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();
318 319 320 321 322 323 324 325 326 327
	{
		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);
		}
	}
328

David Rohr's avatar
David Rohr committed
329
	// ******************************** MAIN CYCLE ******************************************
David Rohr's avatar
David Rohr committed
330

David Rohr's avatar
David Rohr committed
331
	// *** Declaring Private variables for each thread *****
332
	mycomplex_t* proj_mapFFT;
333
	myfloat_t* conv_map = new myfloat_t[param.param_device.NumberPixels * param.param_device.NumberPixels];
334
	mycomplex_t* conv_mapFFT;
335
	myfloat_t sumCONV, sumsquareCONV;
336 337

	//allocating fftw_complex vector
338 339
	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);
340

David Rohr's avatar
David Rohr committed
341
	HighResTimer timer, timer2;
342

343
	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
344 345 346 347

	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
348

David Rohr's avatar
David Rohr committed
349
	for (int iOrient = iOrientStart; iOrient < iOrientEnd; iOrient++)
350
	{
David Rohr's avatar
David Rohr committed
351 352
		// ***************************************************************************************
		// ***** Creating Projection for given orientation and transforming to Fourier space *****
David Rohr's avatar
David Rohr committed
353 354
		if (DebugOutput >= 1) timer2.ResetStart();
		if (DebugOutput >= 2) timer.ResetStart();
355
		createProjection(iOrient, proj_mapFFT);
David Rohr's avatar
David Rohr committed
356
		if (DebugOutput >= 2) printf("Time Projection %d: %f (rank %d)\n", iOrient, timer.GetCurrentElapsedTime(), mpi_rank);
357

David Rohr's avatar
David Rohr committed
358 359
		// ***************************************************************************************
		// ***** **** Internal Loop over convolutions **** *****
360 361
		for (int iConv = 0; iConv < param.nTotCTFs; iConv++)
		{
David Rohr's avatar
David Rohr committed
362
			// *** Calculating convolutions of projection map and crosscorrelations ***
363

364
			if (DebugOutput >= 2) timer.ResetStart();
365
			createConvolutedProjectionMap(iOrient, iConv, proj_mapFFT, conv_map, conv_mapFFT, sumCONV, sumsquareCONV);
David Rohr's avatar
David Rohr committed
366
			if (DebugOutput >= 2) printf("Time Convolution %d %d: %f (rank %d)\n", iOrient, iConv, timer.GetCurrentElapsedTime(), mpi_rank);
367

David Rohr's avatar
David Rohr committed
368 369
			// ***************************************************************************************
			// *** Comparing each calculated convoluted map with all experimental maps ***
370
			if (DebugOutput >= 2) timer.ResetStart();
371
			compareRefMaps(iOrient, iConv, conv_map, conv_mapFFT, sumCONV, sumsquareCONV);
372

373 374 375 376 377 378 379 380 381 382
			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
383
				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);
384
			}
385
		}
David Rohr's avatar
David Rohr committed
386
		if (DebugOutput >= 1) printf("Total time for orientation %d: %f (rank %d)\n", iOrient, timer2.GetCurrentElapsedTime(), mpi_rank);
387 388 389 390
	}
	//deallocating fftw_complex vector
	myfftw_free(proj_mapFFT);
	myfftw_free(conv_mapFFT);
391
	delete[] conv_map;
David Rohr's avatar
David Rohr committed
392

393
	deviceFinishRun();
394 395 396 397 398 399 400 401 402 403
	{
		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;
	}
404

David Rohr's avatar
David Rohr committed
405
	// ************* Writing Out Probabilities ***************
406

David Rohr's avatar
David Rohr committed
407
	// *** Angular Probability ***
David Rohr's avatar
David Rohr committed
408

David Rohr's avatar
David Rohr committed
409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426
#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);
427

David Rohr's avatar
David Rohr committed
428
		//Find MaxProb
429
		MPI_Status mpistatus;
David Rohr's avatar
David Rohr committed
430
		{
David Rohr's avatar
David Rohr committed
431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448
			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)
					{
449
						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
450 451 452 453 454 455 456 457 458 459
					}
					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
460

David Rohr's avatar
David Rohr committed
461 462 463 464 465 466 467 468 469
		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
470

David Rohr's avatar
David Rohr committed
471 472 473 474 475
		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
476

David Rohr's avatar
David Rohr committed
477 478
	//Angle Reduction and Probability summation for individual angles
	if (param.param_device.writeAngles)
479
	{
David Rohr's avatar
David Rohr committed
480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511
		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
512
		delete[] tmp3;
513
	}
David Rohr's avatar
David Rohr committed
514
#endif
515

David Rohr's avatar
David Rohr committed
516
	if (mpi_rank == 0)
517
	{
David Rohr's avatar
David Rohr committed
518 519 520 521 522 523 524 525 526 527 528 529
		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);
530

David Rohr's avatar
David Rohr committed
531
			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";
532

David Rohr's avatar
David Rohr committed
533
			outputProbFile << "RefMap " << iRefMap << " Maximizing Param: ";
534

David Rohr's avatar
David Rohr committed
535 536 537 538 539 540 541 542 543 544 545
			// *** 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";
546

David Rohr's avatar
David Rohr committed
547
			// *** For individual files*** //angProbfile.open ("ANG_PROB_"iRefMap);
548

David Rohr's avatar
David Rohr committed
549
			if(param.param_device.writeAngles)
550
			{
David Rohr's avatar
David Rohr committed
551 552 553
				for (int iOrient = 0; iOrient < param.nTotGridAngles; iOrient++)
				{
					bioem_Probability_angle& pProbAngle = pProb.getProbAngle(iRefMap, iOrient);
554

David Rohr's avatar
David Rohr committed
555 556
					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";
				}
557 558
			}
		}
559

David Rohr's avatar
David Rohr committed
560 561 562 563 564
		if(param.param_device.writeAngles)
		{
			angProbfile.close();
		}
		outputProbFile.close();
565
	}
566

567
	return(0);
568 569
}

570
int bioem::compareRefMaps(int iOrient, int iConv, const myfloat_t* conv_map, mycomplex_t* localmultFFT, myfloat_t sumC, myfloat_t sumsquareC, const int startMap)
571
{
David Rohr's avatar
David Rohr committed
572 573
	//***************************************************************************************
	//***** BioEM routine for comparing reference maps to convoluted maps *****
574
	if (FFTAlgo)
575
	{
David Rohr's avatar
David Rohr committed
576
		//With FFT Algorithm
577 578
		#pragma omp parallel for
		for (int iRefMap = startMap; iRefMap < RefMap.ntotRefMap; iRefMap ++)
579
		{
580
			const int num = omp_get_thread_num();
581
			calculateCCFFT(iRefMap, iOrient, iConv, sumC, sumsquareC, localmultFFT, localCCT[num], lCC[num]);
582 583 584
		}
	}
	else
585
	{
David Rohr's avatar
David Rohr committed
586
		//Without FFT Algorithm
587
		#pragma omp parallel for
588
		for (int iRefMap = startMap; iRefMap < RefMap.ntotRefMap; iRefMap ++)
589
		{
590
			compareRefMapShifted < -1 > (iRefMap, iOrient, iConv, conv_map, pProb, param.param_device, RefMap);
591 592 593 594 595
		}
	}
	return(0);
}

596
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)
597
{
David Rohr's avatar
David Rohr committed
598 599
	//***************************************************************************************
	//***** Calculating cross correlation in FFTALGOrithm *****
Pilar Cossio's avatar
Pilar Cossio committed
600

601
	const mycomplex_t* RefMapFFT = &RefMap.RefMapsFFT[iRefMap * param.FFTMapSize];
602
	for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D; i++)
603
	{
604 605
		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];
606 607
	}

608
	myfftw_execute_dft_c2r(param.fft_plan_c2r_backward, localCCT, lCC);
609

610
	doRefMapFFT(iRefMap, iOrient, iConv, lCC, sumC, sumsquareC, pProb, param.param_device, RefMap);
611
}
612

613
int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
614
{
David Rohr's avatar
David Rohr committed
615
	// **************************************************************************************
David Rohr's avatar
David Rohr committed
616 617
	// ****  BioEM Create Projection routine in Euler angle predefined grid******************
	// ********************* and turns projection into Fourier space ************************
David Rohr's avatar
David Rohr committed
618
	// **************************************************************************************
619

620 621
	cuda_custom_timeslot("Projection", 0);

622 623
	myfloat3_t RotatedPointsModel[Model.nPointsModel];
	myfloat_t rotmat[3][3];
624
	myfloat_t alpha, gam, beta;
625
	myfloat_t* localproj;
626

627
	localproj = lCC[omp_get_thread_num()];
628
	memset(localproj, 0, param.param_device.NumberPixels * param.param_device.NumberPixels * sizeof(*localproj));
629

630 631 632
	alpha = param.angles[iMap].pos[0];
	beta = param.angles[iMap].pos[1];
	gam = param.angles[iMap].pos[2];
633

David Rohr's avatar
David Rohr committed
634
	// **** To see how things are going: cout << "Id " << omp_get_thread_num() <<  " Angs: " << alpha << " " << beta << " " << gam << "\n"; ***
635

David Rohr's avatar
David Rohr committed
636
	// ********** Creat Rotation with pre-defiend grid of orientations**********
637 638 639 640 641 642 643 644 645 646 647
	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++)
648
	{
649 650 651
		RotatedPointsModel[n].pos[0] = 0.0;
		RotatedPointsModel[n].pos[1] = 0.0;
		RotatedPointsModel[n].pos[2] = 0.0;
652
	}
653
	for(int n = 0; n < Model.nPointsModel; n++)
654
	{
655
		for(int k = 0; k < 3; k++)
656
		{
657
			for(int j = 0; j < 3; j++)
658
			{
659
				RotatedPointsModel[n].pos[k] += rotmat[k][j] * Model.points[n].point.pos[j];
660 661 662 663 664 665
			}
		}
	}

	int i, j;

David Rohr's avatar
David Rohr committed
666
	// ************ Projection over the Z axis********************
667
	for(int n = 0; n < Model.nPointsModel; n++)
668 669
	{
		//Getting pixel that represents coordinates & shifting the start at to Numpix/2,Numpix/2 )
670 671
		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);
672

673 674 675 676 677 678
		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;
		}

679
		localproj[i * param.param_device.NumberPixels + j] += Model.points[n].density / Model.NormDen;
680 681
	}

David Rohr's avatar
David Rohr committed
682
	// **** Output Just to check****
683
#ifdef PILAR_DEBUG
684
	if(iMap == 10)
685 686 687 688 689 690
	{
		ofstream myexamplemap;
		ofstream myexampleRot;
		myexamplemap.open ("MAP_i10");
		myexampleRot.open ("Rot_i10");
		myexamplemap << "ANGLES " << alpha << " " << beta << " " << gam << "\n";
691
		for(int k = 0; k < param.param_device.NumberPixels; k++)
692
		{
693
			for(int j = 0; j < param.param_device.NumberPixels; j++) myexamplemap << "\nMAP " << k << " " << j << " " << localproj[k * param.param_device.NumberPixels + j];
694 695
		}
		myexamplemap << " \n";
696
		for(int n = 0; n < Model.nPointsModel; n++)myexampleRot << "\nCOOR " << RotatedPointsModel[n].pos[0] << " " << RotatedPointsModel[n].pos[1] << " " << RotatedPointsModel[n].pos[2];
697 698 699
		myexamplemap.close();
		myexampleRot.close();
	}
700
#endif
701

David Rohr's avatar
David Rohr committed
702 703
	// ***** Converting projection to Fourier Space for Convolution later with kernel****
	// ********** Omp Critical is necessary with FFTW*******
704
	myfftw_execute_dft_r2c(param.fft_plan_r2c_forward, localproj, mapFFT);
705

706 707
	cuda_custom_timeslot_end;

708 709 710
	return(0);
}

711
int bioem::createConvolutedProjectionMap(int iMap, int iConv, mycomplex_t* lproj, myfloat_t* Mapconv, mycomplex_t* localmultFFT, myfloat_t& sumC, myfloat_t& sumsquareC)
712
{
David Rohr's avatar
David Rohr committed
713 714
	// **************************************************************************************
	// ****  BioEM Create Convoluted Projection Map routine, multiplies in Fourier **********
David Rohr's avatar
David Rohr committed
715 716
	// **************** calculated Projection with convoluted precalculated Kernel***********
	// *************** and Backtransforming it to real Space ********************************
David Rohr's avatar
David Rohr committed
717
	// **************************************************************************************
718

719 720
	cuda_custom_timeslot("Convolution", 1);

721
	mycomplex_t* tmp = localCCT[omp_get_thread_num()];
722

David Rohr's avatar
David Rohr committed
723
	// **** Multiplying FFTmap with corresponding kernel ****
724
	const mycomplex_t* refCTF = &param.refCTF[iConv * param.FFTMapSize];
725
	for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D; i++)
726
	{
727 728 729
		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";
730 731
	}

David Rohr's avatar
David Rohr committed
732
	// *** Calculating Cross-correlations of cal-convoluted map with its self *****
733
	sumC = localmultFFT[0][0];
David Rohr's avatar
David Rohr committed
734

735
	sumsquareC = 0;
736
	if (FFTAlgo)
737
	{
738 739 740 741 742 743 744 745 746 747
		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
748

749 750
		myfloat_t norm2 = (myfloat_t) (param.param_device.NumberPixels * param.param_device.NumberPixels);
		sumsquareC = sumsquareC / norm2;
751
	}
752 753 754 755 756 757 758
	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);
759

760 761 762 763 764 765 766 767 768 769
		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
770

771 772
	cuda_custom_timeslot_end;

773
	return(0);
774 775
}

776
int bioem::calcross_cor(myfloat_t* localmap, myfloat_t& sum, myfloat_t& sumsquare)
777
{
David Rohr's avatar
David Rohr committed
778
	// *********************** Routine to calculate Cross correlations***********************
779

780 781
	sum = 0.0;
	sumsquare = 0.0;
782 783 784 785 786
	for (int i = 0; i < param.param_device.NumberPixels; i++)
	{
		for (int j = 0; j < param.param_device.NumberPixels; j++)
		{
			// Calculate Sum of pixels
787
			sum += localmap[i * param.param_device.NumberPixels + j];
788
			// Calculate Sum of pixels squared
789
			sumsquare += localmap[i * param.param_device.NumberPixels + j] * localmap[i * param.param_device.NumberPixels + j];
790 791 792
		}
	}
	return(0);
793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808
}

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

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

int bioem::deviceFinishRun()
{
	return(0);
}
809 810 811 812 813 814 815 816 817 818

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

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