lib/src1/bruker2dicom.cxx

   1 #include "bruker2dicom.h"
   2 #include <boost/filesystem/path.hpp>
   3 #include <boost/filesystem/operations.hpp>
   4 #include "brukerexception.h"
   5
   6 #ifndef PATH_MAX // If not defined yet : do it
   7    #define PATH_MAX 2048
   8 #endif
   9
  10
  11
  12 bool Bruker2Dicom::Execute()
  13 {
  14    // ----- Check input values -----
  15
  16    bool bigEndian = GDCM_NAME_SPACE::Util::IsCurrentProcessorBigEndian();
  17
  18    //if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(InputDirName) )
  19    if ( ! boost::filesystem::is_directory(InputDirName) )
  20    {
  21       std::cout << "KO : [" << InputDirName << "] is not a Directory." << std::endl;
  22       return 0;
  23    }
  24    else
  25    {
  26       if (verbose)
  27          std::cout << "OK : [" << InputDirName << "] is a Directory." << std::endl;
  28    }
  29
  30    std::string strDirNameOut(OutputDirName);
  31    bool res=CreateDirectory(strDirNameOut);
  32    if (!res) {
  33       std::cout << "[" << OutputDirName << "] Directory creation failure " << std::endl;
  34       //exit (0);
  35       throw ( BrukerHopelessException ("Output directory creation failure "));
  36    }
  37
  38    std::string strDirNamein(InputDirName);
  39    GDCM_NAME_SPACE::DirList dirList(strDirNamein, false, true); // DON'T get recursively the list of files
  40    std::string strDirNameout(OutputDirName);
  41
  42 /*
  43    if (listonly)
  44    {
  45       std::cout << "------------List of found files ------------" << std::endl;
  46       dirList.Print();
  47       std::cout << std::endl;
  48       return 1;
  49    }
  50 */
  51
  52 //
  53 // e.g : at level 0, in : B67d1.Bp1
  54 //
  55 //           1  2  3  4  5  6  AdjStatePerStudy  subject
  56 //
  57
  58    GDCM_NAME_SPACE::DirListType fileNames;
  59    fileNames = dirList.GetFilenames();
  60    bool canOpen;
  61    std::string outputFileName;
  62
  63
  64   // BrukerDataSet br_subject;
  65    std::string subject;
  66    subject = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
  67              GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
  68              "subject";
  69    if (verbose)
  70         std::cout << " Subject : [" <<  subject << "]" << std::endl;
  71    canOpen =br_subject.LoadFile(subject);
  72
  73    if (!canOpen)
  74    {
  75       std::cout << "Hopeless! no 'subject' found" << std::endl;
  76       throw ( BrukerHopelessException ("Hopeless! no 'subject' found in root input directory "));
  77       //exit(0);  /// \TODO throw an exception !
  78    }
  79    else
  80    {
  81       br_subject.FillMap();
  82    }
  83    //br_subject.PrintSelf();
  84
  85   // get info for 'Study Description'
  86
  87          BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string");
  88          std::string subject_name = b_name.GetStringValue()[0];
  89          strPatientName = subject_name;
  90          cleanString(subject_name);
  91
  92          BrukerFieldData b_entry=br_subject.GetFieldData("SUBJECT_entry");
  93          std::string subject_entry = b_entry.GetStringValue()[0];
  94          //cleanString(subject_entry);
  95          subject_entry = subject_entry.substr(11, subject_entry.size()-11);
  96
  97          BrukerFieldData b_position=br_subject.GetFieldData("SUBJECT_position");
  98          std::string subject_position = b_position.GetStringValue()[0];
  99          //cleanString(subject_position);
 100          subject_position = subject_position.substr(9, subject_position.size()-9);
 101
 102          BrukerFieldData b_date=br_subject.GetFieldData("SUBJECT_date");
 103          std::string subject_date = b_date.GetStringValue()[0];
 104          strStudyTimeDate = subject_date;
 105          cleanString(subject_date);
 106
 107          BrukerFieldData b_study_name=br_subject.GetFieldData("SUBJECT_study_name");
 108          std::string subject_study_name = b_study_name.GetStringValue()[0];
 109          subject_study_name = subject_study_name.substr(1, subject_study_name.size()-2);
 110          cleanString(subject_date);
 111
 112    // subject_name is already in 'Patient Name'
 113    strStudyDescr = /*subject_name + "." + */ subject_study_name + "." + subject_entry + "." + subject_position + "." + subject_date;
 114
 115    char outputDirName[(unsigned int) PATH_MAX+2];
 116
 117    strStudyUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 118    serieNumber = 0;
 119    instanceNumber = 0;
 120    // -----------------------------------------------------
 121    // Iterate to ALL the objets(files/directories) found in the input directory
 122    // (this is level ZERO)
 123    // each Directory (name : 1, 2, 3, ...) will be a Dicom Serie
 124    // -----------------------------------------------------
 125
 126    GDCM_NAME_SPACE::DirListType::iterator it;
 127
 128    for (it = fileNames.begin();
 129          it != fileNames.end();
 130        ++it)
 131    {
 132       if ( boost::filesystem::is_directory(*it) )
 133       {
 134          if (verbose)
 135             std::cout << "[" << *it << "] is a directory" << std::endl;
 136
 137          //BrukerDataSet br_acqp;
 138          std::string strAcqp;
 139          strAcqp = (*it) +
 140                    GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 141                    "acqp";
 142
 143          br_acqp.LoadFile(strAcqp);
 144          br_acqp.FillMap();
 145
 146          std::string acqp_scan_name;
 147          std::string acqp_method;
 148          std::string acqp_protocol_location;
 149
 150          BrukerFieldData b_protocol_location=br_acqp.GetFieldData("ACQ_protocol_location");
 151          acqp_protocol_location = b_protocol_location.GetStringValue()[0];
 152          cleanString(acqp_protocol_location);
 153
 154          BrukerFieldData b_scan_name=br_acqp.GetFieldData("ACQ_scan_name");
 155          acqp_scan_name = b_scan_name.GetStringValue()[0];
 156          cleanString(acqp_scan_name);
 157
 158          BrukerFieldData b_method=br_acqp.GetFieldData("ACQ_method");
 159          acqp_method = b_method.GetStringValue()[0];
 160          cleanString(acqp_method);
 161
 162          BrukerFieldData b_list_size = br_acqp.GetFieldData("ACQ_O1_list_size");
 163          //b_list_size.PrintSelf(); //JP
 164
 165          nbSlices =  b_list_size.GetIntValue()[0];
 166
 167          strSerieDescr = GDCM_NAME_SPACE::Util::GetName(*it)
 168                        /*  + "." + acqp_protocol_location */ // always the same (in each acquisition)
 169                          + "." + acqp_scan_name
 170                          + "." + acqp_method.c_str();
 171
 172          sprintf(outputDirName, "%s%c%s", OutputDirName.c_str(),
 173                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 174                           strSerieDescr.c_str() );
 175
 176          std::cout << " ================================================================================\n"
 177                    << " === [" << GDCM_NAME_SPACE::Util::GetName(*it) << "] -> [" << strSerieDescr << "]\n"
 178                    << " ================================================================================"
 179                    << std::endl;
 180
 181
 182         if (verbose)
 183            printf ("outputDirName [%s]\n", outputDirName);
 184         try {
 185            DealWithNiveau1(*it, outputDirName);
 186         }
 187         catch (BrukerHopelessException &e)
 188         {
 189          std::cout << "And Exception was thrown in DealWithNiveau1 (" << e.what() << ") " << std::endl;
 190          continue;
 191         }
 192       }
 193    } // end of : for (GDCM_NAME_SPACE::DirListType::iterator it
 194 }
 195
 196
 197 // =====================================================================
 198
 199 void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string currentOutputDirName) {
 200 //
 201 // e.g. : at level 1, in B67d1.Bp1/6
 202 //
 203 // acqp  fid  imnd  pdata  pulseprogram  spnam0  spnam1
 204
 205    bool res = CreateDirectory(currentOutputDirName);
 206
 207    if (!res) {
 208       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 209       throw ( BrukerHopelessException ("Level 1 output directory creation failure "));
 210      // exit (0);
 211    }
 212    GDCM_NAME_SPACE::DirList dirList(level1Directory, false, true); // DON'T get recursively the list of files
 213    GDCM_NAME_SPACE::DirListType fileNames;
 214    fileNames = dirList.GetFilenames();
 215    // -----------------------------------------------------
 216    // Iterate to ALL the objets(files/directories) found in the input directory
 217    // -----------------------------------------------------
 218    GDCM_NAME_SPACE::DirListType::iterator it;
 219
 220    for (it = fileNames.begin();
 221         it != fileNames.end();
 222       ++it)
 223    {
 224       if ( boost::filesystem::is_regular(*it) )
 225       //if ( ! boost::filesystem::is_directory(*it) )
 226       {
 227          if (verbose)
 228             std::cout << "--- [" << *it << "] is a file." << std::endl;
 229       }
 230    }
 231
 232    char outputDirName[(unsigned int) PATH_MAX+2];
 233    //std::string firstName;
 234    bool canOpen;
 235    for (it = fileNames.begin();
 236         it != fileNames.end();
 237       ++it)
 238    {
 239       if ( boost::filesystem::is_directory(*it) )
 240       {
 241          // will be always "pdata" ...
 242          if (verbose)
 243             std::cout << "--- [" << *it << "] is a directory" << std::endl;
 244
 245               /* a recuperer :
 246               if (FileLine.startsWith("##$ACQ_size=")) {
 247               if (FileLine.startsWith("##$NI=")) {
 248               if (FileLine.startsWith("##$NR=")) {
 249               if (FileLine.startsWith("##$ACQ_obj_order=")) {
 250               if (FileLine.startsWith("##$ACQ_word_size=")) {
 251               if (FileLine.startsWith("##$BYTORDA=")) {
 252               if (FileLine.startsWith("##$PULPROG=")) {
 253               */
 254
 255          sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 256                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 257                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str());
 258          //br1.PrintSelf();
 259
 260           std::string strMethod;
 261           //std::string firstName = *(fileNames.begin());
 262
 263           strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin())) +
 264                       GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 265                       "method";
 266             // std::cout << "---strMethod (for method)=> [" << strMethod << "]" << std::endl;
 267           canOpen = br_method.LoadFile(strMethod);
 268           if (!canOpen)
 269           {
 270              strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
 271                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 272                          "imnd";
 273              //std::cout << "---strMethod (for imnd) => [" << strMethod << "]" << std::endl;
 274              canOpen = br_method.LoadFile(strMethod);
 275              if (!canOpen)
 276              {
 277                 std::cout << "Hopeless! neither 'method' nor 'imnd' found in ["
 278                           << level1Directory  << "]; we skip it!" << std::endl;
 279                 continue;
 280                 //throw ( BrukerHopelessException ("Hopeless! neither 'method' nor 'imnd' found "));
 281                 //exit(0);  /// \TODO throw an exception !
 282              }
 283           }
 284           if (verbose)
 285              std::cout << "open => [" << strMethod << "] successfully" << std::endl;
 286           br_method.FillMap();
 287
 288           /* a recuperer :
 289              ##$PVM_Fov (dimension)
 290           */
 291   /*
 292           dans method (pour perfusion  seulement?) :
 293           ##$PVM_ObjOrderList=( 8 )
 294           0 2 4 6 1 3 5 7
 295           ##$PVM_NSPacks=2
 296           ##$PVM_SPackArrNSlices=( 2 )
 297           7 1
 298   */
 299          try {
 300             DealWithNiveau2(*it,outputDirName );
 301          }
 302          catch (BrukerHopelessException &e)
 303          {
 304             std::cout << "And Exception was thrown in DealWithNiveau2 (" << e.what() << ") " << std::endl;
 305             continue;
 306          }
 307       }
 308    }
 309 }
 310
 311 // =====================================================================
 312
 313 void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string currentOutputDirName) {
 314
 315 // e.g. : at level 2 in B67d1.Bp1/6/pdata
 316 //
 317 // acqp  fid  imnd  pdata  pulseprogram  spnam0  spnam1
 318 //
 319
 320    bool res = CreateDirectory(currentOutputDirName);
 321
 322    if (!res) {
 323       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 324       throw ( BrukerHopelessException ("Hopeless! Level2 output directory creation failure"));
 325       //exit (0);
 326    }
 327
 328    GDCM_NAME_SPACE::DirList dirList(level2Directory, false, true); // DON'T get recursively the list of files
 329
 330    GDCM_NAME_SPACE::DirListType fileNames;
 331    fileNames = dirList.GetFilenames();
 332
 333    char outputDirName[(unsigned int) PATH_MAX+2];
 334
 335    // -----------------------------------------------------
 336    // Iterate to ALL the objets(files/directories) found in the input directory
 337    // -----------------------------------------------------
 338    GDCM_NAME_SPACE::DirListType::iterator it;
 339    bool canOpen;
 340
 341    if (verbose)
 342    for (it = fileNames.begin();
 343         it != fileNames.end();
 344       ++it)
 345    {
 346       if ( ! boost::filesystem::is_directory(*it) )
 347       {
 348          std::cout << "--- --- [" << *it << "] is a file.." << std::endl;
 349       }
 350
 351    }
 352
 353    for (it = fileNames.begin();
 354          it != fileNames.end();
 355        ++it)
 356    {
 357       if ( boost::filesystem::is_directory(*it) )
 358       {
 359
 360          if (verbose)
 361             std::cout << "--- --- [" << *it << "] is a directory" << std::endl;
 362
 363         // sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 364         //                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 365         //                                GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
 366   // MUST be 'pdata'!
 367
 368 //
 369 // (interest of previous method :
 370 // If unaware user changed the pdata name, it goes on working
 371 //
 372           std::string str_isa;
 373           str_isa = (*it) +
 374                     GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 375                    "isa";
 376
 377           std::string str_isa_func_name;
 378           canOpen = br_isa.LoadFile(str_isa);
 379           if (!canOpen)
 380           {
 381              sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 382                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 383                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
 384           }
 385           else
 386           {
 387              br_isa.FillMap();
 388              BrukerFieldData b_isa_func_name = br_isa.GetFieldData("ISA_func_name");
 389
 390              str_isa_func_name = b_isa_func_name.GetStringValue()[0];
 391              cleanString(str_isa_func_name);
 392
 393              sprintf(outputDirName, "%s%c%s.%s", currentOutputDirName.c_str(),
 394                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 395                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str(),
 396              str_isa_func_name.c_str());
 397           }
 398           try {
 399              DealWithNiveau3(*it, outputDirName);
 400           }
 401           catch (BrukerHopelessException &e)
 402           {
 403              std::cout << "And Exception was thrown in DealWithNiveau3 (" << e.what() << "); "
 404                        << " We skip [" << level2Directory << "]" << std::endl;
 405              continue;
 406           }
 407       }
 408    }
 409 }
 410
 411
 412 //
 413 // =====================================================================
 414 //
 415
 416 void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string currentOutputDirName){
 417
 418 //
 419 // e.g. at level 3, in
 420
 421    // just to be able to go on checking // JP
 422    if ( GDCM_NAME_SPACE::Util::GetName(level3Directory) != "1")
 423       return;
 424
 425    bool res = CreateDirectory(currentOutputDirName);
 426
 427    if (!res)
 428    {
 429       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 430       throw ( BrukerHopelessException ("Hopeless! Level3 output directory creation failure"));
 431       //exit (0);
 432    }
 433
 434    GDCM_NAME_SPACE::DirList dirList(level3Directory, false, true); // DON'T get recursively the list of files
 435    GDCM_NAME_SPACE::DirListType::iterator it;
 436    GDCM_NAME_SPACE::DirListType fileNames;
 437    fileNames = dirList.GetFilenames();
 438
 439    char original2dseqName       [(unsigned int) PATH_MAX+2];
 440    char currentOutputMhdDirName [(unsigned int) PATH_MAX+2];
 441
 442    char outputMhdFileName       [(unsigned int) PATH_MAX+2];
 443    char output2dseqSliceFileName[(unsigned int) PATH_MAX+6]; // think about extra '.dcm'
 444    char output2dseqName         [(unsigned int) PATH_MAX+6];
 445    char output2dseqCartoName    [(unsigned int) PATH_MAX+6];
 446
 447    char copyFile[PATH_MAX + PATH_MAX + 5]; // Should be enough!
 448    bool canOpen;
 449
 450    //-------------- try d3proc;
 451    char char_d3proc[(unsigned int) PATH_MAX+2];
 452
 453    sprintf(char_d3proc,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"d3proc" );
 454
 455    if (verbose)
 456       std::cout << "d3proc: --- => [" << char_d3proc << "]" << std::endl;
 457    std::string str_d3proc(char_d3proc);
 458    canOpen = br_d3proc.LoadFile(str_d3proc);
 459
 460    if (!canOpen)
 461    {
 462       std::cout << "Hopeless! no 'd3proc' found" << std::endl;
 463       throw ( BrukerHopelessException ("Hopeless! no 'd3proc' found"));
 464       //exit(0);  /// \TODO throw an exception !
 465    }
 466
 467    canOpen = br_d3proc.FillMap();
 468    if (!canOpen)
 469    {
 470       std::cout << "Hopeless! FillMap failed on 'd3proc'" << std::endl;
 471       throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'd3proc'"));
 472       //exit(0);  /// \TODO throw an exception !
 473    }
 474
 475    //-------------- end try d3proc;
 476
 477
 478  // -------------------try reco
 479
 480    char char_reco[(unsigned int) PATH_MAX+2];
 481
 482    sprintf(char_reco,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
 483     //str_d3proc = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
 484     //             GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 485     //             "d3proc";
 486    if (verbose)
 487       std::cout << "reco --- => [" << char_reco << "]" << std::endl;
 488    std::string str_reco(char_reco);
 489    canOpen = br_reco.LoadFile(str_reco);
 490
 491    if (!canOpen) // we try in directory ../1
 492    {
 493       if (verbose)
 494          std::cout << "[" << str_reco << "] not found " << std::endl;
 495       std::string lastDirName = GDCM_NAME_SPACE::Util::GetPath(level3Directory);
 496       //lastDirName = GDCM_NAME_SPACE::Util::GetPath(lastDirName);
 497       sprintf(char_reco,"%s%c1%c%s", lastDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
 498       str_reco=char_reco;
 499       canOpen = br_reco.LoadFile(str_reco);
 500       if (!canOpen)
 501       {
 502          std::cout << "Hopeless! cannot find 'reco' in [" << str_reco << "]"  << std::endl;
 503          throw ( BrukerHopelessException ("Hopeless! cannot find 'reco'"));
 504          //exit(0);  /// \TODO throw an exception !
 505       }
 506    }
 507
 508    canOpen = br_reco.FillMap();
 509    if (!canOpen)
 510    {
 511       std::cout << "Hopeless! FillMap failed on [" << str_reco << "]" << std::endl;
 512       throw ( BrukerHopelessException ("Hopeless!FillMap failed on 'reco'"));
 513       //exit(0);  /// \TODO throw an exception !
 514    }
 515    //std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
 516    // br_reco.PrintSelf();
 517    // std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
 518
 519    // -------------------end try reco
 520
 521
 522    BrukerFieldData bX = br_d3proc.GetFieldData("IM_SIX");
 523    int NX = bX.GetIntValue()[0];
 524
 525    if (verbose)
 526       std::cout << "IM_SIX " << NX << std::endl;
 527    BrukerFieldData bY=br_d3proc.GetFieldData("IM_SIY");
 528    int NY = bY.GetIntValue()[0];
 529
 530    if (verbose)
 531          std::cout << "IM_SIY " << NY << std::endl;
 532    /// \todo : check if there are actually 3 dimensions or only 2
 533
 534    BrukerFieldData bZ= br_d3proc.GetFieldData("IM_SIZ");
 535    int nbFrames = bZ.GetIntValue()[0];
 536    if (verbose)
 537          std::cout << "IM_SIZ " << nbFrames << std::endl;
 538
 539         // WARNING DATTYPE is, either in {ip_short, ip_int, ip_char, ...}, or in {1, 2, 3, ...}
 540
 541    BrukerFieldData bDPT = br_d3proc.GetFieldData("DATTYPE");
 542
 543    std::string mhdDataPixelType;
 544    int pixelSize;
 545    getImhDataType(bDPT, mhdDataPixelType, pixelSize);
 546
 547    BrukerFieldData fov = br_method.GetFieldData("PVM_Fov");
 548    double fovX = fov.GetDoubleValue()[0];
 549    double fovY = fov.GetDoubleValue()[1];
 550    if (verbose)
 551       std::cout << "FOV (ds method) " << fovX << " " << fovY << std::endl;
 552
 553    /// \TODO probabely a more sophisticated accessor will be necessary :
 554    ///  (cf : non contiguous slices, overlapping, slice thickness, space between slices, etc)
 555    BrukerFieldData bsliceDistance = br_method.GetFieldData("PVM_SPackArrSliceDistance");
 556    double sliceDistance = bsliceDistance.GetDoubleValue()[0];
 557
 558    if (mhd)
 559    {
 560       sprintf(currentOutputMhdDirName, "%s%c%s", currentOutputDirName.c_str(),
 561                                GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "MhdFiles");
 562       res = CreateDirectory( currentOutputMhdDirName );
 563       if (!res) {
 564          std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 565          throw ( BrukerHopelessException ("Hopeless!FillMap failed on 'reco'"));
 566          //exit (0);
 567       }
 568
 569       if (verbose)
 570          std::cout << "Directory creation [" <<  currentOutputDirName << "]" << std::endl;
 571    }  // end if mhd
 572
 573    if (verbose)
 574          std::cout << "nbFrames " << nbFrames << std::endl;
 575    if (verbose)
 576          std::cout << "nbSlices " << nbSlices << std::endl;
 577    int k;
 578    int nbInstants = nbFrames/nbSlices;
 579    if (verbose)
 580          std::cout << "nbInstants (deduced )" << nbInstants << std::endl;
 581    int instantNb;
 582    int sliceNb;
 583    FILE *fp;  // for MHD files
 584
 585    sprintf( original2dseqName, "%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "2dseq");
 586
 587 /**/
 588   // \TODO : tenir compte du bazar precedent
 589
 590     // load 2dseq in memory
 591
 592    fp = fopen(original2dseqName, "rb");
 593    if (!fp)
 594    {
 595       std::cout << "Cannot open [" << original2dseqName << "] for reading" << std::endl;
 596       throw ( BrukerHopelessException ("Hopeless! Cannot open '2dseq'"));
 597       //exit (0);
 598    }
 599
 600    unsigned char *buffer_2dseq = new unsigned char[NX*NY*pixelSize*nbSlices*nbInstants];
 601    ///\ TODO : find a safer way to be sure to read everything!
 602    size_t lgr = fread(buffer_2dseq, 1, NX*NY*pixelSize*nbSlices*nbInstants, fp);
 603
 604    // This one will be important!
 605    // ---------------------------
 606    try {
 607       imageSet = CreateImageSet ( );
 608    }
 609    catch (BrukerInitException& e)
 610    {
 611       std::cout <<  "an Exception was throw in CreateImageSet ( ); " << e.what()
 612                 << "catched in DealWithNiveau3" << std::endl;
 613       //return;
 614       throw (e);
 615    }
 616
 617    serieNumber++;
 618    strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 619    if (nbInstants==1) // creer un seul fichier .mhd  pour toutes les Slices! (images natives)
 620    {
 621        if (verbose)
 622           std::cout << "Single instant : do not split" << std::endl;
 623        if (mhd)
 624        {
 625              sprintf(outputMhdFileName, "%s%cMhdData_All_the_Slices.mhd", currentOutputMhdDirName,
 626                                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 627              fp=fopen(outputMhdFileName, "w");
 628              if (!fp)
 629              {
 630                 std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 631                 throw ( BrukerHopelessException ("Hopeless! Cannot open  mhd file for writting"));
 632                 //exit(0);
 633              }
 634              else
 635              {
 636                fprintf(fp, "ObjectType = Image\n");
 637                fprintf(fp, "NDims = 3\n" );
 638                fprintf(fp, "BinaryData = True \n" );
 639                fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 640                fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices );
 641                fprintf(fp, "HeaderSize = %d\n", 0);
 642                fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
 643                fprintf(fp, "Position = 0 0 %d\n", 0 );
 644                fprintf(fp, "Offset = 0 0 0\n" );
 645                fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 646                fprintf(fp, "ElementNumberOfChannels = 1\n" );
 647                fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
 648                fprintf(fp, "ElementDataFile = %s\n", "../2dseq_All_the_Slices" );
 649                fclose(fp);
 650              }
 651              sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices",
 652                                        currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 653              fp=fopen(output2dseqSliceFileName, "wb");
 654              if (!fp)
 655              {
 656                 std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 657                 throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseq file for writting"));
 658              }
 659              else
 660              {
 661                 fwrite( buffer_2dseq, NX*NY*pixelSize, nbSlices, fp);
 662              }
 663              fclose(fp);
 664              serieNumber ++;
 665              strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 666        }  // end if mhd
 667        if (dicom)
 668        {
 669              sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices.dcm",
 670                                        currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 671
 672             /* ----------- Write Dicom Image  ---------------*/
 673              MakeDicomImage(buffer_2dseq,
 674                NX,
 675                NY,
 676                nbFrames,
 677                pixelSize,
 678                fovX/NY, fovY/NY, sliceDistance,
 679                output2dseqSliceFileName,
 680                strPatientName,
 681                day,
 682                strStudyUID,
 683                strSerieUID,
 684                strStudyDescr,
 685                strSerieDescr,
 686                strStudyTimeDate,
 687                0,// index frame number
 688                GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
 689              );
 690        }  // end if dicom
 691    }  // end if nbInstants = 1
 692
 693    else  // more than ONE instant
 694    {
 695           // Interleaved !
 696           // it's (slice1,slide2, ...)t1 ; (slice1,slide2, ...)t2 ; ...
 697
 698          unsigned char *pixelsForCurrentSlice = new unsigned char[NX*NY*pixelSize*nbInstants];
 699
 700          k = 0;
 701          for (sliceNb=0; sliceNb<nbSlices; sliceNb++)
 702          {
 703             if (mhd)
 704             {
 705                sprintf(outputMhdFileName, "%s%cMhdData_%03d.mhd", currentOutputMhdDirName,
 706                                         GDCM_NAME_SPACE::GDCM_FILESEPARATOR, k  );
 707                if (verbose)
 708                   std::cout << "--- Output MHD file [" << outputMhdFileName << "]" << std::endl;
 709                fp=fopen(outputMhdFileName, "w");
 710                if (!fp)
 711                {
 712                    std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 713                    throw ( BrukerHopelessException ("Hopeless! Cannot open  mhd file for writting"));
 714                    //exit(0);
 715                }
 716                else
 717                {
 718             /* ----------- Write MHD Image  ---------------*/
 719                 //if (verbose)
 720                 //   std::cout << "Open sucessfully[" << outputMhdFileName << "] for writting" << std::endl;
 721                    fprintf(fp, "ObjectType = Image\n");
 722                    fprintf(fp, "NDims = 3\n" );
 723                    fprintf(fp, "BinaryData = True \n" );
 724                    fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 725                    fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbInstants);
 726                    fprintf(fp, "HeaderSize = %d\n", 0);
 727                    fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, 1.0 ); // slice distance : no meaning for temporal serie
 728                    fprintf(fp, "Position = 0 0 %d\n", sliceNb );
 729                    fprintf(fp, "Offset = 0 0 0\n" );
 730                    fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 731                    fprintf(fp, "ElementNumberOfChannels = 1\n" );
 732                    fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
 733                    fprintf(fp, "ElementDataFile = ..%c2dseq_Slice_%d\n", GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb );
 734                    fclose(fp);
 735                } // end write MHD
 736
 737                sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d",
 738                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,sliceNb);
 739                fp=fopen(output2dseqSliceFileName, "wb");
 740                if (!fp)
 741                {
 742                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 743                    throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseqSliceFile file for writting"));
 744                    //exit (0);
 745                }
 746                int frameSize = NX*NY*pixelSize;
 747                for (instantNb=0; instantNb<nbInstants; instantNb++)
 748                {
 749 // std::cout << "------------SN " << sliceNb << " IN " << instantNb <<  " T " << nbSlices*instantNb + sliceNb << std::endl;
 750                     fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
 751                             frameSize,
 752                             1, fp);
 753                }
 754                fclose(fp);
 755 // std::cout << "end writting[" << output2dseqSliceFileName << "]" << std::endl;
 756             }  // end if mhd
 757
 758             if (dicom)
 759             {
 760                // desperate try !
 761              /*
 762                sprintf(output2dseqSliceFileName, "%sdummy_buffer",
 763                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 764                fp=fopen(output2dseqSliceFileName, "wb");
 765                if (!fp)
 766                {
 767                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 768                    exit (0);
 769                }
 770                int frameSize = NX*NY*pixelSize;
 771                for (instantNb=0; instantNb<nbInstants; instantNb++)
 772                {
 773 // std::cout << "------------SN " << sliceNb << " IN " << instantNb <<  " T " << nbSlices*instantNb + sliceNb << std::endl;
 774                     fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
 775                             frameSize,
 776                             1, fp);
 777                }
 778                fclose(fp);
 779
 780                fp=fopen(output2dseqSliceFileName, "rb");
 781                if (!fp)
 782                {
 783                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for reading" << std::endl;
 784                    exit (0);
 785                }
 786                fread( pixelsForCurrentSlice,
 787                             frameSize*nbInstants,
 788                             1, fp);
 789                fclose(fp);
 790               // end of desperate try !
 791               */
 792
 793                /* ----------- Write Dicom Image  ---------------*/
 794
 795                int frameSize = NX*NY*pixelSize;
 796                for (instantNb=0; instantNb<nbInstants; instantNb++)
 797                {
 798                   memcpy(pixelsForCurrentSlice + frameSize*instantNb, buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize, frameSize);
 799                }
 800
 801                int indOfFirsImageWithinImageSet =  nbSlices*instantNb;
 802                sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d.dcm",
 803                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb);
 804
 805                MakeDicomImage(
 806                   pixelsForCurrentSlice,
 807                   NX,
 808                   NY,
 809                   nbInstants,
 810                   pixelSize,
 811                   fovX/NY, fovY/NY, sliceDistance,
 812                   output2dseqSliceFileName,
 813                   strPatientName,
 814                   day,
 815                   strStudyUID,
 816                   strSerieUID,
 817                   strStudyDescr,
 818                   strSerieDescr,
 819                   strStudyTimeDate,
 820                   sliceNb*nbInstants,
 821                   GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
 822                );
 823                if (verbose)
 824                   std::cout << "--- Output DCM file [" << output2dseqSliceFileName << "]" << std::endl;
 825
 826            } // en if dicom
 827
 828         k++;
 829         }
 830         delete [] pixelsForCurrentSlice;
 831      }  // end nbInstants == 1
 832    delete [] buffer_2dseq;
 833 /**/
 834
 835
 836    // -----------------------------------------------------
 837    //  deal with MatLab-generated Carto file.
 838    // -----------------------------------------------------
 839
 840    dealWithCarto(fileNames,  NX,  NY,  nbSlices, fovX, fovY, sliceDistance,
 841                    copyFile, currentOutputDirName, outputMhdFileName, output2dseqCartoName);
 842 }
 843
 844
 845 // ===========================================================================================
 846
 847 void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX, int NY, int nbSlices,
 848                                  double fovX, double fovY, double sliceDistance,
 849                                  char *copyFile, std::string &currentOutputDirName,
 850                                  char *outputMhdFileName, char *output2dseqCartoName)
 851 {
 852    // -----------------------------------------------------
 853    //  deal with MatLab-generated Carto file.
 854    // -----------------------------------------------------
 855
 856    char *code[] ={ "ADC", "adc", "TTP", "ttp", "PEAK", "peak", "" };  // add more carto file name identifiers if necessary; end with ""
 857    int icode;
 858    GDCM_NAME_SPACE::DirListType::iterator it;
 859    char file_name_ident[500];
 860    FILE *fp;
 861
 862    // Iterate to ALL the objets(files/directories) found in the input directory
 863    for (it = fileNames.begin();
 864         it != fileNames.end();
 865       ++it)
 866    {
 867       if ( boost::filesystem::is_regular(*it) )
 868       //if ( ! boost::filesystem::is_directory(*it) )
 869       {
 870          if (verbose)
 871             std::cout << "--- [" << *it << "] is a file..." << std::endl;
 872
 873          icode = 0;
 874
 875          while (code[icode][0] != 0)
 876          {
 877             sprintf(file_name_ident, "2dseq.%s",code[icode]); // e.g  "2dseq_ADC"
 878             std::string::size_type loc = (*it).rfind(file_name_ident);
 879
 880             if ( loc != std::string::npos )
 881             {
 882
 883        ///\ TODO : find a safer way to be sure to read everything!
 884               unsigned char *buffer_carto = new unsigned char[NX*NY*sizeof(double)*nbSlices];
 885               fp = fopen ( (*it).c_str(), "rb");
 886               if (!fp){
 887                  std::cout << "Cannot open [" << *it << "] for reading" << std::endl;
 888                  throw ( BrukerHopelessException ("Level 1 Unable to open 'carto' file "));
 889                }
 890                fread(buffer_carto, NX*NY*sizeof(double), nbSlices, fp);
 891
 892                std::cout << "Deal with Carto file :[" <<*it << "], computed length : "
 893                          << NX*NY*sizeof(double)*nbSlices << std::endl;
 894                   std::string lastFileName = GDCM_NAME_SPACE::Util::GetName((*it).c_str());
 895                if (mhd)
 896                {
 897                   // Copy the data file in the new directory
 898                   sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() ,
 899                             currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str());
 900                   system(copyFile);
 901                   sprintf(outputMhdFileName, "%s%c%s%s",
 902                                        currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".mhd" );
 903                   if (verbose)
 904                     std::cout << "--- Output Carto MHD file [" << outputMhdFileName << "]" << std::endl;
 905
 906                   FILE *fp;
 907                   fp=fopen(outputMhdFileName, "w");
 908                   if (!fp)
 909                   {
 910                      std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 911                   }
 912                   else
 913                   {
 914                      fprintf(fp, "ObjectType = Image\n");
 915                      fprintf(fp, "NDims = 3\n" );
 916                      fprintf(fp, "BinaryData = True \n" );
 917                      fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 918                      fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices);
 919                      fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
 920                      fprintf(fp, "HeaderSize = %d\n", 0 );
 921                      fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
 922                      fprintf(fp, "Position = 0 0 0\n" );
 923                      fprintf(fp, "Offset = 0 0 0\n" );
 924                      fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 925                      fprintf(fp, "ElementNumberOfChannels = 1\n" );
 926                      fprintf(fp, "ElementType = %s\n", "MET_DOUBLE" );
 927                      fprintf(fp, "ElementDataFile = %s\n", lastFileName.c_str() );
 928
 929                      fclose(fp);
 930                   }
 931                   if (verbose)
 932                      std::cout << "--- end write Carto MHD file [" << outputMhdFileName << "]" << std::endl;
 933                }  // end if mhd
 934
 935             // ----------- Write Dicom Image  ---------------
 936
 937                if (dicom)
 938                {
 939                   sprintf(output2dseqCartoName, "%s%c%s%s",
 940                                        currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".dcm" );
 941                   if (verbose)
 942                      std::cout << "--- end create name output2dseqCartoName file [" << output2dseqCartoName << "]" << std::endl;
 943
 944                   strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID(); //New SerieUID for each carto.
 945                   std::string strNewSerieDescr(strSerieDescr+ "_" +GDCM_NAME_SPACE::Util::GetName((*it).c_str()));
 946                   MakeDicomImage(buffer_carto,
 947                      NX,
 948                      NY,
 949                      nbSlices,
 950                      8, // pixelSize
 951                      fovX/NY, fovY/NY, sliceDistance,
 952                      output2dseqCartoName,
 953                      strPatientName,
 954                      day,
 955                      strStudyUID,
 956                      strSerieUID,
 957                      strStudyDescr,
 958                      strNewSerieDescr,
 959                      strStudyTimeDate,
 960                      0,
 961                      GDCM_NAME_SPACE::CREATED_IMAGE
 962                   );
 963                }  // end if dicom
 964
 965                delete [] buffer_carto;
 966                if (verbose)
 967                   std::cout << "--- End writing Carto DICOM file [" << output2dseqCartoName << "]" << std::endl;
 968                break; // don't check for more ident on same file name!
 969
 970             }
 971             icode++;
 972          }
 973       }
 974    } // end iterate on files
 975 }
 976
 977
 978 // ==========================================================================================================
 979
 980 bool Bruker2Dicom::CreateDirectory(std::string OutputDirName)
 981 {
 982    std::string systemCommand;
 983
 984    if (verbose)
 985       std::cout << "Check for output directory :[" << OutputDirName << "]."
 986                 <<std::endl;
 987    if ( ! boost::filesystem::is_directory(OutputDirName) )    // dirout not found
 988    {
 989       std::string strDirNameout(OutputDirName);        // to please gcc 4
 990       systemCommand = "mkdir " + strDirNameout;        // create it!
 991       if (verbose)
 992          std::cout << systemCommand << std::endl;
 993       system (systemCommand.c_str());
 994       if ( ! boost::filesystem::is_directory(OutputDirName) ) // be sure it worked
 995       {
 996          if (verbose)
 997             std::cout << "KO : not a dir : [" << OutputDirName << "] (creation failure ?)" << std::endl;
 998          //return 0;
 999          throw ( BrukerHopelessException ("Level 1 output directory creation failure "));
1000       }
1001       else
1002       {
1003          if (verbose)
1004            std::cout << "Directory [" << OutputDirName << "] created." << std::endl;
1005       }
1006    }
1007    else
1008    {
1009        if (verbose)
1010           std::cout << "Output Directory [" << OutputDirName << "] already exists; Used as is." << std::endl;
1011    }
1012
1013    return 1;
1014
1015 }
1016
1017
1018 // ===========================================================================================
1019
1020 /// \TODO move cleanString to 'crea' ?
1021
1022 void Bruker2Dicom::cleanString(std::string &s)
1023 {
1024    int l = s.size();
1025    if (s[l-1] == 0x0A || s[l-1] == 0x0D ) // CR or NL
1026    {
1027       l--;
1028       s = s.substr(0, l);
1029    }
1030    if (s[l-1] == ' ' ) // blank space
1031    {
1032       l--;
1033       s = s.substr(0, l);
1034    }
1035
1036    if (s[0] == '<')
1037       s= s.substr(1,l-2);
1038    std::string repChar("_");
1039    GDCM_NAME_SPACE::Util::ReplaceSpecChar(s, repChar);
1040 }
1041
1042
1043
1044 // ===========================================================================================
1045
1046
1047 void Bruker2Dicom::getImhDataType(BrukerFieldData &bDPT, std::string &mhdDataPixelType, int &pixelSize)
1048 {
1049    if(bDPT.GetDataType() == "string")
1050    {
1051          std::string brukerDataPixelType = bDPT.GetStringValue()[0];
1052          if (verbose)
1053             std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
1054          //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
1055
1056          if (brukerDataPixelType ==  "ip_short") {
1057             mhdDataPixelType = "MET_USHORT";
1058             pixelSize = 2;
1059          }
1060          if (brukerDataPixelType ==  "ip_int") {
1061             mhdDataPixelType = "MET_UINT";
1062             pixelSize = 4;
1063          }
1064          if (brukerDataPixelType ==  "ip_char") {
1065              mhdDataPixelType = "MET_UCHAR";
1066              pixelSize = 1;
1067          }
1068                   /// \TODO : finish the list
1069     /*
1070     case 0 : fp << "ElementType = MET_CHAR" << std::endl;
1071       break;
1072     case 1 : fp << "ElementType = MET_UCHAR" << std::endl;
1073       break;
1074     case 2 : fp << "ElementType = MET_SHORT" << std::endl;
1075       break;
1076     case 3 : fp << "ElementType = MET_USHORT" << std::endl;
1077       break;
1078     case 4 : fp << "ElementType = MET_INT" << std::endl;
1079       break;
1080     case 5 : fp << "ElementType = MET_UINT" << std::endl;
1081       break;
1082     case 6 : fp << "ElementType = MET_FLOAT" << std::endl;
1083       break;
1084     case 7 : fp << "ElementType = MET_DOUBLE" << std::endl;
1085     */
1086     }
1087     else
1088     {
1089          int brukerDataPixelType = bDPT.GetIntValue()[0];
1090          if (verbose)
1091             std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
1092          //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
1093
1094 // Cross your fingers !!!
1095
1096 // pb : found values : 2, 3, 5
1097
1098          if (brukerDataPixelType ==  2) {
1099             mhdDataPixelType = "MET_USHORT";
1100             pixelSize = 2;
1101          }
1102          if (brukerDataPixelType ==  3) {
1103             mhdDataPixelType = "MET_USHORT";
1104             pixelSize = 2;
1105          }
1106          if (brukerDataPixelType ==  1) {
1107             mhdDataPixelType = "MET_UCHAR";
1108             pixelSize = 1;
1109          }
1110     }
1111 }
1112
1113 // ===========================================================================================
1114
1115 std::vector<BrukerImage> Bruker2Dicom::CreateImageSet ( )
1116 {
1117          std::vector<BrukerImage> imageSet;
1118          br_acqp.SetLoopStructure();
1119          std::vector<int> tempVect                      = br_acqp.GetLoopStructure() ;
1120          std::map<std::string, BrukerFieldData> map     = br_acqp.GetBrukerHeaderMap();
1121          bool result                                    = br_acqp.ObjectVaryingProperties.init(map,tempVect);
1122
1123          if (result == false)
1124          {
1125             throw ( BrukerInitException  ("Bruker2Dicom::CreateImageSet failure ") );
1126          }
1127
1128          br_acqp.SetImageLoopStructure();
1129          br_acqp.SetBrukerImageList();
1130          std::vector<std::vector<int> > brukerImageList = br_acqp.GetBrukerImageList();
1131
1132          BrukerImage image(br_acqp,br_reco);
1133          image.Init(br_acqp,br_reco,1);
1134
1135          for(int i=0;i<brukerImageList.size();i++)
1136          {
1137             image.Init(br_acqp,br_reco,i);
1138             imageSet.push_back(image);
1139          }
1140
1141  // Just for checking
1142  /*
1143
1144          std::vector<std::vector <double> > imageOrientation;
1145          std::vector <double> imagePosition;
1146          for(int i=0;i<brukerImageList.size();i++)
1147          {
1148            // fread(buffer_2dseq, NX*NY*pixelSize*nbSlices*nbInstants, 1, fp);
1149
1150            imagePosition = imageSet[i].getTranslationVectorRPS2XYZ();
1151            std::cout << "Position " << imagePosition[0] << " "
1152                      << imagePosition[1] << " "  << imagePosition[2] ;
1153            imageOrientation =  imageSet[i].getRotationMatrixRPS2XYZ();
1154            std::cout << "\t  Orientation " ;
1155            for(int i1=0; i1<3;i1++)for(int i2=0; i2<3;i2++)
1156               std::cout << imageOrientation[i1][i2] << " ";
1157
1158            //std::cout << "\t  Abs Time " << imageSet[i].getAbsoluteTimePosition();
1159            std::cout << "\t  Relat Time " << imageSet[i].getRelativeTimePosition();
1160
1161            std::cout << "\t [";
1162            for (int i3=0; i3<imageSet[i].getLoopStamp().size();i3++)
1163               std::cout << " " << imageSet[i].getLoopStamp()[i3];
1164            std::cout << "]" << std::endl;
1165          }
1166 */
1167    return imageSet;
1168 }
1169
1170 // ===========================================================================================
1171
1172 void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels,
1173               int X,
1174               int Y,
1175               int nbFrames,
1176               int pixelSize,
1177               double spacingX, double spacingY, double sliceDistance,
1178               std::string dcmImageName,
1179               const std::string &patientName,
1180               const char *day,
1181               std::string &studyUID,
1182               std::string &serieUID,
1183               std::string &studyDescr,
1184               std::string &serieDescr,
1185               std::string &strStudyTimeDate,
1186               int imgNum,
1187               GDCM_NAME_SPACE::ImageContentType contentType
1188       )
1189 {
1190    std::ostringstream str;
1191
1192    GDCM_NAME_SPACE::File *file;
1193    file = GDCM_NAME_SPACE::File::New();
1194
1195   // Set the image size
1196    str.str("");
1197    str << X;
1198    file->InsertEntryString(str.str(),0x0028,0x0011,"US"); // Columns
1199    str.str("");
1200    str << Y;
1201    file->InsertEntryString(str.str(),0x0028,0x0010,"US"); // Rows
1202
1203    if (nbFrames != 1)
1204    {
1205       str.str("");
1206       str << nbFrames;
1207       file->InsertEntryString(str.str(),0x0028,0x0008,"IS"); // Number of Frames
1208    }
1209
1210   // Set the pixel type
1211   //      //8, 16, 32, 64 (for double ?)
1212    str.str("");
1213    str << pixelSize*8;
1214    file->InsertEntryString(str.str(),0x0028,0x0100,"US"); // Bits Allocated
1215
1216    file->InsertEntryString(str.str(),0x0028,0x0101,"US"); // Bits Stored
1217
1218    str.str("");
1219    str << pixelSize*8-1;
1220    file->InsertEntryString(str.str(),0x0028,0x0102,"US"); // High Bit
1221
1222   // Set the pixel representation // 0/1 , 0=unsigned
1223    file->InsertEntryString("1",0x0028,0x0103, "US"); // Pixel Representation
1224
1225   // Set the samples per pixel // 1:Grey level, 3:RGB
1226    file->InsertEntryString("1",0x0028,0x0002, "US"); // Samples per Pixel
1227
1228 //  0028 0030 DS 2 Pixel Spacing
1229    str.str("");
1230    str << spacingX << "\\" << spacingY;
1231    file->InsertEntryString(str.str(),0x0028,0x0030, "DS"); // Pixel Spacing
1232
1233  //   0018 0050 DS 1 Slice Thickness
1234    str.str("");
1235    str << sliceDistance;
1236    file->InsertEntryString(str.str(),0x0018,0x0050, "DS");
1237
1238 //    0020 0011 IS 1 Series Number
1239    str.str("");
1240    str << serieNumber;
1241    file->InsertEntryString(str.str(),0x0020,0x0011, "IS");
1242
1243 //    0020|0013 [IS]  [Instance Number]
1244    instanceNumber++;
1245    str.str("");
1246    str << instanceNumber;
1247    file->InsertEntryString(str.str(),0x0020,0x0013, "IS");
1248
1249
1250   // 1.2.840.10008.5.1.4.1.1.4.1 : Enhanced MR Image Storage
1251  //  file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0002, 0x0002, "UI");  // [Media Storage SOP Class UID]
1252   // file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0008, 0x0016, "UI");  // [SOP Class UID]
1253
1254
1255 // OK : MR is NOT multiframe, but I want just a quick an dirty solution
1256
1257 // 1.2.840.10008.5.1.4.1.1.4         MR Image Storage
1258    file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0002, 0x0002, "UI");  // [Media Storage SOP Class UID]
1259    file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0008, 0x0016, "UI");  // [SOP Class UID]
1260
1261   // if (strlen(patientName) != 0)
1262    file->InsertEntryString(patientName.c_str(),0x0010,0x0010, "PN"); // Patient's Name
1263
1264    file->InsertEntryString(studyUID, 0x0020, 0x000d, "UI");
1265    file->InsertEntryString(serieUID, 0x0020, 0x000e, "UI");
1266
1267 //  0008 0020 DA 1 Study Date
1268 //  0008 0030 TM 1 Study Time
1269
1270 /// \TODO split into 2 strings!
1271    file->InsertEntryString(strStudyTimeDate.substr(10,11).c_str(),0x0008,0x0020, "DA");
1272    file->InsertEntryString(strStudyTimeDate.substr(1,8).c_str(),  0x0008,0x0030, "TM");
1273
1274    file->InsertEntryString(studyDescr, 0x0008,0x1030, "LO");  // Study Description
1275    file->InsertEntryString(serieDescr, 0x0008,0x103e, "LO");  // Series Description
1276
1277 //0008|0060 [CS] [Modality]
1278    file->InsertEntryString("MR",0x0008,0x0060, "CS");
1279
1280 // 0020 0037 DS 6 Image Orientation (Patient)
1281    char charImageOrientation[256];
1282
1283 /*
1284 std::cout << "charImageOrientation  " <<
1285                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0] << " " <<
1286                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1] << " " <<
1287                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2] << " " <<
1288                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0] << " " <<
1289                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1] << " " <<
1290                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] << std::endl ;
1291 */
1292    sprintf(charImageOrientation,"%f\\%f\\%f \\ %f\\%f\\%f",
1293                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0],
1294                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1],
1295                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2],
1296                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0],
1297                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1],
1298                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] ) ;
1299
1300    file->InsertEntryString(charImageOrientation,0x0020,0x0037, "DS");
1301
1302
1303 // 0020 0032 DS 3 Image Position (Patient)
1304
1305    char charImagePosition[256];
1306    sprintf(charImagePosition,"%f\\%f\\%f",
1307                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[0],
1308                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[1],
1309                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[2]);
1310
1311    file->InsertEntryString(charImagePosition,0x0020,0x0032, "DS");  //0020 0032 DS 3 Image Position (Patient)
1312
1313
1314
1315 // 0020 0x1041 DS 1 Slice Location
1316 //        sprintf(charImagePosition,"%f",float(imgNum));
1317 //        file->InsertEntryString(charImagePosition,0x0020,0x1041, "DS");
1318 /*
1319   // Set Rescale Intercept
1320         str.str("");
1321         str << div;
1322         file->InsertEntryString(str.str(),0x0028,0x1052,"DS");
1323
1324   // Set Rescale Slope
1325         str.str("");
1326         str << mini;
1327         file->InsertEntryString(str.str(),0x0028,0x1053,"DS");
1328 */
1329
1330    GDCM_NAME_SPACE::FileHelper *fileH;
1331    fileH = GDCM_NAME_SPACE::FileHelper::New(file);
1332    fileH->SetContentType(contentType);
1333
1334    // cast is just to avoid warnings (*no* conversion is performed)
1335    //fileH->SetImageData((uint8_t *)img,int(maxX*maxY)*sizeof(uint16_t)); // troubles when maxX, mayY are *actually* float!
1336
1337 //std::cout << "--------------------------------  X*Y*nbFrames*pixelSize " << X << " " << Y << " " << nbFrames << " " << pixelSize << std::endl;
1338
1339    fileH->SetImageData((uint8_t *)tabPixels, X*Y*nbFrames*pixelSize);
1340    fileH->SetWriteModeToRaw();
1341    fileH->SetWriteTypeToDcmExplVR();
1342    if( !fileH->Write(dcmImageName)) {
1343       std::cout << "Failed for [" << dcmImageName << "]\n"
1344                 << "           File is unwrittable" << std::endl;
1345       file->Delete();
1346       fileH->Delete();
1347       throw ( BrukerHopelessException ("Level 1 Unable to write Dicom file "));
1348    }
1349    if (verbose)
1350       file->Print();
1351
1352    file->Delete();
1353    fileH->Delete();
1354 }
1355
1356