bioem.cpp 21 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  ********
	// *************************************************************************************
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	// *** Inizialzing default variables ***
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	std::string infile, modelfile, mapfile;
	Model.readPDB = false;
	param.writeAngles = false;
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	param.dumpMap = false;
	param.loadMap = false;
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	// *************************************************************************************
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	cout << " ++++++++++++ FROM COMMAND LINE +++++++++++\n\n";
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	// *************************************************************************************
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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;
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			return 1;
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		}
		if (vm.count("help")) {
			cout << "Usage: options_description [options]\n";
			cout << desc;
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			return 1;
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		}

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

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

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

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

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

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

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

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

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	// ****************** Precalculating Necessary Stuff *********************
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	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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	// **************************************************************************************
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	// **Precalculating Routine of Orientation grids, Map crosscorrelations and CTF Kernels**
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	// **************************************************************************************
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	// Generating Grids of orientations
	param.CalculateGridsParam();
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	myfloat_t sum, sumsquare;
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	//Precalculating cross-correlations of maps
	for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap ; iRefMap++)
	{
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		calcross_cor(RefMap.getmap(iRefMap), sum, sumsquare);
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		//Storing Crosscorrelations in Map class
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		RefMap.sum_RefMap[iRefMap] = sum;
		RefMap.sumsquare_RefMap[iRefMap] = sumsquare;
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	}
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	// Precalculating CTF Kernels stored in class Param
	param.CalculateRefCTF();
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	// Precalculating Maps in Fourier space
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	if (FFTAlgo)
	{
		RefMap.PreCalculateMapsFFT(param);
		free(RefMap.maps);
		RefMap.maps = NULL;
	}
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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 ****
	// **************************************************************************************
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	// **** If we want to control the number of threads -> omp_set_num_threads(XX); ******
	// ****************** Declarying class of Probability Pointer  *************************
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	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 ++)
	{
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		pProb[iRefMap].Total = 0.0;
		pProb[iRefMap].Constoadd = -9999999;
		pProb[iRefMap].max_prob = -9999999;
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		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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		}
	}
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	// **************************************************************************************
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	deviceStartRun();

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	// ******************************** MAIN CYCLE ******************************************
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	// *** Declaring Private variables for each thread *****
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	mycomplex_t* proj_mapFFT;
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	myfloat_t* conv_map = new myfloat_t[param.param_device.NumberPixels * param.param_device.NumberPixels];
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	mycomplex_t* conv_mapFFT;
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	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++)
	{
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		// ***************************************************************************************
		// ***** 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 **** *****
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		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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			compareRefMaps(iProjectionOut, iConv, conv_map, 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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	delete[] conv_map;
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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 ++)
	{
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		// **** Total Probability ***
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		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";
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		outputProbFile << "RefMap " << iRefMap << " Maximizing Param: ";

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		// *** Param that maximize probability****
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		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++)
			{
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				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;
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		param.refCTF = NULL;
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	}
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	RefMap.freePointers();
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	return(0);
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}

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int bioem::compareRefMaps(int iProjectionOut, int iConv, const myfloat_t* conv_map, mycomplex_t* localmultFFT, myfloat_t sumC, myfloat_t sumsquareC, const int startMap)
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{
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	if (FFTAlgo)
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	{
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		#pragma omp parallel for
		for (int iRefMap = startMap; iRefMap < RefMap.ntotRefMap; iRefMap ++)
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		{
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			const int num = omp_get_thread_num();
			calculateCCFFT(iRefMap, iProjectionOut, iConv, sumC, sumsquareC, localmultFFT, localCCT[num], lCC[num]);
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		}
	}
	else
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	{
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		#pragma omp parallel for
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		for (int iRefMap = startMap; iRefMap < RefMap.ntotRefMap; iRefMap ++)
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		{
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			compareRefMapShifted < -1 > (iRefMap, iProjectionOut, iConv, conv_map, pProb, param.param_device, RefMap);
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		}
	}
	return(0);
}

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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)
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{
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	const mycomplex_t* RefMapFFT = &RefMap.RefMapsFFT[iRefMap * param.FFTMapSize];
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	for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D; i++)
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	{
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		localCCT[i][0] = localConvFFT[i][0] * RefMapFFT[i][0] + localConvFFT[i][1] * RefMapFFT[i][1];
		localCCT[i][1] = localConvFFT[i][1] * RefMapFFT[i][0] - localConvFFT[i][0] * RefMapFFT[i][1];
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	}

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	myfftw_execute_dft_c2r(param.fft_plan_c2r_backward, localCCT, lCC);
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	doRefMapFFT(iRefMap, iOrient, iConv, lCC, sumC, sumsquareC, pProb, param.param_device, RefMap);
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}
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int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
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{
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	// **************************************************************************************
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	// ****  BioEM Create Projection routine in Euler angle predefined grid******************
	// ********************* and turns projection into Fourier space ************************
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	// **************************************************************************************
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	myfloat3_t RotatedPointsModel[Model.nPointsModel];
	myfloat_t rotmat[3][3];
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	myfloat_t alpha, gam, beta;
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	myfloat_t* localproj;
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	localproj = lCC[omp_get_thread_num()];
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	memset(localproj, 0, param.param_device.NumberPixels * param.param_device.NumberPixels * sizeof(*localproj));
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	alpha = param.angles[iMap].pos[0];
	beta = param.angles[iMap].pos[1];
	gam = param.angles[iMap].pos[2];
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	// **** To see how things are going: cout << "Id " << omp_get_thread_num() <<  " Angs: " << alpha << " " << beta << " " << gam << "\n"; ***
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	// ********** Creat Rotation with pre-defiend grid of orientations**********
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	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++)
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	{
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		RotatedPointsModel[n].pos[0] = 0.0;
		RotatedPointsModel[n].pos[1] = 0.0;
		RotatedPointsModel[n].pos[2] = 0.0;
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	}
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	for(int n = 0; n < Model.nPointsModel; n++)
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	{
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		for(int k = 0; k < 3; k++)
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		{
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			for(int j = 0; j < 3; j++)
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			{
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				RotatedPointsModel[n].pos[k] += rotmat[k][j] * Model.PointsModel[n].pos[j];
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			}
		}
	}

	int i, j;

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	// ************ Projection over the Z axis********************
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	for(int n = 0; n < Model.nPointsModel; n++)
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	{
		//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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	}

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

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	// ***** 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, myfloat_t* Mapconv, mycomplex_t* localmultFFT, myfloat_t& sumC, myfloat_t& sumsquareC)
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{
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	// **************************************************************************************
	// ****  BioEM Create Convoluted Projection Map routine, multiplies in Fourier **********
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	// **************** calculated Projection with convoluted precalculated Kernel***********
	// *************** and Backtransforming it to real Space ********************************
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	// **************************************************************************************
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	mycomplex_t* tmp = localCCT[omp_get_thread_num()];
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	// **** Multiplying FFTmap with corresponding kernel ****
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	const mycomplex_t* refCTF = &param.refCTF[iConv * param.FFTMapSize];
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	for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D; i++)
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	{
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		localmultFFT[i][0] = lproj[i][0] * refCTF[i][0] + lproj[i][1] * refCTF[i][1];
		localmultFFT[i][1] = lproj[i][1] * refCTF[i][0] - lproj[i][0] * refCTF[i][1];
		// cout << "GG " << i << " " << j << " " << refCTF[i][0] << " " << refCTF[i][1] <<" " <<lproj[i][0] <<" " <<lproj[i][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, Mapconv);
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	// *** Calculating Cross-correlations of cal-convoluted map with its self *****
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	sumC = 0;
	sumsquareC = 0;
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	for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberPixels; i++)
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	{
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		sumC += Mapconv[i];
		sumsquareC += Mapconv[i] * Mapconv[i];
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	}
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	// *** The DTF gives an unnormalized value so have to divded by the total number of pixels in Fourier ***
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	// Normalizing
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	myfloat_t norm2 = (myfloat_t) (param.param_device.NumberPixels * param.param_device.NumberPixels);
	myfloat_t norm4 = norm2 * norm2;
	sumC = sumC / norm2;
	sumsquareC = sumsquareC / norm4;
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	return(0);
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}

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int bioem::calcross_cor(myfloat_t* localmap, myfloat_t& sum, myfloat_t& sumsquare)
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{
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	// *********************** Routine to calculate Cross correlations***********************
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	sum = 0.0;
	sumsquare = 0.0;
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	for (int i = 0; i < param.param_device.NumberPixels; i++)
	{
		for (int j = 0; j < param.param_device.NumberPixels; j++)
		{
			// Calculate Sum of pixels
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			sum += localmap[i * param.param_device.NumberPixels + j];
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			// Calculate Sum of pixels squared
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			sumsquare += localmap[i * param.param_device.NumberPixels + j] * localmap[i * param.param_device.NumberPixels + j];
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		}
	}
	return(0);
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}

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

int bioem::deviceStartRun()
{
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	if (FFTAlgo)
	{
		const int count = omp_get_max_threads();
		localCCT = new mycomplex_t*[count];
		lCC = new myfloat_t*[count];
		for (int i = 0;i < count;i++)
		{
			localCCT[i] = (mycomplex_t *) myfftw_malloc(sizeof(mycomplex_t) * param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D);
			lCC[i] = (myfloat_t *) myfftw_malloc(sizeof(myfloat_t) * param.param_device.NumberPixels * param.param_device.NumberPixels);
		}
	}
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	return(0);
}

int bioem::deviceFinishRun()
{
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	if (FFTAlgo)
	{
		const int count = omp_get_max_threads();
		for (int i = 0;i < count;i++)
		{
			myfftw_free(localCCT[i]);
			myfftw_free(lCC[i]);
		}
		delete[] localCCT;
		delete[] lCC;
	}
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	return(0);
}