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           catch (BrukerInitException &e)
 408           {
 409              std::cout << "And Init Exception was thrown in DealWithNiveau3 (" << e.what() << "); "
 410                        << " We skip [" << level2Directory << "]" << std::endl;
 411              continue;
 412           }
 413       }
 414    }
 415 }
 416
 417
 418 //
 419 // =====================================================================
 420 //
 421
 422 void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string currentOutputDirName){
 423
 424 //
 425 // e.g. at level 3, in
 426
 427    // just to be able to go on checking // JP
 428    if ( GDCM_NAME_SPACE::Util::GetName(level3Directory) != "1")
 429       return;
 430
 431    bool res = CreateDirectory(currentOutputDirName);
 432
 433    if (!res)
 434    {
 435       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 436       throw ( BrukerHopelessException ("Hopeless! Level3 output directory creation failure"));
 437       //exit (0);
 438    }
 439
 440    GDCM_NAME_SPACE::DirList dirList(level3Directory, false, true); // DON'T get recursively the list of files
 441    GDCM_NAME_SPACE::DirListType::iterator it;
 442    GDCM_NAME_SPACE::DirListType fileNames;
 443    fileNames = dirList.GetFilenames();
 444
 445    char original2dseqName       [(unsigned int) PATH_MAX+2];
 446    char currentOutputMhdDirName [(unsigned int) PATH_MAX+2];
 447
 448    char outputMhdFileName       [(unsigned int) PATH_MAX+2];
 449    char output2dseqSliceFileName[(unsigned int) PATH_MAX+6]; // think about extra '.dcm'
 450    char output2dseqName         [(unsigned int) PATH_MAX+6];
 451    char output2dseqCartoName    [(unsigned int) PATH_MAX+6];
 452
 453    char copyFile[PATH_MAX + PATH_MAX + 5]; // Should be enough!
 454    bool canOpen;
 455
 456    //-------------- try d3proc;
 457    char char_d3proc[(unsigned int) PATH_MAX+2];
 458
 459    sprintf(char_d3proc,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"d3proc" );
 460
 461    if (verbose)
 462       std::cout << "d3proc: --- => [" << char_d3proc << "]" << std::endl;
 463    std::string str_d3proc(char_d3proc);
 464    canOpen = br_d3proc.LoadFile(str_d3proc);
 465
 466    if (!canOpen)
 467    {
 468       std::cout << "Hopeless! no 'd3proc' found" << std::endl;
 469       throw ( BrukerHopelessException ("Hopeless! no 'd3proc' found"));
 470       //exit(0);  /// \TODO throw an exception !
 471    }
 472
 473    canOpen = br_d3proc.FillMap();
 474    if (!canOpen)
 475    {
 476       std::cout << "Hopeless! FillMap failed on 'd3proc'" << std::endl;
 477       throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'd3proc'"));
 478       //exit(0);  /// \TODO throw an exception !
 479    }
 480
 481    //-------------- end try d3proc;
 482
 483
 484  // -------------------try reco
 485
 486    char char_reco[(unsigned int) PATH_MAX+2];
 487
 488    sprintf(char_reco,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
 489     //str_d3proc = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
 490     //             GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 491     //             "d3proc";
 492    if (verbose)
 493       std::cout << "reco --- => [" << char_reco << "]" << std::endl;
 494    std::string str_reco(char_reco);
 495    canOpen = br_reco.LoadFile(str_reco);
 496
 497    if (!canOpen) // we try in directory ../1
 498    {
 499       if (verbose)
 500          std::cout << "[" << str_reco << "] not found " << std::endl;
 501       std::string lastDirName = GDCM_NAME_SPACE::Util::GetPath(level3Directory);
 502       //lastDirName = GDCM_NAME_SPACE::Util::GetPath(lastDirName);
 503       sprintf(char_reco,"%s%c1%c%s", lastDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
 504       str_reco=char_reco;
 505       canOpen = br_reco.LoadFile(str_reco);
 506       if (!canOpen)
 507       {
 508          std::cout << "Hopeless! cannot find 'reco' in [" << str_reco << "]"  << std::endl;
 509          throw ( BrukerHopelessException ("Hopeless! cannot find 'reco'"));
 510          //exit(0);  /// \TODO throw an exception !
 511       }
 512    }
 513
 514    canOpen = br_reco.FillMap();
 515    if (!canOpen)
 516    {
 517       std::cout << "Hopeless! FillMap failed on [" << str_reco << "]" << std::endl;
 518       throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'reco'"));
 519       //exit(0);  /// \TODO throw an exception !
 520    }
 521    //std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
 522    // br_reco.PrintSelf();
 523    // std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
 524
 525    // -------------------end try reco
 526
 527
 528    BrukerFieldData bX = br_d3proc.GetFieldData("IM_SIX");
 529    int NX = bX.GetIntValue()[0];
 530
 531    if (verbose)
 532       std::cout << "IM_SIX " << NX << std::endl;
 533    BrukerFieldData bY=br_d3proc.GetFieldData("IM_SIY");
 534    int NY = bY.GetIntValue()[0];
 535
 536    if (verbose)
 537          std::cout << "IM_SIY " << NY << std::endl;
 538    /// \todo : check if there are actually 3 dimensions or only 2
 539
 540    BrukerFieldData bZ= br_d3proc.GetFieldData("IM_SIZ");
 541    int nbFrames = bZ.GetIntValue()[0];
 542    if (verbose)
 543          std::cout << "IM_SIZ " << nbFrames << std::endl;
 544
 545         // WARNING DATTYPE is, either in {ip_short, ip_int, ip_char, ...}, or in {1, 2, 3, ...}
 546
 547    BrukerFieldData bDPT = br_d3proc.GetFieldData("DATTYPE");
 548
 549    std::string mhdDataPixelType;
 550    int pixelSize;
 551    getImhDataType(bDPT, mhdDataPixelType, pixelSize);
 552
 553    BrukerFieldData fov = br_method.GetFieldData("PVM_Fov");
 554    double fovX = fov.GetDoubleValue()[0];
 555    double fovY = fov.GetDoubleValue()[1];
 556    if (verbose)
 557       std::cout << "FOV (ds method) " << fovX << " " << fovY << std::endl;
 558
 559    /// \TODO probabely a more sophisticated accessor will be necessary :
 560    ///  (cf : non contiguous slices, overlapping, slice thickness, space between slices, etc)
 561    BrukerFieldData bsliceDistance = br_method.GetFieldData("PVM_SPackArrSliceDistance");
 562    double sliceDistance = bsliceDistance.GetDoubleValue()[0];
 563
 564    if (mhd)
 565    {
 566       sprintf(currentOutputMhdDirName, "%s%c%s", currentOutputDirName.c_str(),
 567                                GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "MhdFiles");
 568       res = CreateDirectory( currentOutputMhdDirName );
 569       if (!res) {
 570          std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 571          throw ( BrukerHopelessException ("Hopeless!FillMap failed on 'reco'"));
 572          //exit (0);
 573       }
 574
 575       if (verbose)
 576          std::cout << "Directory creation [" <<  currentOutputDirName << "]" << std::endl;
 577    }  // end if mhd
 578
 579    if (verbose)
 580          std::cout << "nbFrames " << nbFrames << std::endl;
 581    if (verbose)
 582          std::cout << "nbSlices " << nbSlices << std::endl;
 583    int k;
 584    int nbInstants = nbFrames/nbSlices;
 585    if (verbose)
 586          std::cout << "nbInstants (deduced )" << nbInstants << std::endl;
 587    int instantNb;
 588    int sliceNb;
 589    FILE *fp;  // for MHD files
 590
 591    sprintf( original2dseqName, "%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "2dseq");
 592
 593 /**/
 594   // \TODO : tenir compte du bazar precedent
 595
 596     // load 2dseq in memory
 597
 598    fp = fopen(original2dseqName, "rb");
 599    if (!fp)
 600    {
 601       std::cout << "Cannot open [" << original2dseqName << "] for reading" << std::endl;
 602       throw ( BrukerHopelessException ("Hopeless! Cannot open '2dseq'"));
 603       //exit (0);
 604    }
 605
 606    unsigned char *buffer_2dseq = new unsigned char[NX*NY*pixelSize*nbSlices*nbInstants];
 607    ///\ TODO : find a safer way to be sure to read everything!
 608    size_t lgr = fread(buffer_2dseq, 1, NX*NY*pixelSize*nbSlices*nbInstants, fp);
 609
 610    // This one will be important!
 611    // ---------------------------
 612    try {
 613       imageSet = CreateImageSet ( );
 614    }
 615    catch (BrukerInitException& e)
 616    {
 617       if (verbose)
 618          std::cout <<  "an Init Exception was thrown in CreateImageSet ( ); " << e.what()
 619                    <<  "catched in DealWithNiveau3" << std::endl;
 620       //return;
 621       throw (e);
 622    }
 623
 624    serieNumber++;
 625    strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 626    if (nbInstants==1) // creer un seul fichier .mhd  pour toutes les Slices! (images natives)
 627    {
 628        if (verbose)
 629           std::cout << "Single instant : do not split" << std::endl;
 630        if (mhd)
 631        {
 632              sprintf(outputMhdFileName, "%s%cMhdData_All_the_Slices.mhd", currentOutputMhdDirName,
 633                                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 634              fp=fopen(outputMhdFileName, "w");
 635              if (!fp)
 636              {
 637                 std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 638                 throw ( BrukerHopelessException ("Hopeless! Cannot open  mhd file for writting"));
 639                 //exit(0);
 640              }
 641              else
 642              {
 643                fprintf(fp, "ObjectType = Image\n");
 644                fprintf(fp, "NDims = 3\n" );
 645                fprintf(fp, "BinaryData = True \n" );
 646                fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 647                fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices );
 648                fprintf(fp, "HeaderSize = %d\n", 0);
 649                fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
 650                fprintf(fp, "Position = 0 0 %d\n", 0 );
 651                fprintf(fp, "Offset = 0 0 0\n" );
 652                fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 653                fprintf(fp, "ElementNumberOfChannels = 1\n" );
 654                fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
 655                fprintf(fp, "ElementDataFile = %s\n", "../2dseq_All_the_Slices" );
 656                fclose(fp);
 657              }
 658              sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices",
 659                                        currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 660              fp=fopen(output2dseqSliceFileName, "wb");
 661              if (!fp)
 662              {
 663                 std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 664                 throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseq file for writting"));
 665              }
 666              else
 667              {
 668                 fwrite( buffer_2dseq, NX*NY*pixelSize, nbSlices, fp);
 669              }
 670              fclose(fp);
 671              serieNumber ++;
 672              strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 673        }  // end if mhd
 674        if (dicom)
 675        {
 676              sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices.dcm",
 677                                        currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 678
 679             /* ----------- Write Dicom Image  ---------------*/
 680              MakeDicomImage(buffer_2dseq,
 681                NX,
 682                NY,
 683                nbFrames,
 684                pixelSize,
 685                fovX/NY, fovY/NY, sliceDistance,
 686                output2dseqSliceFileName,
 687                strPatientName,
 688                day,
 689                strStudyUID,
 690                strSerieUID,
 691                strStudyDescr,
 692                strSerieDescr,
 693                strStudyTimeDate,
 694                0,// index frame number
 695                GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
 696              );
 697        }  // end if dicom
 698    }  // end if nbInstants = 1
 699
 700    else  // more than ONE instant
 701    {
 702           // Interleaved !
 703           // it's (slice1,slide2, ...)t1 ; (slice1,slide2, ...)t2 ; ...
 704
 705          unsigned char *pixelsForCurrentSlice = new unsigned char[NX*NY*pixelSize*nbInstants];
 706
 707          k = 0;
 708          for (sliceNb=0; sliceNb<nbSlices; sliceNb++)
 709          {
 710             if (mhd)
 711             {
 712                sprintf(outputMhdFileName, "%s%cMhdData_%03d.mhd", currentOutputMhdDirName,
 713                                         GDCM_NAME_SPACE::GDCM_FILESEPARATOR, k  );
 714                if (verbose)
 715                   std::cout << "--- Output MHD file [" << outputMhdFileName << "]" << std::endl;
 716                fp=fopen(outputMhdFileName, "w");
 717                if (!fp)
 718                {
 719                    std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 720                    throw ( BrukerHopelessException ("Hopeless! Cannot open  mhd file for writting"));
 721                    //exit(0);
 722                }
 723                else
 724                {
 725             /* ----------- Write MHD Image  ---------------*/
 726                 //if (verbose)
 727                 //   std::cout << "Open sucessfully[" << outputMhdFileName << "] for writting" << std::endl;
 728                    fprintf(fp, "ObjectType = Image\n");
 729                    fprintf(fp, "NDims = 3\n" );
 730                    fprintf(fp, "BinaryData = True \n" );
 731                    fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 732                    fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbInstants);
 733                    fprintf(fp, "HeaderSize = %d\n", 0);
 734                    fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, 1.0 ); // slice distance : no meaning for temporal serie
 735                    fprintf(fp, "Position = 0 0 %d\n", sliceNb );
 736                    fprintf(fp, "Offset = 0 0 0\n" );
 737                    fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 738                    fprintf(fp, "ElementNumberOfChannels = 1\n" );
 739                    fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
 740                    fprintf(fp, "ElementDataFile = ..%c2dseq_Slice_%d\n", GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb );
 741                    fclose(fp);
 742                } // end write MHD
 743
 744                sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d",
 745                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,sliceNb);
 746                fp=fopen(output2dseqSliceFileName, "wb");
 747                if (!fp)
 748                {
 749                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 750                    throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseqSliceFile file for writting"));
 751                    //exit (0);
 752                }
 753                int frameSize = NX*NY*pixelSize;
 754                for (instantNb=0; instantNb<nbInstants; instantNb++)
 755                {
 756 // std::cout << "------------SN " << sliceNb << " IN " << instantNb <<  " T " << nbSlices*instantNb + sliceNb << std::endl;
 757                     fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
 758                             frameSize,
 759                             1, fp);
 760                }
 761                fclose(fp);
 762 // std::cout << "end writting[" << output2dseqSliceFileName << "]" << std::endl;
 763             }  // end if mhd
 764
 765             if (dicom)
 766             {
 767                // desperate try !
 768              /*
 769                sprintf(output2dseqSliceFileName, "%sdummy_buffer",
 770                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 771                fp=fopen(output2dseqSliceFileName, "wb");
 772                if (!fp)
 773                {
 774                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 775                    exit (0);
 776                }
 777                int frameSize = NX*NY*pixelSize;
 778                for (instantNb=0; instantNb<nbInstants; instantNb++)
 779                {
 780 // std::cout << "------------SN " << sliceNb << " IN " << instantNb <<  " T " << nbSlices*instantNb + sliceNb << std::endl;
 781                     fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
 782                             frameSize,
 783                             1, fp);
 784                }
 785                fclose(fp);
 786
 787                fp=fopen(output2dseqSliceFileName, "rb");
 788                if (!fp)
 789                {
 790                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for reading" << std::endl;
 791                    exit (0);
 792                }
 793                fread( pixelsForCurrentSlice,
 794                             frameSize*nbInstants,
 795                             1, fp);
 796                fclose(fp);
 797               // end of desperate try !
 798               */
 799
 800                /* ----------- Write Dicom Image  ---------------*/
 801
 802                int frameSize = NX*NY*pixelSize;
 803                for (instantNb=0; instantNb<nbInstants; instantNb++)
 804                {
 805                   memcpy(pixelsForCurrentSlice + frameSize*instantNb, buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize, frameSize);
 806                }
 807
 808                int indOfFirsImageWithinImageSet =  nbSlices*instantNb;
 809                sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d.dcm",
 810                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb);
 811
 812                MakeDicomImage(
 813                   pixelsForCurrentSlice,
 814                   NX,
 815                   NY,
 816                   nbInstants,
 817                   pixelSize,
 818                   fovX/NY, fovY/NY, sliceDistance,
 819                   output2dseqSliceFileName,
 820                   strPatientName,
 821                   day,
 822                   strStudyUID,
 823                   strSerieUID,
 824                   strStudyDescr,
 825                   strSerieDescr,
 826                   strStudyTimeDate,
 827                   sliceNb*nbInstants,
 828                   GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
 829                );
 830                if (verbose)
 831                   std::cout << "--- Output DCM file [" << output2dseqSliceFileName << "]" << std::endl;
 832
 833            } // en if dicom
 834
 835         k++;
 836         }
 837         delete [] pixelsForCurrentSlice;
 838      }  // end nbInstants == 1
 839    delete [] buffer_2dseq;
 840 /**/
 841
 842
 843    // -----------------------------------------------------
 844    //  deal with MatLab-generated Carto file.
 845    // -----------------------------------------------------
 846
 847    dealWithCarto(fileNames,  NX,  NY,  nbSlices, fovX, fovY, sliceDistance,
 848                    copyFile, currentOutputDirName, outputMhdFileName, output2dseqCartoName);
 849 }
 850
 851
 852 // ===========================================================================================
 853
 854 void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX, int NY, int nbSlices,
 855                                  double fovX, double fovY, double sliceDistance,
 856                                  char *copyFile, std::string &currentOutputDirName,
 857                                  char *outputMhdFileName, char *output2dseqCartoName)
 858 {
 859    // -----------------------------------------------------
 860    //  deal with MatLab-generated Carto file.
 861    // -----------------------------------------------------
 862
 863    char *code[] ={ "ADC", "adc", "TTP", "ttp", "PEAK", "peak", "" };  // add more carto file name identifiers if necessary; end with ""
 864    int icode;
 865    GDCM_NAME_SPACE::DirListType::iterator it;
 866    char file_name_ident[500];
 867    FILE *fp;
 868
 869    // Iterate to ALL the objets(files/directories) found in the input directory
 870    for (it = fileNames.begin();
 871         it != fileNames.end();
 872       ++it)
 873    {
 874       if ( boost::filesystem::is_regular(*it) )
 875       //if ( ! boost::filesystem::is_directory(*it) )
 876       {
 877          if (verbose)
 878             std::cout << "--- [" << *it << "] is a file..." << std::endl;
 879
 880          icode = 0;
 881
 882          while (code[icode][0] != 0)
 883          {
 884             sprintf(file_name_ident, "2dseq.%s",code[icode]); // e.g  "2dseq_ADC"
 885             std::string::size_type loc = (*it).rfind(file_name_ident);
 886
 887             if ( loc != std::string::npos )
 888             {
 889
 890        ///\ TODO : find a safer way to be sure to read everything!
 891               unsigned char *buffer_carto = new unsigned char[NX*NY*sizeof(double)*nbSlices];
 892               fp = fopen ( (*it).c_str(), "rb");
 893               if (!fp){
 894                  std::cout << "Cannot open [" << *it << "] for reading" << std::endl;
 895                  throw ( BrukerHopelessException ("Level 1 Unable to open 'carto' file "));
 896                }
 897                fread(buffer_carto, NX*NY*sizeof(double), nbSlices, fp);
 898
 899                std::cout << "Deal with Carto file :[" <<*it << "], computed length : "
 900                          << NX*NY*sizeof(double)*nbSlices << std::endl;
 901                   std::string lastFileName = GDCM_NAME_SPACE::Util::GetName((*it).c_str());
 902                if (mhd)
 903                {
 904                   // Copy the data file in the new directory
 905                   sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() ,
 906                             currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str());
 907                   system(copyFile);
 908                   sprintf(outputMhdFileName, "%s%c%s%s",
 909                                        currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".mhd" );
 910                   if (verbose)
 911                     std::cout << "--- Output Carto MHD file [" << outputMhdFileName << "]" << std::endl;
 912
 913                   FILE *fp;
 914                   fp=fopen(outputMhdFileName, "w");
 915                   if (!fp)
 916                   {
 917                      std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 918                   }
 919                   else
 920                   {
 921                      fprintf(fp, "ObjectType = Image\n");
 922                      fprintf(fp, "NDims = 3\n" );
 923                      fprintf(fp, "BinaryData = True \n" );
 924                      fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 925                      fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices);
 926                      fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
 927                      fprintf(fp, "HeaderSize = %d\n", 0 );
 928                      fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
 929                      fprintf(fp, "Position = 0 0 0\n" );
 930                      fprintf(fp, "Offset = 0 0 0\n" );
 931                      fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 932                      fprintf(fp, "ElementNumberOfChannels = 1\n" );
 933                      fprintf(fp, "ElementType = %s\n", "MET_DOUBLE" );
 934                      fprintf(fp, "ElementDataFile = %s\n", lastFileName.c_str() );
 935
 936                      fclose(fp);
 937                   }
 938                   if (verbose)
 939                      std::cout << "--- end write Carto MHD file [" << outputMhdFileName << "]" << std::endl;
 940                }  // end if mhd
 941
 942             // ----------- Write Dicom Image  ---------------
 943
 944                if (dicom)
 945                {
 946                   sprintf(output2dseqCartoName, "%s%c%s%s",
 947                                        currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".dcm" );
 948                   if (verbose)
 949                      std::cout << "--- end create name output2dseqCartoName file [" << output2dseqCartoName << "]" << std::endl;
 950
 951                   strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID(); //New SerieUID for each carto.
 952                   std::string strNewSerieDescr(strSerieDescr+ "_" +GDCM_NAME_SPACE::Util::GetName((*it).c_str()));
 953                   MakeDicomImage(buffer_carto,
 954                      NX,
 955                      NY,
 956                      nbSlices,
 957                      8, // pixelSize
 958                      fovX/NY, fovY/NY, sliceDistance,
 959                      output2dseqCartoName,
 960                      strPatientName,
 961                      day,
 962                      strStudyUID,
 963                      strSerieUID,
 964                      strStudyDescr,
 965                      strNewSerieDescr,
 966                      strStudyTimeDate,
 967                      0,
 968                      GDCM_NAME_SPACE::CREATED_IMAGE
 969                   );
 970                }  // end if dicom
 971
 972                delete [] buffer_carto;
 973                if (verbose)
 974                   std::cout << "--- End writing Carto DICOM file [" << output2dseqCartoName << "]" << std::endl;
 975                break; // don't check for more ident on same file name!
 976
 977             }
 978             icode++;
 979          }
 980       }
 981    } // end iterate on files
 982 }
 983
 984
 985 // ==========================================================================================================
 986
 987 bool Bruker2Dicom::CreateDirectory(std::string OutputDirName)
 988 {
 989    std::string systemCommand;
 990
 991    if (verbose)
 992       std::cout << "Check for output directory :[" << OutputDirName << "]."
 993                 <<std::endl;
 994    if ( ! boost::filesystem::is_directory(OutputDirName) )    // dirout not found
 995    {
 996       std::string strDirNameout(OutputDirName);        // to please gcc 4
 997       systemCommand = "mkdir " + strDirNameout;        // create it!
 998       if (verbose)
 999          std::cout << systemCommand << std::endl;
1000       system (systemCommand.c_str());
1001       if ( ! boost::filesystem::is_directory(OutputDirName) ) // be sure it worked
1002       {
1003          if (verbose)
1004             std::cout << "KO : not a dir : [" << OutputDirName << "] (creation failure ?)" << std::endl;
1005          //return 0;
1006          throw ( BrukerHopelessException ("Level 1 output directory creation failure "));
1007       }
1008       else
1009       {
1010          if (verbose)
1011            std::cout << "Directory [" << OutputDirName << "] created." << std::endl;
1012       }
1013    }
1014    else
1015    {
1016        if (verbose)
1017           std::cout << "Output Directory [" << OutputDirName << "] already exists; Used as is." << std::endl;
1018    }
1019
1020    return 1;
1021
1022 }
1023
1024
1025 // ===========================================================================================
1026
1027 /// \TODO move cleanString to 'crea' ?
1028
1029 void Bruker2Dicom::cleanString(std::string &s)
1030 {
1031    int l = s.size();
1032    if (s[l-1] == 0x0A || s[l-1] == 0x0D ) // CR or NL
1033    {
1034       l--;
1035       s = s.substr(0, l);
1036    }
1037    if (s[l-1] == ' ' ) // blank space
1038    {
1039       l--;
1040       s = s.substr(0, l);
1041    }
1042
1043    if (s[0] == '<')
1044       s= s.substr(1,l-2);
1045    std::string repChar("_");
1046    GDCM_NAME_SPACE::Util::ReplaceSpecChar(s, repChar);
1047 }
1048
1049
1050
1051 // ===========================================================================================
1052
1053
1054 void Bruker2Dicom::getImhDataType(BrukerFieldData &bDPT, std::string &mhdDataPixelType, int &pixelSize)
1055 {
1056    if(bDPT.GetDataType() == "string")
1057    {
1058          std::string brukerDataPixelType = bDPT.GetStringValue()[0];
1059          if (verbose)
1060             std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
1061          //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
1062
1063          if (brukerDataPixelType ==  "ip_short") {
1064             mhdDataPixelType = "MET_USHORT";
1065             pixelSize = 2;
1066          }
1067          if (brukerDataPixelType ==  "ip_int") {
1068             mhdDataPixelType = "MET_UINT";
1069             pixelSize = 4;
1070          }
1071          if (brukerDataPixelType ==  "ip_char") {
1072              mhdDataPixelType = "MET_UCHAR";
1073              pixelSize = 1;
1074          }
1075                   /// \TODO : finish the list
1076     /*
1077     case 0 : fp << "ElementType = MET_CHAR" << std::endl;
1078       break;
1079     case 1 : fp << "ElementType = MET_UCHAR" << std::endl;
1080       break;
1081     case 2 : fp << "ElementType = MET_SHORT" << std::endl;
1082       break;
1083     case 3 : fp << "ElementType = MET_USHORT" << std::endl;
1084       break;
1085     case 4 : fp << "ElementType = MET_INT" << std::endl;
1086       break;
1087     case 5 : fp << "ElementType = MET_UINT" << std::endl;
1088       break;
1089     case 6 : fp << "ElementType = MET_FLOAT" << std::endl;
1090       break;
1091     case 7 : fp << "ElementType = MET_DOUBLE" << std::endl;
1092     */
1093     }
1094     else
1095     {
1096          int brukerDataPixelType = bDPT.GetIntValue()[0];
1097          if (verbose)
1098             std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
1099          //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
1100
1101 // Cross your fingers !!!
1102
1103 // pb : found values : 2, 3, 5
1104
1105          if (brukerDataPixelType ==  2) {
1106             mhdDataPixelType = "MET_USHORT";
1107             pixelSize = 2;
1108          }
1109          if (brukerDataPixelType ==  3) {
1110             mhdDataPixelType = "MET_USHORT";
1111             pixelSize = 2;
1112          }
1113          if (brukerDataPixelType ==  1) {
1114             mhdDataPixelType = "MET_UCHAR";
1115             pixelSize = 1;
1116          }
1117     }
1118 }
1119
1120 // ===========================================================================================
1121
1122 std::vector<BrukerImage> Bruker2Dicom::CreateImageSet ( )
1123 {
1124          std::vector<BrukerImage> imageSet;
1125          br_acqp.SetLoopStructure();
1126          std::vector<int> tempVect                      = br_acqp.GetLoopStructure() ;
1127          std::map<std::string, BrukerFieldData> map     = br_acqp.GetBrukerHeaderMap();
1128
1129          bool result                                    = br_acqp.ObjectVaryingProperties.init(map,tempVect);
1130
1131          if (result == false)
1132          {
1133             throw ( BrukerInitException  ("ObjectVaryingProperties.init() failure in Bruker2Dicom::CreateImageSet()") );
1134          }
1135
1136          br_acqp.SetImageLoopStructure();
1137          br_acqp.SetBrukerImageList();
1138          std::vector<std::vector<int> > brukerImageList = br_acqp.GetBrukerImageList();
1139
1140          BrukerImage image(br_acqp,br_reco);
1141          image.Init(br_acqp,br_reco,1);
1142
1143          for(int i=0;i<brukerImageList.size();i++)
1144          {
1145             image.Init(br_acqp,br_reco,i);
1146             imageSet.push_back(image);
1147          }
1148
1149  // Just for checking
1150  /*
1151
1152          std::vector<std::vector <double> > imageOrientation;
1153          std::vector <double> imagePosition;
1154          for(int i=0;i<brukerImageList.size();i++)
1155          {
1156            // fread(buffer_2dseq, NX*NY*pixelSize*nbSlices*nbInstants, 1, fp);
1157
1158            imagePosition = imageSet[i].getTranslationVectorRPS2XYZ();
1159            std::cout << "Position " << imagePosition[0] << " "
1160                      << imagePosition[1] << " "  << imagePosition[2] ;
1161            imageOrientation =  imageSet[i].getRotationMatrixRPS2XYZ();
1162            std::cout << "\t  Orientation " ;
1163            for(int i1=0; i1<3;i1++)for(int i2=0; i2<3;i2++)
1164               std::cout << imageOrientation[i1][i2] << " ";CreateImageSet
1165
1166            //std::cout << "\t  Abs Time " << imageSet[i].getAbsoluteTimePosition();
1167            std::cout << "\t  Relat Time " << imageSet[i].getRelativeTimePosition();
1168
1169            std::cout << "\t [";
1170            for (int i3=0; i3<imageSet[i].getLoopStamp().size();i3++)
1171               std::cout << " " << imageSet[i].getLoopStamp()[i3];
1172            std::cout << "]" << std::endl;
1173          }
1174 */
1175    return imageSet;
1176 }
1177
1178 // ===========================================================================================
1179
1180 void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels,
1181               int X,
1182               int Y,
1183               int nbFrames,
1184               int pixelSize,
1185               double spacingX, double spacingY, double sliceDistance,
1186               std::string dcmImageName,
1187               const std::string &patientName,
1188               const char *day,
1189               std::string &studyUID,
1190               std::string &serieUID,
1191               std::string &studyDescr,
1192               std::string &serieDescr,
1193               std::string &strStudyTimeDate,
1194               int imgNum,
1195               GDCM_NAME_SPACE::ImageContentType contentType
1196       )
1197 {
1198    std::ostringstream str;
1199
1200    GDCM_NAME_SPACE::File *file;
1201    file = GDCM_NAME_SPACE::File::New();
1202
1203   // Set the image size
1204    str.str("");
1205    str << X;
1206    file->InsertEntryString(str.str(),0x0028,0x0011,"US"); // Columns
1207    str.str("");
1208    str << Y;
1209    file->InsertEntryString(str.str(),0x0028,0x0010,"US"); // Rows
1210
1211    if (nbFrames != 1)
1212    {
1213       str.str("");
1214       str << nbFrames;
1215       file->InsertEntryString(str.str(),0x0028,0x0008,"IS"); // Number of Frames
1216    }
1217
1218   // Set the pixel type
1219   //      //8, 16, 32, 64 (for double ?)
1220    str.str("");
1221    str << pixelSize*8;
1222    file->InsertEntryString(str.str(),0x0028,0x0100,"US"); // Bits Allocated
1223
1224    file->InsertEntryString(str.str(),0x0028,0x0101,"US"); // Bits Stored
1225
1226    str.str("");
1227    str << pixelSize*8-1;
1228    file->InsertEntryString(str.str(),0x0028,0x0102,"US"); // High Bit
1229
1230   // Set the pixel representation // 0/1 , 0=unsigned
1231    file->InsertEntryString("1",0x0028,0x0103, "US"); // Pixel Representation
1232
1233   // Set the samples per pixel // 1:Grey level, 3:RGB
1234    file->InsertEntryString("1",0x0028,0x0002, "US"); // Samples per Pixel
1235
1236 //  0028 0030 DS 2 Pixel Spacing
1237    str.str("");
1238    str << spacingX << "\\" << spacingY;
1239    file->InsertEntryString(str.str(),0x0028,0x0030, "DS"); // Pixel Spacing
1240
1241  //   0018 0050 DS 1 Slice Thickness
1242    str.str("");
1243    str << sliceDistance;
1244    file->InsertEntryString(str.str(),0x0018,0x0050, "DS");
1245
1246 //    0020 0011 IS 1 Series Number
1247    str.str("");
1248    str << serieNumber;
1249    file->InsertEntryString(str.str(),0x0020,0x0011, "IS");
1250
1251 //    0020|0013 [IS]  [Instance Number]
1252    instanceNumber++;
1253    str.str("");
1254    str << instanceNumber;
1255    file->InsertEntryString(str.str(),0x0020,0x0013, "IS");
1256
1257
1258   // 1.2.840.10008.5.1.4.1.1.4.1 : Enhanced MR Image Storage
1259  //  file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0002, 0x0002, "UI");  // [Media Storage SOP Class UID]
1260   // file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0008, 0x0016, "UI");  // [SOP Class UID]
1261
1262
1263 // OK : MR is NOT multiframe, but I want just a quick an dirty solution
1264
1265 // 1.2.840.10008.5.1.4.1.1.4         MR Image Storage
1266    file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0002, 0x0002, "UI");  // [Media Storage SOP Class UID]
1267    file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0008, 0x0016, "UI");  // [SOP Class UID]
1268
1269   // if (strlen(patientName) != 0)
1270    file->InsertEntryString(patientName.c_str(),0x0010,0x0010, "PN"); // Patient's Name
1271
1272    file->InsertEntryString(studyUID, 0x0020, 0x000d, "UI");
1273    file->InsertEntryString(serieUID, 0x0020, 0x000e, "UI");
1274
1275 //  0008 0020 DA 1 Study Date
1276 //  0008 0030 TM 1 Study Time
1277
1278 /// \TODO split into 2 strings!
1279    file->InsertEntryString(strStudyTimeDate.substr(10,11).c_str(),0x0008,0x0020, "DA");
1280    file->InsertEntryString(strStudyTimeDate.substr(1,8).c_str(),  0x0008,0x0030, "TM");
1281
1282    file->InsertEntryString(studyDescr, 0x0008,0x1030, "LO");  // Study Description
1283    file->InsertEntryString(serieDescr, 0x0008,0x103e, "LO");  // Series Description
1284
1285 //0008|0060 [CS] [Modality]
1286    file->InsertEntryString("MR",0x0008,0x0060, "CS");
1287
1288 // 0020 0037 DS 6 Image Orientation (Patient)
1289    char charImageOrientation[256];
1290
1291 /*
1292 std::cout << "charImageOrientation  " <<
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] << std::endl ;
1299 */
1300    sprintf(charImageOrientation,"%f\\%f\\%f \\ %f\\%f\\%f",
1301                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0],
1302                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1],
1303                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2],
1304                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0],
1305                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1],
1306                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] ) ;
1307
1308    file->InsertEntryString(charImageOrientation,0x0020,0x0037, "DS");
1309
1310
1311 // 0020 0032 DS 3 Image Position (Patient)
1312
1313    char charImagePosition[256];
1314    sprintf(charImagePosition,"%f\\%f\\%f",
1315                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[0],
1316                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[1],
1317                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[2]);
1318
1319    file->InsertEntryString(charImagePosition,0x0020,0x0032, "DS");  //0020 0032 DS 3 Image Position (Patient)
1320
1321
1322
1323 // 0020 0x1041 DS 1 Slice Location
1324 //        sprintf(charImagePosition,"%f",float(imgNum));
1325 //        file->InsertEntryString(charImagePosition,0x0020,0x1041, "DS");
1326 /*
1327   // Set Rescale Intercept
1328         str.str("");
1329         str << div;
1330         file->InsertEntryString(str.str(),0x0028,0x1052,"DS");
1331
1332   // Set Rescale Slope
1333         str.str("");
1334         str << mini;
1335         file->InsertEntryString(str.str(),0x0028,0x1053,"DS");
1336 */
1337
1338    GDCM_NAME_SPACE::FileHelper *fileH;
1339    fileH = GDCM_NAME_SPACE::FileHelper::New(file);
1340    fileH->SetContentType(contentType);
1341
1342    // cast is just to avoid warnings (*no* conversion is performed)
1343    //fileH->SetImageData((uint8_t *)img,int(maxX*maxY)*sizeof(uint16_t)); // troubles when maxX, mayY are *actually* float!
1344
1345 //std::cout << "--------------------------------  X*Y*nbFrames*pixelSize " << X << " " << Y << " " << nbFrames << " " << pixelSize << std::endl;
1346
1347    fileH->SetImageData((uint8_t *)tabPixels, X*Y*nbFrames*pixelSize);
1348    fileH->SetWriteModeToRaw();
1349    fileH->SetWriteTypeToDcmExplVR();
1350    if( !fileH->Write(dcmImageName)) {
1351       std::cout << "Failed for [" << dcmImageName << "]\n"
1352                 << "           File is unwrittable" << std::endl;
1353       file->Delete();
1354       fileH->Delete();
1355       throw ( BrukerHopelessException ("Level 1 Unable to write Dicom file "));
1356    }
1357    if (verbose)
1358       file->Print();
1359
1360    file->Delete();
1361    fileH->Delete();
1362 }
1363
1364