bioem.cpp 23.8 KB
Newer Older
Pilar Cossio's avatar
License  
Pilar Cossio committed
1
2
3
4
/* ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
        < BioEM software for Bayesian inference of Electron Microscopy images>
            Copyright (C) 2014 Pilar Cossio, David Rohr and Gerhard Hummer.
            Max Planck Institute of Biophysics, Frankfurt, Germany.
5

Pilar Cossio's avatar
License  
Pilar Cossio committed
6
7
8
9
                See license statement for terms of distribution.

   ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/

10
11
12
13
14
15
16
17
18
#include <fstream>
#include <boost/program_options.hpp>
#include <iostream>
#include <algorithm>
#include <iterator>
#include <stdio.h>
#include <stdlib.h>
#include <string>
#include <cmath>
19

20
#ifdef WITH_OPENMP
21
#include <omp.h>
22
#endif
23
24
25
26
27
28
29
30
31
32

#include <fftw3.h>
#include <math.h>
#include "cmodules/timer.h"

#include "param.h"
#include "bioem.h"
#include "model.h"
#include "map.h"

33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
#ifdef BIOEM_USE_NVTX
#include "nvToolsExt.h"

const uint32_t colors[] = { 0x0000ff00, 0x000000ff, 0x00ffff00, 0x00ff00ff, 0x0000ffff, 0x00ff0000, 0x00ffffff };
const int num_colors = sizeof(colors)/sizeof(colors[0]);

#define cuda_custom_timeslot(name,cid) { \
	int color_id = cid; \
	color_id = color_id%num_colors;\
	nvtxEventAttributes_t eventAttrib = {0}; \
	eventAttrib.version = NVTX_VERSION; \
	eventAttrib.size = NVTX_EVENT_ATTRIB_STRUCT_SIZE; \
	eventAttrib.colorType = NVTX_COLOR_ARGB; \
	eventAttrib.color = colors[color_id]; \
	eventAttrib.messageType = NVTX_MESSAGE_TYPE_ASCII; \
	eventAttrib.message.ascii = name; \
	nvtxRangePushEx(&eventAttrib); \
}
#define cuda_custom_timeslot_end nvtxRangePop();
#else
#define cuda_custom_timeslot(name,cid)
#define cuda_custom_timeslot_end
#endif
56

57
58
59
60
61
62
63
64
65
66
67
#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)
{
68
69
	copy(v.begin(), v.end(), ostream_iterator<T>(os, " "));
	return os;
70
71
72
73
}

bioem::bioem()
{
74
	FFTAlgo = getenv("FFTALGO") == NULL ? 1 : atoi(getenv("FFTALGO"));
75
	DebugOutput = getenv("BIOEM_DEBUG_OUTPUT") == NULL ? 2 : atoi(getenv("BIOEM_DEBUG_OUTPUT"));
76
77
78
79
80
81
82
83
}

bioem::~bioem()
{
}

int bioem::configure(int ac, char* av[])
{
David Rohr's avatar
David Rohr committed
84
85
86
87
88
	// **************************************************************************************
	// **** Configuration Routine using boost for extracting parameters, models and maps ****
	// **************************************************************************************
	// ****** And Precalculating necessary grids, map crosscorrelations and kernels  ********
	// *************************************************************************************
89

David Rohr's avatar
David Rohr committed
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
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
	if (mpi_rank == 0)
	{
		// *** Inizialzing default variables ***
		std::string infile, modelfile, mapfile;
		Model.readPDB = false;
		param.writeAngles = false;
		param.dumpMap = false;
		param.loadMap = false;
		RefMap.readMRC = false;
		RefMap.readMultMRC = false;

		// *************************************************************************************
		cout << " ++++++++++++ FROM COMMAND LINE +++++++++++\n\n";
		// *************************************************************************************

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

		try {
			po::options_description desc("Command line inputs");
			desc.add_options()
			("Inputfile", po::value<std::string>(), "(Mandatory) Name of input parameter file")
			("Modelfile", po::value< std::string>() , "(Mandatory) Name of model file")
			("Particlesfile", po::value< std::string>(), "(Mandatory) Name of paricles file")
			("ReadPDB", "(Optional) If reading model file in PDB format")
			("ReadMRC", "(Optional) If reading particle file in MRC format")
			("ReadMultipleMRC", "(Optional) If reading Multiple MRCs")
			("DumpMaps", "(Optional) Dump maps after they were red from maps file")
			("LoadMapDump", "(Optional) Read Maps from dump instead of maps file")
			("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);
			p.add("ReadMRC", -1);
			p.add("ReadMultipleMRC", -1);
			p.add("DumpMaps", -1);
			p.add("LoadMapDump", -1);

			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 1;
			}
			if (vm.count("help")) {
				cout << "Usage: options_description [options]\n";
				cout << desc;
				return 1;
			}

			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("ReadMRC"))
			{
				cout << "Reading particle file in MRC format.\n";
				RefMap.readMRC=true;
			}

			if (vm.count("ReadMultipleMRC"))
			{
				cout << "Reading Multiple MRCs.\n";
				RefMap.readMultMRC=true;
			}

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

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

			if (vm.count("Particlesfile"))
			{
				cout << "Paricle file is: "
					 << vm["Particlesfile"].as< std::string >() << "\n";
				mapfile = vm["Particlesfile"].as< std::string >();
			}
David Rohr's avatar
David Rohr committed
196
		}
David Rohr's avatar
David Rohr committed
197
		catch(std::exception& e)
198
		{
David Rohr's avatar
David Rohr committed
199
200
			cout << e.what() << "\n";
			return 1;
201
		}
David Rohr's avatar
David Rohr committed
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
			//check for consitency in multiple MRCs
			if(  RefMap.readMultMRC && not(RefMap.readMRC) ){
			 cout << "For Multiple MRCs command --ReadMRC is necesary too";
			 exit(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
		param.filemap = mapfile.c_str();
		RefMap.readRefMaps(param);
	}
223

David Rohr's avatar
David Rohr committed
224
#ifdef WITH_MPI
225

David Rohr's avatar
David Rohr committed
226
227
#endif
	if (mpi_rank != 0) return(1);
228

David Rohr's avatar
David Rohr committed
229
	// ****************** Precalculating Necessary Stuff *********************
230
	precalculate();
David Rohr's avatar
David Rohr committed
231

232
233
	if (getenv("BIOEM_DEBUG_BREAK"))
	{
234
235
236
		const int cut = atoi(getenv("BIOEM_DEBUG_BREAK"));
		if (param.nTotGridAngles > cut) param.nTotGridAngles = cut;
		if (param.nTotCTFs > cut) param.nTotCTFs = cut;
237
	}
David Rohr's avatar
David Rohr committed
238

239
	pProb.init(RefMap.ntotRefMap, param.nTotGridAngles, *this);
240

241
242
	deviceInit();

243
	return(0);
244
245
}

246
247
248
void bioem::cleanup()
{
	//Deleting allocated pointers
249
	free_device_host(pProb.ptr);
250
251
252
	RefMap.freePointers();
}

253
254
int bioem::precalculate()
{
David Rohr's avatar
David Rohr committed
255
	// **************************************************************************************
David Rohr's avatar
David Rohr committed
256
	// **Precalculating Routine of Orientation grids, Map crosscorrelations and CTF Kernels**
David Rohr's avatar
David Rohr committed
257
	// **************************************************************************************
258

259
260
	// Generating Grids of orientations
	param.CalculateGridsParam();
261

262
263
	// Precalculating CTF Kernels stored in class Param
	param.CalculateRefCTF();
264

265
266
	//Precalculate Maps
	RefMap.precalculate(param, *this);
267

268
	return(0);
269
270
271
272
}

int bioem::run()
{
David Rohr's avatar
David Rohr committed
273
274
275
	// **************************************************************************************
	// **** Main BioEM routine, projects, convolutes and compares with Map using OpenMP ****
	// **************************************************************************************
276

David Rohr's avatar
David Rohr committed
277
278
	// **** If we want to control the number of threads -> omp_set_num_threads(XX); ******
	// ****************** Declarying class of Probability Pointer  *************************
279

280
	printf("\tInitializing Probabilities\n");
281
282
283
	// Inizialzing Probabilites to zero and constant to -Infinity
	for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap; iRefMap ++)
	{
284
285
286
287
288
		bioem_Probability_map& pProbMap = pProb.getProbMap(iRefMap);

		pProbMap.Total = 0.0;
		pProbMap.Constoadd = -9999999;
		pProbMap.max_prob = -9999999;
289
		for (int iOrient = 0; iOrient < param.nTotGridAngles; iOrient ++)
290
		{
291
292
293
294
			bioem_Probability_angle& pProbAngle = pProb.getProbAngle(iRefMap, iOrient);

			pProbAngle.forAngles = 0.0;
			pProbAngle.ConstAngle = -99999999;
295
296
		}
	}
David Rohr's avatar
David Rohr committed
297
	// **************************************************************************************
298
	deviceStartRun();
299
300
301
302
303
304
305
306
307
308
	{
		const int count = omp_get_max_threads();
		localCCT = new mycomplex_t*[count];
		lCC = new myfloat_t*[count];
		for (int i = 0;i < count;i++)
		{
			localCCT[i] = (mycomplex_t *) myfftw_malloc(sizeof(mycomplex_t) * param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D);
			lCC[i] = (myfloat_t *) myfftw_malloc(sizeof(myfloat_t) * param.param_device.NumberPixels * param.param_device.NumberPixels);
		}
	}
309

David Rohr's avatar
David Rohr committed
310
	// ******************************** MAIN CYCLE ******************************************
David Rohr's avatar
David Rohr committed
311

David Rohr's avatar
David Rohr committed
312
	// *** Declaring Private variables for each thread *****
313
	mycomplex_t* proj_mapFFT;
314
	myfloat_t* conv_map = new myfloat_t[param.param_device.NumberPixels * param.param_device.NumberPixels];
315
	mycomplex_t* conv_mapFFT;
316
	myfloat_t sumCONV, sumsquareCONV;
317
318

	//allocating fftw_complex vector
319
320
	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);
321
322
323

	HighResTimer timer;

324
	if (DebugOutput >= 1) 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);
Pilar Cossio's avatar
Pilar Cossio committed
325
//	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)));
326
	for (int iOrient = 0; iOrient < param.nTotGridAngles; iOrient++)
327
	{
David Rohr's avatar
David Rohr committed
328
329
		// ***************************************************************************************
		// ***** Creating Projection for given orientation and transforming to Fourier space *****
330
		if (DebugOutput >= 1) timer.ResetStart();
331
		createProjection(iOrient, proj_mapFFT);
332
		if (DebugOutput >= 1) printf("Time Projection %d: %f\n", iOrient, timer.GetCurrentElapsedTime());
333

David Rohr's avatar
David Rohr committed
334
335
		// ***************************************************************************************
		// ***** **** Internal Loop over convolutions **** *****
336
337
		for (int iConv = 0; iConv < param.nTotCTFs; iConv++)
		{
338
			if (DebugOutput >= 2) printf("\t\tConvolution %d %d\n", iOrient, iConv);
David Rohr's avatar
David Rohr committed
339
			// *** Calculating convolutions of projection map and crosscorrelations ***
340

341
			if (DebugOutput >= 2) timer.ResetStart();
342
			createConvolutedProjectionMap(iOrient, iConv, proj_mapFFT, conv_map, conv_mapFFT, sumCONV, sumsquareCONV);
343
			if (DebugOutput >= 2) printf("Time Convolution %d %d: %f\n", iOrient, iConv, timer.GetCurrentElapsedTime());
344

David Rohr's avatar
David Rohr committed
345
346
			// ***************************************************************************************
			// *** Comparing each calculated convoluted map with all experimental maps ***
347
			if (DebugOutput >= 2) timer.ResetStart();
348
			compareRefMaps(iOrient, iConv, conv_map, conv_mapFFT, sumCONV, sumsquareCONV);
349

350
351
352
353
354
355
356
357
358
359
360
361
			if (DebugOutput >= 2)
			{
				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 *
									  (((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;
				const double nGBs = (double) RefMap.ntotRefMap * (double) nShifts * (double) nShifts *
									(((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;
				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", iOrient, iConv, compTime, nFlops / 1000000000., nGBs / 1000000000., nGBs2 / 1000000000.);
			}
362
363
364
365
366
		}
	}
	//deallocating fftw_complex vector
	myfftw_free(proj_mapFFT);
	myfftw_free(conv_mapFFT);
367
	delete[] conv_map;
David Rohr's avatar
David Rohr committed
368

369
	deviceFinishRun();
370
371
372
373
374
375
376
377
378
379
	{
		const int count = omp_get_max_threads();
		for (int i = 0;i < count;i++)
		{
			myfftw_free(localCCT[i]);
			myfftw_free(lCC[i]);
		}
		delete[] localCCT;
		delete[] lCC;
	}
380

David Rohr's avatar
David Rohr committed
381
	// ************* Writing Out Probabilities ***************
382

David Rohr's avatar
David Rohr committed
383
	// *** Angular Probability ***
384

385
386
387
388
	// if(param.writeAngles){
	ofstream angProbfile;
	angProbfile.open ("ANG_PROB_iRefMap");
	// }
389

390
391
392
393
	ofstream outputProbFile;
	outputProbFile.open ("Output_Probabilities");
	for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap; iRefMap ++)
	{
David Rohr's avatar
David Rohr committed
394
		// **** Total Probability ***
395
396
397
		bioem_Probability_map& pProbMap = pProb.getProbMap(iRefMap);

		outputProbFile << "RefMap " << iRefMap << " Probability  "  << log(pProbMap.Total) + pProbMap.Constoadd + 0.5 * log(M_PI) + (1 - param.param_device.Ntotpi * 0.5)*(log(2 * M_PI) + 1) + log(param.param_device.volu) << " Constant " << pProbMap.Constoadd  << "\n";
398
399
400

		outputProbFile << "RefMap " << iRefMap << " Maximizing Param: ";

David Rohr's avatar
David Rohr committed
401
		// *** Param that maximize probability****
402
403
404
405
406
407
408
409
410
		outputProbFile << (pProbMap.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[pProbMap.max_prob_orient].pos[0] << " ";
		outputProbFile << param.angles[pProbMap.max_prob_orient].pos[1] << " ";
		outputProbFile << param.angles[pProbMap.max_prob_orient].pos[2] << " ";
		outputProbFile << param.CtfParam[pProbMap.max_prob_conv].pos[0] << " ";
		outputProbFile << param.CtfParam[pProbMap.max_prob_conv].pos[1] << " ";
		outputProbFile << param.CtfParam[pProbMap.max_prob_conv].pos[2] << " ";
		outputProbFile << pProbMap.max_prob_cent_x << " ";
		outputProbFile << pProbMap.max_prob_cent_y;
411
		outputProbFile << "\n";
412

David Rohr's avatar
David Rohr committed
413
		// *** For individual files*** //angProbfile.open ("ANG_PROB_"iRefMap);
414

415
		if(param.writeAngles)
416
		{
417
			for (int iOrient = 0; iOrient < param.nTotGridAngles; iOrient++)
418
			{
419
				bioem_Probability_angle& pProbAngle = pProb.getProbAngle(iRefMap, iOrient);
420

421
				angProbfile << " " << iRefMap << " " << param.angles[iOrient].pos[0] << " " << param.angles[iOrient].pos[1] << " " << param.angles[iOrient].pos[2] << " " << log(pProbAngle.forAngles) + pProbAngle.ConstAngle + 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";
422
423
424
			}
		}
	}
425

426
427
	angProbfile.close();
	outputProbFile.close();
428

429
	return(0);
430
431
}

432
int bioem::compareRefMaps(int iOrient, int iConv, const myfloat_t* conv_map, mycomplex_t* localmultFFT, myfloat_t sumC, myfloat_t sumsquareC, const int startMap)
433
{
David Rohr's avatar
David Rohr committed
434
435
	//***************************************************************************************
	//***** BioEM routine for comparing reference maps to convoluted maps *****
436
	if (FFTAlgo)
437
	{
David Rohr's avatar
David Rohr committed
438
		//With FFT Algorithm
439
440
		#pragma omp parallel for
		for (int iRefMap = startMap; iRefMap < RefMap.ntotRefMap; iRefMap ++)
441
		{
442
			const int num = omp_get_thread_num();
443
			calculateCCFFT(iRefMap, iOrient, iConv, sumC, sumsquareC, localmultFFT, localCCT[num], lCC[num]);
444
445
446
		}
	}
	else
447
	{
David Rohr's avatar
David Rohr committed
448
		//Without FFT Algorithm
449
		#pragma omp parallel for
450
		for (int iRefMap = startMap; iRefMap < RefMap.ntotRefMap; iRefMap ++)
451
		{
452
			compareRefMapShifted < -1 > (iRefMap, iOrient, iConv, conv_map, pProb, param.param_device, RefMap);
453
454
455
456
457
		}
	}
	return(0);
}

458
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)
459
{
David Rohr's avatar
David Rohr committed
460
461
	//***************************************************************************************
	//***** Calculating cross correlation in FFTALGOrithm *****
Pilar Cossio's avatar
Pilar Cossio committed
462

463
	const mycomplex_t* RefMapFFT = &RefMap.RefMapsFFT[iRefMap * param.FFTMapSize];
464
	for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D; i++)
465
	{
466
467
		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];
468
469
	}

470
	myfftw_execute_dft_c2r(param.fft_plan_c2r_backward, localCCT, lCC);
471

472
	doRefMapFFT(iRefMap, iOrient, iConv, lCC, sumC, sumsquareC, pProb, param.param_device, RefMap);
473
}
474

475
int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
476
{
David Rohr's avatar
David Rohr committed
477
	// **************************************************************************************
David Rohr's avatar
David Rohr committed
478
479
	// ****  BioEM Create Projection routine in Euler angle predefined grid******************
	// ********************* and turns projection into Fourier space ************************
David Rohr's avatar
David Rohr committed
480
	// **************************************************************************************
481

482
483
	cuda_custom_timeslot("Projection", 0);

484
485
	myfloat3_t RotatedPointsModel[Model.nPointsModel];
	myfloat_t rotmat[3][3];
486
	myfloat_t alpha, gam, beta;
487
	myfloat_t* localproj;
488

489
	localproj = lCC[omp_get_thread_num()];
490
	memset(localproj, 0, param.param_device.NumberPixels * param.param_device.NumberPixels * sizeof(*localproj));
491

492
493
494
	alpha = param.angles[iMap].pos[0];
	beta = param.angles[iMap].pos[1];
	gam = param.angles[iMap].pos[2];
495

David Rohr's avatar
David Rohr committed
496
	// **** To see how things are going: cout << "Id " << omp_get_thread_num() <<  " Angs: " << alpha << " " << beta << " " << gam << "\n"; ***
497

David Rohr's avatar
David Rohr committed
498
	// ********** Creat Rotation with pre-defiend grid of orientations**********
499
500
501
502
503
504
505
506
507
508
509
	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++)
510
	{
511
512
513
		RotatedPointsModel[n].pos[0] = 0.0;
		RotatedPointsModel[n].pos[1] = 0.0;
		RotatedPointsModel[n].pos[2] = 0.0;
514
	}
515
	for(int n = 0; n < Model.nPointsModel; n++)
516
	{
517
		for(int k = 0; k < 3; k++)
518
		{
519
			for(int j = 0; j < 3; j++)
520
			{
521
				RotatedPointsModel[n].pos[k] += rotmat[k][j] * Model.PointsModel[n].pos[j];
522
523
524
525
526
527
			}
		}
	}

	int i, j;

David Rohr's avatar
David Rohr committed
528
	// ************ Projection over the Z axis********************
529
	for(int n = 0; n < Model.nPointsModel; n++)
530
531
	{
		//Getting pixel that represents coordinates & shifting the start at to Numpix/2,Numpix/2 )
532
533
		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);
534

535
536
537
538
539
540
		if (i < 0 || j < 0 || i >= param.param_device.NumberPixels || j >= param.param_device.NumberPixels)
		{
			if (DebugOutput >= 3) cout << "Model Point out of map: " << i << ", " << j << "\n";
			continue;
		}

541
		localproj[i * param.param_device.NumberPixels + j] += Model.densityPointsModel[n] / Model.NormDen;
542
543
	}

David Rohr's avatar
David Rohr committed
544
	// **** Output Just to check****
545
	if(iMap == 10)
546
547
548
549
550
551
	{
		ofstream myexamplemap;
		ofstream myexampleRot;
		myexamplemap.open ("MAP_i10");
		myexampleRot.open ("Rot_i10");
		myexamplemap << "ANGLES " << alpha << " " << beta << " " << gam << "\n";
552
		for(int k = 0; k < param.param_device.NumberPixels; k++)
553
		{
554
			for(int j = 0; j < param.param_device.NumberPixels; j++) myexamplemap << "\nMAP " << k << " " << j << " " << localproj[k * param.param_device.NumberPixels + j];
555
556
		}
		myexamplemap << " \n";
557
		for(int n = 0; n < Model.nPointsModel; n++)myexampleRot << "\nCOOR " << RotatedPointsModel[n].pos[0] << " " << RotatedPointsModel[n].pos[1] << " " << RotatedPointsModel[n].pos[2];
558
559
560
561
		myexamplemap.close();
		myexampleRot.close();
	}

David Rohr's avatar
David Rohr committed
562
563
	// ***** Converting projection to Fourier Space for Convolution later with kernel****
	// ********** Omp Critical is necessary with FFTW*******
564
	myfftw_execute_dft_r2c(param.fft_plan_r2c_forward, localproj, mapFFT);
565

566
567
	cuda_custom_timeslot_end;

568
569
570
	return(0);
}

571
int bioem::createConvolutedProjectionMap(int iMap, int iConv, mycomplex_t* lproj, myfloat_t* Mapconv, mycomplex_t* localmultFFT, myfloat_t& sumC, myfloat_t& sumsquareC)
572
{
David Rohr's avatar
David Rohr committed
573
574
	// **************************************************************************************
	// ****  BioEM Create Convoluted Projection Map routine, multiplies in Fourier **********
David Rohr's avatar
David Rohr committed
575
576
	// **************** calculated Projection with convoluted precalculated Kernel***********
	// *************** and Backtransforming it to real Space ********************************
David Rohr's avatar
David Rohr committed
577
	// **************************************************************************************
578

579
580
	cuda_custom_timeslot("Convolution", 1);

581
	mycomplex_t* tmp = localCCT[omp_get_thread_num()];
582

David Rohr's avatar
David Rohr committed
583
	// **** Multiplying FFTmap with corresponding kernel ****
584
	const mycomplex_t* refCTF = &param.refCTF[iConv * param.FFTMapSize];
585
	for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D; i++)
586
	{
587
588
589
		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";
590
591
	}

592
593
594
	//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);

David Rohr's avatar
David Rohr committed
595
	// **** Bringing convoluted Map to real Space ****
David Rohr's avatar
David Rohr committed
596
	myfftw_execute_dft_c2r(param.fft_plan_c2r_backward, tmp, Mapconv);
597

David Rohr's avatar
David Rohr committed
598
	// *** Calculating Cross-correlations of cal-convoluted map with its self *****
599
600
	sumC = 0;
	sumsquareC = 0;
601
	for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberPixels; i++)
602
	{
David Rohr's avatar
David Rohr committed
603
604
		sumC += Mapconv[i];
		sumsquareC += Mapconv[i] * Mapconv[i];
605
	}
David Rohr's avatar
David Rohr committed
606
	// *** The DTF gives an unnormalized value so have to divded by the total number of pixels in Fourier ***
607
	// Normalizing
608
609
610
611
	myfloat_t norm2 = (myfloat_t) (param.param_device.NumberPixels * param.param_device.NumberPixels);
	myfloat_t norm4 = norm2 * norm2;
	sumC = sumC / norm2;
	sumsquareC = sumsquareC / norm4;
612

613
614
	cuda_custom_timeslot_end;

615
	return(0);
616
617
}

618
int bioem::calcross_cor(myfloat_t* localmap, myfloat_t& sum, myfloat_t& sumsquare)
619
{
David Rohr's avatar
David Rohr committed
620
	// *********************** Routine to calculate Cross correlations***********************
621

622
623
	sum = 0.0;
	sumsquare = 0.0;
624
625
626
627
628
	for (int i = 0; i < param.param_device.NumberPixels; i++)
	{
		for (int j = 0; j < param.param_device.NumberPixels; j++)
		{
			// Calculate Sum of pixels
629
			sum += localmap[i * param.param_device.NumberPixels + j];
630
			// Calculate Sum of pixels squared
631
			sumsquare += localmap[i * param.param_device.NumberPixels + j] * localmap[i * param.param_device.NumberPixels + j];
632
633
634
		}
	}
	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);
}
651
652
653
654
655
656
657
658
659
660

void* bioem::malloc_device_host(size_t size)
{
	return(mallocchk(size));
}

void bioem::free_device_host(void* ptr)
{
	free(ptr);
}