bioem.cpp 21.8 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 57 58 59
	/**************************************************************************************/
	/**** 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;
60 61
	RefMap.dumpMap = false;
	RefMap.loadMap = false;
62 63
        RefMap.readMRC = false;
	RefMap.readMultMRC = false;
64

65 66 67
	/*************************************************************************************/
	cout << " ++++++++++++ FROM COMMAND LINE +++++++++++\n\n";
	/*************************************************************************************/
68

69
	/********************* Command line reading input with BOOST ************************/
70

71 72 73 74 75 76 77
	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")
78 79
                ("ReadMRC", "(Optional) If reading particle file in MRC format")
		 ("ReadMultipleMRC", "(Optional) If reading Multiple MRCs")
80 81
		("DumpMaps", "(Optional) Dump maps after they were red from maps file")
		("LoadMapDump", "(Optional) Read Maps from dump instead of maps file")
82 83 84 85 86 87 88 89
		("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);
90 91
                p.add("ReadMRC", -1);
                p.add("ReadMultipleMRC", -1);
92 93 94
		p.add("DumpMaps", -1);
		p.add("LoadMapDump", -1);

95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127
		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;
		}
128 129 130 131 132 133 134 135 136 137 138
		if (vm.count("ReadMRC"))
                {
                        cout << "Reading particle file in MRC format.\n";
                        RefMap.readMRC=true;
                }
                
		if (vm.count("ReadMultipleMRC"))
                {
                        cout << "Reading Multiple MRCs.\n";
                        RefMap.readMultMRC=true;
                }
139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182

		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();
David Rohr's avatar
David Rohr committed
183

184 185 186 187 188
	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
189

190 191
	deviceInit();

192
	return(0);
193 194 195 196
}

int bioem::precalculate()
{
197 198 199
	/**************************************************************************************/
	/* Precalculating Routine of Orientation grids, Map crosscorrelations and CTF Kernels */
	/**************************************************************************************/
200

201 202
	// Generating Grids of orientations
	param.CalculateGridsParam();
203

204 205 206 207 208 209 210 211 212 213
	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;
	}
214

215 216
	// Precalculating CTF Kernels stored in class Param
	param.CalculateRefCTF();
217

218 219
	// Precalculating Maps in Fourier space
	RefMap.PreCalculateMapsFFT(param);
220

221
	return(0);
222 223 224 225 226
}


int bioem::run()
{
227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242
	/**************************************************************************************/
	/**** 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 ++)
243
		{
244 245 246 247 248
			pProb[iRefMap].forAngles[iOrient]=0.0;
			pProb[iRefMap].ConstAngle[iOrient]=-99999999;
		}
	}
	/**************************************************************************************/
249 250
	deviceStartRun();

251
	/******************************** MAIN CYCLE ******************************************/
David Rohr's avatar
David Rohr committed
252

253 254 255 256 257
	/*** Declaring Private variables for each thread *****/
	mycomplex_t* proj_mapFFT;
	bioem_map conv_map;
	mycomplex_t* conv_mapFFT;
	myfloat_t sumCONV,sumsquareCONV;
258 259

	//allocating fftw_complex vector
260 261
	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);
262 263 264 265 266

	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)));
267 268 269 270
	for (int iProjectionOut = 0; iProjectionOut < param.nTotGridAngles; iProjectionOut++)
	{
		/***************************************************************************************/
		/***** Creating Projection for given orientation and transforming to Fourier space *****/
271
		timer.ResetStart();
272
		createProjection(iProjectionOut, proj_mapFFT);
273 274
		printf("Time Projection %d: %f\n", iProjectionOut, timer.GetCurrentElapsedTime());

275 276 277 278
		/***************************************************************************************/
		/***** **** Internal Loop over convolutions **** *****/
		for (int iConv = 0; iConv < param.nTotCTFs; iConv++)
		{
279
			printf("\t\tConvolution %d %d\n", iProjectionOut, iConv);
280 281
			/*** Calculating convolutions of projection map and crosscorrelations ***/

282
			timer.ResetStart();
283
			createConvolutedProjectionMap(iProjectionOut, iConv, proj_mapFFT, conv_map, conv_mapFFT, sumCONV, sumsquareCONV);
284 285
			printf("Time Convolution %d %d: %f\n", iProjectionOut, iConv, timer.GetCurrentElapsedTime());

286 287
			/***************************************************************************************/
			/*** Comparing each calculated convoluted map with all experimental maps ***/
288
			timer.ResetStart();
289
			compareRefMaps(iProjectionOut, iConv, conv_map, conv_mapFFT, sumCONV, sumsquareCONV);
290

291 292 293
			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 *
294
								  (((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;
295
			const double nGBs = (double) RefMap.ntotRefMap * (double) nShifts * (double) nShifts *
296
								(((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;
297 298 299
			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.);
300 301 302 303 304
		}
	}
	//deallocating fftw_complex vector
	myfftw_free(proj_mapFFT);
	myfftw_free(conv_mapFFT);
David Rohr's avatar
David Rohr committed
305

306 307
	deviceFinishRun();

308
	/************* Writing Out Probabilities ***************/
309

310
	/*** Angular Probability ***/
311

312 313 314 315
	// if(param.writeAngles){
	ofstream angProbfile;
	angProbfile.open ("ANG_PROB_iRefMap");
	// }
316

317 318
	ofstream outputProbFile;
	outputProbFile.open ("Output_Probabilities");
319

320 321 322 323 324 325 326 327 328 329 330 331 332 333 334
	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] << " ";
335 336
		outputProbFile << pProb[iRefMap].max_prob_cent_x << " ";
		outputProbFile << pProb[iRefMap].max_prob_cent_y;
337
		outputProbFile << "\n";
338

339
		/*** For individual files***/ //angProbfile.open ("ANG_PROB_"iRefMap);
340

341
		if(param.writeAngles)
342
		{
343 344 345
			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";
346

347 348 349
			}
		}
	}
350

351 352
	angProbfile.close();
	outputProbFile.close();
353

354
	//Deleting allocated pointers
355

356 357 358 359 360 361 362 363 364 365 366
	if (pProb)
	{
		delete[] pProb;
		pProb = NULL;
	}

	if (param.refCTF)
	{
		delete[] param.refCTF;
		param.refCTF =NULL;
	}
367

368
	if(RefMap.RefMapsFFT)
369
	{
370 371
		delete[] RefMap.RefMapsFFT;
		RefMap.RefMapsFFT = NULL;
372 373
	}
	return(0);
374 375
}

376
int bioem::compareRefMaps(int iProjectionOut, int iConv, const bioem_map& conv_map, mycomplex_t* localmultFFT, myfloat_t sumC, myfloat_t sumsquareC, const int startMap)
377
{
378
	if (FFTAlgo)
379
	{
380
#pragma omp parallel
381 382 383 384 385 386 387 388 389 390 391 392 393 394
		{
			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);

			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 ++)
			{
395
				calculateCCFFT(iRefMap,iProjectionOut, iConv, sumC, sumsquareC, localmultFFT, localCCT,lCC);
396 397 398 399 400 401
			}
			myfftw_free(localCCT);
			myfftw_free(lCC);
		}
	}
	else
402
	{
403 404
#pragma omp parallel for
		for (int iRefMap = startMap; iRefMap < RefMap.ntotRefMap; iRefMap ++)
405
		{
406
			compareRefMapShifted<-1>(iRefMap,iProjectionOut,iConv,conv_map, pProb, param.param_device, RefMap);
407 408 409 410 411
		}
	}
	return(0);
}

412
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)
413
{
414
	const mycomplex_t* RefMapFFT = &RefMap.RefMapsFFT[iRefMap * param.RefMapSize];
415
	for(int i = 0;i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D;i++)
416
	{
417 418
		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];
419 420
	}

421
	myfftw_execute_dft_c2r(param.fft_plan_c2r_backward,localCCT,lCC);
422

423
	doRefMapFFT(iRefMap, iOrient, iConv, lCC, sumC, sumsquareC, pProb, param.param_device, RefMap);
424
}
425

426
int bioem::createProjection(int iMap,mycomplex_t* mapFFT)
427
{
428 429 430 431 432 433 434 435
	/**************************************************************************************/
	/****  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;
436
	myfloat_t* localproj;
437

438
	localproj= (myfloat_t *) myfftw_malloc(sizeof(myfloat_t) *param.param_device.NumberPixels*param.param_device.NumberPixels);
439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481
	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 )
482 483
		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);
484

485
		localproj[i*param.param_device.NumberPixels+j]+=Model.densityPointsModel[n]/Model.NormDen;
486 487 488 489 490 491 492 493 494 495 496 497
	}

	/**** 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++)
		{
498
			for(int j=0; j<param.param_device.NumberPixels; j++) myexamplemap << "\nMAP " << k << " " << j<< " " <<localproj[k*param.param_device.NumberPixels+j];
499 500 501 502 503 504 505 506 507
		}
		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*******/
508
	myfftw_execute_dft_r2c(param.fft_plan_r2c_forward,localproj,mapFFT);
509 510 511 512

	return(0);
}

513
int bioem::createConvolutedProjectionMap(int iMap,int iConv,mycomplex_t* lproj,bioem_map& Mapconv, mycomplex_t* localmultFFT, myfloat_t& sumC, myfloat_t& sumsquareC)
514 515 516 517 518 519 520
{
	/**************************************************************************************/
	/****  BioEM Create Convoluted Projection Map routine, multiplies in Fourier **********
	**************** calculated Projection with convoluted precalculated Kernel**********
	*************** and Backtransforming it to real Space ******************************/
	/**************************************************************************************/

521 522 523 524
	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);
525 526 527

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

528
	const mycomplex_t* refCTF = &param.refCTF[iConv * param.RefMapSize];
529
	for(int i=0;i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D;i++)
530
	{
531 532 533
		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";
534 535
	}

536 537 538
	//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);

539
	/**** Bringing convoluted Map to real Space ****/
540
	myfftw_execute_dft_c2r(param.fft_plan_c2r_backward,tmp,localconvFFT);
541 542 543 544 545 546

	/****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++ )
		{
547
			Mapconv.points[i][j]=localconvFFT[i*param.param_device.NumberPixels+j];
548 549 550 551 552 553
		}
	}

	/*** Calculating Cross-correlations of cal-convoluted map with its self *****/
	sumC=0;
	sumsquareC=0;
554
	for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberPixels; i++)
555
	{
556 557
		sumC += localconvFFT[i];
		sumsquareC += localconvFFT[i] * localconvFFT[i];
558 559 560
	}
	/*** The DTF gives an unnormalized value so have to divded by the total number of pixels in Fourier ***/
	// Normalizing
561 562 563 564
	myfloat_t norm2 = (myfloat_t) (param.param_device.NumberPixels * param.param_device.NumberPixels);
	myfloat_t norm4 = norm2 * norm2;
	sumC = sumC / norm2;
	sumsquareC = sumsquareC / norm4;
565 566

	/**** Freeing fftw_complex created (dont know if omp critical is necessary) ****/
567
	myfftw_free(localconvFFT);
568
	myfftw_free(tmp);
569 570

	return(0);
571 572 573 574
}

int bioem::calcross_cor(bioem_map& localmap,myfloat_t& sum,myfloat_t& sumsquare)
{
575 576 577 578 579 580 581 582 583 584 585 586 587 588 589
	/*********************** 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);
590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605
}

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

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

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