#define DEBUG
#include "genUtil.h"
#include "ctfDeterminationByBayes.h"
-#include "String.h"
+#include "eosString.h"
/*
Example:
} lctfDeterminationByBayesMode;
*/
+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;
+
ctfDeterminationByBayesInfo info;
ctfInfo ctfinfo;
eosBayesDistributionInfo llinfo;
eosBayes out;
+
ctfforbayes ctf;
- int i;
+ intensityforbayes intensity;
+ defocuslikelihoodforbayes likelihood;
+
+ 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;
-
+ /*For Prior*/
leosBayesInit(&out, info.numDistribution, info.numLikelihood, info.mode);
eosBayesCondition(info.fptIn, &out, &llinfo, 0);
- eosBayesPriorWrite(info.fptOut2, &out,0);
- DistributionChangeCheck(&out, 0);
+ eosBayesPriorWrite(&out,0);
+ DistributionChangeCheck(&out, 0, 0);
+ /*For CTF and intensity*/
ctfforbayesInit(info.fptIn2,&ctf,0);
- spatialfrequencyRead(info.fptIn2,&ctf,0);
+ intensityforbayesInit(&intensity,ctf.n,info.MTFmode,info.Ainmode,0);
+ spatialfrequencyRead(info.fptIn2,&ctf,info.rmax,info.rmin,0);
ctfInfoRead(info.fptIn3,&ctfinfo,"",0);
- DEBUGPRINT4("kV:%f Cs:%f Ain:%f ctfMode:%d\n",ctfinfo.kV,ctfinfo.Cs,ctfinfo.Ain,ctfinfo.mode);
- DEBUGPRINT1("flagIn4:%d\n",info.flagIn4);
+ 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);
- /*defocus estimation*/
- for(i=0;i<info.flagIn4;i++){
-
- IntensityRead(info.In4[i],&ctf,0);
-
- DEBUGPRINT("ctf start\n");
- ctfFunctionforbayes(&ctf,out.likelihood,&ctfinfo,out.numLikelihood,i,0);
+ /*ctfInfoflagcheck*/
+ DEBUGPRINT2("flagAliasing:%ld flagSampling:%ld\n",ctfinfo.flagAliasing,ctfinfo.flagSampling);
+ DEBUGPRINT1("NyquistFrequency:%f\n",ctfinfo.NyquistFrequency);
- DEBUGPRINT("likelihood start\n");
+ ctfinfo.flagMolecEnvTable = 0;
+ DEBUGPRINT1("flagMolecEnvTable:%ld\n",ctfinfo.flagMolecEnvTable);
+ ctfinfo.flagElastic = 0;
+ DEBUGPRINT1("flagElastic:%ld\n",ctfinfo.flagElastic);
- defocuslikelihood(ctf,&out,i,0);
- LikelihoodChangeCheck(&out,i,0);
+ 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);
- DEBUGPRINT("estimate start\n");
- eosBayesEstimation(&out,0);
+ 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);
- DistributionChangeCheck(&out,1);
-
- DEBUGPRINT("change start\n");
- eosBayesPosteriortoPrior(&out,0);
- DEBUGPRINT("loop end\n");
+ DEBUGPRINT1("flagIn4:%ld\n",info.flagIn4);
+
+ Rmax = ctf.rmax;
+ Rmin = ctf.rmin;
+ Rintermediate = info.rintermediate;
+ Rfirstpeak = info.rfirstpeak;
+
+ /*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,0,0);
+ DEBUGPRINT("carse search finish\n");
+ ctfforbayescheckIntensityOfMaxPosterior(ctf,out.posterior,out.numDistribution,&ctfinfo,intensity.MTFmode,intensity.Ainmode,1,1);
+
+ /*MTF serch start\n*/
+ DEBUGPRINT("MTF,B search start\n");
+ ctf.rmax = Rmax;
+ ctf.rmin = Rintermediate;
+ DEBUGPRINT2("set R range:%f~%f\n",ctf.rmin,ctf.rmax);
+ DEBUGPRINT("----maxflagcheck----\n");
+ #ifdef DEBUG
+ for(i=0;i<out.numDistribution;i++){
+ printf("dist%d:%d\n",i,(out.posterior[i].maxposteriorflag));
}
+ #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 \n");
+ out.prior[4].resetflag = 1;
+ eosBayesProbabilityReset(info.fptIn,&out,10,0);
+
+ 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");
- eosBayesPriorWrite(info.fptOut,&out,0);
+ DEBUGPRINT("----maxflagcheck----\n");
+ #ifdef DEBUG
+ for(i=0;i<out.numDistribution;i++){
+ printf("dist%d:%d\n",i,(out.posterior[i].maxposteriorflag));
+ }
+ #endif
+
+ ctfforbayescheckIntensityOfMaxPosterior(ctf,out.posterior,out.numDistribution,&ctfinfo,intensity.MTFmode,intensity.Ainmode,1,1);
+
+
+ /*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,4);
+
+ DEBUGPRINT("set canstantflag of Ain");
+ out.posterior[3].constantflag = 1;
+ out.posterior[5].constantflag = 1;
+
+ DEBUGPRINT("set resetflag of df,k\n");
+ out.prior[0].resetflag = 1;
+ out.prior[1].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++){
+ printf("dist%d:%d\n",i,(out.posterior[i].maxposteriorflag));
+ }
+ #endif
+
+ 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,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 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,k\n");
+ out.prior[0].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));
+ printf("rangechange%d:%d\n",i,(out.posterior[i].rangechangeflag));
+
+ }
+ #endif
+
+ 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);
+
+
+ /*Defocus ref*/
+ DEBUGPRINT("defocus refinement start\n");
+ 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,4);
+
+ DEBUGPRINT("set canstantflag of Ain");
+ out.posterior[3].constantflag = 0;
+ out.posterior[5].constantflag = 0;
+
+ 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);
+
+ DistributionChangeCheck(&out, 6, 0);
+ defocusLikelihoodInit(&likelihood,&out,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);
+
+ eosBayesPosteriorWrite(&out,0);
+ ctfforbayesFree(&ctf,&intensity,&likelihood,out.numLikelihood);
+
+ eosBayesFree(&out);
+
exit(EXIT_SUCCESS);
}
+void DefocusEstimationLoop(ctfDeterminationByBayesInfo info, eosBayes* out, ctfInfo* ctfinfo, ctfforbayes* ctf, intensityforbayes* intensity, defocuslikelihoodforbayes* likelihood, int count,int mode){
+ int i;
+
+ defocusLikelihoodInit(likelihood,out,mode);
+ DEBUGPRINT("In DefocusEstimationLoop\n");
+ for(i=0;i<info.flagIn4;i++){
+
+ intensityRead(info.In4[i],intensity,i,0);
+ DEBUGPRINT("ctf start\n");
+ ctfFunctionforbayes(ctf,intensity,out,ctfinfo,likelihood,count,1);
+
+ DEBUGPRINT("estimate start\n");
+ eosBayesEstimation(out,0);
+ DistributionChangeCheck(out,count,1);
+
+ DEBUGPRINT("change start\n");
+ eosBayesPosteriortoPrior(out,0);
+
+ }
+
+}
+
void
additionalUsage()
{
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