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);
}