bioem.cpp 25.6 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 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 62
	RefMap.dumpMap = false;
	RefMap.loadMap = false;

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 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165
		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();
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

187 188 189 190 191 192 193 194 195 196
	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;
	}
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()
{
210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225
	/**************************************************************************************/
	/**** 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 ++)
226
		{
227 228 229 230 231
			pProb[iRefMap].forAngles[iOrient]=0.0;
			pProb[iRefMap].ConstAngle[iOrient]=-99999999;
		}
	}
	/**************************************************************************************/
232 233
	deviceStartRun();

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

236 237 238 239 240
	/*** Declaring Private variables for each thread *****/
	mycomplex_t* proj_mapFFT;
	bioem_map conv_map;
	mycomplex_t* conv_mapFFT;
	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();
272 273 274 275 276 277 278 279 280
			if (FFTAlgo == 0)
			{
				compareRefMaps(iProjectionOut, iConv, conv_map);
			}
			else
			{
				compareRefMaps2(iProjectionOut, iConv,conv_mapFFT,sumCONV,sumsquareCONV);
			}

281 282 283
			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 *
284
								  (((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;
285
			const double nGBs = (double) RefMap.ntotRefMap * (double) nShifts * (double) nShifts *
286
								(((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;
287 288 289
			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.);
290 291 292 293 294
		}
	}
	//deallocating fftw_complex vector
	myfftw_free(proj_mapFFT);
	myfftw_free(conv_mapFFT);
David Rohr's avatar
David Rohr committed
295

296 297
	deviceFinishRun();

298
	/************* Writing Out Probabilities ***************/
299

300
	/*** Angular Probability ***/
301

302 303 304 305
	// if(param.writeAngles){
	ofstream angProbfile;
	angProbfile.open ("ANG_PROB_iRefMap");
	// }
306

307 308
	ofstream outputProbFile;
	outputProbFile.open ("Output_Probabilities");
309

310 311 312 313 314 315 316 317 318 319 320 321 322 323 324
	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] << " ";
325 326
		outputProbFile << pProb[iRefMap].max_prob_cent_x << " ";
		outputProbFile << pProb[iRefMap].max_prob_cent_y;
327
		outputProbFile << "\n";
328

329
		/*** For individual files***/ //angProbfile.open ("ANG_PROB_"iRefMap);
330

331
		if(param.writeAngles)
332
		{
333 334 335
			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";
336

337 338 339
			}
		}
	}
340

341 342
	angProbfile.close();
	outputProbFile.close();
343

344
	//Deleting allocated pointers
345

346 347 348 349 350 351 352 353 354 355 356
	if (pProb)
	{
		delete[] pProb;
		pProb = NULL;
	}

	if (param.refCTF)
	{
		delete[] param.refCTF;
		param.refCTF =NULL;
	}
357

358 359 360 361 362 363
	if(RefMap.RefMapFFT)
	{
		delete[] RefMap.RefMapFFT;
		RefMap.RefMapFFT = NULL;
	}
	return(0);
364 365
}

366
int bioem::compareRefMaps(int iProjectionOut, int iConv, const bioem_map& conv_map, const int startMap)
367
{
368
#pragma omp parallel for
369 370 371 372 373
	for (int iRefMap = startMap; iRefMap < RefMap.ntotRefMap; iRefMap ++)
	{
		compareRefMapShifted<-1>(iRefMap,iProjectionOut,iConv,conv_map, pProb, param.param_device, RefMap);
	}
	return(0);
374 375
}

376
int bioem::compareRefMaps2(int iOrient, int iConv, mycomplex_t* localConvFFT,myfloat_t sumC,myfloat_t sumsquareC)
377
{
378
#pragma omp parallel
379
	{
380 381 382 383
		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);
384

385 386 387 388 389 390 391
		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 ++)
392
		{
393
			calculateCCFFT(iRefMap,iOrient, iConv, sumC,sumsquareC, localConvFFT, localCCT,lCC);
394 395 396 397
		}
		myfftw_free(localCCT);
		myfftw_free(lCC);
	}
398

399 400 401 402
	return(0);
}

/////////////NEW ROUTINE ////////////////
403
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)
404
{
405
	for(int i = 0;i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D;i++)
406
	{
407 408
		localCCT[i][0] = localConvFFT[i][0] * RefMap.RefMapFFT[iRefMap].cpoints[i][0] + localConvFFT[i][1] * RefMap.RefMapFFT[iRefMap].cpoints[i][1];
		localCCT[i][1] = localConvFFT[i][1] * RefMap.RefMapFFT[iRefMap].cpoints[i][0] - localConvFFT[i][0] * RefMap.RefMapFFT[iRefMap].cpoints[i][1];
409 410
	}

411
	myfftw_execute_dft_c2r(param.fft_plan_c2r_backward,localCCT,lCC);
412 413 414 415 416 417

// 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)
		{
418
			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);
419 420 421
		}
		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)
		{
422
			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);
423 424 425 426 427 428
		}
	}
	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)
		{
429
			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);
430 431 432
		}
		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)
		{
433
			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);
434 435
		}
	}
436

437 438
	return (0);
}
439

440
inline int bioem::calProb(int iRefMap,int iOrient, int iConv,myfloat_t sumC,myfloat_t sumsquareC, int value, int disx, int disy)
441
{
442

443 444 445
	/********************************************************/
	/*********** Calculates the BioEM probability ***********/
	/********************************************************/
446

447
	const myfloat_t ForLogProb = (sumsquareC * param.param_device.Ntotpi - sumC * sumC);
448

449
		// Products of different cross-correlations (first element in formula)
450 451
		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;
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

		//******* 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;
479 480
				pProb[iRefMap].max_prob_cent_x = disx;
				pProb[iRefMap].max_prob_cent_y = disy;
481 482 483 484 485
				pProb[iRefMap].max_prob_orient = iOrient;
				pProb[iRefMap].max_prob_conv = iConv;
			}
		}
	return (0);
486 487 488
}


489
int bioem::createProjection(int iMap,mycomplex_t* mapFFT)
490
{
491 492 493 494 495 496 497 498
	/**************************************************************************************/
	/****  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;
499
	myfloat_t* localproj;
500

501
	localproj= (myfloat_t *) myfftw_malloc(sizeof(myfloat_t) *param.param_device.NumberPixels*param.param_device.NumberPixels);
502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545
	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 )
546 547
		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);
548

549
		localproj[i*param.param_device.NumberPixels+j]+=Model.densityPointsModel[n]/Model.NormDen;
550 551 552 553 554 555 556 557 558 559 560 561
	}

	/**** 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++)
		{
562
			for(int j=0; j<param.param_device.NumberPixels; j++) myexamplemap << "\nMAP " << k << " " << j<< " " <<localproj[k*param.param_device.NumberPixels+j];
563 564 565 566 567 568 569 570 571
		}
		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*******/
572
	myfftw_execute_dft_r2c(param.fft_plan_r2c_forward,localproj,mapFFT);
573 574 575 576

	return(0);
}

577
int bioem::createConvolutedProjectionMap(int iMap,int iConv,mycomplex_t* lproj,bioem_map& Mapconv, mycomplex_t* localmultFFT, myfloat_t& sumC, myfloat_t& sumsquareC)
578 579 580 581 582 583 584
{
	/**************************************************************************************/
	/****  BioEM Create Convoluted Projection Map routine, multiplies in Fourier **********
	**************** calculated Projection with convoluted precalculated Kernel**********
	*************** and Backtransforming it to real Space ******************************/
	/**************************************************************************************/

585 586 587 588
	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);
589 590 591

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

592
	for(int i=0;i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D;i++)
593
	{
594 595 596
		localmultFFT[i][0] = lproj[i][0] * param.refCTF[iConv].cpoints[i][0] + lproj[i][1] * param.refCTF[iConv].cpoints[i][1];
		localmultFFT[i][1] = lproj[i][1] * param.refCTF[iConv].cpoints[i][0] - lproj[i][0] * param.refCTF[iConv].cpoints[i][1];
		// cout << "GG " << i << " " << j << " " << param.refCTF[iConv].cpoints[i][0] << " " <<param.refCTF[iConv].cpoints[i][1] <<" " <<lproj[i][0] <<" " <<lproj[i][1] << "\n";
597 598
	}

599 600 601
	//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);

602
	/**** Bringing convoluted Map to real Space ****/
603
	myfftw_execute_dft_c2r(param.fft_plan_c2r_backward,tmp,localconvFFT);
604 605 606 607 608 609

	/****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++ )
		{
610
			Mapconv.points[i][j]=localconvFFT[i*param.param_device.NumberPixels+j];
611 612 613 614 615 616
		}
	}

	/*** Calculating Cross-correlations of cal-convoluted map with its self *****/
	sumC=0;
	sumsquareC=0;
617
	for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberPixels; i++)
618
	{
619 620
		sumC += localconvFFT[i];
		sumsquareC += localconvFFT[i] * localconvFFT[i];
621 622 623
	}
	/*** The DTF gives an unnormalized value so have to divded by the total number of pixels in Fourier ***/
	// Normalizing
624 625 626 627
	myfloat_t norm2 = (myfloat_t) (param.param_device.NumberPixels * param.param_device.NumberPixels);
	myfloat_t norm4 = norm2 * norm2;
	sumC = sumC / norm2;
	sumsquareC = sumsquareC / norm4;
628 629

	/**** Freeing fftw_complex created (dont know if omp critical is necessary) ****/
630
	myfftw_free(localconvFFT);
631
	myfftw_free(tmp);
632 633

	return(0);
634 635 636 637
}

int bioem::calcross_cor(bioem_map& localmap,myfloat_t& sum,myfloat_t& sumsquare)
{
638 639 640 641 642 643 644 645 646 647 648 649 650 651 652
	/*********************** 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);
653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668
}

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

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

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