bioem.cpp 26.7 KB
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#include <fstream>
#include <boost/program_options.hpp>
#include <iostream>
#include <algorithm>
#include <iterator>
#include <stdio.h>
#include <stdlib.h>
#include <string>
#include <cmath>
#include <omp.h>

#include <fftw3.h>
#include <math.h>
#include "cmodules/timer.h"

#include "param.h"
#include "bioem.h"
#include "model.h"
#include "map.h"


#include "bioem_algorithm.h"


using namespace boost;
namespace po = boost::program_options;

using namespace std;

// A helper function of Boost
template<class T>
ostream& operator<<(ostream& os, const vector<T>& v)
{
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	copy(v.begin(), v.end(), ostream_iterator<T>(os, " "));
	return os;
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}

bioem::bioem()
{
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	FFTAlgo = getenv("FFTALGO") == NULL ? 0 : atoi(getenv("FFTALGO"));
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}

bioem::~bioem()
{
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}

int bioem::configure(int ac, char* av[])
{
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	/**************************************************************************************/
	/**** Configuration Routine using boost for extracting parameters, models and maps ****/
	/**************************************************************************************/
	/****** And Precalculating necessary grids, map crosscorrelations and kernels  ********/
	/*************************************************************************************/

	/*** Inizialzing default variables ***/
	std::string infile,modelfile,mapfile;
	Model.readPDB=false;
	param.writeAngles=false;
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	RefMap.dumpMap = false;
	RefMap.loadMap = false;

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	/*************************************************************************************/
	cout << " ++++++++++++ FROM COMMAND LINE +++++++++++\n\n";
	/*************************************************************************************/
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	/********************* Command line reading input with BOOST ************************/
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	try {
		po::options_description desc("Command line inputs");
		desc.add_options()
		("Inputfile", po::value<std::string>(), "Name of input parameter file")
		("Modelfile", po::value< std::string>() , "Name of model file")
		("Particlesfile", po::value< std::string>(), "Name of paricles file")
		("ReadPDB", "(Optional) If reading model file in PDB format")
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		("DumpMaps", "(Optional) Dump maps after they were red from maps file")
		("LoadMapDump", "(Optional) Read Maps from dump instead of maps file")
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		("help", "(Optional) Produce help message")
		;

		po::positional_options_description p;
		p.add("Inputfile", -1);
		p.add("Modelfile", -1);
		p.add("Particlesfile", -1);
		p.add("ReadPDB", -1);
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		p.add("DumpMaps", -1);
		p.add("LoadMapDump", -1);

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		po::variables_map vm;
		po::store(po::command_line_parser(ac, av).
				  options(desc).positional(p).run(), vm);
		po::notify(vm);

		if((ac < 6)) {
			std::cout << desc << std::endl;
			return 0;
		}
		if (vm.count("help")) {
			cout << "Usage: options_description [options]\n";
			cout << desc;
			return 0;
		}

		if (vm.count("Inputfile"))
		{
			cout << "Input file is: ";
			cout << vm["Inputfile"].as< std::string >()<< "\n";
			infile=vm["Inputfile"].as< std::string >();
		}
		if (vm.count("Modelfile"))
		{
			cout << "Model file is: "
				 << vm["Modelfile"].as<  std::string  >() << "\n";
			modelfile=vm["Modelfile"].as<  std::string  >();
		}

		if (vm.count("ReadPDB"))
		{
			cout << "Reading model file in PDB format.\n";
			Model.readPDB=true;
		}

		if (vm.count("DumpMaps"))
		{
			cout << "Dumping Maps after reading from file.\n";
			RefMap.dumpMap = true;
		}

		if (vm.count("LoadMapDump"))
		{
			cout << "Loading Map dump.\n";
			RefMap.loadMap = true;
		}

		if (vm.count("Particlesfile"))
		{
			cout << "Paricle file is: "
				 << vm["Particlesfile"].as< std::string >() << "\n";
			mapfile=vm["Particlesfile"].as< std::string >();
		}
	}
	catch(std::exception& e)
	{
		cout << e.what() << "\n";
		return 1;
	}

	/********************* Reading Parameter Input ***************************/
	// copying inputfile to param class
	param.fileinput = infile.c_str();
	param.readParameters();

	/********************* Reading Model Input ******************************/
	// copying modelfile to model class
	Model.filemodel = modelfile.c_str();
	Model.readModel();

	/********************* Reading Particle Maps Input **********************/
	/********* HERE: PROBLEM if maps dont fit on the memory!! ***************/
	// copying mapfile to ref map class
	RefMap.filemap = mapfile.c_str();
	RefMap.readRefMaps(param);

	/****************** Precalculating Necessary Stuff *********************/
	precalculate();
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	if (getenv("BIOEM_DEBUG_BREAK"))
	{
		param.nTotGridAngles = atoi(getenv("BIOEM_DEBUG_BREAK"));
		param.nTotCTFs = atoi(getenv("BIOEM_DEBUG_BREAK"));
	}
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	deviceInit();

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	return(0);
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}

int bioem::precalculate()
{
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	/**************************************************************************************/
	/* Precalculating Routine of Orientation grids, Map crosscorrelations and CTF Kernels */
	/**************************************************************************************/
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	// Generating Grids of orientations
	param.CalculateGridsParam();
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	myfloat_t sum,sumsquare;

	//Precalculating cross-correlations of maps
	for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap ; iRefMap++)
	{
		calcross_cor(RefMap.Ref[iRefMap],sum,sumsquare);
		//Storing Crosscorrelations in Map class
		RefMap.sum_RefMap[iRefMap]=sum;
		RefMap.sumsquare_RefMap[iRefMap]=sumsquare;
	}
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	// Precalculating CTF Kernels stored in class Param
	param.CalculateRefCTF();
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	// Precalculating Maps in Fourier space
	RefMap.PreCalculateMapsFFT(param);
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	return(0);
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}


int bioem::run()
{
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	/**************************************************************************************/
	/**** 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); ******/
	/****************** Declarying class of Probability Pointer  *************************/
	pProb = new bioem_Probability[RefMap.ntotRefMap];

	printf("\tInitializing\n");
	// Inizialzing Probabilites to zero and constant to -Infinity
	for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap; iRefMap ++)
	{
		pProb[iRefMap].Total=0.0;
		pProb[iRefMap].Constoadd=-9999999;
		pProb[iRefMap].max_prob=-9999999;
		for (int iOrient = 0; iOrient < param.nTotGridAngles; iOrient ++)
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		{
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			pProb[iRefMap].forAngles[iOrient]=0.0;
			pProb[iRefMap].ConstAngle[iOrient]=-99999999;
		}
	}
	/**************************************************************************************/
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	deviceStartRun();

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	/******************************** MAIN CYCLE ******************************************/
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	/*** Declaring Private variables for each thread *****/
	mycomplex_t* proj_mapFFT;
	bioem_map conv_map;
	mycomplex_t* conv_mapFFT;
	myfloat_t sumCONV,sumsquareCONV;
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	//allocating fftw_complex vector
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	proj_mapFFT= (mycomplex_t *) myfftw_malloc(sizeof(mycomplex_t) * param.param_device.NumberPixels*param.param_device.NumberFFTPixels1D);
	conv_mapFFT= (mycomplex_t *) myfftw_malloc(sizeof(mycomplex_t) * param.param_device.NumberPixels*param.param_device.NumberFFTPixels1D);
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	HighResTimer timer;

	printf("\tMain Loop (GridAngles %d, CTFs %d, RefMaps %d, Shifts (%d/%d)²), Pixels %d²\n", param.nTotGridAngles, param.nTotCTFs, RefMap.ntotRefMap, 2 * param.param_device.maxDisplaceCenter + param.param_device.GridSpaceCenter, param.param_device.GridSpaceCenter, param.param_device.NumberPixels);
	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)));
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	for (int iProjectionOut = 0; iProjectionOut < param.nTotGridAngles; iProjectionOut++)
	{
		/***************************************************************************************/
		/***** Creating Projection for given orientation and transforming to Fourier space *****/
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		timer.ResetStart();
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		createProjection(iProjectionOut, proj_mapFFT);
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		printf("Time Projection %d: %f\n", iProjectionOut, timer.GetCurrentElapsedTime());

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		/***************************************************************************************/
		/***** **** Internal Loop over convolutions **** *****/
		for (int iConv = 0; iConv < param.nTotCTFs; iConv++)
		{
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			printf("\t\tConvolution %d %d\n", iProjectionOut, iConv);
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			/*** Calculating convolutions of projection map and crosscorrelations ***/

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			timer.ResetStart();
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			createConvolutedProjectionMap(iProjectionOut,iConv,proj_mapFFT,conv_map,conv_mapFFT,sumCONV,sumsquareCONV);
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			printf("Time Convolution %d %d: %f\n", iProjectionOut, iConv, timer.GetCurrentElapsedTime());

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			/***************************************************************************************/
			/*** Comparing each calculated convoluted map with all experimental maps ***/
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			timer.ResetStart();
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			if (FFTAlgo == 0)
			{
				compareRefMaps(iProjectionOut, iConv, conv_map);
			}
			else
			{
				compareRefMaps2(iProjectionOut, iConv,conv_mapFFT,sumCONV,sumsquareCONV);
			}

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			const double compTime = timer.GetCurrentElapsedTime();
			const int nShifts = 2 * param.param_device.maxDisplaceCenter / param.param_device.GridSpaceCenter + 1;
			const double nFlops = (double) RefMap.ntotRefMap * (double) nShifts * (double) nShifts *
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								  (((double) param.param_device.NumberPixels - (double) param.param_device.maxDisplaceCenter / 2.) * ((double) param.param_device.NumberPixels - (double) param.param_device.maxDisplaceCenter / 2.) * 5. + 25.) / compTime;
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			const double nGBs = (double) RefMap.ntotRefMap * (double) nShifts * (double) nShifts *
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								(((double) param.param_device.NumberPixels - (double) param.param_device.maxDisplaceCenter / 2.) * ((double) param.param_device.NumberPixels - (double) param.param_device.maxDisplaceCenter / 2.) * 2. + 8.) * (double) sizeof(myfloat_t) / compTime;
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			const double nGBs2 = (double) RefMap.ntotRefMap * ((double) param.param_device.NumberPixels * (double) param.param_device.NumberPixels + 8.) * (double) sizeof(myfloat_t) / compTime;

			printf("Time Comparison %d %d: %f sec (%f GFlops, %f GB/s (cached), %f GB/s)\n", iProjectionOut, iConv, compTime, nFlops / 1000000000., nGBs / 1000000000., nGBs2 / 1000000000.);
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		}
	}
	//deallocating fftw_complex vector
	myfftw_free(proj_mapFFT);
	myfftw_free(conv_mapFFT);
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	deviceFinishRun();

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	/************* Writing Out Probabilities ***************/
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	/*** Angular Probability ***/
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	// if(param.writeAngles){
	ofstream angProbfile;
	angProbfile.open ("ANG_PROB_iRefMap");
	// }
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	ofstream outputProbFile;
	outputProbFile.open ("Output_Probabilities");
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	for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap; iRefMap ++)
	{
		/**** 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 << " Maximizing Param: ";

		/*** 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 << 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[2] << " ";
		outputProbFile << param.CtfParam[pProb[iRefMap].max_prob_conv].pos[0] << " ";
		outputProbFile << param.CtfParam[pProb[iRefMap].max_prob_conv].pos[1] << " ";
		outputProbFile << param.CtfParam[pProb[iRefMap].max_prob_conv].pos[2] << " ";
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		outputProbFile << pProb[iRefMap].max_prob_cent_x << " ";
		outputProbFile << pProb[iRefMap].max_prob_cent_y;
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		outputProbFile << "\n";
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		/*** For individual files***/ //angProbfile.open ("ANG_PROB_"iRefMap);
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		if(param.writeAngles)
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		{
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			for (int iProjectionOut = 0; iProjectionOut < param.nTotGridAngles; iProjectionOut++)
			{
				angProbfile << " " << iRefMap << " " << param.angles[iProjectionOut].pos[0] << " " << param.angles[iProjectionOut].pos[1] << " " << param.angles[iProjectionOut].pos[2] << " " << log(pProb[iRefMap].forAngles[iProjectionOut])+pProb[iRefMap].ConstAngle[iProjectionOut]+0.5*log(M_PI)+(1-param.param_device.Ntotpi*0.5)*(log(2*M_PI)+1)+log(param.param_device.volu) << " " << log(param.param_device.volu) << "\n";
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			}
		}
	}
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	angProbfile.close();
	outputProbFile.close();
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	//Deleting allocated pointers
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	if (pProb)
	{
		delete[] pProb;
		pProb = NULL;
	}

	if (param.refCTF)
	{
		delete[] param.refCTF;
		param.refCTF =NULL;
	}
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	if(RefMap.RefMapFFT)
	{
		delete[] RefMap.RefMapFFT;
		RefMap.RefMapFFT = NULL;
	}
	return(0);
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}

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int bioem::compareRefMaps(int iProjectionOut, int iConv, const bioem_map& conv_map, const int startMap)
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{
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#pragma omp parallel for
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	for (int iRefMap = startMap; iRefMap < RefMap.ntotRefMap; iRefMap ++)
	{
		compareRefMapShifted<-1>(iRefMap,iProjectionOut,iConv,conv_map, pProb, param.param_device, RefMap);
	}
	return(0);
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}

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int bioem::compareRefMaps2(int iOrient, int iConv, mycomplex_t* localConvFFT,myfloat_t sumC,myfloat_t sumsquareC)
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{
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#pragma omp parallel
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	{
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		mycomplex_t *localCCT;
		myfloat_t *lCC;
		localCCT= (mycomplex_t *) myfftw_malloc(sizeof(mycomplex_t) *param.param_device.NumberPixels*param.param_device.NumberFFTPixels1D);
		lCC= (myfloat_t *) myfftw_malloc(sizeof(myfloat_t) *param.param_device.NumberPixels*param.param_device.NumberPixels);
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		const int num_threads = omp_get_num_threads();
		const int thread_id = omp_get_thread_num();
		const int mapsPerThread = (RefMap.ntotRefMap + num_threads - 1) / num_threads;
		const int iStart = thread_id * mapsPerThread;
		const int iEnd = min(RefMap.ntotRefMap, (thread_id + 1) * mapsPerThread);

		for (int iRefMap = iStart; iRefMap < iEnd; iRefMap ++)
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		{
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			calculateCCFFT(iRefMap,iOrient, iConv, sumC,sumsquareC, localConvFFT, localCCT,lCC);
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		}
		myfftw_free(localCCT);
		myfftw_free(lCC);
	}
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	return(0);
}

/////////////NEW ROUTINE ////////////////
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inline int bioem::calculateCCFFT(int iRefMap, int iOrient, int iConv, myfloat_t sumC,myfloat_t sumsquareC, mycomplex_t* localConvFFT,mycomplex_t* localCCT,myfloat_t* lCC)
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{
	for(int i=0; i < param.param_device.NumberPixels ; i++ )
	{
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		for(int j=0; j < param.param_device.NumberFFTPixels1D ; j++ )
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		{
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			localCCT[i*param.param_device.NumberFFTPixels1D+j][0]=localConvFFT[i*param.param_device.NumberFFTPixels1D+j][0]*RefMap.RefMapFFT[iRefMap].cpoints[i*param.param_device.NumberFFTPixels1D+j][0]+localConvFFT[i*param.param_device.NumberFFTPixels1D+j][1]*RefMap.RefMapFFT[iRefMap].cpoints[i*param.param_device.NumberFFTPixels1D+j][1];
			localCCT[i*param.param_device.NumberFFTPixels1D+j][1]=localConvFFT[i*param.param_device.NumberFFTPixels1D+j][1]*RefMap.RefMapFFT[iRefMap].cpoints[i*param.param_device.NumberFFTPixels1D+j][0]-localConvFFT[i*param.param_device.NumberFFTPixels1D+j][0]*RefMap.RefMapFFT[iRefMap].cpoints[i*param.param_device.NumberFFTPixels1D+j][1];
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		}
	}

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	myfftw_execute_dft_c2r(param.fft_plan_c2r_backward,localCCT,lCC);
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// Storing CORRELATIONS FOR CORRESPONDING DISPLACEMENTS & Normalizing after Backward FFT
	for (int cent_x = 0; cent_x <= param.param_device.maxDisplaceCenter; cent_x=cent_x+param.param_device.GridSpaceCenter)
	{
		for (int cent_y = 0; cent_y <= param.param_device.maxDisplaceCenter; cent_y=cent_y+param.param_device.GridSpaceCenter)
		{
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			calProb(iRefMap, iOrient, iConv, sumC, sumsquareC, (myfloat_t) lCC[cent_x*param.param_device.NumberPixels+cent_y]/ (myfloat_t) (param.param_device.NumberPixels * param.param_device.NumberPixels), cent_x, cent_y);
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		}
		for (int cent_y = param.param_device.NumberPixels-param.param_device.maxDisplaceCenter; cent_y < param.param_device.NumberPixels; cent_y=cent_y+param.param_device.GridSpaceCenter)
		{
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			calProb(iRefMap, iOrient, iConv, sumC, sumsquareC, (myfloat_t) lCC[cent_x*param.param_device.NumberPixels+cent_y]/ (myfloat_t) (param.param_device.NumberPixels*param.param_device.NumberPixels), cent_x, param.param_device.NumberPixels-cent_y);
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		}
	}
	for (int cent_x = param.param_device.NumberPixels-param.param_device.maxDisplaceCenter; cent_x < param.param_device.NumberPixels; cent_x=cent_x+param.param_device.GridSpaceCenter)
	{
		for (int cent_y = 0; cent_y < param.param_device.maxDisplaceCenter; cent_y=cent_y+param.param_device.GridSpaceCenter)
		{
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			calProb(iRefMap, iOrient, iConv, sumC, sumsquareC, (myfloat_t) lCC[cent_x*param.param_device.NumberPixels+cent_y]/ (myfloat_t) (param.param_device.NumberPixels*param.param_device.NumberPixels), param.param_device.NumberPixels-cent_x, cent_y);
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		}
		for (int cent_y = param.param_device.NumberPixels-param.param_device.maxDisplaceCenter; cent_y <= param.param_device.NumberPixels; cent_y=cent_y+param.param_device.GridSpaceCenter)
		{
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			calProb(iRefMap, iOrient, iConv, sumC, sumsquareC, (myfloat_t) lCC[cent_x*param.param_device.NumberPixels+cent_y]/ (myfloat_t) (param.param_device.NumberPixels*param.param_device.NumberPixels), param.param_device.NumberPixels-cent_x, param.param_device.NumberPixels-cent_y);
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		}
	}
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	return (0);
}
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inline int bioem::calProb(int iRefMap,int iOrient, int iConv,myfloat_t sumC,myfloat_t sumsquareC, int value, int disx, int disy)
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{
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	/********************************************************/
	/*********** Calculates the BioEM probability ***********/
	/********************************************************/
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	const myfloat_t ForLogProb = (sumsquareC * param.param_device.Ntotpi - sumC * sumC);
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		// Products of different cross-correlations (first element in formula)
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		const myfloat_t firstele = param.param_device.Ntotpi * (RefMap.sumsquare_RefMap[iRefMap] * sumsquareC -   value * value) +
								   2 * RefMap.sum_RefMap[iRefMap] * sumC *   value - RefMap.sumsquare_RefMap[iRefMap] * sumC * sumC - RefMap.sum_RefMap[iRefMap] * RefMap.sum_RefMap[iRefMap] * sumsquareC;
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		//******* Calculating log of Prob*********/
		// As in fortran code: logpro=(3-Ntotpi)*0.5*log(firstele/pConvMap[iOrient].ForLogProbfromConv[iConv])+(Ntotpi*0.5-2)*log(Ntotpi-2)-0.5*log(pConvMap[iOrient].ForLogProbfromConv[iConv])+0.5*log(PI)+(1-Ntotpi*0.5)*(log(2*PI)+1);
		const myfloat_t logpro = (3 - param.param_device.Ntotpi) * 0.5 * log(firstele) + (param.param_device.Ntotpi * 0.5 - 2) * log((param.param_device.Ntotpi - 2) * ForLogProb);
//   cout << n <<" " << firstele << " "<< logpro << "\n";
		{
			/*******  Summing total Probabilities *************/
			/******* Need a constant because of numerical divergence*****/
			if(pProb[iRefMap].Constoadd < logpro)
			{
				pProb[iRefMap].Total = pProb[iRefMap].Total * exp(-logpro + pProb[iRefMap].Constoadd);
				pProb[iRefMap].Constoadd = logpro;
			}
			pProb[iRefMap].Total += exp(logpro - pProb[iRefMap].Constoadd);

			//Summing probabilities for each orientation
			if(pProb[iRefMap].ConstAngle[iOrient] < logpro)
			{
				pProb[iRefMap].forAngles[iOrient] = pProb[iRefMap].forAngles[iOrient] * exp(-logpro + pProb[iRefMap].ConstAngle[iOrient]);
				pProb[iRefMap].ConstAngle[iOrient] = logpro;
			}
			pProb[iRefMap].forAngles[iOrient] += exp(logpro - pProb[iRefMap].ConstAngle[iOrient]);

			/********** Getting parameters that maximize the probability ***********/
			if(pProb[iRefMap].max_prob < logpro)
			{
				pProb[iRefMap].max_prob = logpro;
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				pProb[iRefMap].max_prob_cent_x = disx;
				pProb[iRefMap].max_prob_cent_y = disy;
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				pProb[iRefMap].max_prob_orient = iOrient;
				pProb[iRefMap].max_prob_conv = iConv;
			}
		}
	return (0);
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}


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int bioem::createProjection(int iMap,mycomplex_t* mapFFT)
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{
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	/**************************************************************************************/
	/****  BioEM Create Projection routine in Euler angle predefined grid****************
	********************* and turns projection into Fourier space **********************/
	/**************************************************************************************/

	myfloat3_t RotatedPointsModel[Model.nPointsModel];
	myfloat_t rotmat[3][3];
	myfloat_t alpha, gam,beta;
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	myfloat_t* localproj;
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	localproj= (myfloat_t *) myfftw_malloc(sizeof(myfloat_t) *param.param_device.NumberPixels*param.param_device.NumberPixels);
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	memset(localproj,0,param.param_device.NumberPixels*param.param_device.NumberPixels*sizeof(*localproj));

	alpha=param.angles[iMap].pos[0];
	beta=param.angles[iMap].pos[1];
	gam=param.angles[iMap].pos[2];

	/**** 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**********/

	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][2]=sin(gam)*sin(beta);
	rotmat[1][0]=-sin(gam)*cos(alpha)-cos(beta)*sin(alpha)*cos(gam);
	rotmat[1][1]=-sin(gam)*sin(alpha)+cos(beta)*cos(alpha)*cos(gam);
	rotmat[1][2]=cos(gam)*sin(beta);
	rotmat[2][0]=sin(beta)*sin(alpha);
	rotmat[2][1]=-sin(beta)*cos(alpha);
	rotmat[2][2]=cos(beta);


	for(int n=0; n< Model.nPointsModel; n++)
	{
		RotatedPointsModel[n].pos[0]=0.0;
		RotatedPointsModel[n].pos[1]=0.0;
		RotatedPointsModel[n].pos[2]=0.0;
	}
	for(int n=0; n< Model.nPointsModel; n++)
	{
		for(int k=0; k< 3; k++)
		{
			for(int j=0; j< 3; j++)
			{
				RotatedPointsModel[n].pos[k]+=rotmat[k][j]*Model.PointsModel[n].pos[j];
			}
		}
	}

	int i, j;

	/************ Projection over the Z axis********************/
	for(int n=0; n< Model.nPointsModel; n++)
	{
		//Getting pixel that represents coordinates & shifting the start at to Numpix/2,Numpix/2 )
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		i=floor(RotatedPointsModel[n].pos[0]/param.pixelSize+ (myfloat_t) param.param_device.NumberPixels / 2.0f + 0.5f);
		j=floor(RotatedPointsModel[n].pos[1]/param.pixelSize+ (myfloat_t) param.param_device.NumberPixels / 2.0f + 0.5f);
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		localproj[i*param.param_device.NumberPixels+j]+=Model.densityPointsModel[n]/Model.NormDen;
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	}

	/**** Output Just to check****/
	if(iMap==10)
	{
		ofstream myexamplemap;
		ofstream myexampleRot;
		myexamplemap.open ("MAP_i10");
		myexampleRot.open ("Rot_i10");
		myexamplemap << "ANGLES " << alpha << " " << beta << " " << gam << "\n";
		for(int k=0; k<param.param_device.NumberPixels; k++)
		{
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			for(int j=0; j<param.param_device.NumberPixels; j++) myexamplemap << "\nMAP " << k << " " << j<< " " <<localproj[k*param.param_device.NumberPixels+j];
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		}
		myexamplemap << " \n";
		for(int n=0; n< Model.nPointsModel; n++)myexampleRot << "\nCOOR " << RotatedPointsModel[n].pos[0] << " " << RotatedPointsModel[n].pos[1] << " " << RotatedPointsModel[n].pos[2];
		myexamplemap.close();
		myexampleRot.close();
	}

	/***** Converting projection to Fourier Space for Convolution later with kernel****/
	/********** Omp Critical is necessary with FFTW*******/
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	myfftw_execute_dft_r2c(param.fft_plan_r2c_forward,localproj,mapFFT);
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	return(0);
}

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int bioem::createConvolutedProjectionMap(int iMap,int iConv,mycomplex_t* lproj,bioem_map& Mapconv, mycomplex_t* localmultFFT, myfloat_t& sumC, myfloat_t& sumsquareC)
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{
	/**************************************************************************************/
	/****  BioEM Create Convoluted Projection Map routine, multiplies in Fourier **********
	**************** calculated Projection with convoluted precalculated Kernel**********
	*************** and Backtransforming it to real Space ******************************/
	/**************************************************************************************/

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	myfloat_t* localconvFFT;
	localconvFFT= (myfloat_t *) myfftw_malloc(sizeof(myfloat_t)*param.param_device.NumberPixels*param.param_device.NumberPixels);
	mycomplex_t* tmp;
	tmp = (mycomplex_t*) myfftw_malloc(sizeof(mycomplex_t) * param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D);
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	/**** Multiplying FFTmap with corresponding kernel ****/

	for(int i=0; i < param.param_device.NumberPixels ; i++ )
	{
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		for(int j=0; j < param.param_device.NumberFFTPixels1D ; j++ )
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		{   //Projection*CONJ(KERNEL)
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			localmultFFT[i*param.param_device.NumberFFTPixels1D+j][0]=lproj[i*param.param_device.NumberFFTPixels1D+j][0]*param.refCTF[iConv].cpoints[i*param.param_device.NumberFFTPixels1D+j][0]+lproj[i*param.param_device.NumberFFTPixels1D+j][1]*param.refCTF[iConv].cpoints[i*param.param_device.NumberFFTPixels1D+j][1];
			localmultFFT[i*param.param_device.NumberFFTPixels1D+j][1]=lproj[i*param.param_device.NumberFFTPixels1D+j][1]*param.refCTF[iConv].cpoints[i*param.param_device.NumberFFTPixels1D+j][0]-lproj[i*param.param_device.NumberFFTPixels1D+j][0]*param.refCTF[iConv].cpoints[i*param.param_device.NumberFFTPixels1D+j][1];
			// cout << "GG " << i << " " << j << " " << param.refCTF[iConv].cpoints[i*param.param_device.NumberFFTPixels1D+j][0] << " " <<param.refCTF[iConv].cpoints[i*param.param_device.NumberFFTPixels1D+j][1] <<" " <<lproj[i*param.param_device.NumberFFTPixels1D+j][0] <<" " <<lproj[i*param.param_device.NumberFFTPixels1D+j][1] << "\n";
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		}
	}

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	//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);

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	/**** Bringing convoluted Map to real Space ****/
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	myfftw_execute_dft_c2r(param.fft_plan_c2r_backward,tmp,localconvFFT);
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	/****Asigning convolution fftw_complex to bioem_map ****/
	for(int i=0; i < param.param_device.NumberPixels ; i++ )
	{
		for(int j=0; j < param.param_device.NumberPixels ; j++ )
		{
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			Mapconv.points[i][j]=localconvFFT[i*param.param_device.NumberPixels+j];
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		}
	}

	/*** Calculating Cross-correlations of cal-convoluted map with its self *****/
	sumC=0;
	sumsquareC=0;
	for(int i=0; i < param.param_device.NumberPixels ; i++ )
	{
		for(int j=0; j < param.param_device.NumberPixels ; j++ )
		{
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			sumC+=localconvFFT[i*param.param_device.NumberPixels+j];
			sumsquareC+=localconvFFT[i*param.param_device.NumberPixels+j]*localconvFFT[i*param.param_device.NumberPixels+j];
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		}
	}
	/*** The DTF gives an unnormalized value so have to divded by the total number of pixels in Fourier ***/
	// Normalizing
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	sumC=sumC/ (myfloat_t) (param.param_device.NumberPixels*param.param_device.NumberPixels);
	sumsquareC=sumsquareC / pow((myfloat_t) param.param_device.NumberPixels,4);
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	/**** Freeing fftw_complex created (dont know if omp critical is necessary) ****/
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	myfftw_free(localconvFFT);
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	myfftw_free(tmp);
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	return(0);
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}

int bioem::calcross_cor(bioem_map& localmap,myfloat_t& sum,myfloat_t& sumsquare)
{
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	/*********************** Routine to calculate Cross correlations***********************/

	sum=0.0;
	sumsquare=0.0;
	for (int i = 0; i < param.param_device.NumberPixels; i++)
	{
		for (int j = 0; j < param.param_device.NumberPixels; j++)
		{
			// Calculate Sum of pixels
			sum += localmap.points[i][j];
			// Calculate Sum of pixels squared
			sumsquare += localmap.points[i][j]*localmap.points[i][j];
		}
	}
	return(0);
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}

int bioem::deviceInit()
{
	return(0);
}

int bioem::deviceStartRun()
{
	return(0);
}

int bioem::deviceFinishRun()
{
	return(0);
}