bioem.cpp 54.3 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

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

Pilar Cossio's avatar
Pilar Cossio committed
293
    if(!param.printModel)param.CalculateGridsParam(Inputanglefile.c_str());
294
    }
295
296
297
298
299
#ifdef WITH_MPI
  if (mpi_size > 1)
    {
      if (DebugOutput >= 2 && mpi_rank == 0) timer.ResetStart();
      MPI_Bcast(&param, sizeof(param), MPI_BYTE, 0, MPI_COMM_WORLD);
Pilar Cossio's avatar
Pilar Cossio committed
300
301
      //We have to reinitialize all pointers !!!!!!!!!!!!!!
      if (mpi_rank != 0) param.angprior = NULL;
Pilar Cossio's avatar
Pilar Cossio committed
302

Pilar Cossio's avatar
Pilar Cossio committed
303
//  cout << "HERE MPI " << param.nTotGridAngles << " " << param.nTotGridAngles  * sizeof(myfloat3_t*) << "\n";
Pilar Cossio's avatar
Pilar Cossio committed
304
305
   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);
306
307
308
309
310
311
312

     //Allocating memory for prior	
//   if (mpi_rank != 0){//param.angprior = (myfloat_t*)  mallocchk(3* param.nTotGridAngles * sizeof (myfloat_t*));
    //  delete[] param.angprior;
  //  param.angprior = new myfloat_t[param.NotUn_angles] ;

//
Pilar Cossio's avatar
Pilar Cossio committed
313
#ifdef PILAR_DEBUG
314
	for(int n=0;n<param.nTotGridAngles;n++){
Pilar Cossio's avatar
Pilar Cossio committed
315
	  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
316
317

#endif
318
319
320
321
322
323
324
325
326
327
      //refCtf, CtfParam, angles automatically filled by precalculare function below

      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
328

329
330
331
332
333
    }
#endif
  // ****************** Precalculating Necessary Stuff *********************
  if (DebugOutput >= 2 && mpi_rank == 0) timer.ResetStart();
  param.PrepareFFTs();
334

335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
  if (DebugOutput >= 2 && mpi_rank == 0)
    {
      printf("Time Prepare FFTs %f\n", timer.GetCurrentElapsedTime());
      timer.ResetStart();
    }
  precalculate();

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

  return(0);
365
366
}

367
368
void bioem::cleanup()
{
369
 //Deleting allocated pointers
370
371
  free_device_host(pProb.ptr);
  RefMap.freePointers();
372
373
}

374
375
int bioem::precalculate()
{
376
377
378
379
380
381
  // **************************************************************************************
  // **Precalculating Routine of Orientation grids, Map crosscorrelations and CTF Kernels**
  // **************************************************************************************
  HighResTimer timer;

  // Generating Grids of orientations 
382
 // param.CalculateGridsParam();                
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401

  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);
402
403
404
405
}

int bioem::run()
{
David Rohr's avatar
David Rohr committed
406

407
408
409
  // **************************************************************************************
  // ********** Secondary routine for printing out the only best projection ***************
  // **************************************************************************************
David Rohr's avatar
David Rohr committed
410

411
  if(mpi_rank == 0 && param.printModel){ //Only works for 1 MPI process (not parallelized)
412

413
414
415
416
417
    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;
418

419
420
421
    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);
422

423
    cout << "...... Calculating Projection .......................\n " ;
424

425
    createProjection(0, proj_mapsFFT);
426

427
    cout << "...... Calculating Convolution .......................\n " ;
David Rohr's avatar
David Rohr committed
428

429
    createConvolutedProjectionMap(0, 0, proj_mapsFFT, conv_map, conv_mapFFT, sumCONV, sumsquareCONV);
430

431
  }
432

433
434
435
  // **************************************************************************************
  // **** Main BioEM routine, projects, convolutes and compares with Map using OpenMP ****
  // **************************************************************************************
436

437
438
  // **** 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
439

440
  if (mpi_rank == 0) printf("\tInitializing Probabilities\n");
441

442

443
444
445
446
  // 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
447

448
      pProbMap.Total = 0.0;
449
450
      pProbMap.Constoadd = -FLT_MAX; //Problem if using double presicion

451
      if (param.param_device.writeAngles)
452
	{
453
454
455
456
457
	  for (int iOrient = 0; iOrient < param.nTotGridAngles; iOrient ++)
	    {
	      bioem_Probability_angle& pProbAngle = pProb.getProbAngle(iRefMap, iOrient);

	      pProbAngle.forAngles = 0.0;
458
	      pProbAngle.ConstAngle = -FLT_MAX;
459
460
	    }
	}
461

462
      if (param.param_device.writeCC)
463
	{      int  cc=0;
464
	  for (int cent_x = 0; cent_x < param.param_device.NumberPixels; cent_x = cent_x + param.param_device.CCdisplace)
465
	    {
466
	      for (int cent_y = 0; cent_y < param.param_device.NumberPixels; cent_y = cent_y + param.param_device.CCdisplace)
467
		{
468
		  bioem_Probability_cc& pProbCC = pProb.getProbCC(iRefMap, cc);
469
470
471
472
473
474
475
476
477
		  //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++;
478
		}
479
	    }
480
       if(!FFTAlgo){cout << "Cross correlation calculation must be with enviormental variable FFTALGO=1\n"; exit(1);}
481
482
	}                 
    }
483
484
485

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

486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
  // **************************************************************************************
  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
  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);

Pilar Cossio's avatar
Pilar Cossio committed
507
508
509
  if(mpi_size > param.nTotGridAngles){
    cout << "EXIT: Wrong MPI setup More MPI processes than orientations\n"; exit(1);
  }
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
  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;

  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);
#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);
527

528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
      for (int iOrient = iOrientAtOnce; iOrient < iTmpEnd;iOrient++)
	{
	  mycomplex_t* proj_mapFFT = &proj_mapsFFT[(iOrient - iOrientAtOnce) * ProjMapSize];
	  // ***************************************************************************************
	  // ***** **** Internal Loop over convolutions **** *****
	  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);

	      // ***************************************************************************************
	      // *** Comparing each calculated convoluted map with all experimental maps ***
	      if (DebugOutput >= 2) timer.ResetStart();
544
545
546
547
548
549
550
     	      myfloat_t amp,pha,env;

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

	      compareRefMaps(iOrient, iConv, amp, pha, env, conv_map, conv_mapFFT, sumCONV, sumsquareCONV);
551
552

	      if (DebugOutput >= 2)
553
		{
554
555
556
557
558
559
560
561
562
		  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);
563
		}
564
565
566
567
568
569
	    }
	  if (DebugOutput >= 1)
	    {
	      printf("\tTotal time for projection %d: %f (rank %d)\n", iOrient, timer2.GetCurrentElapsedTime(), mpi_rank);
	      timer2.ResetStart();
	    }
570
	}
571
572
573
574
575
    }
  //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
576

577
  deviceFinishRun();
578

579
  // ************* Writing Out Probabilities ***************
580

581
  // *** Angular Probability ***
David Rohr's avatar
David Rohr committed
582

David Rohr's avatar
David Rohr committed
583
#ifdef WITH_MPI
584
585
586
587
588
589
590
591
592
593
594
595
596
  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);
597

598
599
600
601
602
603
604
605
606
	for (int i = 0;i < RefMap.ntotRefMap;i++)
	  {
	    bioem_Probability_map& pProbMap = pProb.getProbMap(i);
	    tmp1[i] = pProbMap.Total * exp(pProbMap.Constoadd - tmp2[i]);
	  }
	MPI_Reduce(tmp1, tmp3, RefMap.ntotRefMap, MY_MPI_FLOAT, MPI_SUM, 0, MPI_COMM_WORLD);

	//Find MaxProb
	MPI_Status mpistatus;
David Rohr's avatar
David Rohr committed
607
	{
608
609
610
611
612
613
	  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;
614
              //temporary array that has the mpirank for the highest pProb.constant
615
616
617
618
619
	    }
	  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
620
		{
621
		  if (mpi_rank == 0) printf("Error: Could not find highest probability\n");
David Rohr's avatar
David Rohr committed
622
		}
623
	      else if (tmpi2[i] != 0) //Skip if rank 0 already has highest probability
David Rohr's avatar
David Rohr committed
624
		{
625
626
627
628
629
630
631
632
		  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
633
		}
634
635
636
	    }
	  delete[] tmpi1;
	  delete[] tmpi2;
637
	}
638

David Rohr's avatar
David Rohr committed
639
	if (mpi_rank == 0)
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
	  {
	    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)
657
	{
658
659
660
661
662
663
	  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++)
	    {
664
665
666
667
668
	 for (int j = 0;j < param.nTotGridAngles;j++)
                {
//	      tmp1[i] = pProb.getProbMap(i).Constoadd;
//	      bioem_Probability_angle& pProbAngle = pProb.getProbAngle(i, j);
              tmp1[i * param.nTotGridAngles + j]= pProb.getProbAngle(i, j).ConstAngle;
669
	    }
670
671
	 }

672
673
674
675
	  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
676
		{
677
678
		  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
679
		}
680
681
682
683
684
	    }
	  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++)
685
		{
686
687
688
689
690
691
		  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];
		    }
692
		}
693
694
695
696
697
698
699
	    }
	  delete[] tmp1;
	  delete[] tmp2;
	  delete[] tmp3;
	}
    }
#endif
David Rohr's avatar
David Rohr committed
700

701
702
  if (mpi_rank == 0)
    {
703
 
704
705
      // Output for Angle Probability File
      ofstream angProbfile;
706
707
708
      if(param.param_device.writeAngles)
	{
	  angProbfile.open ("ANG_PROB");
709
	  angProbfile <<"************************* HEADER:: NOTATION *******************************************\n";
710
711
          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" ;};
712
	  angProbfile <<"************************* HEADER:: NOTATION *******************************************\n";
Pilar Cossio's avatar
Pilar Cossio committed
713
714
//          angProbfile <<"Model Used: " << modelfile.c_str() << "\n";
//          angProbfile <<"Input Used: " << infile.c_str() << "\n";
715
	}
716
      // Output for Cross Correlation File
717
718
719
720
      ofstream ccProbfile;
      if(param.param_device.writeCC)
	{
	  ccProbfile.open ("CROSS_CORRELATION");
721
	  ccProbfile <<"************************* HEADER:: NOTATION *******************************************\n";
722
723
724
          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";
725
          ccProbfile <<"************************* HEADER:: NOTATION *******************************************\n";
726
727
	}

728
729
730
731
732
733
734
735
736
      // 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{
737
	  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";}
738
739
740
741
742
      }else { 
	if(param.usepsf){
	  //     if( localcc[rx * param.param_device.NumberPixels + ry] <
	  outputProbFile << "Notation= RefMap:  MapNumber ; Maximizing Param: MaxLogProb - q1 - q2 - q3 - PSF amp - PSF phase - PSF envelope - center x - center y - normalization - offsett \n";
	}else{
743
          outputProbFile << "Notation= RefMap:  MapNumber ; Maximizing Param: MaxLogProb - q1 - q2 - q3 - CTF amp - CTF defocus - CTF B-Env - center x - center y - normalization - offsett \n";
744
        }}
745
      if(param.writeCTF) outputProbFile << " RefMap:  MapNumber ; CTFMaxParm: defocus - b-Env (B ref. Penzeck 2010)\n";
746
747
748
      outputProbFile <<"************************* HEADER:: NOTATION *******************************************\n\n";

      // Loop over reference maps
749

750
751
752
753
754
      for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap; iRefMap ++)
	{
	  // **** Total Probability ***
	  bioem_Probability_map& pProbMap = pProb.getProbMap(iRefMap);

755
	  //Controll for Value of Total Probability
Pilar Cossio's avatar
Pilar Cossio committed
756
          // cout << pProbMap.Total << " " <<  pProbMap.Constoadd << " " << FLT_MAX <<" " << log(FLT_MAX) << "\n";
757
758
          if(pProbMap.Total>1.e-38){

759
760
761
762
763
764
765
766
767
768
769
770
	    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: ";

	    // *** Param that maximize probability****
	    outputProbFile << (pProbMap.Constoadd + 0.5 * log(M_PI) + (1 - param.param_device.Ntotpi * 0.5) * (log(2 * M_PI) + 1) + log(param.param_device.volu)) << " ";
	    outputProbFile << param.angles[pProbMap.max.max_prob_orient].pos[0] << " [ ] ";
	    outputProbFile << param.angles[pProbMap.max.max_prob_orient].pos[1] << " [ ] ";
	    outputProbFile << param.angles[pProbMap.max.max_prob_orient].pos[2] << " [ ] ";
	    outputProbFile << param.CtfParam[pProbMap.max.max_prob_conv].pos[0] << " [ ] ";
	    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] ";}
Pilar Cossio's avatar
Pilar Cossio committed
771
	    if(!param.usepsf){outputProbFile << param.CtfParam[pProbMap.max.max_prob_conv].pos[2] << " [A²] ";}
772
773
774
775
776
777
            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] " ;
	    outputProbFile << pProbMap.max.max_prob_norm << " [ ] " ; 
	    outputProbFile << pProbMap.max.max_prob_mu << " [ ] ";
	    outputProbFile << "\n";
778
	  }else{ 
779
780
781
782
783
784
785
786
787
788
789
790
791
	    outputProbFile << "PROBLEM!! with Map " << iRefMap << "Numerical Integrated Probability = 0.0; Options for error: \n - Try re-normalizing experimental map \n -looking at your model density. \n - Maybe radius is less than pixel size (If so try KEYWORD NO_PROJECT_RADIUS in parameter inputfile)\n";
	    outputProbFile << "RefMap: " << iRefMap << "Most probabily Numerical Constant Out of Float-point range: " << pProbMap.Constoadd  << "\n"; }

	  // 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] "; 
792
	    outputProbFile << 4*M_PI*M_PI*param.CtfParam[pProbMap.max.max_prob_conv].pos[2]/denomi << " [A²] \n";
793
	  }
794

795
	  // Writing Individual Angle probabilities
796
797
798
	  if(param.param_device.writeAngles)
	    {
	      for (int iOrient = 0; iOrient < param.nTotGridAngles; iOrient++)
David Rohr's avatar
David Rohr committed
799
		{
800
		  bioem_Probability_angle& pProbAngle = pProb.getProbAngle(iRefMap, iOrient);
801

802
803
804
805
806
807
808
809
810
811
812
                 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.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";
		    }
813
814
		}
	    }
815
	
816
817
	  // Writing Cross-Correlations if requiered
	  if(param.param_device.writeCC){
818

819
820
821
822
823
	    int  cc=0;
	    int halfPix;
	    int rx=0;
	    int ry=0;
	    myfloat_t localcc[ (param.param_device.NumberPixels+1) * (param.param_device.NumberPixels+1) ];
824

825
826
	    halfPix = param.param_device.NumberPixels / 2 ;
	    // Ordering the centers of the Cross Correlation
827

828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
	    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;
		  }
	      }

	    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;
		    }
		    cc++;
		  }
		//              ccProbfile << "\n";
	      }
	    if(!param.ignoreCCoff){
	      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
872
		{
873
		  for (int ry = param.param_device.CCdisplace; ry < param.param_device.NumberPixels ; ry = ry + param.param_device.CCdisplace)
874
		    {
875
876
877
878
879
880
		     if(localcc[ rx * param.param_device.NumberPixels + ry ] > -FLT_MAX){
			ccProbfile << "RefMap: "<< iRefMap << " " << rx << " " << ry << " " << localcc[ rx * param.param_device.NumberPixels + ry ] << "\n" ;
			}else{
			ccProbfile << "RefMap: "<< iRefMap << " " << rx << " " << ry << " " << -FLT_MAX << "\n" ;
			}
		      //				 cout << " cc " << rx << " " << ry << " " << localcc[ rx * param.param_device.NumberPixels + ry ] <<"\n" ;
881
		    }
882
883
884
885
		  ccProbfile << "\n";
		}			
	    }else{
	      for (int rx = param.param_device.CCdisplace; rx < param.param_device.NumberPixels ; rx++)
886
		{
887
		  for (int ry = param.param_device.CCdisplace; ry < param.param_device.NumberPixels ; ry++)
888
		    {
889
890
891
892
893
		if(localcc[ rx * param.param_device.NumberPixels + ry ] > -FLT_MAX){
                        ccProbfile << "RefMap: "<< iRefMap << " " << rx << " " << ry << " " << localcc[ rx * param.param_device.NumberPixels + ry ] << "\n" ;
                        }else{
                        ccProbfile << "RefMap: "<< iRefMap << " " << rx << " " << ry << " " << -FLT_MAX << "\n" ;
                        }
894
		    }
895
		  ccProbfile << "\n";
896
		}
897

898
	    }
899
	  }
900
	}
901

902
903
904
905
906
907
908
909
      if(param.param_device.writeAngles)
	{
	  angProbfile.close();
	}

      if(param.param_device.writeCC)
	{
	  ccProbfile.close();
910
	}
911

912
913
914
915
      outputProbFile.close();
    }

  return(0);
916
917
}

918
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)
919
{
920

921
922
923
924
925
926
927
  //***************************************************************************************
  //***** 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 ++)
928
	{
929
	  const int num = omp_get_thread_num();
930
	  calculateCCFFT(iRefMap, iOrient, iConv, amp, pha, env, sumC, sumsquareC, localmultFFT, param.fft_scratch_complex[num], param.fft_scratch_real[num]);
931
	}
932
933
934
935
936
937
    }
  else
    {
      //Without FFT Algorithm
#pragma omp parallel for schedule(dynamic, 1)
      for (int iRefMap = startMap; iRefMap < RefMap.ntotRefMap; iRefMap ++)
938
	{
939
	  compareRefMapShifted < -1 > (iRefMap, iOrient, iConv, conv_map, pProb, param.param_device, RefMap);
940
	}
941
942
    }
  return(0);
943
944
}

945
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)
946
{
947
948
  //***************************************************************************************
  //***** Calculating cross correlation in FFTALGOrithm *****
Pilar Cossio's avatar
Pilar Cossio committed
949

950
951
952
953
954
955
  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];
    }
956

957
  myfftw_execute_dft_c2r(param.fft_plan_c2r_backward, localCCT, lCC);
958

959
  doRefMapFFT(iRefMap, iOrient, iConv, amp, pha, env, lCC, sumC, sumsquareC, pProb, param.param_device, RefMap);
Pilar Cossio's avatar
Pilar Cossio committed
960
961

#ifdef PILAR_DEBUG
962
963
  if (param.param_device.writeCC)
    {      int  cc=0;
964
      for (int cent_x = 0; cent_x < param.param_device.NumberPixels ; cent_x = cent_x + param.param_device.CCdisplace)
965
	{
966
	  for (int cent_y = 0; cent_y < param.param_device.NumberPixels ; cent_y = cent_y + param.param_device.CCdisplace)
967
968
969
970
971
972
	    {
	      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
973
974
#endif

975
}
976

977
int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
978
{
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
  // **************************************************************************************
  // ****  BioEM Create Projection routine in Euler angle predefined grid******************
  // ********************* 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));

994
995
  if(param.doquater){

996
997
    myfloat_t quater[4],cq[4],temp[4];
    myfloat_t a[4];
998
    //quaternion
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
    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++)
      {
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
	//Rotation with quaterion

	// Initial coords	
	a[0]=0.;
	a[1]=Model.points[n].point.pos[0];
	a[2]=Model.points[n].point.pos[1];
	a[3]=Model.points[n].point.pos[2];

	temp[0]=a[0]*cq[0]-a[1]*cq[1]-a[2]*cq[2]-a[3]*cq[3];
	temp[1]=a[0]*cq[1]+a[1]*cq[0]+a[2]*cq[3]-a[3]*cq[2];
	temp[2]=a[0]*cq[2]-a[1]*cq[3]+a[2]*cq[0]+a[3]*cq[1];
	temp[3]=a[0]*cq[3]+a[1]*cq[2]-a[2]*cq[1]+a[3]*cq[0];

	// First coordinate is zero Going back to real space
        RotatedPointsModel[n].pos[0] = quater[0]*temp[1]+quater[1]*temp[0]+quater[2]*temp[3]-quater[3]*temp[2];
	RotatedPointsModel[n].pos[1] = quater[0]*temp[2]-quater[1]*temp[3]+quater[2]*temp[0]+quater[3]*temp[1];
        RotatedPointsModel[n].pos[2] = quater[0]*temp[3]+quater[1]*temp[2]-quater[2]*temp[1]+quater[3]*temp[0]; 
    
    
1031
      }
1032
1033


1034
1035
1036
1037
1038
  } else{
    // Doing Euler angles instead of Quaternions
    alpha = param.angles[iMap].pos[0];
    beta = param.angles[iMap].pos[1];
    gam = param.angles[iMap].pos[2];
1039

1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
    //*** To see how things are going:
#ifdef PILAR_DEBUG 
    cout << "Id " << omp_get_thread_num() <<  " Angs: " << alpha << " " << beta << " " << gam << "\n"; 
#endif
    // ********** Creat Rotation with pre-defiend grid of orientations**********
    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++)
      {
	RotatedPointsModel[n].pos[0] = 0.0;
	RotatedPointsModel[n].pos[1] = 0.0;
	RotatedPointsModel[n].pos[2] = 0.0;
      }
    for(int n = 0; n < Model.nPointsModel; n++)
      {
	for(int k = 0; k < 3; k++)
	  {
	    for(int j = 0; j < 3; j++)
	      {
		RotatedPointsModel[n].pos[k] += rotmat[k][j] * Model.points[n].point.pos[j];
	      }
	  }
      }
1071

1072
  }
1073

1074
1075
  if(param.printrotmod) {
    for(int n = 0; n < Model.nPointsModel; n++) cout << "ROTATED " << iMap << " " << n <<" "<< RotatedPointsModel[n].pos[0] << " " << RotatedPointsModel[n].pos[1] << " " <<  RotatedPointsModel[n].pos[2] << "\n";
1076

1077
  }
1078
  int i, j;
1079

1080
1081
1082
1083
1084
  //********** Projection with radius ***************
  if(param.doaaradius)
    {
      int irad;
      myfloat_t dist, rad2;
Pilar Cossio's avatar
Pilar Cossio committed
1085

1086
1087
      for(int n = 0; n < Model.nPointsModel; n++)
	{
1088
	  if(Model.points[n].radius < param.pixelSize){
Pilar Cossio's avatar
Pilar Cossio committed
1089
1090
1091
1092
1093
1094
1095
1096
	 //   cout << "Radius less than Pixel size: use keyword NO_PROJECT_RADIUS in inputfile\n";
          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);

          if (i < 0 || j < 0 || i >= param.param_device.NumberPixels || j >= param.param_device.NumberPixels)
            {
              if (DebugOutput >= 0) cout << "WARNING:::: Model Point out of Projection map: " << i << ", " << j << "\n";
              //              continue;
1097
              if(not param.ignorepointsout)exit(1);
Pilar Cossio's avatar
Pilar Cossio committed
1098
1099
1100
1101
1102
1103
1104
            }

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

	 // exit(1);
	  }else{

1105
	  //Getting Centers of Sphere
Pilar Cossio's avatar
Pilar Cossio committed
1106
1107
	  i = floor(RotatedPointsModel[n].pos[0] / param.pixelSize + (myfloat_t) param.param_device.NumberPixels / 2.0f + 0.5f) -param.shiftX;
	  j = floor(RotatedPointsModel[n].pos[1] / param.pixelSize + (myfloat_t) param.param_device.NumberPixels / 2.0f + 0.5f) -param.shiftY;
1108
	  //Getting the radius
Pilar Cossio's avatar
Pilar Cossio committed
1109
	  irad=int( Model.points[n].radius / param.pixelSize ) + 1;
1110
1111
	  rad2= Model.points[n].radius * Model.points[n].radius;

1112
	  if (i < 0 || j < 0 || i >= param.param_device.NumberPixels || j >= param.param_device.NumberPixels)
Pilar Cossio's avatar
Pilar Cossio committed
1113
1114
            {
              if (DebugOutput >= 0) cout << "WARNING::: Model Point out of Projection map: " << i << ", " << j << "\n";
1115
1116
	      cout << "Model point " << n << "Rotation: " << iMap <<" "<< RotatedPointsModel[n].pos[0] << " " << RotatedPointsModel[n].pos[1] << " " <<  RotatedPointsModel[n].pos[2] << "\n";
	      cout << "Original coor " << n <<" " << Model.points[n].point.pos[0] << " " << Model.points[n].point.pos[1] << " " <<Model.points[n].point.pos[2] << "\n";
Pilar Cossio's avatar
Pilar Cossio committed
1117
	      cout << "WARNING: Angle orient " << n << " " <<  param.angles[iMap].pos[0] << " " <<  param.angles[iMap].pos[1] << " " << param.angles[iMap].pos[2] <<  " out " << i << " " << j << "\n";
1118
1119
	      cout << "WARNING: MPI rank " << mpi_rank <<"\n";
	      //              continue;
1120
	      if(not param.ignorepointsout)exit(1);
Pilar Cossio's avatar
Pilar Cossio committed
1121
1122
1123
            }


1124
	  //Projecting over the radius
Pilar Cossio's avatar
Pilar Cossio committed
1125
	  for(int ii= i - irad; ii < i + irad + 1 ; ii++)
1126
	    {	
Pilar Cossio's avatar
Pilar Cossio committed
1127
	      for(int jj = j - irad; jj < j + irad + 1 ; jj++)
1128
		{
Pilar Cossio's avatar
Pilar Cossio committed
1129
		  dist= ( (myfloat_t) (ii-i)*(ii-i)+(jj-j)*(jj-j) ) *  param.pixelSize *  param.pixelSize ; //at pixel center
1130
1131
		  if( dist < rad2 )
		    {
Pilar Cossio's avatar
Pilar Cossio committed
1132
1133
1134
1135
		      localproj[ii * param.param_device.NumberPixels + jj] += param.pixelSize * param.pixelSize * 2 * sqrt( rad2 - dist ) * Model.points[n].density
			* 3 / (4 * M_PI * Model.points[n].radius * rad2 );
//			cout << "TT " << ii << " " << jj << " " << localproj[ii * param.param_device.NumberPixels + jj] << " " <<  sqrt( rad2 - dist )  << " " <<  (4 * M_PI * Model.points[n].radius * rad2 )/3. << " " << param.pixelSize *  param.pixelSize * 2 * sqrt( rad2 - dist ) <<  "\n"; 
                       // This is the number of electrons that this piece of volume contributes (from the full circle)
1136
		    }
Pilar Cossio's avatar