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Commit 0392963f authored by Pilar Cossio's avatar Pilar Cossio
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Included Input Checks

parent 92e7d74a
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Showing with 217 additions and 127 deletions
bioem.cpp
View file @ 0392963f
...@@ -47,11 +47,11 @@ bioem::~bioem() ...@@ -47,11 +47,11 @@ bioem::~bioem()
int bioem::configure(int ac, char* av[]) int bioem::configure(int ac, char* av[])
{ {
/**************************************************************************************/ //**************************************************************************************
/**** Configuration Routine using boost for extracting parameters, models and maps ****/ //**** Configuration Routine using boost for extracting parameters, models and maps ****
/**************************************************************************************/ //**************************************************************************************
/****** And Precalculating necessary grids, map crosscorrelations and kernels ********/ //****** And Precalculating necessary grids, map crosscorrelations and kernels ********
/*************************************************************************************/ //*************************************************************************************
/*** Inizialzing default variables ***/ /*** Inizialzing default variables ***/
std::string infile,modelfile,mapfile; std::string infile,modelfile,mapfile;
...@@ -61,19 +61,20 @@ int bioem::configure(int ac, char* av[]) ...@@ -61,19 +61,20 @@ int bioem::configure(int ac, char* av[])
RefMap.loadMap = false; RefMap.loadMap = false;
RefMap.readMRC = false; RefMap.readMRC = false;
RefMap.readMultMRC = false; RefMap.readMultMRC = false;
/*************************************************************************************/ //*************************************************************************************
cout << " ++++++++++++ FROM COMMAND LINE +++++++++++\n\n"; cout << "+++++++++++++ FROM COMMAND LINE +++++++++++\n\n";
/*************************************************************************************/ //*************************************************************************************
/********************* Command line reading input with BOOST ************************/ //********************* Command line reading input with BOOST ************************
try { try {
po::options_description desc("Command line inputs"); po::options_description desc("Command line inputs");
desc.add_options() desc.add_options()
("Inputfile", po::value<std::string>(), "Name of input parameter file") ("Inputfile", po::value<std::string>(), "(Mandatory) Name of input parameter file")
("Modelfile", po::value< std::string>() , "Name of model file") ("Modelfile", po::value< std::string>() , "(Mandatory) Name of model file")
("Particlesfile", po::value< std::string>(), "Name of paricles file") ("Particlesfile", po::value< std::string>(), "(Mandatory) Name of paricles file")
("ReadPDB", "(Optional) If reading model file in PDB format") ("ReadPDB", "(Optional) If reading model file in PDB format")
("ReadMRC", "(Optional) If reading particle file in MRC format") ("ReadMRC", "(Optional) If reading particle file in MRC format")
("ReadMultipleMRC", "(Optional) If reading Multiple MRCs") ("ReadMultipleMRC", "(Optional) If reading Multiple MRCs")
...@@ -98,8 +99,9 @@ int bioem::configure(int ac, char* av[]) ...@@ -98,8 +99,9 @@ int bioem::configure(int ac, char* av[])
po::notify(vm); po::notify(vm);
if((ac < 6)) { if((ac < 6)) {
std::cout << desc << std::endl; std::cout << desc << std::endl;
return 0; exit(1);
return 0;
} }
if (vm.count("help")) { if (vm.count("help")) {
cout << "Usage: options_description [options]\n"; cout << "Usage: options_description [options]\n";
...@@ -111,7 +113,7 @@ int bioem::configure(int ac, char* av[]) ...@@ -111,7 +113,7 @@ int bioem::configure(int ac, char* av[])
{ {
cout << "Input file is: "; cout << "Input file is: ";
cout << vm["Inputfile"].as< std::string >()<< "\n"; cout << vm["Inputfile"].as< std::string >()<< "\n";
infile=vm["Inputfile"].as< std::string >(); infile=vm["Inputfile"].as< std::string >();
} }
if (vm.count("Modelfile")) if (vm.count("Modelfile"))
{ {
...@@ -162,23 +164,23 @@ int bioem::configure(int ac, char* av[]) ...@@ -162,23 +164,23 @@ int bioem::configure(int ac, char* av[])
return 1; return 1;
} }
/********************* Reading Parameter Input ***************************/ //********************* Reading Parameter Input ***************************
// copying inputfile to param class // copying inputfile to param class
param.fileinput = infile.c_str(); param.fileinput = infile.c_str();
param.readParameters(); param.readParameters();
/********************* Reading Model Input ******************************/ //********************* Reading Model Input ******************************
// copying modelfile to model class // copying modelfile to model class
Model.filemodel = modelfile.c_str(); Model.filemodel = modelfile.c_str();
Model.readModel(); Model.readModel();
/********************* Reading Particle Maps Input **********************/ //********************* Reading Particle Maps Input **********************
/********* HERE: PROBLEM if maps dont fit on the memory!! ***************/ //********* HERE: PROBLEM if maps dont fit on the memory!! ***************
// copying mapfile to ref map class // copying mapfile to ref map class
RefMap.filemap = mapfile.c_str(); RefMap.filemap = mapfile.c_str();
RefMap.readRefMaps(param); RefMap.readRefMaps(param);
/****************** Precalculating Necessary Stuff *********************/ //****************** Precalculating Necessary Stuff *********************
precalculate(); precalculate();
if (getenv("BIOEM_DEBUG_BREAK")) if (getenv("BIOEM_DEBUG_BREAK"))
...@@ -194,9 +196,9 @@ int bioem::configure(int ac, char* av[]) ...@@ -194,9 +196,9 @@ int bioem::configure(int ac, char* av[])
int bioem::precalculate() int bioem::precalculate()
{ {
/**************************************************************************************/ //**************************************************************************************
/* Precalculating Routine of Orientation grids, Map crosscorrelations and CTF Kernels */ //* Precalculating Routine of Orientation grids, Map crosscorrelations and CTF Kernels *
/**************************************************************************************/ //**************************************************************************************
// Generating Grids of orientations // Generating Grids of orientations
param.CalculateGridsParam(); param.CalculateGridsParam();
...@@ -224,12 +226,12 @@ int bioem::precalculate() ...@@ -224,12 +226,12 @@ int bioem::precalculate()
int bioem::run() int bioem::run()
{ {
/**************************************************************************************/ //**************************************************************************************
/**** Main BioEM routine, projects, convolutes and compares with Map using OpenMP ****/ //**** Main BioEM routine, projects, convolutes and compares with Map using OpenMP ****
/**************************************************************************************/ //**************************************************************************************
/**** If we want to control the number of threads -> omp_set_num_threads(XX); ******/ //**** If we want to control the number of threads -> omp_set_num_threads(XX); ******
/****************** Declarying class of Probability Pointer *************************/ //****************** Declarying class of Probability Pointer *************************
pProb = new bioem_Probability[RefMap.ntotRefMap]; pProb = new bioem_Probability[RefMap.ntotRefMap];
printf("\tInitializing\n"); printf("\tInitializing\n");
...@@ -245,12 +247,12 @@ int bioem::run() ...@@ -245,12 +247,12 @@ int bioem::run()
pProb[iRefMap].ConstAngle[iOrient]=-99999999; pProb[iRefMap].ConstAngle[iOrient]=-99999999;
} }
} }
/**************************************************************************************/ //**************************************************************************************
deviceStartRun(); deviceStartRun();
/******************************** MAIN CYCLE ******************************************/ //******************************** MAIN CYCLE ******************************************
/*** Declaring Private variables for each thread *****/ //*** Declaring Private variables for each thread *****
mycomplex_t* proj_mapFFT; mycomplex_t* proj_mapFFT;
bioem_map conv_map; bioem_map conv_map;
mycomplex_t* conv_mapFFT; mycomplex_t* conv_mapFFT;
...@@ -266,25 +268,25 @@ int bioem::run() ...@@ -266,25 +268,25 @@ int bioem::run()
printf("\tInner Loop Count (%d %d %d) %lld\n", param.param_device.maxDisplaceCenter, param.param_device.GridSpaceCenter, param.param_device.NumberPixels, (long long int) (param.param_device.NumberPixels * param.param_device.NumberPixels * (2 * param.param_device.maxDisplaceCenter / param.param_device.GridSpaceCenter + 1) * (2 * param.param_device.maxDisplaceCenter / param.param_device.GridSpaceCenter + 1))); printf("\tInner Loop Count (%d %d %d) %lld\n", param.param_device.maxDisplaceCenter, param.param_device.GridSpaceCenter, param.param_device.NumberPixels, (long long int) (param.param_device.NumberPixels * param.param_device.NumberPixels * (2 * param.param_device.maxDisplaceCenter / param.param_device.GridSpaceCenter + 1) * (2 * param.param_device.maxDisplaceCenter / param.param_device.GridSpaceCenter + 1)));
for (int iProjectionOut = 0; iProjectionOut < param.nTotGridAngles; iProjectionOut++) for (int iProjectionOut = 0; iProjectionOut < param.nTotGridAngles; iProjectionOut++)
{ {
/***************************************************************************************/ //***************************************************************************************
/***** Creating Projection for given orientation and transforming to Fourier space *****/ //***** Creating Projection for given orientation and transforming to Fourier space *****
timer.ResetStart(); timer.ResetStart();
createProjection(iProjectionOut, proj_mapFFT); createProjection(iProjectionOut, proj_mapFFT);
printf("Time Projection %d: %f\n", iProjectionOut, timer.GetCurrentElapsedTime()); printf("Time Projection %d: %f\n", iProjectionOut, timer.GetCurrentElapsedTime());
/***************************************************************************************/ //***************************************************************************************
/***** **** Internal Loop over convolutions **** *****/ //***** **** Internal Loop over convolutions **** *****
for (int iConv = 0; iConv < param.nTotCTFs; iConv++) for (int iConv = 0; iConv < param.nTotCTFs; iConv++)
{ {
printf("\t\tConvolution %d %d\n", iProjectionOut, iConv); printf("\t\tConvolution %d %d\n", iProjectionOut, iConv);
/*** Calculating convolutions of projection map and crosscorrelations ***/ //*** Calculating convolutions of projection map and crosscorrelations ***
timer.ResetStart(); timer.ResetStart();
createConvolutedProjectionMap(iProjectionOut, iConv, proj_mapFFT, conv_map, conv_mapFFT, sumCONV, sumsquareCONV); createConvolutedProjectionMap(iProjectionOut, iConv, proj_mapFFT, conv_map, conv_mapFFT, sumCONV, sumsquareCONV);
printf("Time Convolution %d %d: %f\n", iProjectionOut, iConv, timer.GetCurrentElapsedTime()); printf("Time Convolution %d %d: %f\n", iProjectionOut, iConv, timer.GetCurrentElapsedTime());
/***************************************************************************************/ //***************************************************************************************
/*** Comparing each calculated convoluted map with all experimental maps ***/ //*** Comparing each calculated convoluted map with all experimental maps ***
timer.ResetStart(); timer.ResetStart();
compareRefMaps(iProjectionOut, iConv, conv_map, conv_mapFFT, sumCONV, sumsquareCONV); compareRefMaps(iProjectionOut, iConv, conv_map, conv_mapFFT, sumCONV, sumsquareCONV);
...@@ -305,9 +307,9 @@ int bioem::run() ...@@ -305,9 +307,9 @@ int bioem::run()
deviceFinishRun(); deviceFinishRun();
/************* Writing Out Probabilities ***************/ //************* Writing Out Probabilities ***************
/*** Angular Probability ***/ //*** Angular Probability ***
// if(param.writeAngles){ // if(param.writeAngles){
ofstream angProbfile; ofstream angProbfile;
...@@ -319,12 +321,12 @@ int bioem::run() ...@@ -319,12 +321,12 @@ int bioem::run()
for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap; iRefMap ++) for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap; iRefMap ++)
{ {
/**** Total Probability ***/ //**** Total Probability ***
outputProbFile << "RefMap " << iRefMap << " Probability " << log(pProb[iRefMap].Total)+pProb[iRefMap].Constoadd+0.5*log(M_PI)+(1-param.param_device.Ntotpi*0.5)*(log(2*M_PI)+1)+log(param.param_device.volu) << " Constant " << pProb[iRefMap].Constoadd << "\n"; outputProbFile << "RefMap " << iRefMap << " Probability " << log(pProb[iRefMap].Total)+pProb[iRefMap].Constoadd+0.5*log(M_PI)+(1-param.param_device.Ntotpi*0.5)*(log(2*M_PI)+1)+log(param.param_device.volu) << " Constant " << pProb[iRefMap].Constoadd << "\n";
outputProbFile << "RefMap " << iRefMap << " Maximizing Param: "; outputProbFile << "RefMap " << iRefMap << " Maximizing Param: ";
/*** Param that maximize probability****/ //*** Param that maximize probability****
outputProbFile << (pProb[iRefMap].max_prob + 0.5 * log(M_PI) + (1 - param.param_device.Ntotpi * 0.5) * (log(2 * M_PI) + 1) + log(param.param_device.volu)) << " "; outputProbFile << (pProb[iRefMap].max_prob + 0.5 * log(M_PI) + (1 - param.param_device.Ntotpi * 0.5) * (log(2 * M_PI) + 1) + log(param.param_device.volu)) << " ";
outputProbFile << param.angles[pProb[iRefMap].max_prob_orient].pos[0] << " "; outputProbFile << param.angles[pProb[iRefMap].max_prob_orient].pos[0] << " ";
outputProbFile << param.angles[pProb[iRefMap].max_prob_orient].pos[1] << " "; outputProbFile << param.angles[pProb[iRefMap].max_prob_orient].pos[1] << " ";
...@@ -336,7 +338,7 @@ int bioem::run() ...@@ -336,7 +338,7 @@ int bioem::run()
outputProbFile << pProb[iRefMap].max_prob_cent_y; outputProbFile << pProb[iRefMap].max_prob_cent_y;
outputProbFile << "\n"; outputProbFile << "\n";
/*** For individual files***/ //angProbfile.open ("ANG_PROB_"iRefMap); //*** For individual files*** //angProbfile.open ("ANG_PROB_"iRefMap);
if(param.writeAngles) if(param.writeAngles)
{ {
...@@ -375,7 +377,11 @@ int bioem::run() ...@@ -375,7 +377,11 @@ int bioem::run()
int bioem::compareRefMaps(int iProjectionOut, int iConv, const bioem_map& conv_map, mycomplex_t* localmultFFT, myfloat_t sumC, myfloat_t sumsquareC, const int startMap) int bioem::compareRefMaps(int iProjectionOut, int iConv, const bioem_map& conv_map, mycomplex_t* localmultFFT, myfloat_t sumC, myfloat_t sumsquareC, const int startMap)
{ {
if (FFTAlgo)
//***************************************************************************************
//***** BioEM routine for comparing reference maps to convoluted maps *****
if (FFTAlgo) //IF using the fft algorithm
{ {
#pragma omp parallel #pragma omp parallel
{ {
...@@ -411,6 +417,10 @@ int bioem::compareRefMaps(int iProjectionOut, int iConv, const bioem_map& conv_m ...@@ -411,6 +417,10 @@ int bioem::compareRefMaps(int iProjectionOut, int iConv, const bioem_map& conv_m
inline void bioem::calculateCCFFT(int iRefMap, int iOrient, int iConv, myfloat_t sumC,myfloat_t sumsquareC, mycomplex_t* localConvFFT,mycomplex_t* localCCT,myfloat_t* lCC) inline void bioem::calculateCCFFT(int iRefMap, int iOrient, int iConv, myfloat_t sumC,myfloat_t sumsquareC, mycomplex_t* localConvFFT,mycomplex_t* localCCT,myfloat_t* lCC)
{ {
//***************************************************************************************
//***** Calculating cross correlation in FFTALGOrithm *****
const mycomplex_t* RefMapFFT = &RefMap.RefMapsFFT[iRefMap * param.RefMapSize]; const mycomplex_t* RefMapFFT = &RefMap.RefMapsFFT[iRefMap * param.RefMapSize];
for(int i = 0;i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D;i++) for(int i = 0;i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D;i++)
{ {
...@@ -425,10 +435,10 @@ inline void bioem::calculateCCFFT(int iRefMap, int iOrient, int iConv, myfloat_t ...@@ -425,10 +435,10 @@ inline void bioem::calculateCCFFT(int iRefMap, int iOrient, int iConv, myfloat_t
int bioem::createProjection(int iMap,mycomplex_t* mapFFT) int bioem::createProjection(int iMap,mycomplex_t* mapFFT)
{ {
/**************************************************************************************/ //**************************************************************************************
/**** BioEM Create Projection routine in Euler angle predefined grid**************** //**** BioEM Create Projection routine in Euler angle predefined grid****************
********************* and turns projection into Fourier space **********************/ //********************* and turns projection into Fourier space **********************
/**************************************************************************************/ //**************************************************************************************
myfloat3_t RotatedPointsModel[Model.nPointsModel]; myfloat3_t RotatedPointsModel[Model.nPointsModel];
myfloat_t rotmat[3][3]; myfloat_t rotmat[3][3];
...@@ -442,9 +452,9 @@ int bioem::createProjection(int iMap,mycomplex_t* mapFFT) ...@@ -442,9 +452,9 @@ int bioem::createProjection(int iMap,mycomplex_t* mapFFT)
beta=param.angles[iMap].pos[1]; beta=param.angles[iMap].pos[1];
gam=param.angles[iMap].pos[2]; gam=param.angles[iMap].pos[2];
/**** To see how things are going: cout << "Id " << omp_get_thread_num() << " Angs: " << alpha << " " << beta << " " << gam << "\n"; ***/ //**** To see how things are going: cout << "Id " << omp_get_thread_num() << " Angs: " << alpha << " " << beta << " " << gam << "\n"; ***
/********** Creat Rotation with pre-defiend grid of orientations**********/ //********** Creat Rotation with pre-defiend grid of orientations**********
rotmat[0][0]=cos(gam)*cos(alpha)-cos(beta)*sin(alpha)*sin(gam); rotmat[0][0]=cos(gam)*cos(alpha)-cos(beta)*sin(alpha)*sin(gam);
rotmat[0][1]=cos(gam)*sin(alpha)+cos(beta)*cos(alpha)*sin(gam); rotmat[0][1]=cos(gam)*sin(alpha)+cos(beta)*cos(alpha)*sin(gam);
...@@ -475,7 +485,7 @@ int bioem::createProjection(int iMap,mycomplex_t* mapFFT) ...@@ -475,7 +485,7 @@ int bioem::createProjection(int iMap,mycomplex_t* mapFFT)
int i, j; int i, j;
/************ Projection over the Z axis********************/ //************ Projection over the Z axis********************
for(int n=0; n< Model.nPointsModel; n++) for(int n=0; n< Model.nPointsModel; n++)
{ {
//Getting pixel that represents coordinates & shifting the start at to Numpix/2,Numpix/2 ) //Getting pixel that represents coordinates & shifting the start at to Numpix/2,Numpix/2 )
...@@ -485,7 +495,7 @@ int bioem::createProjection(int iMap,mycomplex_t* mapFFT) ...@@ -485,7 +495,7 @@ int bioem::createProjection(int iMap,mycomplex_t* mapFFT)
localproj[i*param.param_device.NumberPixels+j]+=Model.densityPointsModel[n]/Model.NormDen; localproj[i*param.param_device.NumberPixels+j]+=Model.densityPointsModel[n]/Model.NormDen;
} }
/**** Output Just to check****/ //**** Output Just to check****
if(iMap==10) if(iMap==10)
{ {
ofstream myexamplemap; ofstream myexamplemap;
...@@ -503,8 +513,8 @@ int bioem::createProjection(int iMap,mycomplex_t* mapFFT) ...@@ -503,8 +513,8 @@ int bioem::createProjection(int iMap,mycomplex_t* mapFFT)
myexampleRot.close(); myexampleRot.close();
} }
/***** Converting projection to Fourier Space for Convolution later with kernel****/ //***** Converting projection to Fourier Space for Convolution later with kernel****
/********** Omp Critical is necessary with FFTW*******/ //********** Omp Critical is necessary with FFTW*******
myfftw_execute_dft_r2c(param.fft_plan_r2c_forward,localproj,mapFFT); myfftw_execute_dft_r2c(param.fft_plan_r2c_forward,localproj,mapFFT);
return(0); return(0);
...@@ -512,18 +522,18 @@ int bioem::createProjection(int iMap,mycomplex_t* mapFFT) ...@@ -512,18 +522,18 @@ int bioem::createProjection(int iMap,mycomplex_t* mapFFT)
int bioem::createConvolutedProjectionMap(int iMap,int iConv,mycomplex_t* lproj,bioem_map& Mapconv, mycomplex_t* localmultFFT, myfloat_t& sumC, myfloat_t& sumsquareC) int bioem::createConvolutedProjectionMap(int iMap,int iConv,mycomplex_t* lproj,bioem_map& Mapconv, mycomplex_t* localmultFFT, myfloat_t& sumC, myfloat_t& sumsquareC)
{ {
/**************************************************************************************/ //**************************************************************************************
/**** BioEM Create Convoluted Projection Map routine, multiplies in Fourier ********** //**** BioEM Create Convoluted Projection Map routine, multiplies in Fourier **********
**************** calculated Projection with convoluted precalculated Kernel********** //**************** calculated Projection with convoluted precalculated Kernel**********
*************** and Backtransforming it to real Space ******************************/ //*************** and Backtransforming it to real Space ******************************
/**************************************************************************************/ //**************************************************************************************
myfloat_t* localconvFFT; myfloat_t* localconvFFT;
localconvFFT= (myfloat_t *) myfftw_malloc(sizeof(myfloat_t)*param.param_device.NumberPixels*param.param_device.NumberPixels); localconvFFT= (myfloat_t *) myfftw_malloc(sizeof(myfloat_t)*param.param_device.NumberPixels*param.param_device.NumberPixels);
mycomplex_t* tmp; mycomplex_t* tmp;
tmp = (mycomplex_t*) myfftw_malloc(sizeof(mycomplex_t) * param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D); tmp = (mycomplex_t*) myfftw_malloc(sizeof(mycomplex_t) * param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D);
/**** Multiplying FFTmap with corresponding kernel ****/ //**** Multiplying FFTmap with corresponding kernel ****
const mycomplex_t* refCTF = &param.refCTF[iConv * param.RefMapSize]; const mycomplex_t* refCTF = &param.refCTF[iConv * param.RefMapSize];
for(int i=0;i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D;i++) for(int i=0;i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D;i++)
...@@ -536,10 +546,10 @@ int bioem::createConvolutedProjectionMap(int iMap,int iConv,mycomplex_t* lproj,b ...@@ -536,10 +546,10 @@ int bioem::createConvolutedProjectionMap(int iMap,int iConv,mycomplex_t* lproj,b
//FFTW_C2R will destroy the input array, so we have to work on a copy here //FFTW_C2R will destroy the input array, so we have to work on a copy here
memcpy(tmp, localmultFFT, sizeof(mycomplex_t) * param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D); memcpy(tmp, localmultFFT, sizeof(mycomplex_t) * param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D);
/**** Bringing convoluted Map to real Space ****/ //**** Bringing convoluted Map to real Space ****
myfftw_execute_dft_c2r(param.fft_plan_c2r_backward,tmp,localconvFFT); myfftw_execute_dft_c2r(param.fft_plan_c2r_backward,tmp,localconvFFT);
/****Asigning convolution fftw_complex to bioem_map ****/ //****Asigning convolution fftw_complex to bioem_map ****
for(int i=0; i < param.param_device.NumberPixels ; i++ ) for(int i=0; i < param.param_device.NumberPixels ; i++ )
{ {
for(int j=0; j < param.param_device.NumberPixels ; j++ ) for(int j=0; j < param.param_device.NumberPixels ; j++ )
...@@ -548,7 +558,7 @@ int bioem::createConvolutedProjectionMap(int iMap,int iConv,mycomplex_t* lproj,b ...@@ -548,7 +558,7 @@ int bioem::createConvolutedProjectionMap(int iMap,int iConv,mycomplex_t* lproj,b
} }
} }
/*** Calculating Cross-correlations of cal-convoluted map with its self *****/ //*** Calculating Cross-correlations of cal-convoluted map with its self *****
sumC=0; sumC=0;
sumsquareC=0; sumsquareC=0;
for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberPixels; i++) for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberPixels; i++)
...@@ -556,14 +566,14 @@ int bioem::createConvolutedProjectionMap(int iMap,int iConv,mycomplex_t* lproj,b ...@@ -556,14 +566,14 @@ int bioem::createConvolutedProjectionMap(int iMap,int iConv,mycomplex_t* lproj,b
sumC += localconvFFT[i]; sumC += localconvFFT[i];
sumsquareC += localconvFFT[i] * localconvFFT[i]; sumsquareC += localconvFFT[i] * localconvFFT[i];
} }
/*** The DTF gives an unnormalized value so have to divded by the total number of pixels in Fourier ***/ //*** The DTF gives an unnormalized value so have to divded by the total number of pixels in Fourier ***
// Normalizing // Normalizing
myfloat_t norm2 = (myfloat_t) (param.param_device.NumberPixels * param.param_device.NumberPixels); myfloat_t norm2 = (myfloat_t) (param.param_device.NumberPixels * param.param_device.NumberPixels);
myfloat_t norm4 = norm2 * norm2; myfloat_t norm4 = norm2 * norm2;
sumC = sumC / norm2; sumC = sumC / norm2;
sumsquareC = sumsquareC / norm4; sumsquareC = sumsquareC / norm4;
/**** Freeing fftw_complex created (dont know if omp critical is necessary) ****/ //**** Freeing fftw_complex created (dont know if omp critical is necessary) ****
myfftw_free(localconvFFT); myfftw_free(localconvFFT);
myfftw_free(tmp); myfftw_free(tmp);
...@@ -572,7 +582,7 @@ int bioem::createConvolutedProjectionMap(int iMap,int iConv,mycomplex_t* lproj,b ...@@ -572,7 +582,7 @@ int bioem::createConvolutedProjectionMap(int iMap,int iConv,mycomplex_t* lproj,b
int bioem::calcross_cor(bioem_map& localmap,myfloat_t& sum,myfloat_t& sumsquare) int bioem::calcross_cor(bioem_map& localmap,myfloat_t& sum,myfloat_t& sumsquare)
{ {
/*********************** Routine to calculate Cross correlations***********************/ //*********************** Routine to calculate Cross correlations***********************
sum=0.0; sum=0.0;
sumsquare=0.0; sumsquare=0.0;
......
main.cpp
View file @ 0392963f
...@@ -21,9 +21,9 @@ ...@@ -21,9 +21,9 @@
int main(int argc, char* argv[]) int main(int argc, char* argv[])
{ {
/**************************************************************************************/ //*************************************************************************************
/********************************* Main BioEM code **********************************/ //********************************* Main BioEM code **********************************
/************************************************************************************/ //*************************************************************************************
#pragma omp parallel #pragma omp parallel
{ {
...@@ -43,17 +43,17 @@ int main(int argc, char* argv[]) ...@@ -43,17 +43,17 @@ int main(int argc, char* argv[])
bio = new bioem; bio = new bioem;
} }
/************ Configuration and Pre-calculating necessary objects *****************/ //************ Configuration and Pre-calculating necessary objects *********************
printf("Configuring\n"); printf("Configuring\n");
bio->configure(argc,argv); bio->configure(argc,argv);
/******************************* Run BioEM routine ******************************/ //******************************* Run BioEM routine ************************************
printf("Running\n"); printf("Running\n");
timer.Start(); timer.Start();
bio->run(); bio->run();
timer.Stop(); timer.Stop();
/************************************ End **********************************/ //************************************ End ***********************************************
printf ("The code ran for %f seconds.\n", timer.GetElapsedTime()); printf ("The code ran for %f seconds.\n", timer.GetElapsedTime());
delete bio; delete bio;
......
map.cpp
View file @ 0392963f
...@@ -13,9 +13,9 @@ using namespace std; ...@@ -13,9 +13,9 @@ using namespace std;
int bioem_RefMap::readRefMaps(bioem_param& param) int bioem_RefMap::readRefMaps(bioem_param& param)
{ {
/**************************************************************************************/ //**************************************************************************************
/***********************Reading reference Particle Maps************************/ //***********************Reading reference Particle Maps************************
/**************************************************************************************/ //**************************************************************************************
if (loadMap) if (loadMap)
{ {
FILE* fp = fopen("maps.dump", "rb"); FILE* fp = fopen("maps.dump", "rb");
...@@ -34,7 +34,7 @@ int bioem_RefMap::readRefMaps(bioem_param& param) ...@@ -34,7 +34,7 @@ int bioem_RefMap::readRefMaps(bioem_param& param)
fclose(fp); fclose(fp);
cout << "Particle Maps read from Map Dump \nTotal Number of particles: " << ntotRefMap ; cout << "Particle Maps read from Map Dump \nTotal Number of particles: " << ntotRefMap ;
cout << "\n+++++++++++++++++++++++++++++++++++++++++ \n"; cout << "\n+++++++++++++++++++++++++++++++++++++++ \n";
} }
else else
{ {
...@@ -79,11 +79,13 @@ int bioem_RefMap::readRefMaps(bioem_param& param) ...@@ -79,11 +79,13 @@ int bioem_RefMap::readRefMaps(bioem_param& param)
for(int i=3;i<100;i++)mapname[i] = {0}; for(int i=3;i<100;i++)mapname[i] = {0};
} }
cout << "\n+++++++++++++++++++++++++++++++++++++++++++ \n";
cout << "Particle Maps read from MULTIPLE MRC Files in: " << filemap << "\n" ; cout << "Particle Maps read from MULTIPLE MRC Files in: " << filemap << "\n" ;
} else { } else {
read_MRC(filemap,param); read_MRC(filemap,param);
cout << "\n++++++++++++++++++++++++++++++++++++++++++ \n";
cout << "Particle Maps read from ONE MRC File: " << filemap << "\n" ; cout << "Particle Maps read from ONE MRC File: " << filemap << "\n" ;
} }
...@@ -160,6 +162,7 @@ int bioem_RefMap::readRefMaps(bioem_param& param) ...@@ -160,6 +162,7 @@ int bioem_RefMap::readRefMaps(bioem_param& param)
} }
cout << "."; cout << ".";
ntotRefMap=nummap+1; ntotRefMap=nummap+1;
cout << "\n++++++++++++++++++++++++++++++++++++++++++ \n";
cout << "Particle Maps read from Standard File\n" ; cout << "Particle Maps read from Standard File\n" ;
} }
cout << "Total Number of particles: " << ntotRefMap ; cout << "Total Number of particles: " << ntotRefMap ;
...@@ -184,9 +187,9 @@ int bioem_RefMap::readRefMaps(bioem_param& param) ...@@ -184,9 +187,9 @@ int bioem_RefMap::readRefMaps(bioem_param& param)
int bioem_RefMap::PreCalculateMapsFFT(bioem_param& param) int bioem_RefMap::PreCalculateMapsFFT(bioem_param& param)
{ {
/**************************************************************************************/