bioem.cpp 24.3 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
226 227 228 229 230 231 232 233
	MPI_Bcast(&param, sizeof(param), MPI_BYTE, 0, MPI_COMM_WORLD);
	//refCtf, CtfParam, angles automatically filled by precalculare function below
	
	MPI_Bcast(&Model, sizeof(Model), MPI_BYTE, 0, MPI_COMM_WORLD);
	Model.points = (bioem_model::bioem_model_point*) mallocchk(sizeof(bioem_model::bioem_model_point) * Model.nPointsModel);
	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
234 235
#endif
	if (mpi_rank != 0) return(1);
236

David Rohr's avatar
David Rohr committed
237
	// ****************** Precalculating Necessary Stuff *********************
238
	param.PrepareFFTs();
239
	precalculate();
David Rohr's avatar
David Rohr committed
240

241 242
	if (getenv("BIOEM_DEBUG_BREAK"))
	{
243 244 245
		const int cut = atoi(getenv("BIOEM_DEBUG_BREAK"));
		if (param.nTotGridAngles > cut) param.nTotGridAngles = cut;
		if (param.nTotCTFs > cut) param.nTotCTFs = cut;
246
	}
David Rohr's avatar
David Rohr committed
247

248
	pProb.init(RefMap.ntotRefMap, param.nTotGridAngles, *this);
249

250 251
	deviceInit();

252
	return(0);
253 254
}

255 256 257
void bioem::cleanup()
{
	//Deleting allocated pointers
258
	free_device_host(pProb.ptr);
259 260 261
	RefMap.freePointers();
}

262 263
int bioem::precalculate()
{
David Rohr's avatar
David Rohr committed
264
	// **************************************************************************************
David Rohr's avatar
David Rohr committed
265
	// **Precalculating Routine of Orientation grids, Map crosscorrelations and CTF Kernels**
David Rohr's avatar
David Rohr committed
266
	// **************************************************************************************
267

268 269
	// Generating Grids of orientations
	param.CalculateGridsParam();
270

271 272
	// Precalculating CTF Kernels stored in class Param
	param.CalculateRefCTF();
273

274 275
	//Precalculate Maps
	RefMap.precalculate(param, *this);
276

277
	return(0);
278 279 280 281
}

int bioem::run()
{
David Rohr's avatar
David Rohr committed
282 283 284
	// **************************************************************************************
	// **** Main BioEM routine, projects, convolutes and compares with Map using OpenMP ****
	// **************************************************************************************
285

David Rohr's avatar
David Rohr committed
286 287
	// **** If we want to control the number of threads -> omp_set_num_threads(XX); ******
	// ****************** Declarying class of Probability Pointer  *************************
288

289
	printf("\tInitializing Probabilities\n");
290 291 292
	// Inizialzing Probabilites to zero and constant to -Infinity
	for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap; iRefMap ++)
	{
293 294 295 296 297
		bioem_Probability_map& pProbMap = pProb.getProbMap(iRefMap);

		pProbMap.Total = 0.0;
		pProbMap.Constoadd = -9999999;
		pProbMap.max_prob = -9999999;
298
		if (param.param_device.writeAngles)
299
		{
300 301 302
			for (int iOrient = 0; iOrient < param.nTotGridAngles; iOrient ++)
			{
				bioem_Probability_angle& pProbAngle = pProb.getProbAngle(iRefMap, iOrient);
303

304 305 306
				pProbAngle.forAngles = 0.0;
				pProbAngle.ConstAngle = -99999999;
			}
307 308
		}
	}
David Rohr's avatar
David Rohr committed
309
	// **************************************************************************************
310
	deviceStartRun();
311 312 313 314 315 316 317 318 319 320
	{
		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);
		}
	}
321

David Rohr's avatar
David Rohr committed
322
	// ******************************** MAIN CYCLE ******************************************
David Rohr's avatar
David Rohr committed
323

David Rohr's avatar
David Rohr committed
324
	// *** Declaring Private variables for each thread *****
325
	mycomplex_t* proj_mapFFT;
326
	myfloat_t* conv_map = new myfloat_t[param.param_device.NumberPixels * param.param_device.NumberPixels];
327
	mycomplex_t* conv_mapFFT;
328
	myfloat_t sumCONV, sumsquareCONV;
329 330

	//allocating fftw_complex vector
331 332
	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);
333 334 335

	HighResTimer timer;

336
	if (DebugOutput >= 1) printf("\tMain Loop (GridAngles %d, CTFs %d, RefMaps %d, Shifts (%d/%d)²), Pixels %d²\n", param.nTotGridAngles, param.nTotCTFs, RefMap.ntotRefMap, 2 * param.param_device.maxDisplaceCenter + param.param_device.GridSpaceCenter, param.param_device.GridSpaceCenter, param.param_device.NumberPixels);
Pilar Cossio's avatar
Pilar Cossio committed
337
//	printf("\tInner Loop Count (%d %d %d) %lld\n", param.param_device.maxDisplaceCenter, param.param_device.GridSpaceCenter, param.param_device.NumberPixels, (long long int) (param.param_device.NumberPixels * param.param_device.NumberPixels * (2 * param.param_device.maxDisplaceCenter / param.param_device.GridSpaceCenter + 1) * (2 * param.param_device.maxDisplaceCenter / param.param_device.GridSpaceCenter + 1)));
338
	for (int iOrient = 0; iOrient < param.nTotGridAngles; iOrient++)
339
	{
David Rohr's avatar
David Rohr committed
340 341
		// ***************************************************************************************
		// ***** Creating Projection for given orientation and transforming to Fourier space *****
342
		if (DebugOutput >= 1) timer.ResetStart();
343
		createProjection(iOrient, proj_mapFFT);
344
		if (DebugOutput >= 1) printf("Time Projection %d: %f\n", iOrient, timer.GetCurrentElapsedTime());
345

David Rohr's avatar
David Rohr committed
346 347
		// ***************************************************************************************
		// ***** **** Internal Loop over convolutions **** *****
348 349
		for (int iConv = 0; iConv < param.nTotCTFs; iConv++)
		{
350
			if (DebugOutput >= 2) printf("\t\tConvolution %d %d\n", iOrient, iConv);
David Rohr's avatar
David Rohr committed
351
			// *** Calculating convolutions of projection map and crosscorrelations ***
352

353
			if (DebugOutput >= 2) timer.ResetStart();
354
			createConvolutedProjectionMap(iOrient, iConv, proj_mapFFT, conv_map, conv_mapFFT, sumCONV, sumsquareCONV);
355
			if (DebugOutput >= 2) printf("Time Convolution %d %d: %f\n", iOrient, iConv, timer.GetCurrentElapsedTime());
356

David Rohr's avatar
David Rohr committed
357 358
			// ***************************************************************************************
			// *** Comparing each calculated convoluted map with all experimental maps ***
359
			if (DebugOutput >= 2) timer.ResetStart();
360
			compareRefMaps(iOrient, iConv, conv_map, conv_mapFFT, sumCONV, sumsquareCONV);
361

362 363 364 365 366 367 368 369 370 371 372 373
			if (DebugOutput >= 2)
			{
				const double compTime = timer.GetCurrentElapsedTime();
				const int nShifts = 2 * param.param_device.maxDisplaceCenter / param.param_device.GridSpaceCenter + 1;
				const double nFlops = (double) RefMap.ntotRefMap * (double) nShifts * (double) nShifts *
									  (((double) param.param_device.NumberPixels - (double) param.param_device.maxDisplaceCenter / 2.) * ((double) param.param_device.NumberPixels - (double) param.param_device.maxDisplaceCenter / 2.) * 5. + 25.) / compTime;
				const double nGBs = (double) RefMap.ntotRefMap * (double) nShifts * (double) nShifts *
									(((double) param.param_device.NumberPixels - (double) param.param_device.maxDisplaceCenter / 2.) * ((double) param.param_device.NumberPixels - (double) param.param_device.maxDisplaceCenter / 2.) * 2. + 8.) * (double) sizeof(myfloat_t) / compTime;
				const double nGBs2 = (double) RefMap.ntotRefMap * ((double) param.param_device.NumberPixels * (double) param.param_device.NumberPixels + 8.) * (double) sizeof(myfloat_t) / compTime;

				printf("Time Comparison %d %d: %f sec (%f GFlops, %f GB/s (cached), %f GB/s)\n", iOrient, iConv, compTime, nFlops / 1000000000., nGBs / 1000000000., nGBs2 / 1000000000.);
			}
374 375 376 377 378
		}
	}
	//deallocating fftw_complex vector
	myfftw_free(proj_mapFFT);
	myfftw_free(conv_mapFFT);
379
	delete[] conv_map;
David Rohr's avatar
David Rohr committed
380

381
	deviceFinishRun();
382 383 384 385 386 387 388 389 390 391
	{
		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;
	}
392

David Rohr's avatar
David Rohr committed
393
	// ************* Writing Out Probabilities ***************
394

David Rohr's avatar
David Rohr committed
395
	// *** Angular Probability ***
396

397
	ofstream angProbfile;
398
	if(param.param_device.writeAngles)
399 400 401
	{
		angProbfile.open ("ANG_PROB");
	}
402

403 404 405 406
	ofstream outputProbFile;
	outputProbFile.open ("Output_Probabilities");
	for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap; iRefMap ++)
	{
David Rohr's avatar
David Rohr committed
407
		// **** Total Probability ***
408 409 410
		bioem_Probability_map& pProbMap = pProb.getProbMap(iRefMap);

		outputProbFile << "RefMap " << iRefMap << " Probability  "  << log(pProbMap.Total) + pProbMap.Constoadd + 0.5 * log(M_PI) + (1 - param.param_device.Ntotpi * 0.5)*(log(2 * M_PI) + 1) + log(param.param_device.volu) << " Constant " << pProbMap.Constoadd  << "\n";
411 412 413

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

David Rohr's avatar
David Rohr committed
414
		// *** Param that maximize probability****
415 416 417 418 419 420 421 422 423
		outputProbFile << (pProbMap.max_prob + 0.5 * log(M_PI) + (1 - param.param_device.Ntotpi * 0.5) * (log(2 * M_PI) + 1) + log(param.param_device.volu)) << " ";
		outputProbFile << param.angles[pProbMap.max_prob_orient].pos[0] << " ";
		outputProbFile << param.angles[pProbMap.max_prob_orient].pos[1] << " ";
		outputProbFile << param.angles[pProbMap.max_prob_orient].pos[2] << " ";
		outputProbFile << param.CtfParam[pProbMap.max_prob_conv].pos[0] << " ";
		outputProbFile << param.CtfParam[pProbMap.max_prob_conv].pos[1] << " ";
		outputProbFile << param.CtfParam[pProbMap.max_prob_conv].pos[2] << " ";
		outputProbFile << pProbMap.max_prob_cent_x << " ";
		outputProbFile << pProbMap.max_prob_cent_y;
424
		outputProbFile << "\n";
425

David Rohr's avatar
David Rohr committed
426
		// *** For individual files*** //angProbfile.open ("ANG_PROB_"iRefMap);
427

428
		if(param.param_device.writeAngles)
429
		{
430
			for (int iOrient = 0; iOrient < param.nTotGridAngles; iOrient++)
431
			{
432
				bioem_Probability_angle& pProbAngle = pProb.getProbAngle(iRefMap, iOrient);
433

434
				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";
435 436 437
			}
		}
	}
438

439
	if(param.param_device.writeAngles)
440 441 442
	{
		angProbfile.close();
	}
443
	outputProbFile.close();
444

445
	return(0);
446 447
}

448
int bioem::compareRefMaps(int iOrient, int iConv, const myfloat_t* conv_map, mycomplex_t* localmultFFT, myfloat_t sumC, myfloat_t sumsquareC, const int startMap)
449
{
David Rohr's avatar
David Rohr committed
450 451
	//***************************************************************************************
	//***** BioEM routine for comparing reference maps to convoluted maps *****
452
	if (FFTAlgo)
453
	{
David Rohr's avatar
David Rohr committed
454
		//With FFT Algorithm
455 456
		#pragma omp parallel for
		for (int iRefMap = startMap; iRefMap < RefMap.ntotRefMap; iRefMap ++)
457
		{
458
			const int num = omp_get_thread_num();
459
			calculateCCFFT(iRefMap, iOrient, iConv, sumC, sumsquareC, localmultFFT, localCCT[num], lCC[num]);
460 461 462
		}
	}
	else
463
	{
David Rohr's avatar
David Rohr committed
464
		//Without FFT Algorithm
465
		#pragma omp parallel for
466
		for (int iRefMap = startMap; iRefMap < RefMap.ntotRefMap; iRefMap ++)
467
		{
468
			compareRefMapShifted < -1 > (iRefMap, iOrient, iConv, conv_map, pProb, param.param_device, RefMap);
469 470 471 472 473
		}
	}
	return(0);
}

474
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)
475
{
David Rohr's avatar
David Rohr committed
476 477
	//***************************************************************************************
	//***** Calculating cross correlation in FFTALGOrithm *****
Pilar Cossio's avatar
Pilar Cossio committed
478

479
	const mycomplex_t* RefMapFFT = &RefMap.RefMapsFFT[iRefMap * param.FFTMapSize];
480
	for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D; i++)
481
	{
482 483
		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];
484 485
	}

486
	myfftw_execute_dft_c2r(param.fft_plan_c2r_backward, localCCT, lCC);
487

488
	doRefMapFFT(iRefMap, iOrient, iConv, lCC, sumC, sumsquareC, pProb, param.param_device, RefMap);
489
}
490

491
int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
492
{
David Rohr's avatar
David Rohr committed
493
	// **************************************************************************************
David Rohr's avatar
David Rohr committed
494 495
	// ****  BioEM Create Projection routine in Euler angle predefined grid******************
	// ********************* and turns projection into Fourier space ************************
David Rohr's avatar
David Rohr committed
496
	// **************************************************************************************
497

498 499
	cuda_custom_timeslot("Projection", 0);

500 501
	myfloat3_t RotatedPointsModel[Model.nPointsModel];
	myfloat_t rotmat[3][3];
502
	myfloat_t alpha, gam, beta;
503
	myfloat_t* localproj;
504

505
	localproj = lCC[omp_get_thread_num()];
506
	memset(localproj, 0, param.param_device.NumberPixels * param.param_device.NumberPixels * sizeof(*localproj));
507

508 509 510
	alpha = param.angles[iMap].pos[0];
	beta = param.angles[iMap].pos[1];
	gam = param.angles[iMap].pos[2];
511

David Rohr's avatar
David Rohr committed
512
	// **** To see how things are going: cout << "Id " << omp_get_thread_num() <<  " Angs: " << alpha << " " << beta << " " << gam << "\n"; ***
513

David Rohr's avatar
David Rohr committed
514
	// ********** Creat Rotation with pre-defiend grid of orientations**********
515 516 517 518 519 520 521 522 523 524 525
	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++)
526
	{
527 528 529
		RotatedPointsModel[n].pos[0] = 0.0;
		RotatedPointsModel[n].pos[1] = 0.0;
		RotatedPointsModel[n].pos[2] = 0.0;
530
	}
531
	for(int n = 0; n < Model.nPointsModel; n++)
532
	{
533
		for(int k = 0; k < 3; k++)
534
		{
535
			for(int j = 0; j < 3; j++)
536
			{
537
				RotatedPointsModel[n].pos[k] += rotmat[k][j] * Model.points[n].point.pos[j];
538 539 540 541 542 543
			}
		}
	}

	int i, j;

David Rohr's avatar
David Rohr committed
544
	// ************ Projection over the Z axis********************
545
	for(int n = 0; n < Model.nPointsModel; n++)
546 547
	{
		//Getting pixel that represents coordinates & shifting the start at to Numpix/2,Numpix/2 )
548 549
		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);
550

551 552 553 554 555 556
		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;
		}

557
		localproj[i * param.param_device.NumberPixels + j] += Model.points[n].density / Model.NormDen;
558 559
	}

David Rohr's avatar
David Rohr committed
560
	// **** Output Just to check****
561
#ifdef PILAR_DEBUG
562
	if(iMap == 10)
563 564 565 566 567 568
	{
		ofstream myexamplemap;
		ofstream myexampleRot;
		myexamplemap.open ("MAP_i10");
		myexampleRot.open ("Rot_i10");
		myexamplemap << "ANGLES " << alpha << " " << beta << " " << gam << "\n";
569
		for(int k = 0; k < param.param_device.NumberPixels; k++)
570
		{
571
			for(int j = 0; j < param.param_device.NumberPixels; j++) myexamplemap << "\nMAP " << k << " " << j << " " << localproj[k * param.param_device.NumberPixels + j];
572 573
		}
		myexamplemap << " \n";
574
		for(int n = 0; n < Model.nPointsModel; n++)myexampleRot << "\nCOOR " << RotatedPointsModel[n].pos[0] << " " << RotatedPointsModel[n].pos[1] << " " << RotatedPointsModel[n].pos[2];
575 576 577
		myexamplemap.close();
		myexampleRot.close();
	}
578
#endif
579

David Rohr's avatar
David Rohr committed
580 581
	// ***** Converting projection to Fourier Space for Convolution later with kernel****
	// ********** Omp Critical is necessary with FFTW*******
582
	myfftw_execute_dft_r2c(param.fft_plan_r2c_forward, localproj, mapFFT);
583

584 585
	cuda_custom_timeslot_end;

586 587 588
	return(0);
}

589
int bioem::createConvolutedProjectionMap(int iMap, int iConv, mycomplex_t* lproj, myfloat_t* Mapconv, mycomplex_t* localmultFFT, myfloat_t& sumC, myfloat_t& sumsquareC)
590
{
David Rohr's avatar
David Rohr committed
591 592
	// **************************************************************************************
	// ****  BioEM Create Convoluted Projection Map routine, multiplies in Fourier **********
David Rohr's avatar
David Rohr committed
593 594
	// **************** calculated Projection with convoluted precalculated Kernel***********
	// *************** and Backtransforming it to real Space ********************************
David Rohr's avatar
David Rohr committed
595
	// **************************************************************************************
596

597 598
	cuda_custom_timeslot("Convolution", 1);

599
	mycomplex_t* tmp = localCCT[omp_get_thread_num()];
600

David Rohr's avatar
David Rohr committed
601
	// **** Multiplying FFTmap with corresponding kernel ****
602
	const mycomplex_t* refCTF = &param.refCTF[iConv * param.FFTMapSize];
603
	for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D; i++)
604
	{
605 606 607
		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";
608 609
	}

610 611 612
	//FFTW_C2R will destroy the input array, so we have to work on a copy here
	memcpy(tmp, localmultFFT, sizeof(mycomplex_t) * param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D);

David Rohr's avatar
David Rohr committed
613
	// **** Bringing convoluted Map to real Space ****
David Rohr's avatar
David Rohr committed
614
	myfftw_execute_dft_c2r(param.fft_plan_c2r_backward, tmp, Mapconv);
615

David Rohr's avatar
David Rohr committed
616
	// *** Calculating Cross-correlations of cal-convoluted map with its self *****
617 618
	sumC = 0;
	sumsquareC = 0;
619
	for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberPixels; i++)
620
	{
David Rohr's avatar
David Rohr committed
621 622
		sumC += Mapconv[i];
		sumsquareC += Mapconv[i] * Mapconv[i];
623
	}
David Rohr's avatar
David Rohr committed
624
	// *** The DTF gives an unnormalized value so have to divded by the total number of pixels in Fourier ***
625
	// Normalizing
626 627 628 629
	myfloat_t norm2 = (myfloat_t) (param.param_device.NumberPixels * param.param_device.NumberPixels);
	myfloat_t norm4 = norm2 * norm2;
	sumC = sumC / norm2;
	sumsquareC = sumsquareC / norm4;
630

631 632
	cuda_custom_timeslot_end;

633
	return(0);
634 635
}

636
int bioem::calcross_cor(myfloat_t* localmap, myfloat_t& sum, myfloat_t& sumsquare)
637
{
David Rohr's avatar
David Rohr committed
638
	// *********************** Routine to calculate Cross correlations***********************
639

640 641
	sum = 0.0;
	sumsquare = 0.0;
642 643 644 645 646
	for (int i = 0; i < param.param_device.NumberPixels; i++)
	{
		for (int j = 0; j < param.param_device.NumberPixels; j++)
		{
			// Calculate Sum of pixels
647
			sum += localmap[i * param.param_device.NumberPixels + j];
648
			// Calculate Sum of pixels squared
649
			sumsquare += localmap[i * param.param_device.NumberPixels + j] * localmap[i * param.param_device.NumberPixels + j];
650 651 652
		}
	}
	return(0);
653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668
}

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

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

int bioem::deviceFinishRun()
{
	return(0);
}
669 670 671 672 673 674 675 676 677 678

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

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