bioem.cpp 56.2 KB
Newer Older
Pilar Cossio's avatar
License    
Pilar Cossio committed
1
/* ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2
   < BioEM software for Bayesian inference of Electron Microscopy images>
3
   Copyright (C) 2016 Pilar Cossio, David Rohr and Gerhard Hummer.
4
   Max Planck Institute of Biophysics, Frankfurt, Germany.
5

6
   See license statement for terms of distribution.
Pilar Cossio's avatar
License    
Pilar Cossio committed
7
8
9

   ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/

10
11
#include <mpi.h>

12
13
14
15
16
#define MPI_CHK(expr)							\
  if (expr != MPI_SUCCESS)						\
    {									\
      fprintf(stderr, "Error in MPI function %s: %d\n", __FILE__, __LINE__); \
    }
17

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

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

#include "param.h"
#include "bioem.h"
#include "model.h"
#include "map.h"
40
#include "MersenneTwister.h"
41

42
43
44
45
46
47
#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]);

48
49
50
51
52
53
54
55
56
57
58
59
#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);			\
  }
60
61
62
63
64
#define cuda_custom_timeslot_end nvtxRangePop();
#else
#define cuda_custom_timeslot(name,cid)
#define cuda_custom_timeslot_end
#endif
65

66
67
68
69
70
71
72
#include "bioem_algorithm.h"

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

using namespace std;

73
/* For dvl nodes in hydra with problem in boost
74
75
76
   namespace std {
   typedef decltype(nullptr) nullptr_t;
   }*/
77

78
79
80
81
// A helper function of Boost
template<class T>
ostream& operator<<(ostream& os, const vector<T>& v)
{
82
83
  copy(v.begin(), v.end(), ostream_iterator<T>(os, " "));
  return os;
84
85
86
87
}

bioem::bioem()
{
88
89
90
  FFTAlgo = getenv("FFTALGO") == NULL ? 1 : atoi(getenv("FFTALGO"));
  DebugOutput = getenv("BIOEM_DEBUG_OUTPUT") == NULL ? 2 : atoi(getenv("BIOEM_DEBUG_OUTPUT"));
  nProjectionsAtOnce = getenv("BIOEM_PROJECTIONS_AT_ONCE") == NULL ? 1 : atoi(getenv("BIOEM_PROJECTIONS_AT_ONCE"));
91
92
93
94
95
96
97
98
}

bioem::~bioem()
{
}

int bioem::configure(int ac, char* av[])
{
99
100
101
102
103
104
105
106
  // **************************************************************************************
  // **** Configuration Routine using boost for extracting parameters, models and maps ****
  // **************************************************************************************
  // ****** And Precalculating necessary grids, map crosscorrelations and kernels  ********
  // *************************************************************************************

  HighResTimer timer;

107
  std::string infile, modelfile, mapfile,Inputanglefile,Inputbestmap; 
108
109
110
111
112
113
114
115
116
117
118
  if (mpi_rank == 0)
    {
      // *** Inizialzing default variables ***
      std::string infile, modelfile, mapfile,Inputanglefile,Inputbestmap;
      Model.readPDB = false;
      param.param_device.writeAngles = false;
      param.dumpMap = false;
      param.loadMap = false;
      RefMap.readMRC = false;
      RefMap.readMultMRC = false;
      param.notuniformangles=false;
Pilar Cossio's avatar
Pilar Cossio committed
119
      yesoutfilename=false;
120
121
122
123
124
125
126
127
128
129
130
131
132
133

      // *************************************************************************************
      cout << " ++++++++++++ FROM COMMAND LINE +++++++++++\n\n";
      // *************************************************************************************

      // ********************* Command line reading input with BOOST ************************

      try {
	po::options_description desc("Command line inputs");
	desc.add_options()
	  ("Modelfile", po::value< std::string>() , "(Mandatory) Name of model file")
	  ("Particlesfile", po::value< std::string>(), "if BioEM (Mandatory) Name of paricles file")
	  ("Inputfile", po::value<std::string>(), "if BioEM (Mandatory) Name of input parameter file") 
	  ("PrintBestCalMap", po::value< std::string>(), "(Optional) Only print best calculated map (file nec.). NO BioEM (!)")
134
	  ("ReadOrientation", po::value< std::string>(), "(Optional) Read orientation list instead of uniform grid (file nec.)")
135
136
137
138
139
	  ("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")
Pilar Cossio's avatar
Pilar Cossio committed
140
	  ("OutputFile",  po::value< std::string>(), "(Optional) For changing the outputfile name")
141
142
143
144
145
146
147
148
149
150
151
	  ("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);
152
	p.add("ReadOrientation",-1);
153
154
155
	p.add("PrintBestCalMap",-1);
	p.add("DumpMaps", -1);
	p.add("LoadMapDump", -1);
Pilar Cossio's avatar
Pilar Cossio committed
156
        p.add("OutputFile",-1);
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171

	po::variables_map vm;
	po::store(po::command_line_parser(ac, av).
		  options(desc).positional(p).run(), vm);
	po::notify(vm);

	if((ac < 4)) {
	  std::cout << desc << std::endl;
	  return 1;
	}
	if (vm.count("help")) {
	  cout << "Usage: options_description [options]\n";
	  cout << desc;
	  return 1;
	}
172

173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
	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;
	  }
190
	if (vm.count("ReadOrientation"))
191
	  {
192
193
194
195
196
197
198
199
	    cout << "Reading Orientation from file: "
		 << vm["ReadOrientation"].as<  std::string  >() << "\n";
	    cout << "Important! if using Quaternions, include \n";
	    cout << "QUATERNIONS keyword in INPUT PARAMETER FILE\n";
	    cout << "First row in file should be the total number of orientations (int)\n";
	    cout << "Euler angle format should be alpha (12.6f) beta (12.6f) gamma (12.6f)\n";
	    cout << "Quaternion format q1 (12.6f) q2 (12.6f) q3 (12.6f) q4 (12.6f)\n";
	    Inputanglefile = vm["ReadOrientation"].as<  std::string  >();
200
201
	    param.notuniformangles=true;
	  }
Pilar Cossio's avatar
Pilar Cossio committed
202
203
	if (vm.count("OutputFile"))
          {
204
205
206
207
	    OutfileName = vm["OutputFile"].as< std::string >();
	    cout << "Writing OUTPUT to: " <<  vm["OutputFile"].as<  std::string  >() << "\n";
	    yesoutfilename=true;
	  }
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
	if (vm.count("PrintBestCalMap"))
	  {
	    cout << "Reading Euler Angles from file: "
		 << vm["PrintBestCalMap"].as<  std::string  >() << "\n";
	    Inputbestmap = vm["PrintBestCalMap"].as<  std::string  >();
	    param.printModel=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 >();
	  }
      }
      catch(std::exception& e)
	{
	  cout << e.what() << "\n";
	  return 1;
	}
David Rohr's avatar
David Rohr committed
252

253
254
      //check for consitency in multiple MRCs
      if(RefMap.readMultMRC && not(RefMap.readMRC))
David Rohr's avatar
David Rohr committed
255
	{
256
257
258
	  cout << "For Multiple MRCs command --ReadMRC is necesary too";
	  exit(1);
	}
David Rohr's avatar
David Rohr committed
259

260
261
262
263
      if(!Model.readPDB){
	cout << "Note: Reading model in simple text format (not PDB)\n";
	cout << "----  x   y   z  radius  density ------- \n";
      } 
David Rohr's avatar
David Rohr committed
264

265
266
267
268
      if (DebugOutput >= 2 && mpi_rank == 0) timer.ResetStart();
      // ********************* Reading Parameter Input ***************************
      if(!param.printModel){
	// Standard definition for BioEM
Pilar Cossio's avatar
Pilar Cossio committed
269
	param.readParameters(infile.c_str());
David Rohr's avatar
David Rohr committed
270

271
272
	// ********************* Reading Particle Maps Input **********************
	RefMap.readRefMaps(param, mapfile.c_str());
David Rohr's avatar
David Rohr committed
273

274

275
276
      } else{
	// Reading parameters for only writting down Best projection
277

278
279
	param.forprintBest(Inputbestmap.c_str());
      }	
280

281
      // ********************* Reading Model Input ******************************
282
      Model.readModel(param, modelfile.c_str());
David Rohr's avatar
David Rohr committed
283

284
      cout << "**NOTE:: look at file COORDREAD to confirm that the Model coordinates are correct\n";
David Rohr's avatar
David Rohr committed
285

286
      if (DebugOutput >= 2 && mpi_rank == 0) printf("Reading Input Data Time: %f\n", timer.GetCurrentElapsedTime());
287
    
288
      if(param.param_device.writeCC && mpi_size>1){
289
290
	cout << "Exiting::: WRITE CROSS-CORRELATION ONLY VAILD FOR 1 MPI PROCESS\n";
        exit(1);
291
      }
Pilar Cossio's avatar
Pilar Cossio committed
292

293
294
      // Generating Grids of orientations 
      if(!param.printModel)param.CalculateGridsParam(Inputanglefile.c_str());
295
    }
296

297
#ifdef WITH_MPI
298

Pilar Cossio's avatar
Pilar Cossio committed
299

300
301

  // ********************* MPI inizialization/ Transfer of parameters******************
302
303
304
305
  if (mpi_size > 1)
    {
      if (DebugOutput >= 2 && mpi_rank == 0) timer.ResetStart();
      MPI_Bcast(&param, sizeof(param), MPI_BYTE, 0, MPI_COMM_WORLD);
306
      //We have to reinitialize all pointers !!!!!!!!!!!!
Pilar Cossio's avatar
Pilar Cossio committed
307
      if (mpi_rank != 0) param.angprior = NULL;
Pilar Cossio's avatar
Pilar Cossio committed
308

309
310
      if (mpi_rank != 0)param.angles =  (myfloat3_t*) mallocchk(param.nTotGridAngles  * sizeof (myfloat3_t));
      MPI_Bcast(param.angles, param.nTotGridAngles  * sizeof (myfloat3_t),MPI_BYTE, 0, MPI_COMM_WORLD);
311

Pilar Cossio's avatar
Pilar Cossio committed
312
#ifdef PILAR_DEBUG
313
314
      for(int n=0;n<param.nTotGridAngles;n++){
	cout << "CHECK: Angle orient " << mpi_rank << " "<< n << " " <<  param.angles[n].pos[0] << " " <<  param.angles[n].pos[1] << " " << param.angles[n].pos[2] << " " << param.angles[n].quat4  << " " << "\n";} 
Pilar Cossio's avatar
Pilar Cossio committed
315
316

#endif
317
      //****refCtf, CtfParam, angles automatically filled by precalculate function bellow
318
319
320
321
322
323
324
325
326

      MPI_Bcast(&Model, sizeof(Model), MPI_BYTE, 0, MPI_COMM_WORLD);
      if (mpi_rank != 0) 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);

      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);
      if (DebugOutput >= 2 && mpi_rank == 0) printf("MPI Broadcast of Input Data %f\n", timer.GetCurrentElapsedTime());
Pilar Cossio's avatar
Pilar Cossio committed
327

328
329
    }
#endif
330

331
332
333
  // ****************** Precalculating Necessary Stuff *********************
  if (DebugOutput >= 2 && mpi_rank == 0) timer.ResetStart();
  param.PrepareFFTs();
334

335
336
337
338
339
340
341
  if (DebugOutput >= 2 && mpi_rank == 0)
    {
      printf("Time Prepare FFTs %f\n", timer.GetCurrentElapsedTime());
      timer.ResetStart();
    }
  precalculate();

342
  // ****************** For debugging *********************
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
  if (getenv("BIOEM_DEBUG_BREAK"))
    {
      const int cut = atoi(getenv("BIOEM_DEBUG_BREAK"));
      if (param.nTotGridAngles > cut) param.nTotGridAngles = cut;
      if (param.nTotCTFs > cut) param.nTotCTFs = cut;
    }

  if (DebugOutput >= 2 && mpi_rank == 0)
    {
      printf("Time Precalculate %f\n", timer.GetCurrentElapsedTime());
      timer.ResetStart();
    }
  if(!param.printModel)pProb.init(RefMap.ntotRefMap, param.nTotGridAngles, param.nTotCC, *this);

  if (DebugOutput >= 2 && mpi_rank == 0)
    {
      printf("Time Init Probabilities %f\n", timer.GetCurrentElapsedTime());
      timer.ResetStart();
    }
362
363
364

  // ****************** Initializng pointers *********************

365
  deviceInit();
366

367
368
369
  if (DebugOutput >= 2 && mpi_rank == 0) printf("Time Device Init %f\n", timer.GetCurrentElapsedTime());

  return(0);
370
371
}

372
373
void bioem::cleanup()
{
374
  //Deleting allocated pointers
375
376
  free_device_host(pProb.ptr);
  RefMap.freePointers();
377
378
}

379
380
int bioem::precalculate()
{
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
  // **************************************************************************************
  // **Precalculating Routine of Orientation grids, Map crosscorrelations and CTF Kernels**
  // **************************************************************************************
  HighResTimer timer;
  if (DebugOutput >= 3)
    {
      printf("\tTime Precalculate Grids Param: %f\n", timer.GetCurrentElapsedTime());
      timer.ResetStart();
    }
  // Precalculating CTF Kernels stored in class Param
  param.CalculateRefCTF();

  if (DebugOutput >= 3)
    {
      printf("\tTime Precalculate CTFs: %f\n", timer.GetCurrentElapsedTime());
      timer.ResetStart();
    }
  //Precalculate Maps
  if(!param.printModel) RefMap.precalculate(param, *this);
  if (DebugOutput >= 3) printf("\tTime Precalculate Maps: %f\n", timer.GetCurrentElapsedTime());

  return(0);
403
404
405
406
}

int bioem::run()
{
David Rohr's avatar
David Rohr committed
407

408
409
410
  // **************************************************************************************
  // ********** Secondary routine for printing out the only best projection ***************
  // **************************************************************************************
David Rohr's avatar
David Rohr committed
411

412
  if(mpi_rank == 0 && param.printModel){ //Only works for 1 MPI process (not parallelized)
413

414
415
416
417
418
    cout << "\nAnalysis for printing best projection::: \n \n" ; 
    mycomplex_t* proj_mapsFFT;
    myfloat_t* conv_map = NULL;
    mycomplex_t* conv_mapFFT;
    myfloat_t sumCONV, sumsquareCONV;
419

420
421
422
    proj_mapsFFT = (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);
    conv_map = (myfloat_t*) myfftw_malloc(sizeof(myfloat_t) * param.param_device.NumberPixels * param.param_device.NumberPixels);
423

424
    cout << "...... Calculating Projection .......................\n " ;
425

426
    createProjection(0, proj_mapsFFT);
427

428
    cout << "...... Calculating Convolution .......................\n " ;
David Rohr's avatar
David Rohr committed
429

430
    createConvolutedProjectionMap(0, 0, proj_mapsFFT, conv_map, conv_mapFFT, sumCONV, sumsquareCONV);
431

432
  }
433

434
435
436
  // **************************************************************************************
  // **** Main BioEM routine, projects, convolutes and compares with Map using OpenMP ****
  // **************************************************************************************
437

438
439
  // **** If we want to control the number of threads -> omp_set_num_threads(XX); ******
  // ****************** Declarying class of Probability Pointer  *************************
David Rohr's avatar
David Rohr committed
440

441
  if (mpi_rank == 0) printf("\tInitializing Probabilities\n");
442

Pilar Cossio's avatar
Pilar Cossio committed
443
444
445
446
  // Contros for MPI
  if(mpi_size > param.nTotGridAngles){
    cout << "EXIT: Wrong MPI setup More MPI processes than orientations\n"; exit(1);
  }
447

448
449
450
451
  // Inizialzing Probabilites to zero and constant to -Infinity
  for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap; iRefMap ++)
    {
      bioem_Probability_map& pProbMap = pProb.getProbMap(iRefMap);
David Rohr's avatar
David Rohr committed
452

453
      pProbMap.Total = 0.0;
454
455
      pProbMap.Constoadd = -FLT_MAX; //Problem if using double presicion

456
      if (param.param_device.writeAngles)
457
	{
458
459
460
461
462
	  for (int iOrient = 0; iOrient < param.nTotGridAngles; iOrient ++)
	    {
	      bioem_Probability_angle& pProbAngle = pProb.getProbAngle(iRefMap, iOrient);

	      pProbAngle.forAngles = 0.0;
463
	      pProbAngle.ConstAngle = -FLT_MAX;
464
465
	    }
	}
466

467
      if (param.param_device.writeCC)
468
	{      int  cc=0;
469
	  for (int cent_x = 0; cent_x < param.param_device.NumberPixels; cent_x = cent_x + param.param_device.CCdisplace)
470
	    {
471
	      for (int cent_y = 0; cent_y < param.param_device.NumberPixels; cent_y = cent_y + param.param_device.CCdisplace)
472
		{
473
		  bioem_Probability_cc& pProbCC = pProb.getProbCC(iRefMap, cc);
474
475
476
477
478
479
480
481
482
		  //Debuggin:: cout << iRefMap << " " << cc << " " << cent_x << " " << cent_y << "\n";

		  if(!param.param_device.CCwithBayes) {
		    pProbCC.forCC=-FLT_MAX;
		  }else {
		    pProbCC.forCC = 0.0;
		    pProbCC.ConstCC=-FLT_MAX;
		  }
		  cc++;
483
		}
484
	    }
485
	  if(!FFTAlgo){cout << "Cross correlation calculation must be with enviormental variable FFTALGO=1\n"; exit(1);}
486
487
	}                 
    }
488
489
490

  if(!FFTAlgo){cout << "Remark: Not using FFT algorithm. Not using Prior in B-Env.";}

491
  // **************************************************************************************
492

493
494
495
496
497
498
499
500
501
502
503
  deviceStartRun();

  // ******************************** MAIN CYCLE ******************************************

  mycomplex_t* proj_mapsFFT;
  myfloat_t* conv_map = NULL;
  mycomplex_t* conv_mapFFT;
  myfloat_t sumCONV, sumsquareCONV;

  //allocating fftw_complex vector
  const int ProjMapSize = (param.FFTMapSize + 64) & ~63;	//Make sure this is properly aligned for fftw..., Actually this should be ensureb by using FFTMapSize, but it is not due to a bug in CUFFT which cannot handle padding properly
504
  //******** Alocating Vectors *************
505
506
507
508
509
510
511
512
513
  proj_mapsFFT = (mycomplex_t *) myfftw_malloc(sizeof(mycomplex_t) * ProjMapSize * nProjectionsAtOnce);
  conv_mapFFT = (mycomplex_t *) myfftw_malloc(sizeof(mycomplex_t) * param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D);
  if (!FFTAlgo) conv_map = (myfloat_t*) myfftw_malloc(sizeof(myfloat_t) * param.param_device.NumberPixels * param.param_device.NumberPixels);
             

  HighResTimer timer, timer2;

  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);

514
515


516
517
518
519
  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;

520
521
522

  // **************************Loop Over orientations***************************************

523
524
525
526
527
528
529
  for (int iOrientAtOnce = iOrientStart; iOrientAtOnce < iOrientEnd; iOrientAtOnce += nProjectionsAtOnce)
    {
      // ***************************************************************************************
      // ***** Creating Projection for given orientation and transforming to Fourier space *****
      if (DebugOutput >= 1) timer2.ResetStart();
      if (DebugOutput >= 2) timer.ResetStart();
      int iTmpEnd = std::min(iOrientEnd, iOrientAtOnce + nProjectionsAtOnce);
530
531
532

      // **************************Parallel orientations for projections at once***************

533
534
535
536
537
538
#pragma omp parallel for
      for (int iOrient = iOrientAtOnce; iOrient < iTmpEnd;iOrient++)
	{
	  createProjection(iOrient, &proj_mapsFFT[(iOrient - iOrientAtOnce) * ProjMapSize]);
	}
      if (DebugOutput >= 2) printf("\tTime Projection %d: %f (rank %d)\n", iOrientAtOnce, timer.GetCurrentElapsedTime(), mpi_rank);
539

540
541
542
      for (int iOrient = iOrientAtOnce; iOrient < iTmpEnd;iOrient++)
	{
	  mycomplex_t* proj_mapFFT = &proj_mapsFFT[(iOrient - iOrientAtOnce) * ProjMapSize];
543

544
	  // ***************************************************************************************
545
546
	  // ***** **** Internal Loop over PSF/CTF convolutions **** *****

547
548
549
550
551
552
553
554
	  for (int iConv = 0; iConv < param.nTotCTFs; iConv++)
	    {
	      // *** Calculating convolutions of projection map and crosscorrelations ***

	      if (DebugOutput >= 2) timer.ResetStart();
	      createConvolutedProjectionMap(iOrient, iConv, proj_mapFFT, conv_map, conv_mapFFT, sumCONV, sumsquareCONV);
	      if (DebugOutput >= 2) printf("\t\tTime Convolution %d %d: %f (rank %d)\n", iOrient, iConv, timer.GetCurrentElapsedTime(), mpi_rank);

555
	  
556
	      if (DebugOutput >= 2) timer.ResetStart();
557
558
559
560
561
562
     	      myfloat_t amp,pha,env;

              amp=param.CtfParam[iConv].pos[0];
              pha=param.CtfParam[iConv].pos[1];
              env=param.CtfParam[iConv].pos[2];

563
564
565
	      // ******************Internal loop over Reference images CUDA or OpenMP******************
	      // *** Comparing each calculated convoluted map with all experimental maps ***

566
	      compareRefMaps(iOrient, iConv, amp, pha, env, conv_map, conv_mapFFT, sumCONV, sumsquareCONV);
567
568

	      if (DebugOutput >= 2)
569
		{
570
571
572
573
574
575
576
577
578
		  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("\t\tTime 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);
579
		}
580
581
582
583
584
585
	    }
	  if (DebugOutput >= 1)
	    {
	      printf("\tTotal time for projection %d: %f (rank %d)\n", iOrient, timer2.GetCurrentElapsedTime(), mpi_rank);
	      timer2.ResetStart();
	    }
586
	}
587
588
589
590
591
    }
  //deallocating fftw_complex vector
  myfftw_free(proj_mapsFFT);
  myfftw_free(conv_mapFFT);
  if (!FFTAlgo) myfftw_free(conv_map);
David Rohr's avatar
David Rohr committed
592

593
  deviceFinishRun();
594
595


596
597

  // ************* Collecing all the probabilities from MPI replicas ***************
David Rohr's avatar
David Rohr committed
598

David Rohr's avatar
David Rohr committed
599
#ifdef WITH_MPI
600
601
602
603
604
605
606
607
608
609
610
611
612
  if (mpi_size > 1)
    {
      if (DebugOutput >= 1 && 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);
613

614
615
616
	for (int i = 0;i < RefMap.ntotRefMap;i++)
	  {
	    bioem_Probability_map& pProbMap = pProb.getProbMap(i);
617
618
619
#ifdef PILAR_DEBUG
	    cout << "Reduction " << mpi_rank << " Map " << i << " Prob " << pProbMap.Total << " Const " << pProbMap.Constoadd  << "\n";     
#endif
620
	    tmp1[i] = pProbMap.Total * exp(pProbMap.Constoadd - tmp2[i]);
621

622
623
624
625
626
	  }
	MPI_Reduce(tmp1, tmp3, RefMap.ntotRefMap, MY_MPI_FLOAT, MPI_SUM, 0, MPI_COMM_WORLD);

	//Find MaxProb
	MPI_Status mpistatus;
David Rohr's avatar
David Rohr committed
627
	{
628
629
630
631
632
633
	  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;
634
              //temporary array that has the mpirank for the highest pProb.constant
635
636
637
638
639
	    }
	  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)
David Rohr's avatar
David Rohr committed
640
		{
641
		  if (mpi_rank == 0) printf("Error: Could not find highest probability\n");
David Rohr's avatar
David Rohr committed
642
		}
643
	      else if (tmpi2[i] != 0) //Skip if rank 0 already has highest probability
David Rohr's avatar
David Rohr committed
644
		{
645
646
647
648
649
650
651
652
		  if (mpi_rank == 0)
		    {
		      MPI_Recv(&pProb.getProbMap(i).max, sizeof(pProb.getProbMap(i).max), MPI_BYTE, tmpi2[i], i, MPI_COMM_WORLD, &mpistatus);
		    }
		  else if (mpi_rank == tmpi2[i])
		    {
		      MPI_Send(&pProb.getProbMap(i).max, sizeof(pProb.getProbMap(i).max), MPI_BYTE, 0, i, MPI_COMM_WORLD);
		    }
David Rohr's avatar
David Rohr committed
653
		}
654
655
656
	    }
	  delete[] tmpi1;
	  delete[] tmpi2;
657
	}
658

David Rohr's avatar
David Rohr committed
659
	if (mpi_rank == 0)
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
	  {
	    for (int i = 0;i < RefMap.ntotRefMap;i++)
	      {
		bioem_Probability_map& pProbMap = pProb.getProbMap(i);
		pProbMap.Total = tmp3[i];
		pProbMap.Constoadd = tmp2[i];
	      }
	  }

	delete[] tmp1;
	delete[] tmp2;
	delete[] tmp3;
	if (DebugOutput >= 1 && mpi_rank == 0 && mpi_size > 1) printf("Time MPI Reduction: %f\n", timer.GetCurrentElapsedTime());
      }

      //Angle Reduction and Probability summation for individual angles
      if (param.param_device.writeAngles)
677
	{
678
679
680
681
682
683
	  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++)
	    {
684
	      for (int j = 0;j < param.nTotGridAngles;j++)
685
                {
686
687
688
689
		  //	      tmp1[i] = pProb.getProbMap(i).Constoadd;
		  //	      bioem_Probability_angle& pProbAngle = pProb.getProbAngle(i, j);
		  tmp1[i * param.nTotGridAngles + j]= pProb.getProbAngle(i, j).ConstAngle;
		}
690
	    }
691

692
693
694
695
	  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++)
David Rohr's avatar
David Rohr committed
696
		{
697
698
		  bioem_Probability_angle& pProbAngle = pProb.getProbAngle(i, j);
		  tmp1[i * param.nTotGridAngles + j] = pProbAngle.forAngles * exp(pProbAngle.ConstAngle - tmp2[i * param.nTotGridAngles + j]);
David Rohr's avatar
David Rohr committed
699
		}
700
701
702
703
704
	    }
	  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++)
705
		{
706
707
708
709
710
711
		  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];
		    }
712
		}
713
714
715
716
717
718
719
	    }
	  delete[] tmp1;
	  delete[] tmp2;
	  delete[] tmp3;
	}
    }
#endif
David Rohr's avatar
David Rohr committed
720

721
722

  // ************* Writing Out Probabilities ***************
723
724
  if (mpi_rank == 0)
    {
725
 
726
727
      // Output for Angle Probability File
      ofstream angProbfile;
728
729
730
      if(param.param_device.writeAngles)
	{
	  angProbfile.open ("ANG_PROB");
731
	  angProbfile <<"************************* HEADER:: NOTATION *******************************************\n";
732
733
          if(!param.doquater){ angProbfile <<" RefMap:  MapNumber ; alpha[rad] - beta[rad] - gamma[rad] - logP - cal log Probability + Constant: Numerical Const.+ log (volume) + prior ang\n" ;}
	  else { angProbfile <<" RefMap:  MapNumber ; q1 - q2 -q3 - logP- cal log Probability + Constant: Numerical Const. + log (volume) + prior ang\n" ;};
734
	  angProbfile <<"************************* HEADER:: NOTATION *******************************************\n";
735
736
	  //          angProbfile <<"Model Used: " << modelfile.c_str() << "\n";
	  //          angProbfile <<"Input Used: " << infile.c_str() << "\n";
737
	}
738
      // Output for Cross Correlation File
739
740
741
742
      ofstream ccProbfile;
      if(param.param_device.writeCC)
	{
	  ccProbfile.open ("CROSS_CORRELATION");
743
	  ccProbfile <<"************************* HEADER:: NOTATION *******************************************\n";
744
745
746
          ccProbfile <<" RefMap:  MapNumber ; Pixel x - Pixel y - Cross-Correlation \n";
          ccProbfile <<"Note that the highest Cross-correlation is the best.\n";
          ccProbfile <<"If the particles are flipped, include the keyward FLIPPED in the Param file.\n";
747
          ccProbfile <<"************************* HEADER:: NOTATION *******************************************\n";
748
749
	}

750
751
752
753
754
755
756
757
758
      // Output for Standard Probability
      ofstream outputProbFile;
      if(!yesoutfilename)OutfileName="Output_Probabilities";
      outputProbFile.open (OutfileName.c_str());
      outputProbFile <<"************************* HEADER:: NOTATION *******************************************\n";   
      outputProbFile << "Notation= RefMap:  MapNumber ; LogProb natural logarithm of posterior Probability ; Constant: Numerical Const. for adding Probabilities \n";
      if(!param.doquater){
	if(param.usepsf){
	  outputProbFile << "Notation= RefMap:  MapNumber ; Maximizing Param: MaxLogProb - alpha[rad] - beta[rad] - gamma[rad] - PSF amp - PSF phase - PSF envelope - center x - center y - normalization - offsett \n";}else{
759
	  outputProbFile << "Notation= RefMap:  MapNumber ; Maximizing Param: MaxLogProb - alpha[rad] - beta[rad] - gamma[rad] - CTF amp - CTF defocus - CTF B-Env - center x - center y - normalization - offsett \n";}
760
761
762
      }else { 
	if(param.usepsf){
	  //     if( localcc[rx * param.param_device.NumberPixels + ry] <
Pilar Cossio's avatar
Pilar Cossio committed
763
	  outputProbFile << "Notation= RefMap:  MapNumber ; Maximizing Param: MaxLogProb - q1 - q2 - q3 - q4 -PSF amp - PSF phase - PSF envelope - center x - center y - normalization - offsett \n";
764
	}else{
Pilar Cossio's avatar
Pilar Cossio committed
765
          outputProbFile << "Notation= RefMap:  MapNumber ; Maximizing Param: MaxLogProb - q1 - q2 - q3 - q4 - CTF amp - CTF defocus - CTF B-Env - center x - center y - normalization - offsett \n";
766
        }}
767
      if(param.writeCTF) outputProbFile << " RefMap:  MapNumber ; CTFMaxParm: defocus - b-Env (B ref. Penzeck 2010)\n";
Pilar Cossio's avatar
Pilar Cossio committed
768
      if(param.yespriorAngles) outputProbFile << "**** Remark: Using Prior Proability in Angles ****\n";
769
770
      outputProbFile <<"************************* HEADER:: NOTATION *******************************************\n\n";

Pilar Cossio's avatar
Pilar Cossio committed
771
       
772
      // Loop over reference maps
773
      // ************* Over all maps ***************
774

775
776
777
778
779
      for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap; iRefMap ++)
	{
	  // **** Total Probability ***
	  bioem_Probability_map& pProbMap = pProb.getProbMap(iRefMap);

780
	  //Controll for Value of Total Probability
Pilar Cossio's avatar
Pilar Cossio committed
781
          // cout << pProbMap.Total << " " <<  pProbMap.Constoadd << " " << FLT_MAX <<" " << log(FLT_MAX) << "\n";
782
783
          if(pProbMap.Total>1.e-38){

784
785
	    outputProbFile << "RefMap: " << iRefMap << " LogProb:  "  << 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";
	    outputProbFile << "RefMap: " << iRefMap << " Maximizing Param: ";
786
787
788
            // *** Param that maximize probability****
            outputProbFile << (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)) << " ";

789

790
	  }else{ 
791
792
793
794
795
796
797
798
799
	    outputProbFile << "Warining! with Map " << iRefMap << "Numerical Integrated Probability without constant = 0.0;\n";
	    outputProbFile << "Warining RefMap: " << iRefMap << "Check that constant is finite: " << pProbMap.Constoadd  << "\n"; 
	    outputProbFile << "Warining RefMap: i) check model, ii) check refmap , iii) check GPU on/off command inconsitency\n";
	    //	    outputProbFile << "Warning! " << iRefMap << " LogProb:  "  << 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";
	  }
	  //	    outputProbFile << "RefMap: " << iRefMap << " Maximizing Param: ";

	  // *** 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)) << " ";
Pilar Cossio's avatar
Pilar Cossio committed
800
801
802
803
804
805

	  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] << " [] ";
	  if(param.doquater)outputProbFile << param.angles[pProbMap.max.max_prob_orient].quat4 << " [] "; 
	  outputProbFile << param.CtfParam[pProbMap.max.max_prob_conv].pos[0] << " [] ";
806
807
808
809
810
811
	  if(!param.usepsf){outputProbFile << param.CtfParam[pProbMap.max.max_prob_conv].pos[1]/ 2.f /M_PI / param.elecwavel * 0.0001 << " [micro-m] ";
	  }else{outputProbFile << param.CtfParam[pProbMap.max.max_prob_conv].pos[1] << " [1/A²] ";}
	  if(!param.usepsf){outputProbFile << param.CtfParam[pProbMap.max.max_prob_conv].pos[2] << " [A²] ";}
	  else{outputProbFile << param.CtfParam[pProbMap.max.max_prob_conv].pos[2] << " [1/A²] ";}
	  outputProbFile << pProbMap.max.max_prob_cent_x << " [pix] ";
	  outputProbFile << pProbMap.max.max_prob_cent_y << " [pix] " ;
Pilar Cossio's avatar
Pilar Cossio committed
812
813
	  outputProbFile << pProbMap.max.max_prob_norm << " [] " ; 
	  outputProbFile << pProbMap.max.max_prob_mu << " [] ";
814
	  outputProbFile << "\n";
815
816
817
818
819
820
821
822
823
824
825

	  // Writing out CTF parameters if requiered
	  if(param.writeCTF && param.usepsf){

	    myfloat_t denomi;
	    denomi = param.CtfParam[pProbMap.max.max_prob_conv].pos[1] * param.CtfParam[pProbMap.max.max_prob_conv].pos[1] + 
	      param.CtfParam[pProbMap.max.max_prob_conv].pos[2] * param.CtfParam[pProbMap.max.max_prob_conv].pos[2];
	    outputProbFile << "RefMap: " << iRefMap << " CTFMaxParam: ";
	    //		  outputProbFile <<  2*M_PI*param.CtfParam[pProbMap.max.max_prob_conv].pos[1]/denomi/param.elecwavel << " [micro-m]; ";
	    //		 outputProbFile << param.CtfParam[pProbMap.max.max_prob_conv].pos[1] << param.CtfParam[pProbMap.max.max_prob_conv].pos[2] << denomi ;
	    outputProbFile <<  2*M_PI*param.CtfParam[pProbMap.max.max_prob_conv].pos[1]/denomi/param.elecwavel*0.0001 << " [micro-m] "; 
826
	    outputProbFile << 4*M_PI*M_PI*param.CtfParam[pProbMap.max.max_prob_conv].pos[2]/denomi << " [A²] \n";
827
	  }
828

829
	  //*************** Writing Individual Angle probabilities
830
831
832
	  if(param.param_device.writeAngles)
	    {
	      for (int iOrient = 0; iOrient < param.nTotGridAngles; iOrient++)
David Rohr's avatar
David Rohr committed
833
		{
834
		  bioem_Probability_angle& pProbAngle = pProb.getProbAngle(iRefMap, iOrient);
835

836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
		  myfloat_t logp=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);
		  if(!param.doquater){
		    // For Euler Angles
		    if(param.yespriorAngles){
		      logp+=param.angprior[iOrient];
		      angProbfile << " " << iRefMap << " " << param.angles[iOrient].pos[0] << " " << param.angles[iOrient].pos[1] << " " << param.angles[iOrient].pos[2] << " " << logp << " Separated: "
				  << 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) << " " << param.angprior[iOrient] << "\n";
		    } else
		      {
			angProbfile << " " << iRefMap << " " << param.angles[iOrient].pos[0] << " " << param.angles[iOrient].pos[1] << " " << param.angles[iOrient].pos[2] << " " <<  logp << " Separated: "<<
			  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) << "\n";
		      }
		  }else {
		    // Samething but for Quaternions
		    if(param.yespriorAngles){
		      logp+=param.angprior[iOrient];
		      angProbfile << " " << iRefMap << " " << param.angles[iOrient].pos[0] << " " << param.angles[iOrient].pos[1] << " " << param.angles[iOrient].pos[2] << " " << param.angles[iOrient].quat4 << " " << logp << " Separated: " << 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) << " " << param.angprior[iOrient] << "\n";
		    } else
		      {
			angProbfile << " " << iRefMap << " " << param.angles[iOrient].pos[0] << " " << param.angles[iOrient].pos[1] << " " << param.angles[iOrient].pos[2] << " " << param.angles[iOrient].quat4 << " " << logp << " Separated: "<<
			  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) << "\n";
		      }
		  }
859
860
		}
	    }
861
	
862
	  //************* Writing Cross-Correlations if requiered
863
	  if(param.param_device.writeCC){
864

865
866
867
868
869
	    int  cc=0;
	    int halfPix;
	    int rx=0;
	    int ry=0;
	    myfloat_t localcc[ (param.param_device.NumberPixels+1) * (param.param_device.NumberPixels+1) ];
Pilar Cossio's avatar
Pilar Cossio committed
870
            int used[(param.param_device.NumberPixels+1) * (param.param_device.NumberPixels+1)];
871

872
873
	    halfPix = param.param_device.NumberPixels / 2 ;
	    // Ordering the centers of the Cross Correlation
874

875
876
877
878
879
	    for (int rx = 0; rx < param.param_device.NumberPixels ; rx++)
	      {
		for (int ry = 0; ry < param.param_device.NumberPixels ; ry++)
		  {
		    localcc[ rx * param.param_device.NumberPixels + ry ] = 0.0;
Pilar Cossio's avatar
Pilar Cossio committed
880
			used[ rx * param.param_device.NumberPixels + ry ]= 0;
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
		  }
	      }

	    for (int cent_x = 0; cent_x < param.param_device.NumberPixels ; cent_x = cent_x + param.param_device.CCdisplace)
	      {
		for (int cent_y = 0; cent_y < param.param_device.NumberPixels ; cent_y = cent_y + param.param_device.CCdisplace)
		  {
		    //localcc[ rx * param.param_device.NumberPixels + ry ] = 0.0;
		    bioem_Probability_cc& pProbCC = pProb.getProbCC(iRefMap, cc);

		    // Applying Periodic boundary conditions to the CC
		    if(cent_x < halfPix && cent_y < halfPix){
		      //	ccProbfile << " " << iRefMap << " " << (myfloat_t) halfPix  - cent_x << " " << halfPix - cent_y << " " << pProbCC.forCC <<"\n";
		      rx = halfPix  - cent_x;
		      ry = halfPix  - cent_y;}
		    if(cent_x >= halfPix && cent_y < halfPix){
		      //      ccProbfile << " " << iRefMap << " " << (myfloat_t) 3 * halfPix  - cent_x << " " << halfPix - cent_y << " " << pProbCC.forCC <<"\n"; 
		      rx = 3 * halfPix  - cent_x;
		      ry = halfPix  - cent_y;}
		    if(cent_x < halfPix && cent_y >= halfPix){
		      //      ccProbfile << " " << iRefMap << " " << (myfloat_t) halfPix  - cent_x << " " << 3 * halfPix - cent_y << " " << pProbCC.forCC <<"\n";
		      rx = halfPix  - cent_x;
		      ry = 3 * halfPix  - cent_y;}
		    if(cent_x >= halfPix && cent_y >= halfPix){
		      //        ccProbfile << " " << iRefMap << " " << 3* halfPix  - cent_x << " " << 3 * halfPix - cent_y << " " << pProbCC.forCC <<"\n";
		      rx = 3 * halfPix  - cent_x;
		      ry = 3 * halfPix  - cent_y;}
		    //						cout << " TT " << cent_x << " " << rx << " " << cent_y << " " << ry << " " <<  pProbCC.forCC << "\n";
		    if(!param.param_device.CCwithBayes){
		      localcc[ rx * param.param_device.NumberPixels + ry ] = pProbCC.forCC;
		    }else{ 
		      localcc[ rx * param.param_device.NumberPixels + ry ] = log(pProbCC.forCC)+pProbCC.ConstCC;
		    }
Pilar Cossio's avatar
Pilar Cossio committed
914
 			used[ rx * param.param_device.NumberPixels + ry] = 1;
915
916
917
918
919
		    cc++;
		  }
		//              ccProbfile << "\n";
	      }
	    if(!param.ignoreCCoff){
Pilar Cossio's avatar
Pilar Cossio committed
920
/*	      for (int rx = param.param_device.CCdisplace; rx < param.param_device.NumberPixels ; rx = rx + param.param_device.CCdisplace)
David Rohr's avatar
David Rohr committed
921
		{
922
		  for (int ry = param.param_device.CCdisplace; ry < param.param_device.NumberPixels ; ry = ry + param.param_device.CCdisplace)
Pilar Cossio's avatar
Pilar Cossio committed
923
924
925
926
927
928
929
		    {*/
  for (int rx = param.param_device.CCdisplace; rx < param.param_device.NumberPixels ; rx++)
                {
                  for (int ry = param.param_device.CCdisplace; ry < param.param_device.NumberPixels ; ry++)
                    {

		      if(used[ rx * param.param_device.NumberPixels + ry ] == 1){
930
			ccProbfile << "RefMap: "<< iRefMap << " " << rx << " " << ry << " " << localcc[ rx * param.param_device.NumberPixels + ry ] << "\n" ;
931
		      }else{
Pilar Cossio's avatar
Pilar Cossio committed
932
			if(localcc[ rx * param.param_device.NumberPixels + ry ] <= -FLT_MAX)ccProbfile << "RefMap: "<< iRefMap << " " << rx << " " << ry << " " << -FLT_MAX << "\n" ;
933
		      }
934
		      //				 cout << " cc " << rx << " " << ry << " " << localcc[ rx * param.param_device.NumberPixels + ry ] <<"\n" ;
935
		    }
Pilar Cossio's avatar
Pilar Cossio committed
936
	//	  ccProbfile << "\n";
937
938
939
		}			
	    }else{
	      for (int rx = param.param_device.CCdisplace; rx < param.param_device.NumberPixels ; rx++)
940
		{
941
		  for (int ry = param.param_device.CCdisplace; ry < param.param_device.NumberPixels ; ry++)
942
		    {
Pilar Cossio's avatar
Pilar Cossio committed
943
                         if(used[ rx * param.param_device.NumberPixels + ry ] == 1){
944
                        ccProbfile << "RefMap: "<< iRefMap << " " << rx << " " << ry << " " << localcc[ rx * param.param_device.NumberPixels + ry ] << "\n" ;
945
		      }else{
Pilar Cossio's avatar
Pilar Cossio committed
946
                        if(localcc[ rx * param.param_device.NumberPixels + ry ] <= -FLT_MAX)ccProbfile << "RefMap: "<< iRefMap << " " << rx << " " << ry << " " << -FLT_MAX << "\n" ;
947
		      }
948
		    }
Pilar Cossio's avatar
Pilar Cossio committed
949
	//	  ccProbfile << "\n";
950
		}
951

952
	    }
953
	  }
954
	}
955

956
957
958
959
960
961
962
963
      if(param.param_device.writeAngles)
	{
	  angProbfile.close();
	}

      if(param.param_device.writeCC)
	{
	  ccProbfile.close();
964
	}
965

966
967
968
969
      outputProbFile.close();
    }

  return(0);
970
971
}

972
int bioem::compareRefMaps(int iOrient, int iConv,  myfloat_t amp, myfloat_t pha, myfloat_t env, const myfloat_t* conv_map, mycomplex_t* localmultFFT, myfloat_t sumC, myfloat_t sumsquareC, const int startMap)
973
{
974

975
976
977
978
979
980
981
  //***************************************************************************************
  //***** BioEM routine for comparing reference maps to convoluted maps *****
  if (FFTAlgo)
    {
      //With FFT Algorithm
#pragma omp parallel for schedule(dynamic, 1)
      for (int iRefMap = startMap; iRefMap < RefMap.ntotRefMap; iRefMap ++)
982
	{
983
	  const int num = omp_get_thread_num();
984
	  calculateCCFFT(iRefMap, iOrient, iConv, amp, pha, env, sumC, sumsquareC, localmultFFT, param.fft_scratch_complex[num], param.fft_scratch_real[num]);
985
	}
986
987
988
989
990
991
    }
  else
    {
      //Without FFT Algorithm
#pragma omp parallel for schedule(dynamic, 1)
      for (int iRefMap = startMap; iRefMap < RefMap.ntotRefMap; iRefMap ++)
992
	{
993
	  compareRefMapShifted < -1 > (iRefMap, iOrient, iConv, conv_map, pProb, param.param_device, RefMap);
994
	}
995
996
    }
  return(0);
997
998
}

999
inline void bioem::calculateCCFFT(int iRefMap, int iOrient, int iConv,  myfloat_t amp, myfloat_t pha, myfloat_t env, myfloat_t sumC, myfloat_t sumsquareC, mycomplex_t* localConvFFT, mycomplex_t* localCCT, myfloat_t* lCC)
1000
{
1001
1002
  //***************************************************************************************
  //***** Calculating cross correlation in FFTALGOrithm *****
Pilar Cossio's avatar
Pilar Cossio committed
1003

1004
1005
1006
1007
1008
1009
  for(int i = 0; i < param.param_device.NumberPixels; i++)
    {
      for(int j = 0; j < param.param_device.NumberPixels; j++) lCC[i * param.param_device.NumberPixels + j] = 0.f; 
    }


1010
1011
1012
1013
1014
1015
  const mycomplex_t* RefMapFFT = &RefMap.RefMapsFFT[iRefMap * param.FFTMapSize];
  for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D; i++)
    {
      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];
    }
1016

1017
  myfftw_execute_dft_c2r(param.fft_plan_c2r_backward, localCCT, lCC);
1018
1019
 
  // printf("HereCC %p %f %d %d %d %d \n", &lCC[139 * param.param_device.NumberPixels + 139],lCC[139 * param.param_device.NumberPixels + 139],mpi_rank,iConv,iOrient,iRefMap);
1020

1021
  doRefMapFFT(iRefMap, iOrient, iConv, amp, pha, env, lCC, sumC, sumsquareC, pProb, param.param_device, RefMap);
Pilar Cossio's avatar
Pilar Cossio committed
1022

1023

Pilar Cossio's avatar
Pilar Cossio committed
1024
#ifdef PILAR_DEBUG
1025
1026
  if (param.param_device.writeCC)
    {      int  cc=0;
1027
      for (int cent_x = 0; cent_x < param.param_device.NumberPixels ; cent_x = cent_x + param.param_device.CCdisplace)
1028
	{
1029
	  for (int cent_y = 0; cent_y < param.param_device.NumberPixels ; cent_y = cent_y + param.param_device.CCdisplace)
1030
1031
1032
1033
1034
1035
	    {
	      cout << "CHECKCC " << " " << cent_x << " " << cent_y <<" " << lCC[cent_x * param.param_device.NumberPixels + cent_y] / (myfloat_t) (param.param_device.NumberPixels * param.param_device.NumberPixels ) << "\n";
	      cc++;
	    }
	}
    }
Pilar Cossio's avatar
Pilar Cossio committed
1036
1037
#endif

1038
}
1039

1040
int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
1041
{
1042
  // **************************************************************************************
1043
  // ****  BioEM Create Projection routine in Euler angles / Quaternions ******************
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
  // ********************* and turns projection into Fourier space ************************
  // **************************************************************************************

  cuda_custom_timeslot("Projection", 0);

  myfloat3_t RotatedPointsModel[Model.nPointsModel];
  myfloat_t rotmat[3][3];
  myfloat_t alpha, gam, beta;
  myfloat_t* localproj;

  localproj = param.fft_scratch_real[omp_get_thread_num()];
  memset(localproj, 0, param.param_device.NumberPixels * param.param_device.NumberPixels * sizeof(*localproj));

1057
1058
  //*************** Rotating the model ****************************
  //*************** Quaternions ****************************
1059
1060
  if(param.doquater){

1061
1062
    myfloat_t quater[4],cq[4],temp[4];
    myfloat_t a[4];
1063
    //quaternion
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
    quater[1]=param.angles[iMap].pos[1];
    quater[2]=param.angles[iMap].pos[2];
    quater[3]=param.angles[iMap].pos[0];  
    quater[0]=param.angles[iMap].quat4;

    // its conjugate
    cq[0]=quater[0];
    cq[1]=-quater[1];
    cq[2]=-quater[2];
    cq[3]=-quater[3];

    for(int n = 0; n < Model.nPointsModel; n++)
      {