bioem.cpp 21.6 KB
Newer Older
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33
#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)
{
34 35
	copy(v.begin(), v.end(), ostream_iterator<T>(os, " "));
	return os;
36 37 38 39
}

bioem::bioem()
{
40
	FFTAlgo = getenv("FFTALGO") == NULL ? 0 : atoi(getenv("FFTALGO"));
41 42 43 44
}

bioem::~bioem()
{
David Rohr's avatar
David Rohr committed
45

46 47 48 49
}

int bioem::configure(int ac, char* av[])
{
50 51 52 53 54 55 56
	/**************************************************************************************/
	/**** Configuration Routine using boost for extracting parameters, models and maps ****/
	/**************************************************************************************/
	/****** And Precalculating necessary grids, map crosscorrelations and kernels  ********/
	/*************************************************************************************/

	/*** Inizialzing default variables ***/
57 58 59
	std::string infile, modelfile, mapfile;
	Model.readPDB = false;
	param.writeAngles = false;
60 61
	param.dumpMap = false;
	param.loadMap = false;
62

63 64 65
	/*************************************************************************************/
	cout << " ++++++++++++ FROM COMMAND LINE +++++++++++\n\n";
	/*************************************************************************************/
66

67
	/********************* Command line reading input with BOOST ************************/
68

69 70 71 72 73 74 75
	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")
76 77
		("DumpMaps", "(Optional) Dump maps after they were red from maps file")
		("LoadMapDump", "(Optional) Read Maps from dump instead of maps file")
78 79 80 81 82 83 84 85
		("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);
86 87 88
		p.add("DumpMaps", -1);
		p.add("LoadMapDump", -1);

89 90 91 92 93 94 95
		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;
96
			return 1;
97 98 99 100
		}
		if (vm.count("help")) {
			cout << "Usage: options_description [options]\n";
			cout << desc;
101
			return 1;
102 103 104 105 106
		}

		if (vm.count("Inputfile"))
		{
			cout << "Input file is: ";
107 108
			cout << vm["Inputfile"].as< std::string >() << "\n";
			infile = vm["Inputfile"].as< std::string >();
109 110 111 112 113
		}
		if (vm.count("Modelfile"))
		{
			cout << "Model file is: "
				 << vm["Modelfile"].as<  std::string  >() << "\n";
114
			modelfile = vm["Modelfile"].as<  std::string  >();
115 116 117 118 119
		}

		if (vm.count("ReadPDB"))
		{
			cout << "Reading model file in PDB format.\n";
120
			Model.readPDB = true;
121 122 123 124 125
		}

		if (vm.count("DumpMaps"))
		{
			cout << "Dumping Maps after reading from file.\n";
126
			param.dumpMap = true;
127 128 129 130 131
		}

		if (vm.count("LoadMapDump"))
		{
			cout << "Loading Map dump.\n";
132
			param.loadMap = true;
133 134 135 136 137 138
		}

		if (vm.count("Particlesfile"))
		{
			cout << "Paricle file is: "
				 << vm["Particlesfile"].as< std::string >() << "\n";
139
			mapfile = vm["Particlesfile"].as< std::string >();
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160
		}
	}
	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
161
	param.filemap = mapfile.c_str();
162 163 164 165
	RefMap.readRefMaps(param);

	/****************** Precalculating Necessary Stuff *********************/
	precalculate();
David Rohr's avatar
David Rohr committed
166

167 168 169 170 171
	if (getenv("BIOEM_DEBUG_BREAK"))
	{
		param.nTotGridAngles = atoi(getenv("BIOEM_DEBUG_BREAK"));
		param.nTotCTFs = atoi(getenv("BIOEM_DEBUG_BREAK"));
	}
David Rohr's avatar
David Rohr committed
172

173 174
	deviceInit();

175
	return(0);
176 177 178 179
}

int bioem::precalculate()
{
180 181 182
	/**************************************************************************************/
	/* Precalculating Routine of Orientation grids, Map crosscorrelations and CTF Kernels */
	/**************************************************************************************/
183

184 185
	// Generating Grids of orientations
	param.CalculateGridsParam();
186

187
	myfloat_t sum, sumsquare;
188 189 190 191

	//Precalculating cross-correlations of maps
	for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap ; iRefMap++)
	{
192
		calcross_cor(RefMap.getmap(iRefMap), sum, sumsquare);
193
		//Storing Crosscorrelations in Map class
194 195
		RefMap.sum_RefMap[iRefMap] = sum;
		RefMap.sumsquare_RefMap[iRefMap] = sumsquare;
196
	}
197

198 199
	// Precalculating CTF Kernels stored in class Param
	param.CalculateRefCTF();
200

201 202
	// Precalculating Maps in Fourier space
	RefMap.PreCalculateMapsFFT(param);
203

204
	return(0);
205 206 207 208 209
}


int bioem::run()
{
210 211 212 213 214 215 216 217 218 219 220 221
	/**************************************************************************************/
	/**** 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 ++)
	{
222 223 224
		pProb[iRefMap].Total = 0.0;
		pProb[iRefMap].Constoadd = -9999999;
		pProb[iRefMap].max_prob = -9999999;
225
		for (int iOrient = 0; iOrient < param.nTotGridAngles; iOrient ++)
226
		{
227 228
			pProb[iRefMap].forAngles[iOrient] = 0.0;
			pProb[iRefMap].ConstAngle[iOrient] = -99999999;
229 230 231
		}
	}
	/**************************************************************************************/
232 233
	deviceStartRun();

234
	/******************************** MAIN CYCLE ******************************************/
David Rohr's avatar
David Rohr committed
235

236 237
	/*** Declaring Private variables for each thread *****/
	mycomplex_t* proj_mapFFT;
238
	myfloat_t* conv_map = new myfloat_t[param.param_device.NumberPixels * param.param_device.NumberPixels];
239
	mycomplex_t* conv_mapFFT;
240
	myfloat_t sumCONV, sumsquareCONV;
241 242

	//allocating fftw_complex vector
243 244
	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);
245 246 247 248 249

	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)));
250 251 252 253
	for (int iProjectionOut = 0; iProjectionOut < param.nTotGridAngles; iProjectionOut++)
	{
		/***************************************************************************************/
		/***** Creating Projection for given orientation and transforming to Fourier space *****/
254
		timer.ResetStart();
255
		createProjection(iProjectionOut, proj_mapFFT);
256 257
		printf("Time Projection %d: %f\n", iProjectionOut, timer.GetCurrentElapsedTime());

258 259 260 261
		/***************************************************************************************/
		/***** **** Internal Loop over convolutions **** *****/
		for (int iConv = 0; iConv < param.nTotCTFs; iConv++)
		{
262
			printf("\t\tConvolution %d %d\n", iProjectionOut, iConv);
263 264
			/*** Calculating convolutions of projection map and crosscorrelations ***/

265
			timer.ResetStart();
266
			createConvolutedProjectionMap(iProjectionOut, iConv, proj_mapFFT, conv_map, conv_mapFFT, sumCONV, sumsquareCONV);
267 268
			printf("Time Convolution %d %d: %f\n", iProjectionOut, iConv, timer.GetCurrentElapsedTime());

269 270
			/***************************************************************************************/
			/*** Comparing each calculated convoluted map with all experimental maps ***/
271
			timer.ResetStart();
272
			compareRefMaps(iProjectionOut, iConv, conv_map, conv_mapFFT, sumCONV, sumsquareCONV);
273

274 275 276
			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 *
277
								  (((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;
278
			const double nGBs = (double) RefMap.ntotRefMap * (double) nShifts * (double) nShifts *
279
								(((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;
280 281 282
			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.);
283 284 285 286 287
		}
	}
	//deallocating fftw_complex vector
	myfftw_free(proj_mapFFT);
	myfftw_free(conv_mapFFT);
288
	delete[] conv_map;
David Rohr's avatar
David Rohr committed
289

290 291
	deviceFinishRun();

292
	/************* Writing Out Probabilities ***************/
293

294
	/*** Angular Probability ***/
295

296 297 298 299
	// if(param.writeAngles){
	ofstream angProbfile;
	angProbfile.open ("ANG_PROB_iRefMap");
	// }
300

301 302
	ofstream outputProbFile;
	outputProbFile.open ("Output_Probabilities");
303

304 305 306
	for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap; iRefMap ++)
	{
		/**** Total Probability ***/
307
		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";
308 309 310 311 312 313 314 315 316 317 318

		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] << " ";
319 320
		outputProbFile << pProb[iRefMap].max_prob_cent_x << " ";
		outputProbFile << pProb[iRefMap].max_prob_cent_y;
321
		outputProbFile << "\n";
322

323
		/*** For individual files***/ //angProbfile.open ("ANG_PROB_"iRefMap);
324

325
		if(param.writeAngles)
326
		{
327 328
			for (int iProjectionOut = 0; iProjectionOut < param.nTotGridAngles; iProjectionOut++)
			{
329
				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";
330

331 332 333
			}
		}
	}
334

335 336
	angProbfile.close();
	outputProbFile.close();
337

338
	//Deleting allocated pointers
339

340 341 342 343 344 345 346 347 348
	if (pProb)
	{
		delete[] pProb;
		pProb = NULL;
	}

	if (param.refCTF)
	{
		delete[] param.refCTF;
349
		param.refCTF = NULL;
350
	}
351

352
	RefMap.freePointers();
353
	return(0);
354 355
}

356
int bioem::compareRefMaps(int iProjectionOut, int iConv, const myfloat_t* conv_map, mycomplex_t* localmultFFT, myfloat_t sumC, myfloat_t sumsquareC, const int startMap)
357
{
358
	if (FFTAlgo)
359
	{
360
		#pragma omp parallel
361 362 363
		{
			mycomplex_t *localCCT;
			myfloat_t *lCC;
364 365
			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);
366 367 368 369 370 371 372 373 374

			const int num_threads = omp_get_num_threads();
			const int thread_id = omp_get_thread_num();
			const int mapsPerThread = (RefMap.ntotRefMap - startMap + num_threads - 1) / num_threads;
			const int iStart = startMap + thread_id * mapsPerThread;
			const int iEnd = min(RefMap.ntotRefMap, startMap + (thread_id + 1) * mapsPerThread);

			for (int iRefMap = iStart; iRefMap < iEnd; iRefMap ++)
			{
375
				calculateCCFFT(iRefMap, iProjectionOut, iConv, sumC, sumsquareC, localmultFFT, localCCT, lCC);
376 377 378 379 380 381
			}
			myfftw_free(localCCT);
			myfftw_free(lCC);
		}
	}
	else
382
	{
383
		#pragma omp parallel for
384
		for (int iRefMap = startMap; iRefMap < RefMap.ntotRefMap; iRefMap ++)
385
		{
386
			compareRefMapShifted < -1 > (iRefMap, iProjectionOut, iConv, conv_map, pProb, param.param_device, RefMap);
387 388 389 390 391
		}
	}
	return(0);
}

392
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)
393
{
394
	const mycomplex_t* RefMapFFT = &RefMap.RefMapsFFT[iRefMap * param.FFTMapSize];
395
	for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D; i++)
396
	{
397 398
		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];
399 400
	}

401
	myfftw_execute_dft_c2r(param.fft_plan_c2r_backward, localCCT, lCC);
402

403
	doRefMapFFT(iRefMap, iOrient, iConv, lCC, sumC, sumsquareC, pProb, param.param_device, RefMap);
404
}
405

406
int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
407
{
408 409 410 411 412 413 414
	/**************************************************************************************/
	/****  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];
415
	myfloat_t alpha, gam, beta;
416
	myfloat_t* localproj;
417

418 419
	localproj = (myfloat_t *) myfftw_malloc(sizeof(myfloat_t) * param.param_device.NumberPixels * param.param_device.NumberPixels);
	memset(localproj, 0, param.param_device.NumberPixels * param.param_device.NumberPixels * sizeof(*localproj));
420

421 422 423
	alpha = param.angles[iMap].pos[0];
	beta = param.angles[iMap].pos[1];
	gam = param.angles[iMap].pos[2];
424 425 426 427 428

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

429 430 431 432 433 434 435 436 437 438 439
	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++)
440
	{
441 442 443
		RotatedPointsModel[n].pos[0] = 0.0;
		RotatedPointsModel[n].pos[1] = 0.0;
		RotatedPointsModel[n].pos[2] = 0.0;
444
	}
445
	for(int n = 0; n < Model.nPointsModel; n++)
446
	{
447
		for(int k = 0; k < 3; k++)
448
		{
449
			for(int j = 0; j < 3; j++)
450
			{
451
				RotatedPointsModel[n].pos[k] += rotmat[k][j] * Model.PointsModel[n].pos[j];
452 453 454 455 456 457 458
			}
		}
	}

	int i, j;

	/************ Projection over the Z axis********************/
459
	for(int n = 0; n < Model.nPointsModel; n++)
460 461
	{
		//Getting pixel that represents coordinates & shifting the start at to Numpix/2,Numpix/2 )
462 463
		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);
464

465
		localproj[i * param.param_device.NumberPixels + j] += Model.densityPointsModel[n] / Model.NormDen;
466 467 468
	}

	/**** Output Just to check****/
469
	if(iMap == 10)
470 471 472 473 474 475
	{
		ofstream myexamplemap;
		ofstream myexampleRot;
		myexamplemap.open ("MAP_i10");
		myexampleRot.open ("Rot_i10");
		myexamplemap << "ANGLES " << alpha << " " << beta << " " << gam << "\n";
476
		for(int k = 0; k < param.param_device.NumberPixels; k++)
477
		{
478
			for(int j = 0; j < param.param_device.NumberPixels; j++) myexamplemap << "\nMAP " << k << " " << j << " " << localproj[k * param.param_device.NumberPixels + j];
479 480
		}
		myexamplemap << " \n";
481
		for(int n = 0; n < Model.nPointsModel; n++)myexampleRot << "\nCOOR " << RotatedPointsModel[n].pos[0] << " " << RotatedPointsModel[n].pos[1] << " " << RotatedPointsModel[n].pos[2];
482 483 484 485 486 487
		myexamplemap.close();
		myexampleRot.close();
	}

	/***** Converting projection to Fourier Space for Convolution later with kernel****/
	/********** Omp Critical is necessary with FFTW*******/
488
	myfftw_execute_dft_r2c(param.fft_plan_r2c_forward, localproj, mapFFT);
489 490 491 492

	return(0);
}

493
int bioem::createConvolutedProjectionMap(int iMap, int iConv, mycomplex_t* lproj, myfloat_t* Mapconv, mycomplex_t* localmultFFT, myfloat_t& sumC, myfloat_t& sumsquareC)
494 495 496 497 498 499 500
{
	/**************************************************************************************/
	/****  BioEM Create Convoluted Projection Map routine, multiplies in Fourier **********
	**************** calculated Projection with convoluted precalculated Kernel**********
	*************** and Backtransforming it to real Space ******************************/
	/**************************************************************************************/

501
	myfloat_t* localconvFFT;
502
	localconvFFT = (myfloat_t *) myfftw_malloc(sizeof(myfloat_t) * param.param_device.NumberPixels * param.param_device.NumberPixels);
503 504
	mycomplex_t* tmp;
	tmp = (mycomplex_t*) myfftw_malloc(sizeof(mycomplex_t) * param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D);
505 506 507

	/**** Multiplying FFTmap with corresponding kernel ****/

508
	const mycomplex_t* refCTF = &param.refCTF[iConv * param.FFTMapSize];
509
	for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D; i++)
510
	{
511 512 513
		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";
514 515
	}

516 517 518
	//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);

519
	/**** Bringing convoluted Map to real Space ****/
520
	myfftw_execute_dft_c2r(param.fft_plan_c2r_backward, tmp, localconvFFT);
521 522

	/****Asigning convolution fftw_complex to bioem_map ****/
523
	for(int i = 0; i < param.param_device.NumberPixels ; i++ )
524
	{
525
		for(int j = 0; j < param.param_device.NumberPixels ; j++ )
526
		{
527
			Mapconv[i * param.param_device.NumberPixels + j] = localconvFFT[i * param.param_device.NumberPixels + j];
528 529 530 531
		}
	}

	/*** Calculating Cross-correlations of cal-convoluted map with its self *****/
532 533
	sumC = 0;
	sumsquareC = 0;
534
	for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberPixels; i++)
535
	{
536 537
		sumC += localconvFFT[i];
		sumsquareC += localconvFFT[i] * localconvFFT[i];
538 539 540
	}
	/*** The DTF gives an unnormalized value so have to divded by the total number of pixels in Fourier ***/
	// Normalizing
541 542 543 544
	myfloat_t norm2 = (myfloat_t) (param.param_device.NumberPixels * param.param_device.NumberPixels);
	myfloat_t norm4 = norm2 * norm2;
	sumC = sumC / norm2;
	sumsquareC = sumsquareC / norm4;
545 546

	/**** Freeing fftw_complex created (dont know if omp critical is necessary) ****/
547
	myfftw_free(localconvFFT);
548
	myfftw_free(tmp);
549 550

	return(0);
551 552
}

553
int bioem::calcross_cor(myfloat_t* localmap, myfloat_t& sum, myfloat_t& sumsquare)
554
{
555 556
	/*********************** Routine to calculate Cross correlations***********************/

557 558
	sum = 0.0;
	sumsquare = 0.0;
559 560 561 562 563
	for (int i = 0; i < param.param_device.NumberPixels; i++)
	{
		for (int j = 0; j < param.param_device.NumberPixels; j++)
		{
			// Calculate Sum of pixels
564
			sum += localmap[i * param.param_device.NumberPixels + j];
565
			// Calculate Sum of pixels squared
566
			sumsquare += localmap[i * param.param_device.NumberPixels + j] * localmap[i * param.param_device.NumberPixels + j];
567 568 569
		}
	}
	return(0);
570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585
}

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

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

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