bioem.cpp 24.6 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
			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);
David Rohr's avatar
David Rohr committed
288

289
290
	deviceFinishRun();

291
	/************* Writing Out Probabilities ***************/
292

293
	/*** Angular Probability ***/
294

295
296
297
298
	// if(param.writeAngles){
	ofstream angProbfile;
	angProbfile.open ("ANG_PROB_iRefMap");
	// }
299

300
301
	ofstream outputProbFile;
	outputProbFile.open ("Output_Probabilities");
302

303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
	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] << " ";
318
319
		outputProbFile << pProb[iRefMap].max_prob_cent_x << " ";
		outputProbFile << pProb[iRefMap].max_prob_cent_y;
320
		outputProbFile << "\n";
321

322
		/*** For individual files***/ //angProbfile.open ("ANG_PROB_"iRefMap);
323

324
		if(param.writeAngles)
325
		{
326
327
328
			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";
329

330
331
332
			}
		}
	}
333

334
335
	angProbfile.close();
	outputProbFile.close();
336

337
	//Deleting allocated pointers
338

339
340
341
342
343
344
345
346
347
348
349
	if (pProb)
	{
		delete[] pProb;
		pProb = NULL;
	}

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

351
352
353
354
355
356
	if(RefMap.RefMapFFT)
	{
		delete[] RefMap.RefMapFFT;
		RefMap.RefMapFFT = NULL;
	}
	return(0);
357
358
}

359
int bioem::compareRefMaps(int iProjectionOut, int iConv, const bioem_map& conv_map, mycomplex_t* localmultFFT, myfloat_t sumC, myfloat_t sumsquareC, const int startMap)
360
{
361
	if (FFTAlgo)
362
	{
363
#pragma omp parallel
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
		{
			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 ++)
			{
				calculateCCFFT(iRefMap,iProjectionOut, iConv, sumC,sumsquareC, localmultFFT, localCCT,lCC);
			}
			myfftw_free(localCCT);
			myfftw_free(lCC);
		}
	}
	else
385
	{
386
387
#pragma omp parallel for
		for (int iRefMap = startMap; iRefMap < RefMap.ntotRefMap; iRefMap ++)
388
		{
389
			compareRefMapShifted<-1>(iRefMap,iProjectionOut,iConv,conv_map, pProb, param.param_device, RefMap);
390
391
392
393
394
395
		}
	}
	return(0);
}

/////////////NEW ROUTINE ////////////////
396
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)
397
{
398
	for(int i = 0;i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D;i++)
399
	{
400
401
		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];
402
403
	}

404
	myfftw_execute_dft_c2r(param.fft_plan_c2r_backward,localCCT,lCC);
405
406
407
408
409
410

// 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)
		{
411
			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);
412
413
414
		}
		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)
		{
415
			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);
416
417
418
419
420
421
		}
	}
	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)
		{
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), param.param_device.NumberPixels-cent_x, cent_y);
423
424
425
		}
		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)
		{
426
			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);
427
428
		}
	}
429

430
431
	return (0);
}
432

433
inline int bioem::calProb(int iRefMap,int iOrient, int iConv,myfloat_t sumC,myfloat_t sumsquareC, float value, int disx, int disy)
434
{
435

436
437
438
	/********************************************************/
	/*********** Calculates the BioEM probability ***********/
	/********************************************************/
439

440
	const myfloat_t logpro = calc_logpro(param.param_device, sumC, sumsquareC, value, RefMap.sum_RefMap[iRefMap], RefMap.sumsquare_RefMap[iRefMap]);
441

442
443
444
445
446
447
448
449
	//update_prob<-1>(logpro, iRefMap, iOrient, iConv, disx, disy, pProb);
	//GCC is too stupid to inline properly, so the code is copied here
    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);
450

451
452
453
454
455
456
	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]);
457

458
459
460
461
462
463
464
465
	if(pProb[iRefMap].max_prob < logpro)
	{
		pProb[iRefMap].max_prob = logpro;
		pProb[iRefMap].max_prob_cent_x = disx;
		pProb[iRefMap].max_prob_cent_y = disy;
		pProb[iRefMap].max_prob_orient = iOrient;
		pProb[iRefMap].max_prob_conv = iConv;
	}
466
467

	return (0);
468
469
470
}


471
int bioem::createProjection(int iMap,mycomplex_t* mapFFT)
472
{
473
474
475
476
477
478
479
480
	/**************************************************************************************/
	/****  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;
481
	myfloat_t* localproj;
482

483
	localproj= (myfloat_t *) myfftw_malloc(sizeof(myfloat_t) *param.param_device.NumberPixels*param.param_device.NumberPixels);
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
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
	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 )
528
529
		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);
530

531
		localproj[i*param.param_device.NumberPixels+j]+=Model.densityPointsModel[n]/Model.NormDen;
532
533
534
535
536
537
538
539
540
541
542
543
	}

	/**** 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++)
		{
544
			for(int j=0; j<param.param_device.NumberPixels; j++) myexamplemap << "\nMAP " << k << " " << j<< " " <<localproj[k*param.param_device.NumberPixels+j];
545
546
547
548
549
550
551
552
553
		}
		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*******/
554
	myfftw_execute_dft_r2c(param.fft_plan_r2c_forward,localproj,mapFFT);
555
556
557
558

	return(0);
}

559
int bioem::createConvolutedProjectionMap(int iMap,int iConv,mycomplex_t* lproj,bioem_map& Mapconv, mycomplex_t* localmultFFT, myfloat_t& sumC, myfloat_t& sumsquareC)
560
561
562
563
564
565
566
{
	/**************************************************************************************/
	/****  BioEM Create Convoluted Projection Map routine, multiplies in Fourier **********
	**************** calculated Projection with convoluted precalculated Kernel**********
	*************** and Backtransforming it to real Space ******************************/
	/**************************************************************************************/

567
568
569
570
	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);
571
572
573

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

574
	for(int i=0;i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D;i++)
575
	{
576
577
578
		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";
579
580
	}

581
582
583
	//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);

584
	/**** Bringing convoluted Map to real Space ****/
585
	myfftw_execute_dft_c2r(param.fft_plan_c2r_backward,tmp,localconvFFT);
586
587
588
589
590
591

	/****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++ )
		{
592
			Mapconv.points[i][j]=localconvFFT[i*param.param_device.NumberPixels+j];
593
594
595
596
597
598
		}
	}

	/*** Calculating Cross-correlations of cal-convoluted map with its self *****/
	sumC=0;
	sumsquareC=0;
599
	for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberPixels; i++)
600
	{
601
602
		sumC += localconvFFT[i];
		sumsquareC += localconvFFT[i] * localconvFFT[i];
603
604
605
	}
	/*** The DTF gives an unnormalized value so have to divded by the total number of pixels in Fourier ***/
	// Normalizing
606
607
608
609
	myfloat_t norm2 = (myfloat_t) (param.param_device.NumberPixels * param.param_device.NumberPixels);
	myfloat_t norm4 = norm2 * norm2;
	sumC = sumC / norm2;
	sumsquareC = sumsquareC / norm4;
610
611

	/**** Freeing fftw_complex created (dont know if omp critical is necessary) ****/
612
	myfftw_free(localconvFFT);
613
	myfftw_free(tmp);
614
615

	return(0);
616
617
618
619
}

int bioem::calcross_cor(bioem_map& localmap,myfloat_t& sum,myfloat_t& sumsquare)
{
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
	/*********************** 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);
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
}

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

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

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