bioem.cpp 23.6 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 18
#include <fstream>
#include <boost/program_options.hpp>
#include <iostream>
#include <algorithm>
#include <iterator>
#include <stdio.h>
#include <stdlib.h>
#include <string>
#include <cmath>
19

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

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

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

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

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

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

57 58 59 60 61 62 63 64 65 66 67
#include "bioem_algorithm.h"

using namespace boost;
namespace po = boost::program_options;

using namespace std;

// A helper function of Boost
template<class T>
ostream& operator<<(ostream& os, const vector<T>& v)
{
68 69
	copy(v.begin(), v.end(), ostream_iterator<T>(os, " "));
	return os;
70 71 72 73
}

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

bioem::~bioem()
{
}

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

David Rohr's avatar
David Rohr committed
90
	// *** Inizialzing default variables ***
91 92 93
	std::string infile, modelfile, mapfile;
	Model.readPDB = false;
	param.writeAngles = false;
94 95
	param.dumpMap = false;
	param.loadMap = false;
David Rohr's avatar
David Rohr committed
96 97
	RefMap.readMRC = false;
	RefMap.readMultMRC = false;
98

David Rohr's avatar
David Rohr committed
99
	// *************************************************************************************
100
	cout << " ++++++++++++ FROM COMMAND LINE +++++++++++\n\n";
David Rohr's avatar
David Rohr committed
101
	// *************************************************************************************
102

David Rohr's avatar
David Rohr committed
103
	// ********************* Command line reading input with BOOST ************************
104

105 106
	try {
		po::options_description desc("Command line inputs");
David Rohr's avatar
David Rohr committed
107 108 109 110 111 112 113 114 115 116 117
		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")
		;
David Rohr's avatar
David Rohr committed
118

119 120 121 122 123 124

		po::positional_options_description p;
		p.add("Inputfile", -1);
		p.add("Modelfile", -1);
		p.add("Particlesfile", -1);
		p.add("ReadPDB", -1);
David Rohr's avatar
David Rohr committed
125 126
		p.add("ReadMRC", -1);
		p.add("ReadMultipleMRC", -1);
127 128 129
		p.add("DumpMaps", -1);
		p.add("LoadMapDump", -1);

130 131 132 133 134 135 136
		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;
137
			return 1;
138 139 140 141
		}
		if (vm.count("help")) {
			cout << "Usage: options_description [options]\n";
			cout << desc;
142
			return 1;
143 144 145 146 147
		}

		if (vm.count("Inputfile"))
		{
			cout << "Input file is: ";
148 149
			cout << vm["Inputfile"].as< std::string >() << "\n";
			infile = vm["Inputfile"].as< std::string >();
150 151 152 153 154
		}
		if (vm.count("Modelfile"))
		{
			cout << "Model file is: "
				 << vm["Modelfile"].as<  std::string  >() << "\n";
155
			modelfile = vm["Modelfile"].as<  std::string  >();
156 157 158 159 160
		}

		if (vm.count("ReadPDB"))
		{
			cout << "Reading model file in PDB format.\n";
161
			Model.readPDB = true;
162 163
		}

David Rohr's avatar
David Rohr committed
164 165 166 167 168 169 170 171 172 173 174
		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;
		}
175 176 177 178

		if (vm.count("DumpMaps"))
		{
			cout << "Dumping Maps after reading from file.\n";
179
			param.dumpMap = true;
180 181 182 183 184
		}

		if (vm.count("LoadMapDump"))
		{
			cout << "Loading Map dump.\n";
185
			param.loadMap = true;
186 187 188 189 190 191
		}

		if (vm.count("Particlesfile"))
		{
			cout << "Paricle file is: "
				 << vm["Particlesfile"].as< std::string >() << "\n";
192
			mapfile = vm["Particlesfile"].as< std::string >();
193 194 195 196 197 198 199
		}
	}
	catch(std::exception& e)
	{
		cout << e.what() << "\n";
		return 1;
	}
Pilar Cossio's avatar
Pilar Cossio committed
200 201 202 203 204
        //check for consitency in multiple MRCs
        if(  RefMap.readMultMRC && not(RefMap.readMRC) ){
         cout << "For Multiple MRCs command --ReadMRC is necesary too";
         exit(1);
        }
David Rohr's avatar
David Rohr committed
205
	// ********************* Reading Parameter Input ***************************
206 207 208 209
	// copying inputfile to param class
	param.fileinput = infile.c_str();
	param.readParameters();

David Rohr's avatar
David Rohr committed
210
	// ********************* Reading Model Input ******************************
211 212 213 214
	// copying modelfile to model class
	Model.filemodel = modelfile.c_str();
	Model.readModel();

David Rohr's avatar
David Rohr committed
215 216
	// ********************* Reading Particle Maps Input **********************
	// ********* HERE: PROBLEM if maps dont fit on the memory!! ***************
217
	// copying mapfile to ref map class
218
	param.filemap = mapfile.c_str();
219 220
	RefMap.readRefMaps(param);

David Rohr's avatar
David Rohr committed
221
	// ****************** Precalculating Necessary Stuff *********************
222
	precalculate();
David Rohr's avatar
David Rohr committed
223

224 225
	if (getenv("BIOEM_DEBUG_BREAK"))
	{
226 227 228
		const int cut = atoi(getenv("BIOEM_DEBUG_BREAK"));
		if (param.nTotGridAngles > cut) param.nTotGridAngles = cut;
		if (param.nTotCTFs > cut) param.nTotCTFs = cut;
229
	}
David Rohr's avatar
David Rohr committed
230

231
	pProb.init(RefMap.ntotRefMap, param.nTotGridAngles, *this);
232

233 234
	deviceInit();

235
	return(0);
236 237
}

238 239 240
void bioem::cleanup()
{
	//Deleting allocated pointers
241
	free_device_host(pProb.ptr);
242 243 244
	RefMap.freePointers();
}

245 246
int bioem::precalculate()
{
David Rohr's avatar
David Rohr committed
247
	// **************************************************************************************
David Rohr's avatar
David Rohr committed
248
	// **Precalculating Routine of Orientation grids, Map crosscorrelations and CTF Kernels**
David Rohr's avatar
David Rohr committed
249
	// **************************************************************************************
250

251 252
	// Generating Grids of orientations
	param.CalculateGridsParam();
253

254 255
	// Precalculating CTF Kernels stored in class Param
	param.CalculateRefCTF();
256

257 258
	//Precalculate Maps
	RefMap.precalculate(param, *this);
259

260
	return(0);
261 262 263 264
}

int bioem::run()
{
David Rohr's avatar
David Rohr committed
265 266 267
	// **************************************************************************************
	// **** Main BioEM routine, projects, convolutes and compares with Map using OpenMP ****
	// **************************************************************************************
268

David Rohr's avatar
David Rohr committed
269 270
	// **** If we want to control the number of threads -> omp_set_num_threads(XX); ******
	// ****************** Declarying class of Probability Pointer  *************************
271

272
	printf("\tInitializing Probabilities\n");
273 274 275
	// Inizialzing Probabilites to zero and constant to -Infinity
	for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap; iRefMap ++)
	{
276 277 278 279 280
		bioem_Probability_map& pProbMap = pProb.getProbMap(iRefMap);

		pProbMap.Total = 0.0;
		pProbMap.Constoadd = -9999999;
		pProbMap.max_prob = -9999999;
281
		for (int iOrient = 0; iOrient < param.nTotGridAngles; iOrient ++)
282
		{
283 284 285 286
			bioem_Probability_angle& pProbAngle = pProb.getProbAngle(iRefMap, iOrient);

			pProbAngle.forAngles = 0.0;
			pProbAngle.ConstAngle = -99999999;
287 288
		}
	}
David Rohr's avatar
David Rohr committed
289
	// **************************************************************************************
290
	deviceStartRun();
291 292 293 294 295 296 297 298 299 300
	{
		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);
		}
	}
301

David Rohr's avatar
David Rohr committed
302
	// ******************************** MAIN CYCLE ******************************************
David Rohr's avatar
David Rohr committed
303

David Rohr's avatar
David Rohr committed
304
	// *** Declaring Private variables for each thread *****
305
	mycomplex_t* proj_mapFFT;
306
	myfloat_t* conv_map = new myfloat_t[param.param_device.NumberPixels * param.param_device.NumberPixels];
307
	mycomplex_t* conv_mapFFT;
308
	myfloat_t sumCONV, sumsquareCONV;
309 310

	//allocating fftw_complex vector
311 312
	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);
313 314 315

	HighResTimer timer;

316
	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
317
//	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)));
318
	for (int iOrient = 0; iOrient < param.nTotGridAngles; iOrient++)
319
	{
David Rohr's avatar
David Rohr committed
320 321
		// ***************************************************************************************
		// ***** Creating Projection for given orientation and transforming to Fourier space *****
322
		if (DebugOutput >= 1) timer.ResetStart();
323
		createProjection(iOrient, proj_mapFFT);
324
		if (DebugOutput >= 1) printf("Time Projection %d: %f\n", iOrient, timer.GetCurrentElapsedTime());
325

David Rohr's avatar
David Rohr committed
326 327
		// ***************************************************************************************
		// ***** **** Internal Loop over convolutions **** *****
328 329
		for (int iConv = 0; iConv < param.nTotCTFs; iConv++)
		{
330
			if (DebugOutput >= 2) printf("\t\tConvolution %d %d\n", iOrient, iConv);
David Rohr's avatar
David Rohr committed
331
			// *** Calculating convolutions of projection map and crosscorrelations ***
332

333
			if (DebugOutput >= 2) timer.ResetStart();
334
			createConvolutedProjectionMap(iOrient, iConv, proj_mapFFT, conv_map, conv_mapFFT, sumCONV, sumsquareCONV);
335
			if (DebugOutput >= 2) printf("Time Convolution %d %d: %f\n", iOrient, iConv, timer.GetCurrentElapsedTime());
336

David Rohr's avatar
David Rohr committed
337 338
			// ***************************************************************************************
			// *** Comparing each calculated convoluted map with all experimental maps ***
339
			if (DebugOutput >= 2) timer.ResetStart();
340
			compareRefMaps(iOrient, iConv, conv_map, conv_mapFFT, sumCONV, sumsquareCONV);
341

342 343 344 345 346 347 348 349 350 351 352 353
			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.);
			}
354 355 356 357 358
		}
	}
	//deallocating fftw_complex vector
	myfftw_free(proj_mapFFT);
	myfftw_free(conv_mapFFT);
359
	delete[] conv_map;
David Rohr's avatar
David Rohr committed
360

361
	deviceFinishRun();
362 363 364 365 366 367 368 369 370 371
	{
		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;
	}
372

David Rohr's avatar
David Rohr committed
373
	// ************* Writing Out Probabilities ***************
374

David Rohr's avatar
David Rohr committed
375
	// *** Angular Probability ***
376

377 378 379 380
	// if(param.writeAngles){
	ofstream angProbfile;
	angProbfile.open ("ANG_PROB_iRefMap");
	// }
381

382 383 384 385
	ofstream outputProbFile;
	outputProbFile.open ("Output_Probabilities");
	for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap; iRefMap ++)
	{
David Rohr's avatar
David Rohr committed
386
		// **** Total Probability ***
387 388 389
		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";
390 391 392

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

David Rohr's avatar
David Rohr committed
393
		// *** Param that maximize probability****
394 395 396 397 398 399 400 401 402
		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;
403
		outputProbFile << "\n";
404

David Rohr's avatar
David Rohr committed
405
		// *** For individual files*** //angProbfile.open ("ANG_PROB_"iRefMap);
406

407
		if(param.writeAngles)
408
		{
409
			for (int iOrient = 0; iOrient < param.nTotGridAngles; iOrient++)
410
			{
411
				bioem_Probability_angle& pProbAngle = pProb.getProbAngle(iRefMap, iOrient);
412

413
				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";
414 415 416
			}
		}
	}
417

418 419
	angProbfile.close();
	outputProbFile.close();
420

421
	return(0);
422 423
}

424
int bioem::compareRefMaps(int iOrient, int iConv, const myfloat_t* conv_map, mycomplex_t* localmultFFT, myfloat_t sumC, myfloat_t sumsquareC, const int startMap)
425
{
David Rohr's avatar
David Rohr committed
426 427
	//***************************************************************************************
	//***** BioEM routine for comparing reference maps to convoluted maps *****
428
	if (FFTAlgo)
429
	{
David Rohr's avatar
David Rohr committed
430
		//With FFT Algorithm
431 432
		#pragma omp parallel for
		for (int iRefMap = startMap; iRefMap < RefMap.ntotRefMap; iRefMap ++)
433
		{
434
			const int num = omp_get_thread_num();
435
			calculateCCFFT(iRefMap, iOrient, iConv, sumC, sumsquareC, localmultFFT, localCCT[num], lCC[num]);
436 437 438
		}
	}
	else
439
	{
David Rohr's avatar
David Rohr committed
440
		//Without FFT Algorithm
441
		#pragma omp parallel for
442
		for (int iRefMap = startMap; iRefMap < RefMap.ntotRefMap; iRefMap ++)
443
		{
444
			compareRefMapShifted < -1 > (iRefMap, iOrient, iConv, conv_map, pProb, param.param_device, RefMap);
445 446 447 448 449
		}
	}
	return(0);
}

450
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)
451
{
David Rohr's avatar
David Rohr committed
452 453
	//***************************************************************************************
	//***** Calculating cross correlation in FFTALGOrithm *****
Pilar Cossio's avatar
Pilar Cossio committed
454

455
	const mycomplex_t* RefMapFFT = &RefMap.RefMapsFFT[iRefMap * param.FFTMapSize];
456
	for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D; i++)
457
	{
458 459
		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];
460 461
	}

462
	myfftw_execute_dft_c2r(param.fft_plan_c2r_backward, localCCT, lCC);
463

464
	doRefMapFFT(iRefMap, iOrient, iConv, lCC, sumC, sumsquareC, pProb, param.param_device, RefMap);
465
}
466

467
int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
468
{
David Rohr's avatar
David Rohr committed
469
	// **************************************************************************************
David Rohr's avatar
David Rohr committed
470 471
	// ****  BioEM Create Projection routine in Euler angle predefined grid******************
	// ********************* and turns projection into Fourier space ************************
David Rohr's avatar
David Rohr committed
472
	// **************************************************************************************
473

474 475
	cuda_custom_timeslot("Projection", 0);

476 477
	myfloat3_t RotatedPointsModel[Model.nPointsModel];
	myfloat_t rotmat[3][3];
478
	myfloat_t alpha, gam, beta;
479
	myfloat_t* localproj;
480

481
	localproj = lCC[omp_get_thread_num()];
482
	memset(localproj, 0, param.param_device.NumberPixels * param.param_device.NumberPixels * sizeof(*localproj));
483

484 485 486
	alpha = param.angles[iMap].pos[0];
	beta = param.angles[iMap].pos[1];
	gam = param.angles[iMap].pos[2];
487

David Rohr's avatar
David Rohr committed
488
	// **** To see how things are going: cout << "Id " << omp_get_thread_num() <<  " Angs: " << alpha << " " << beta << " " << gam << "\n"; ***
489

David Rohr's avatar
David Rohr committed
490
	// ********** Creat Rotation with pre-defiend grid of orientations**********
491 492 493 494 495 496 497 498 499 500 501
	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++)
502
	{
503 504 505
		RotatedPointsModel[n].pos[0] = 0.0;
		RotatedPointsModel[n].pos[1] = 0.0;
		RotatedPointsModel[n].pos[2] = 0.0;
506
	}
507
	for(int n = 0; n < Model.nPointsModel; n++)
508
	{
509
		for(int k = 0; k < 3; k++)
510
		{
511
			for(int j = 0; j < 3; j++)
512
			{
513
				RotatedPointsModel[n].pos[k] += rotmat[k][j] * Model.PointsModel[n].pos[j];
514 515 516 517 518 519
			}
		}
	}

	int i, j;

David Rohr's avatar
David Rohr committed
520
	// ************ Projection over the Z axis********************
521
	for(int n = 0; n < Model.nPointsModel; n++)
522 523
	{
		//Getting pixel that represents coordinates & shifting the start at to Numpix/2,Numpix/2 )
524 525
		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);
526

527 528 529 530 531 532
		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;
		}

533
		localproj[i * param.param_device.NumberPixels + j] += Model.densityPointsModel[n] / Model.NormDen;
534 535
	}

David Rohr's avatar
David Rohr committed
536
	// **** Output Just to check****
537
	if(iMap == 10)
538 539 540 541 542 543
	{
		ofstream myexamplemap;
		ofstream myexampleRot;
		myexamplemap.open ("MAP_i10");
		myexampleRot.open ("Rot_i10");
		myexamplemap << "ANGLES " << alpha << " " << beta << " " << gam << "\n";
544
		for(int k = 0; k < param.param_device.NumberPixels; k++)
545
		{
546
			for(int j = 0; j < param.param_device.NumberPixels; j++) myexamplemap << "\nMAP " << k << " " << j << " " << localproj[k * param.param_device.NumberPixels + j];
547 548
		}
		myexamplemap << " \n";
549
		for(int n = 0; n < Model.nPointsModel; n++)myexampleRot << "\nCOOR " << RotatedPointsModel[n].pos[0] << " " << RotatedPointsModel[n].pos[1] << " " << RotatedPointsModel[n].pos[2];
550 551 552 553
		myexamplemap.close();
		myexampleRot.close();
	}

David Rohr's avatar
David Rohr committed
554 555
	// ***** Converting projection to Fourier Space for Convolution later with kernel****
	// ********** Omp Critical is necessary with FFTW*******
556
	myfftw_execute_dft_r2c(param.fft_plan_r2c_forward, localproj, mapFFT);
557

558 559
	cuda_custom_timeslot_end;

560 561 562
	return(0);
}

563
int bioem::createConvolutedProjectionMap(int iMap, int iConv, mycomplex_t* lproj, myfloat_t* Mapconv, mycomplex_t* localmultFFT, myfloat_t& sumC, myfloat_t& sumsquareC)
564
{
David Rohr's avatar
David Rohr committed
565 566
	// **************************************************************************************
	// ****  BioEM Create Convoluted Projection Map routine, multiplies in Fourier **********
David Rohr's avatar
David Rohr committed
567 568
	// **************** calculated Projection with convoluted precalculated Kernel***********
	// *************** and Backtransforming it to real Space ********************************
David Rohr's avatar
David Rohr committed
569
	// **************************************************************************************
570

571 572
	cuda_custom_timeslot("Convolution", 1);

573
	mycomplex_t* tmp = localCCT[omp_get_thread_num()];
574

David Rohr's avatar
David Rohr committed
575
	// **** Multiplying FFTmap with corresponding kernel ****
576
	const mycomplex_t* refCTF = &param.refCTF[iConv * param.FFTMapSize];
577
	for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D; i++)
578
	{
579 580 581
		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";
582 583
	}

584 585 586
	//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
587
	// **** Bringing convoluted Map to real Space ****
David Rohr's avatar
David Rohr committed
588
	myfftw_execute_dft_c2r(param.fft_plan_c2r_backward, tmp, Mapconv);
589

David Rohr's avatar
David Rohr committed
590
	// *** Calculating Cross-correlations of cal-convoluted map with its self *****
591 592
	sumC = 0;
	sumsquareC = 0;
593
	for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberPixels; i++)
594
	{
David Rohr's avatar
David Rohr committed
595 596
		sumC += Mapconv[i];
		sumsquareC += Mapconv[i] * Mapconv[i];
597
	}
David Rohr's avatar
David Rohr committed
598
	// *** The DTF gives an unnormalized value so have to divded by the total number of pixels in Fourier ***
599
	// Normalizing
600 601 602 603
	myfloat_t norm2 = (myfloat_t) (param.param_device.NumberPixels * param.param_device.NumberPixels);
	myfloat_t norm4 = norm2 * norm2;
	sumC = sumC / norm2;
	sumsquareC = sumsquareC / norm4;
604

605 606
	cuda_custom_timeslot_end;

607
	return(0);
608 609
}

610
int bioem::calcross_cor(myfloat_t* localmap, myfloat_t& sum, myfloat_t& sumsquare)
611
{
David Rohr's avatar
David Rohr committed
612
	// *********************** Routine to calculate Cross correlations***********************
613

614 615
	sum = 0.0;
	sumsquare = 0.0;
616 617 618 619 620
	for (int i = 0; i < param.param_device.NumberPixels; i++)
	{
		for (int j = 0; j < param.param_device.NumberPixels; j++)
		{
			// Calculate Sum of pixels
621
			sum += localmap[i * param.param_device.NumberPixels + j];
622
			// Calculate Sum of pixels squared
623
			sumsquare += localmap[i * param.param_device.NumberPixels + j] * localmap[i * param.param_device.NumberPixels + j];
624 625 626
		}
	}
	return(0);
627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642
}

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

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

int bioem::deviceFinishRun()
{
	return(0);
}
643 644 645 646 647 648 649 650 651 652

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

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