bioem.cpp 28.6 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
#include <mpi.h>

#define MPI_CHK(expr) \
	if (expr != MPI_SUCCESS) \
	{ \
		fprintf(stderr, "Error in MPI function %s: %d\n", __FILE__, __LINE__); \
	}

18
19
20
21
22
23
24
25
26
#include <fstream>
#include <boost/program_options.hpp>
#include <iostream>
#include <algorithm>
#include <iterator>
#include <stdio.h>
#include <stdlib.h>
#include <string>
#include <cmath>
27

28
#ifdef WITH_OPENMP
29
#include <omp.h>
30
#endif
31
32
33
34
35
36
37
38
39
40

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

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

41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
#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
64

65
66
67
68
69
70
71
72
73
74
75
#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)
{
76
77
	copy(v.begin(), v.end(), ostream_iterator<T>(os, " "));
	return os;
78
79
80
81
}

bioem::bioem()
{
82
	FFTAlgo = getenv("FFTALGO") == NULL ? 1 : atoi(getenv("FFTALGO"));
83
	DebugOutput = getenv("BIOEM_DEBUG_OUTPUT") == NULL ? 2 : atoi(getenv("BIOEM_DEBUG_OUTPUT"));
84
85
86
87
88
89
90
91
}

bioem::~bioem()
{
}

int bioem::configure(int ac, char* av[])
{
David Rohr's avatar
David Rohr committed
92
93
94
95
96
	// **************************************************************************************
	// **** Configuration Routine using boost for extracting parameters, models and maps ****
	// **************************************************************************************
	// ****** And Precalculating necessary grids, map crosscorrelations and kernels  ********
	// *************************************************************************************
97

David Rohr's avatar
David Rohr committed
98
99
100
101
102
	if (mpi_rank == 0)
	{
		// *** Inizialzing default variables ***
		std::string infile, modelfile, mapfile;
		Model.readPDB = false;
103
		param.param_device.writeAngles = false;
David Rohr's avatar
David Rohr committed
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
196
197
198
199
200
201
202
203
		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
204
		}
David Rohr's avatar
David Rohr committed
205
		catch(std::exception& e)
206
		{
David Rohr's avatar
David Rohr committed
207
208
			cout << e.what() << "\n";
			return 1;
209
		}
David Rohr's avatar
David Rohr committed
210
211
212
213
214
215
			//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 ***************************
216
		param.readParameters(infile.c_str());
David Rohr's avatar
David Rohr committed
217
218

		// ********************* Reading Model Input ******************************
219
		Model.readModel(modelfile.c_str());
David Rohr's avatar
David Rohr committed
220
221

		// ********************* Reading Particle Maps Input **********************
222
		RefMap.readRefMaps(param, mapfile.c_str());
David Rohr's avatar
David Rohr committed
223
	}
224

David Rohr's avatar
David Rohr committed
225
#ifdef WITH_MPI
226
227
	MPI_Bcast(&param, sizeof(param), MPI_BYTE, 0, MPI_COMM_WORLD);
	//refCtf, CtfParam, angles automatically filled by precalculare function below
David Rohr's avatar
David Rohr committed
228

229
	MPI_Bcast(&Model, sizeof(Model), MPI_BYTE, 0, MPI_COMM_WORLD);
David Rohr's avatar
David Rohr committed
230
	if (mpi_rank != 0) Model.points = (bioem_model::bioem_model_point*) mallocchk(sizeof(bioem_model::bioem_model_point) * Model.nPointsModel);
231
	MPI_Bcast(Model.points, sizeof(bioem_model::bioem_model_point) * Model.nPointsModel, MPI_BYTE, 0, MPI_COMM_WORLD);
David Rohr's avatar
David Rohr committed
232

David Rohr's avatar
David Rohr committed
233
234
235
	MPI_Bcast(&RefMap, sizeof(RefMap), MPI_BYTE, 0, MPI_COMM_WORLD);
	if (mpi_rank != 0) RefMap.maps = (myfloat_t*) mallocchk(RefMap.refMapSize * sizeof(myfloat_t) * RefMap.ntotRefMap);
	MPI_Bcast(RefMap.maps, RefMap.refMapSize * sizeof(myfloat_t) * RefMap.ntotRefMap, MPI_BYTE, 0, MPI_COMM_WORLD);
David Rohr's avatar
David Rohr committed
236
#endif
237

David Rohr's avatar
David Rohr committed
238
	// ****************** Precalculating Necessary Stuff *********************
239
	param.PrepareFFTs();
240
	precalculate();
David Rohr's avatar
David Rohr committed
241

242
243
	if (getenv("BIOEM_DEBUG_BREAK"))
	{
244
245
246
		const int cut = atoi(getenv("BIOEM_DEBUG_BREAK"));
		if (param.nTotGridAngles > cut) param.nTotGridAngles = cut;
		if (param.nTotCTFs > cut) param.nTotCTFs = cut;
247
	}
David Rohr's avatar
David Rohr committed
248

249
	pProb.init(RefMap.ntotRefMap, param.nTotGridAngles, *this);
250

251
252
	deviceInit();

253
	return(0);
254
255
}

256
257
258
void bioem::cleanup()
{
	//Deleting allocated pointers
259
	free_device_host(pProb.ptr);
260
261
262
	RefMap.freePointers();
}

263
264
int bioem::precalculate()
{
David Rohr's avatar
David Rohr committed
265
	// **************************************************************************************
David Rohr's avatar
David Rohr committed
266
	// **Precalculating Routine of Orientation grids, Map crosscorrelations and CTF Kernels**
David Rohr's avatar
David Rohr committed
267
	// **************************************************************************************
268

269
270
	// Generating Grids of orientations
	param.CalculateGridsParam();
271

272
273
	// Precalculating CTF Kernels stored in class Param
	param.CalculateRefCTF();
274

275
276
	//Precalculate Maps
	RefMap.precalculate(param, *this);
277

278
	return(0);
279
280
281
282
}

int bioem::run()
{
David Rohr's avatar
David Rohr committed
283
284
285
	// **************************************************************************************
	// **** Main BioEM routine, projects, convolutes and compares with Map using OpenMP ****
	// **************************************************************************************
David Rohr's avatar
David Rohr committed
286

287
288
	if (param.printModel)
	{
David Rohr's avatar
David Rohr committed
289

290
291
292
		//....
		return(0);
	}
293

David Rohr's avatar
David Rohr committed
294
295
	// **** If we want to control the number of threads -> omp_set_num_threads(XX); ******
	// ****************** Declarying class of Probability Pointer  *************************
296

David Rohr's avatar
David Rohr committed
297
	if (mpi_rank == 0) printf("\tInitializing Probabilities\n");
298
299
300
	// Inizialzing Probabilites to zero and constant to -Infinity
	for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap; iRefMap ++)
	{
301
302
303
304
		bioem_Probability_map& pProbMap = pProb.getProbMap(iRefMap);

		pProbMap.Total = 0.0;
		pProbMap.Constoadd = -9999999;
305
		if (param.param_device.writeAngles)
306
		{
307
308
309
			for (int iOrient = 0; iOrient < param.nTotGridAngles; iOrient ++)
			{
				bioem_Probability_angle& pProbAngle = pProb.getProbAngle(iRefMap, iOrient);
310

311
312
313
				pProbAngle.forAngles = 0.0;
				pProbAngle.ConstAngle = -99999999;
			}
314
315
		}
	}
David Rohr's avatar
David Rohr committed
316
	// **************************************************************************************
317
	deviceStartRun();
318
319
320
321
	{
		const int count = omp_get_max_threads();
		localCCT = new mycomplex_t*[count];
		lCC = new myfloat_t*[count];
322
		#pragma omp parallel
323
		{
324
325
326
327
328
329
			#pragma omp critical
			{
				const int i = omp_get_thread_num();
				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);
			}
330
331
		}
	}
332

David Rohr's avatar
David Rohr committed
333
	// ******************************** MAIN CYCLE ******************************************
David Rohr's avatar
David Rohr committed
334

David Rohr's avatar
David Rohr committed
335
	// *** Declaring Private variables for each thread *****
336
	mycomplex_t* proj_mapFFT;
337
	myfloat_t* conv_map = new myfloat_t[param.param_device.NumberPixels * param.param_device.NumberPixels];
338
	mycomplex_t* conv_mapFFT;
339
	myfloat_t sumCONV, sumsquareCONV;
340
341

	//allocating fftw_complex vector
342
343
	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);
344

David Rohr's avatar
David Rohr committed
345
	HighResTimer timer, timer2;
346

347
	if (DebugOutput >= 1 && mpi_rank == 0) printf("\tMain Loop GridAngles %d, CTFs %d, RefMaps %d, Shifts (%d/%d)², Pixels %d², OMP Threads %d, MPI Ranks %d\n", param.nTotGridAngles, param.nTotCTFs, RefMap.ntotRefMap, 2 * param.param_device.maxDisplaceCenter + param.param_device.GridSpaceCenter, param.param_device.GridSpaceCenter, param.param_device.NumberPixels, omp_get_max_threads(), mpi_size);
David Rohr's avatar
David Rohr committed
348
349
350
351

	const int iOrientStart = (int) ((long long int) mpi_rank * param.nTotGridAngles / mpi_size);
	int iOrientEnd = (int) ((long long int) (mpi_rank + 1) * param.nTotGridAngles / mpi_size);
	if (iOrientEnd > param.nTotGridAngles) iOrientEnd = param.nTotGridAngles;
David Rohr's avatar
David Rohr committed
352

David Rohr's avatar
David Rohr committed
353
	for (int iOrient = iOrientStart; iOrient < iOrientEnd; iOrient++)
354
	{
David Rohr's avatar
David Rohr committed
355
356
		// ***************************************************************************************
		// ***** Creating Projection for given orientation and transforming to Fourier space *****
David Rohr's avatar
David Rohr committed
357
358
		if (DebugOutput >= 1) timer2.ResetStart();
		if (DebugOutput >= 2) timer.ResetStart();
359
		createProjection(iOrient, proj_mapFFT);
David Rohr's avatar
David Rohr committed
360
		if (DebugOutput >= 2) printf("Time Projection %d: %f (rank %d)\n", iOrient, timer.GetCurrentElapsedTime(), mpi_rank);
361

David Rohr's avatar
David Rohr committed
362
363
		// ***************************************************************************************
		// ***** **** Internal Loop over convolutions **** *****
364
365
		for (int iConv = 0; iConv < param.nTotCTFs; iConv++)
		{
David Rohr's avatar
David Rohr committed
366
			// *** Calculating convolutions of projection map and crosscorrelations ***
367

368
			if (DebugOutput >= 2) timer.ResetStart();
369
			createConvolutedProjectionMap(iOrient, iConv, proj_mapFFT, conv_map, conv_mapFFT, sumCONV, sumsquareCONV);
David Rohr's avatar
David Rohr committed
370
			if (DebugOutput >= 2) printf("Time Convolution %d %d: %f (rank %d)\n", iOrient, iConv, timer.GetCurrentElapsedTime(), mpi_rank);
371

David Rohr's avatar
David Rohr committed
372
373
			// ***************************************************************************************
			// *** Comparing each calculated convoluted map with all experimental maps ***
374
			if (DebugOutput >= 2) timer.ResetStart();
375
			compareRefMaps(iOrient, iConv, conv_map, conv_mapFFT, sumCONV, sumsquareCONV);
376

377
378
379
380
381
382
383
384
385
386
			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;

David Rohr's avatar
David Rohr committed
387
				printf("Time Comparison %d %d: %f sec (%f GFlops, %f GB/s (cached), %f GB/s) (rank %d)\n", iOrient, iConv, compTime, nFlops / 1000000000., nGBs / 1000000000., nGBs2 / 1000000000., mpi_rank);
388
			}
389
		}
David Rohr's avatar
David Rohr committed
390
		if (DebugOutput >= 1) printf("Total time for orientation %d: %f (rank %d)\n", iOrient, timer2.GetCurrentElapsedTime(), mpi_rank);
391
392
393
394
	}
	//deallocating fftw_complex vector
	myfftw_free(proj_mapFFT);
	myfftw_free(conv_mapFFT);
395
	delete[] conv_map;
David Rohr's avatar
David Rohr committed
396

397
	deviceFinishRun();
398
399
400
401
402
403
404
405
406
407
	{
		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;
	}
408

David Rohr's avatar
David Rohr committed
409
	// ************* Writing Out Probabilities ***************
410

David Rohr's avatar
David Rohr committed
411
	// *** Angular Probability ***
David Rohr's avatar
David Rohr committed
412

David Rohr's avatar
David Rohr committed
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
#ifdef WITH_MPI
	if (DebugOutput >= 2 && mpi_rank == 0) timer.ResetStart();
	//Reduce Constant and summarize probabilities
	{
		myfloat_t* tmp1 = new myfloat_t[RefMap.ntotRefMap];
		myfloat_t* tmp2 = new myfloat_t[RefMap.ntotRefMap];
		myfloat_t* tmp3 = new myfloat_t[RefMap.ntotRefMap];
		for (int i = 0;i < RefMap.ntotRefMap;i++)
		{
				tmp1[i] = pProb.getProbMap(i).Constoadd;
		}
		MPI_Allreduce(tmp1, tmp2, RefMap.ntotRefMap, MY_MPI_FLOAT, MPI_MAX, MPI_COMM_WORLD);
		for (int i = 0;i < RefMap.ntotRefMap;i++)
		{
			bioem_Probability_map& pProbMap = pProb.getProbMap(i);
			tmp1[i] = pProbMap.Total * exp(pProbMap.Constoadd - tmp2[i]);
		}
		MPI_Reduce(tmp1, tmp3, RefMap.ntotRefMap, MY_MPI_FLOAT, MPI_SUM, 0, MPI_COMM_WORLD);
431

David Rohr's avatar
David Rohr committed
432
		//Find MaxProb
433
		MPI_Status mpistatus;
David Rohr's avatar
David Rohr committed
434
		{
David Rohr's avatar
David Rohr committed
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
			int* tmpi1 = new int[RefMap.ntotRefMap];
			int* tmpi2 = new int[RefMap.ntotRefMap];
			for (int i = 0;i < RefMap.ntotRefMap;i++)
			{
				bioem_Probability_map& pProbMap = pProb.getProbMap(i);
				tmpi1[i] = tmp2[i] <= pProbMap.Constoadd ? mpi_rank : -1;
			}
			MPI_Allreduce(tmpi1, tmpi2, RefMap.ntotRefMap, MPI_INT, MPI_MAX, MPI_COMM_WORLD);
			for (int i = 0;i < RefMap.ntotRefMap;i++)
			{
				if (tmpi2[i] == -1)
				{
					if (mpi_rank == 0) printf("Error: Could not find highest probability\n");
				}
				else if (tmpi2[i] != 0) //Skip if rank 0 already has highest probability
				{
					if (mpi_rank == 0)
					{
453
						MPI_Recv(&pProb.getProbMap(i).max, sizeof(pProb.getProbMap(i).max), MPI_BYTE, tmpi2[i], i, MPI_COMM_WORLD, &mpistatus);
David Rohr's avatar
David Rohr committed
454
455
456
457
458
459
460
461
462
463
					}
					else if (mpi_rank == tmpi2[i])
					{
						MPI_Send(&pProb.getProbMap(i).max, sizeof(pProb.getProbMap(i).max), MPI_BYTE, 0, i, MPI_COMM_WORLD);
					}
				}
			}
			delete[] tmpi1;
			delete[] tmpi2;
		}
David Rohr's avatar
David Rohr committed
464

David Rohr's avatar
David Rohr committed
465
466
467
468
469
470
471
472
473
		if (mpi_rank == 0)
		{
			for (int i = 0;i < RefMap.ntotRefMap;i++)
			{
					bioem_Probability_map& pProbMap = pProb.getProbMap(i);
					pProbMap.Total = tmp3[i];
					pProbMap.Constoadd = tmp2[i];
			}
		}
David Rohr's avatar
David Rohr committed
474

David Rohr's avatar
David Rohr committed
475
476
477
478
479
		delete[] tmp1;
		delete[] tmp2;
		delete[] tmp3;
		if (DebugOutput >= 2 && mpi_rank == 0) printf("Time MPI Reduction: %f\n", timer.GetCurrentElapsedTime());
	}
David Rohr's avatar
David Rohr committed
480

David Rohr's avatar
David Rohr committed
481
482
	//Angle Reduction and Probability summation for individual angles
	if (param.param_device.writeAngles)
483
	{
David Rohr's avatar
David Rohr committed
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
		const int count = RefMap.ntotRefMap * param.nTotGridAngles;
		myfloat_t* tmp1 = new myfloat_t[count];
		myfloat_t* tmp2 = new myfloat_t[count];
		myfloat_t* tmp3 = new myfloat_t[count];
		for (int i = 0;i < RefMap.ntotRefMap;i++)
		{
				tmp1[i] = pProb.getProbMap(i).Constoadd;
		}
		MPI_Allreduce(tmp1, tmp2, count, MY_MPI_FLOAT, MPI_MAX, MPI_COMM_WORLD);
		for (int i = 0;i < RefMap.ntotRefMap;i++)
		{
			for (int j = 0;j < param.nTotGridAngles;j++)
			{
				bioem_Probability_angle& pProbAngle = pProb.getProbAngle(i, j);
				tmp1[i * param.nTotGridAngles + j] = pProbAngle.forAngles * exp(pProbAngle.ConstAngle - tmp2[i * param.nTotGridAngles + j]);
			}
		}
		MPI_Reduce(tmp1, tmp3, count, MY_MPI_FLOAT, MPI_SUM, 0, MPI_COMM_WORLD);
		if (mpi_rank == 0)
		{
			for (int i = 0;i < RefMap.ntotRefMap;i++)
			{
				for (int j = 0;j < param.nTotGridAngles;j++)
				{
					bioem_Probability_angle& pProbAngle = pProb.getProbAngle(i, j);
					pProbAngle.forAngles = tmp3[i * param.nTotGridAngles + j];
					pProbAngle.ConstAngle = tmp2[i * param.nTotGridAngles + j];
				}
			}
		}
		delete[] tmp1;
		delete[] tmp2;
David Rohr's avatar
David Rohr committed
516
		delete[] tmp3;
517
	}
David Rohr's avatar
David Rohr committed
518
#endif
519

David Rohr's avatar
David Rohr committed
520
	if (mpi_rank == 0)
521
	{
David Rohr's avatar
David Rohr committed
522
523
524
525
526
527
528
529
530
531
532
533
		ofstream angProbfile;
		if(param.param_device.writeAngles)
		{
			angProbfile.open ("ANG_PROB");
		}

		ofstream outputProbFile;
		outputProbFile.open ("Output_Probabilities");
		for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap; iRefMap ++)
		{
			// **** Total Probability ***
			bioem_Probability_map& pProbMap = pProb.getProbMap(iRefMap);
534

David Rohr's avatar
David Rohr committed
535
			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";
536

David Rohr's avatar
David Rohr committed
537
			outputProbFile << "RefMap " << iRefMap << " Maximizing Param: ";
538

David Rohr's avatar
David Rohr committed
539
540
541
542
543
544
545
546
547
548
549
			// *** Param that maximize probability****
			outputProbFile << (pProbMap.Constoadd + 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.max_prob_orient].pos[0] << " ";
			outputProbFile << param.angles[pProbMap.max.max_prob_orient].pos[1] << " ";
			outputProbFile << param.angles[pProbMap.max.max_prob_orient].pos[2] << " ";
			outputProbFile << param.CtfParam[pProbMap.max.max_prob_conv].pos[0] << " ";
			outputProbFile << param.CtfParam[pProbMap.max.max_prob_conv].pos[1] << " ";
			outputProbFile << param.CtfParam[pProbMap.max.max_prob_conv].pos[2] << " ";
			outputProbFile << pProbMap.max.max_prob_cent_x << " ";
			outputProbFile << pProbMap.max.max_prob_cent_y;
			outputProbFile << "\n";
550

David Rohr's avatar
David Rohr committed
551
			// *** For individual files*** //angProbfile.open ("ANG_PROB_"iRefMap);
552

David Rohr's avatar
David Rohr committed
553
			if(param.param_device.writeAngles)
554
			{
David Rohr's avatar
David Rohr committed
555
556
557
				for (int iOrient = 0; iOrient < param.nTotGridAngles; iOrient++)
				{
					bioem_Probability_angle& pProbAngle = pProb.getProbAngle(iRefMap, iOrient);
558

David Rohr's avatar
David Rohr committed
559
560
					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";
				}
561
562
			}
		}
563

David Rohr's avatar
David Rohr committed
564
565
566
567
568
		if(param.param_device.writeAngles)
		{
			angProbfile.close();
		}
		outputProbFile.close();
569
	}
570

571
	return(0);
572
573
}

574
int bioem::compareRefMaps(int iOrient, int iConv, const myfloat_t* conv_map, mycomplex_t* localmultFFT, myfloat_t sumC, myfloat_t sumsquareC, const int startMap)
575
{
David Rohr's avatar
David Rohr committed
576
577
	//***************************************************************************************
	//***** BioEM routine for comparing reference maps to convoluted maps *****
578
	if (FFTAlgo)
579
	{
David Rohr's avatar
David Rohr committed
580
		//With FFT Algorithm
581
582
		#pragma omp parallel for
		for (int iRefMap = startMap; iRefMap < RefMap.ntotRefMap; iRefMap ++)
583
		{
584
			const int num = omp_get_thread_num();
585
			calculateCCFFT(iRefMap, iOrient, iConv, sumC, sumsquareC, localmultFFT, localCCT[num], lCC[num]);
586
587
588
		}
	}
	else
589
	{
David Rohr's avatar
David Rohr committed
590
		//Without FFT Algorithm
591
		#pragma omp parallel for
592
		for (int iRefMap = startMap; iRefMap < RefMap.ntotRefMap; iRefMap ++)
593
		{
594
			compareRefMapShifted < -1 > (iRefMap, iOrient, iConv, conv_map, pProb, param.param_device, RefMap);
595
596
597
598
599
		}
	}
	return(0);
}

600
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)
601
{
David Rohr's avatar
David Rohr committed
602
603
	//***************************************************************************************
	//***** Calculating cross correlation in FFTALGOrithm *****
Pilar Cossio's avatar
Pilar Cossio committed
604

605
	const mycomplex_t* RefMapFFT = &RefMap.RefMapsFFT[iRefMap * param.FFTMapSize];
606
	for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D; i++)
607
	{
608
609
		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];
610
611
	}

612
	myfftw_execute_dft_c2r(param.fft_plan_c2r_backward, localCCT, lCC);
613

614
	doRefMapFFT(iRefMap, iOrient, iConv, lCC, sumC, sumsquareC, pProb, param.param_device, RefMap);
615
}
616

617
int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
618
{
David Rohr's avatar
David Rohr committed
619
	// **************************************************************************************
David Rohr's avatar
David Rohr committed
620
621
	// ****  BioEM Create Projection routine in Euler angle predefined grid******************
	// ********************* and turns projection into Fourier space ************************
David Rohr's avatar
David Rohr committed
622
	// **************************************************************************************
623

624
625
	cuda_custom_timeslot("Projection", 0);

626
627
	myfloat3_t RotatedPointsModel[Model.nPointsModel];
	myfloat_t rotmat[3][3];
628
	myfloat_t alpha, gam, beta;
629
	myfloat_t* localproj;
630

631
	localproj = lCC[omp_get_thread_num()];
632
	memset(localproj, 0, param.param_device.NumberPixels * param.param_device.NumberPixels * sizeof(*localproj));
633

634
635
636
	alpha = param.angles[iMap].pos[0];
	beta = param.angles[iMap].pos[1];
	gam = param.angles[iMap].pos[2];
637

David Rohr's avatar
David Rohr committed
638
	// **** To see how things are going: cout << "Id " << omp_get_thread_num() <<  " Angs: " << alpha << " " << beta << " " << gam << "\n"; ***
639

David Rohr's avatar
David Rohr committed
640
	// ********** Creat Rotation with pre-defiend grid of orientations**********
641
642
643
644
645
646
647
648
649
650
651
	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++)
652
	{
653
654
655
		RotatedPointsModel[n].pos[0] = 0.0;
		RotatedPointsModel[n].pos[1] = 0.0;
		RotatedPointsModel[n].pos[2] = 0.0;
656
	}
657
	for(int n = 0; n < Model.nPointsModel; n++)
658
	{
659
		for(int k = 0; k < 3; k++)
660
		{
661
			for(int j = 0; j < 3; j++)
662
			{
663
				RotatedPointsModel[n].pos[k] += rotmat[k][j] * Model.points[n].point.pos[j];
664
665
666
667
668
669
			}
		}
	}

	int i, j;

David Rohr's avatar
David Rohr committed
670
	// ************ Projection over the Z axis********************
671
	for(int n = 0; n < Model.nPointsModel; n++)
672
673
	{
		//Getting pixel that represents coordinates & shifting the start at to Numpix/2,Numpix/2 )
674
675
		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);
676

677
678
679
680
681
682
		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;
		}

683
		localproj[i * param.param_device.NumberPixels + j] += Model.points[n].density / Model.NormDen;
684
685
	}

David Rohr's avatar
David Rohr committed
686
	// **** Output Just to check****
687
#ifdef PILAR_DEBUG
688
	if(iMap == 10)
689
690
691
692
693
694
	{
		ofstream myexamplemap;
		ofstream myexampleRot;
		myexamplemap.open ("MAP_i10");
		myexampleRot.open ("Rot_i10");
		myexamplemap << "ANGLES " << alpha << " " << beta << " " << gam << "\n";
695
		for(int k = 0; k < param.param_device.NumberPixels; k++)
696
		{
697
			for(int j = 0; j < param.param_device.NumberPixels; j++) myexamplemap << "\nMAP " << k << " " << j << " " << localproj[k * param.param_device.NumberPixels + j];
698
699
		}
		myexamplemap << " \n";
700
		for(int n = 0; n < Model.nPointsModel; n++)myexampleRot << "\nCOOR " << RotatedPointsModel[n].pos[0] << " " << RotatedPointsModel[n].pos[1] << " " << RotatedPointsModel[n].pos[2];
701
702
703
		myexamplemap.close();
		myexampleRot.close();
	}
704
#endif
705

David Rohr's avatar
David Rohr committed
706
707
	// ***** Converting projection to Fourier Space for Convolution later with kernel****
	// ********** Omp Critical is necessary with FFTW*******
708
	myfftw_execute_dft_r2c(param.fft_plan_r2c_forward, localproj, mapFFT);
709

710
711
	cuda_custom_timeslot_end;

712
713
714
	return(0);
}

715
int bioem::createConvolutedProjectionMap(int iMap, int iConv, mycomplex_t* lproj, myfloat_t* Mapconv, mycomplex_t* localmultFFT, myfloat_t& sumC, myfloat_t& sumsquareC)
716
{
David Rohr's avatar
David Rohr committed
717
718
	// **************************************************************************************
	// ****  BioEM Create Convoluted Projection Map routine, multiplies in Fourier **********
David Rohr's avatar
David Rohr committed
719
720
	// **************** calculated Projection with convoluted precalculated Kernel***********
	// *************** and Backtransforming it to real Space ********************************
David Rohr's avatar
David Rohr committed
721
	// **************************************************************************************
722

723
724
	cuda_custom_timeslot("Convolution", 1);

725
	mycomplex_t* tmp = localCCT[omp_get_thread_num()];
726

David Rohr's avatar
David Rohr committed
727
	// **** Multiplying FFTmap with corresponding kernel ****
728
	const mycomplex_t* refCTF = &param.refCTF[iConv * param.FFTMapSize];
729
	for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D; i++)
730
	{
731
732
733
		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";
734
735
	}

David Rohr's avatar
David Rohr committed
736
	// *** Calculating Cross-correlations of cal-convoluted map with its self *****
737
	sumC = localmultFFT[0][0];
David Rohr's avatar
David Rohr committed
738

739
	sumsquareC = 0;
740
	if (FFTAlgo)
741
	{
742
743
744
745
746
747
748
749
750
751
		for(int i = 0; i < param.param_device.NumberPixels; i++)
		{
			for (int j = 1;j < param.param_device.NumberFFTPixels1D;j++)
			{
				int k = i * param.param_device.NumberFFTPixels1D + j;
				sumsquareC += (localmultFFT[k][0] * localmultFFT[k][0] + localmultFFT[k][1] * localmultFFT[k][1]) * 2;
			}
			int k = i * param.param_device.NumberFFTPixels1D;
			sumsquareC += localmultFFT[k][0] * localmultFFT[k][0] + localmultFFT[k][1] * localmultFFT[k][1];
		}
David Rohr's avatar
David Rohr committed
752

753
754
		myfloat_t norm2 = (myfloat_t) (param.param_device.NumberPixels * param.param_device.NumberPixels);
		sumsquareC = sumsquareC / norm2;
755
	}
756
757
758
759
760
761
762
	else
	{
		//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);

		// **** Bringing convoluted Map to real Space ****
		myfftw_execute_dft_c2r(param.fft_plan_c2r_backward, tmp, Mapconv);
763

764
765
766
767
768
769
770
771
772
773
		for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberPixels; i++)
		{
			sumsquareC += Mapconv[i] * Mapconv[i];
			sumC += Mapconv[i];
		}

		myfloat_t norm2 = (myfloat_t) (param.param_device.NumberPixels * param.param_device.NumberPixels);
		myfloat_t norm4 = norm2 * norm2;
		sumsquareC = sumsquareC / norm4;
	}
David Rohr's avatar
David Rohr committed
774

775
776
	cuda_custom_timeslot_end;

777
	return(0);
778
779
}

780
int bioem::calcross_cor(myfloat_t* localmap, myfloat_t& sum, myfloat_t& sumsquare)
781
{
David Rohr's avatar
David Rohr committed
782
	// *********************** Routine to calculate Cross correlations***********************
783

784
785
	sum = 0.0;
	sumsquare = 0.0;
786
787
788
789
790
	for (int i = 0; i < param.param_device.NumberPixels; i++)
	{
		for (int j = 0; j < param.param_device.NumberPixels; j++)
		{
			// Calculate Sum of pixels
791
			sum += localmap[i * param.param_device.NumberPixels + j];
792
			// Calculate Sum of pixels squared
793
			sumsquare += localmap[i * param.param_device.NumberPixels + j] * localmap[i * param.param_device.NumberPixels + j];
794
795
796
		}
	}
	return(0);
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
}

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

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

int bioem::deviceFinishRun()
{
	return(0);
}
813
814
815
816
817
818
819
820
821
822

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

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