain:%f Cc:%f MTF:%f ctfMode:%ld\n",ctfinfo.kV,ctfinfo.Cs,ctfinfo.Ain,ctfinfo.Cc,ctfinfo.BofMTF,ctfinfo.mode);
+
+
+  /*ctfInfoflagcheck*/
+  DEBUGPRINT2("flagAliasing:%ld flagSampling:%ld\n",ctfinfo.flagAliasing,ctfinfo.flagSampling);
+  DEBUGPRINT1("NyquistFrequency:%f\n",ctfinfo.NyquistFrequency);
+
+  ctfinfo.flagMolecEnvTable = 0;
+  DEBUGPRINT1("flagMolecEnvTable:%ld\n",ctfinfo.flagMolecEnvTable);
+  ctfinfo.flagElastic = 0;
+  DEBUGPRINT1("flagElastic:%ld\n",ctfinfo.flagElastic);
+
+  ctfinfo.flagWithInElasticTable = 0;
+  DEBUGPRINT1("flagWithInElasticEnvTable:%ld\n",ctfinfo.flagWithInElasticTable);
+  ctfinfo.flagInElastic = 0;
+  DEBUGPRINT1("flagInElastic:%ld\n",ctfinfo.flagInElastic);
+  ctfinfo.flagWithInElastic = 0;
+  DEBUGPRINT1("flagWithInElastic:%ld\n",ctfinfo.flagWithInElastic);
+
+  ctfinfo.flagVibration = 0;
+  DEBUGPRINT1("flagVibration:%ld\n",ctfinfo.flagVibration);
+  ctfinfo.VibrationMode = 0;
+  DEBUGPRINT1("VibrationMode:%ld\n",ctfinfo.VibrationMode);
+ 
+  ctfinfo.Magnification = 0;
+  DEBUGPRINT1("Magnification:%f\n",ctfinfo.Magnification);
+  ctfinfo.flagMagnification = 0;
+  DEBUGPRINT1("flagMagnification:%ld\n",ctfinfo.flagMagnification);
+
+
   DEBUGPRINT1("flagIn4:%ld\n",info.flagIn4);
 
   Rmax = ctf.rmax;
   Rmin = ctf.rmin;
   Rintermediate = info.rintermediate;
+  Rfirstpeak = info.rfirstpeak;
 
-  /*global carse search*/
+  /*global carse search B*/
   DEBUGPRINT("carse search start\n");
+  ctf.rmax = Rmax;
+  ctf.rmin = Rintermediate;
   DEBUGPRINT2("set R range:%f~%f\n",ctf.rmin,ctf.rmax);
-  DefocusEstimationLoop(info,&out,&ctfinfo,&ctf,&intensity,&likelihood,0);
+  DefocusEstimationLoop(info,&out,&ctfinfo,&ctf,&intensity,&likelihood,0,0);
   DEBUGPRINT("carse search finish\n");
   ctfforbayescheckIntensityOfMaxPosterior(ctf,out.posterior,out.numDistribution,&ctfinfo,intensity.MTFmode,intensity.Ainmode,1,1);
 
-  /*MTF,B serch start\n*/
+  /*MTF serch start\n*/
   DEBUGPRINT("MTF,B search start\n");
-  ctf.rmax = Rintermediate;
-  ctf.rmin = Rmin;
+  ctf.rmax = Rmax;
+  ctf.rmin = Rintermediate;
   DEBUGPRINT2("set R range:%f~%f\n",ctf.rmin,ctf.rmax);
-
-  DEBUGPRINT("set maxposteriorflag of MTF,B\n");
-  eosBayesMaxposteriorflagSet(&out,0);
-  eosBayesMaxposteriorflagSet(&out,1);
-  eosBayesMaxposteriorflagSet(&out,3);
-
   DEBUGPRINT("----maxflagcheck----\n");
   #ifdef DEBUG
   for(i=0;i<out.numDistribution;i++){
@@ -113,16 +141,24 @@ main(int argc, char* argv[])
   #endif
 
   DEBUGPRINT("set canstantflag of Ain");
+  out.posterior[0].constantflag = 1;
+  out.posterior[1].constantflag = 1;
+  out.posterior[3].constantflag = 1;
   out.posterior[5].constantflag = 1;
 
-  DEBUGPRINT("set resetflag of df,A,k\n");
-  out.prior[2].resetflag = 1;
+  DEBUGPRINT("set resetflag of \n");
   out.prior[4].resetflag = 1;
-  eosBayesProbabilityReset(info.fptIn,&out,5,0);
+  eosBayesProbabilityReset(info.fptIn,&out,10,0);
 
-  DefocusEstimationLoop(info,&out,&ctfinfo,&ctf,&intensity,&likelihood,1);
-  DEBUGPRINT("MTF,B search finish\n");
+  DEBUGPRINT("set rangechangeflag of B\n");
+  eosBayesRangeChangeflagSet(&out,2,0.95,100);
+  eosBayesProbabilityRangeChange(&out,0);
 
+  DistributionChangeCheck(&out, 1, 0);
+
+  DefocusEstimationLoop(info,&out,&ctfinfo,&ctf,&intensity,&likelihood,1,1);
+  DEBUGPRINT("MTF,B search finish\n");
+  
   DEBUGPRINT("----maxflagcheck----\n");
   #ifdef DEBUG
   for(i=0;i<out.numDistribution;i++){
@@ -132,25 +168,31 @@ main(int argc, char* argv[])
 
   ctfforbayescheckIntensityOfMaxPosterior(ctf,out.posterior,out.numDistribution,&ctfinfo,intensity.MTFmode,intensity.Ainmode,1,1);
 
-  /*df,A serch*/
-  DEBUGPRINT("df, A, k search start\n");
+
+  /*df,A B serch*/
+  DEBUGPRINT("df, A, B search start\n");
   ctf.rmax = Rintermediate;
   ctf.rmin = Rmin;
   DEBUGPRINT2("set R range:%f~%f\n",ctf.rmin,ctf.rmax);
 
   DEBUGPRINT("set maxposteriorflag of MTF,B\n");
-  eosBayesMaxposteriorflagSet(&out,2);
   eosBayesMaxposteriorflagSet(&out,4);
 
-  DEBUGPRINT("set canstantflag of k and Ain");
+  DEBUGPRINT("set canstantflag of Ain");
+  out.posterior[3].constantflag = 1;
   out.posterior[5].constantflag = 1;
 
-  DEBUGPRINT("set resetflag of df,A,k\n");
+  DEBUGPRINT("set resetflag of df,k\n");
   out.prior[0].resetflag = 1;
   out.prior[1].resetflag = 1;
-  out.prior[2].resetflag = 1;
   eosBayesProbabilityReset(info.fptIn,&out,1,0);
 
+  DEBUGPRINT("set rangechangeflag of B\n");
+  eosBayesRangeChangeflagSet(&out,2,0.95,20);
+  eosBayesProbabilityRangeChange(&out,0);
+
+
+  DistributionChangeCheck(&out, 4, 0);
   DEBUGPRINT("----maxflagcheck----\n");
   #ifdef DEBUG
   for(i=0;i<out.numDistribution;i++){
@@ -158,162 +200,83 @@ main(int argc, char* argv[])
   }
   #endif
 
-  DefocusEstimationLoop(info,&out,&ctfinfo,&ctf,&intensity,&likelihood,1);
-  DEBUGPRINT("A,df,A search finish\n");
+  DefocusEstimationLoop(info,&out,&ctfinfo,&ctf,&intensity,&likelihood,4,1);
+  DEBUGPRINT("A,B,df search finish\n");
   ctfforbayescheckIntensityOfMaxPosterior(ctf,out.posterior,out.numDistribution,&ctfinfo,intensity.MTFmode,intensity.Ainmode,1,1);
 
-  /*df serch*/
-  DEBUGPRINT("df serch start\n");
+
+  /*df,A, B 2 serch*/
+  DEBUGPRINT("df, A, B search 2 start\n");
   ctf.rmax = Rintermediate;
   ctf.rmin = Rmin;
   DEBUGPRINT2("set R range:%f~%f\n",ctf.rmin,ctf.rmax);
 
-  DEBUGPRINT("set maxposteriorflag of defocus,A,B\n");
-  eosBayesMaxposteriorflagSet(&out,1);
-  eosBayesMaxposteriorflagSet(&out,2);
-  eosBayesMaxposteriorflagSet(&out,3);
+  DEBUGPRINT("set maxposteriorflag of MTF,B\n");
   eosBayesMaxposteriorflagSet(&out,4);
 
   DEBUGPRINT("set canstantflag of Ain");
+  out.posterior[3].constantflag = 1;
   out.posterior[5].constantflag = 1;
 
-  DEBUGPRINT("set resetflag of df\n");
+  DEBUGPRINT("set resetflag of df,k\n");
   out.prior[0].resetflag = 1;
   eosBayesProbabilityReset(info.fptIn,&out,5,0);
 
-  DEBUGPRINT("----maxflagcheck----\n");
-  #ifdef DEBUG
-  for(i=0;i<out.numDistribution;i++){
-       printf("dist%d:%d\n",i,(out.posterior[i].maxposteriorflag));
-  }
-  #endif
 
-  DefocusEstimationLoop(info,&out,&ctfinfo,&ctf,&intensity,&likelihood,1);
-  DEBUGPRINT("df search finish\n");
-  ctfforbayescheckIntensityOfMaxPosterior(ctf,out.posterior,out.numDistribution,&ctfinfo,intensity.MTFmode,intensity.Ainmode,1,1);
-  
-  /*MTF refinement*/
-  DEBUGPRINT("MTF refinement\n");
-  ctf.rmax = Rmax;
-  ctf.rmin = Rmin;
-  DEBUGPRINT2("set R range:%f~%f\n",ctf.rmin,ctf.rmax);
- 
-  DEBUGPRINT("set maxposteriorflag of defocus,A,B,k\n");
-  eosBayesMaxposteriorflagSet(&out,0);
-  eosBayesMaxposteriorflagSet(&out,1);
-  eosBayesMaxposteriorflagSet(&out,2);
-  eosBayesMaxposteriorflagSet(&out,3);
-
-  DEBUGPRINT("set canstantflag of Ain");
-  out.posterior[5].constantflag = 1;
-
-  DEBUGPRINT("set resetflag of MTF\n");
-  out.prior[4].resetflag = 1;
-  eosBayesProbabilityReset(info.fptIn,&out,5,0);
+  DEBUGPRINT("set rangechangeflag of A\n");
+  eosBayesRangeChangeflagSet(&out,1,0.95,20);
+  eosBayesRangeChangeflagSet(&out,2,0.95,20);
+  eosBayesProbabilityRangeChange(&out,0);
 
+  DistributionChangeCheck(&out, 5, 0);
   DEBUGPRINT("----maxflagcheck----\n");
   #ifdef DEBUG
   for(i=0;i<out.numDistribution;i++){
        printf("dist%d:%d\n",i,(out.posterior[i].maxposteriorflag));
-  }
-  #endif
+       printf("rangechange%d:%d\n",i,(out.posterior[i].rangechangeflag));
 
-  DefocusEstimationLoop(info,&out,&ctfinfo,&ctf,&intensity,&likelihood,1);
-  DEBUGPRINT("MTF refinement finish\n");
-  ctfforbayescheckIntensityOfMaxPosterior(ctf,out.posterior,out.numDistribution,&ctfinfo,intensity.MTFmode,intensity.Ainmode,1,1);
-
-  /*B refinement*/
-  DEBUGPRINT("B,refinement\n");
-  ctf.rmax = Rintermediate;
-  ctf.rmin = Rmin;
-  DEBUGPRINT2("set R range:%f~%f\n",ctf.rmin,ctf.rmax);
- 
-  DEBUGPRINT("set maxposteriorflag of defocus,A,k,MTF\n");
-  eosBayesMaxposteriorflagSet(&out,0);
-  eosBayesMaxposteriorflagSet(&out,1);
-  eosBayesMaxposteriorflagSet(&out,3);
-  eosBayesMaxposteriorflagSet(&out,4);
-
-  DEBUGPRINT("set canstantflag of Ain");
-  out.posterior[5].constantflag = 1;
-
-  DEBUGPRINT("set resetflag of B\n");
-  out.prior[2].resetflag = 1;
-  eosBayesProbabilityReset(info.fptIn,&out,5,0);
-
-  DEBUGPRINT("----maxflagcheck----\n");
-  #ifdef DEBUG
-  for(i=0;i<out.numDistribution;i++){
-       printf("dist%d:%d\n",i,(out.posterior[i].maxposteriorflag));
   }
   #endif
 
-  DefocusEstimationLoop(info,&out,&ctfinfo,&ctf,&intensity,&likelihood,1);
-  DEBUGPRINT("B refinement finish\n");
+  DefocusEstimationLoop(info,&out,&ctfinfo,&ctf,&intensity,&likelihood,5,1);
+  DEBUGPRINT("A,df,k search finish\n");
   ctfforbayescheckIntensityOfMaxPosterior(ctf,out.posterior,out.numDistribution,&ctfinfo,intensity.MTFmode,intensity.Ainmode,1,1);
 
 
-  /*df serch 2*/
-  DEBUGPRINT("df serch 2 start\n");
-  ctf.rmax = Rintermediate;
-  ctf.rmin = Rmin;
-  DEBUGPRINT2("set R range:%f~%f\n",ctf.rmin,ctf.rmax);
-
-  DEBUGPRINT("set maxposteriorflag of defocus,A,B\n");
-  eosBayesMaxposteriorflagSet(&out,1);
-  eosBayesMaxposteriorflagSet(&out,2);
-  eosBayesMaxposteriorflagSet(&out,3);
-  eosBayesMaxposteriorflagSet(&out,4);
-
-  DEBUGPRINT("set canstantflag of Ain");
-  out.posterior[5].constantflag = 1;
-
-  DEBUGPRINT("set resetflag of df\n");
-  out.prior[0].resetflag = 1;
-  eosBayesProbabilityReset(info.fptIn,&out,5,0);
-
-  DEBUGPRINT("----maxflagcheck----\n");
-  #ifdef DEBUG
-  for(i=0;i<out.numDistribution;i++){
-       printf("dist%d:%d\n",i,(out.posterior[i].maxposteriorflag));
-  }
-  #endif
-
-  DefocusEstimationLoop(info,&out,&ctfinfo,&ctf,&intensity,&likelihood,1);
-  DEBUGPRINT("df search2 finish\n");
-  ctfforbayescheckIntensityOfMaxPosterior(ctf,out.posterior,out.numDistribution,&ctfinfo,intensity.MTFmode,intensity.Ainmode,1,1);
-
-  /*defocus refinement*/
-  
+  /*Defocus ref*/
   DEBUGPRINT("defocus refinement start\n");
-  ctf.rmax = Rintermediate;
-  ctf.rmin = Rmin;
+  ctf.rmax = Rmax;
+  ctf.rmin = Rfirstpeak;
   DEBUGPRINT2("set R range:%f~%f\n",ctf.rmin,ctf.rmax);
 
   DEBUGPRINT("set maxposteriorflag of defocus,A,B,MTF\n");
   out.posterior[0].maxposteriorflag = 0;
   out.posterior[1].maxposteriorflag = 0;
   out.posterior[3].maxposteriorflag = 0;
+  out.posterior[4].maxposteriorflag = 0;
   out.posterior[5].maxposteriorflag = 0;
-  eosBayesMaxposteriorflagSet(&out,2);
-  eosBayesMaxposteriorflagSet(&out,4);
+  // eosBayesMaxposteriorflagSet(&out,4);
 
-  DEBUGPRINT("set canstantflag of k and Ain");
+  DEBUGPRINT("set canstantflag of Ain");
+  out.posterior[3].constantflag = 0;
   out.posterior[5].constantflag = 0;
 
-  DEBUGPRINT("set refmode\n");
-  out.posterior[0].refmode = 1;
-  out.posterior[1].refmode = 1;
-  out.posterior[2].refmode = 0;
-  out.posterior[3].refmode = 1;
-  out.posterior[4].refmode = 0;
-  out.posterior[5].refmode = 2;
+  DEBUGPRINT("set resetflag of df,k\n");
+  out.prior[3].resetflag = 1;
+  out.prior[5].resetflag = 1;
+  eosBayesProbabilityReset(info.fptIn,&out,1,0);
+
+  DEBUGPRINT("set rangechangeflag of A\n");
+  eosBayesRangeChangeflagSet(&out,0,0.70,10);
+  eosBayesRangeChangeflagSet(&out,1,0.95,20);
+  eosBayesRangeChangeflagSet(&out,2,0.95,20);
+  eosBayesRangeChangeflagSet(&out,4,0.40,5);
+  eosBayesProbabilityRangeChange(&out,0);
 
-  eosBayesRefinementCondition(info.fptIn,&out,&llinfo,5,0);  
-  DistributionChangeCheck(&out, 0);
+  DistributionChangeCheck(&out, 6, 0);
   defocusLikelihoodInit(&likelihood,&out,1);
 
-  DefocusEstimationLoop(info,&out,&ctfinfo,&ctf,&intensity,&likelihood,1);
+  DefocusEstimationLoop(info,&out,&ctfinfo,&ctf,&intensity,&likelihood,6,1);
   DEBUGPRINT("defocus refinement finish\n");
   ctfforbayescheckIntensityOfMaxPosterior(ctf,out.posterior,out.numDistribution,&ctfinfo,intensity.MTFmode,intensity.Ainmode,1,1);
 
@@ -326,7 +289,7 @@ main(int argc, char* argv[])
   exit(EXIT_SUCCESS);
 }
 
-void DefocusEstimationLoop(ctfDeterminationByBayesInfo info, eosBayes* out, ctfInfo* ctfinfo, ctfforbayes* ctf, intensityforbayes* intensity, defocuslikelihoodforbayes* likelihood, int mode){
+void DefocusEstimationLoop(ctfDeterminationByBayesInfo info, eosBayes* out, ctfInfo* ctfinfo, ctfforbayes* ctf, intensityforbayes* intensity, defocuslikelihoodforbayes* likelihood, int count,int mode){
   int i;
 
   defocusLikelihoodInit(likelihood,out,mode);
@@ -335,11 +298,11 @@ void DefocusEstimationLoop(ctfDeterminationByBayesInfo info, eosBayes* out, ctfI
 
        intensityRead(info.In4[i],intensity,i,0);
        DEBUGPRINT("ctf start\n");
-       ctfFunctionforbayes(ctf,intensity,out,ctfinfo,likelihood,0,1);
+       ctfFunctionforbayes(ctf,intensity,out,ctfinfo,likelihood,count,1);
 
        DEBUGPRINT("estimate start\n");
        eosBayesEstimation(out,0);
-       DistributionChangeCheck(out,1);
+       DistributionChangeCheck(out,count,1);
   
        DEBUGPRINT("change start\n");
        eosBayesPosteriortoPrior(out,0);
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