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 directory name -----
  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    // ----- Check output directory name -----
  31
  32    std::string strDirNameOut(OutputDirName);
  33    bool res=CreateDirectory(strDirNameOut);
  34    if (!res) {
  35       std::cout << "[" << OutputDirName << "] Directory creation failure " << std::endl;
  36       //exit (0);
  37       throw ( BrukerHopelessException ("Output directory creation failure "));
  38    }
  39
  40    std::string strDirNamein(InputDirName);
  41    GDCM_NAME_SPACE::DirList dirList(strDirNamein, false, true); // DON'T get recursively the list of files
  42    std::string strDirNameout(OutputDirName);
  43
  44 /*
  45    if (listonly)
  46    {
  47       std::cout << "------------List of found files ------------" << std::endl;
  48       dirList.Print();
  49       std::cout << std::endl;
  50       return 1;
  51    }
  52 */
  53
  54 //
  55 // e.g : at level 0, in : B67d1.Bp1
  56 //
  57 //           1  2  3  4  5  6  AdjStatePerStudy  subject
  58 //
  59
  60    GDCM_NAME_SPACE::DirListType fileNames;
  61    fileNames = dirList.GetFilenames();
  62    bool canOpen;
  63    std::string outputFileName;
  64
  65
  66   // BrukerDataSet br_subject;
  67    std::string subject;
  68    subject = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
  69              GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
  70              "subject";
  71    if (verbose)
  72         std::cout << " Subject : [" <<  subject << "]" << std::endl;
  73    canOpen =br_subject.LoadFile(subject);
  74
  75    if (!canOpen)
  76    {
  77       std::cout << "Hopeless! no 'subject' found" << std::endl;
  78       throw ( BrukerHopelessException ("Hopeless! no 'subject' found in root input directory "));
  79       //exit(0);  /// \TODO throw an exception !
  80    }
  81    else
  82    {
  83       br_subject.FillMap();
  84    }
  85    //br_subject.PrintSelf();
  86
  87   // get info for 'Study Description'
  88
  89     BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string");
  90     std::string subject_name = b_name.GetStringValue()[0];
  91     strPatientName = subject_name;
  92     cleanString(subject_name);
  93
  94     // creation directory : 'nom du patient'
  95     std::string tempStringPatDir(OutputDirName);
  96     tempStringPatDir = tempStringPatDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + subject_name;
  97
  98     res=CreateDirectory(tempStringPatDir);
  99     if (!res) {
 100        std::cout << "[" << tempStringPatDir << "] Directory creation failure " << std::endl;
 101        throw ( BrukerHopelessException ("Patient directory creation failure "));
 102     }
 103
 104     BrukerFieldData b_entry=br_subject.GetFieldData("SUBJECT_entry");
 105     std::string subject_entry = b_entry.GetStringValue()[0];
 106     //cleanString(subject_entry);
 107     subject_entry = subject_entry.substr(11, subject_entry.size()-11);
 108
 109     BrukerFieldData b_position=br_subject.GetFieldData("SUBJECT_position");
 110     std::string subject_position = b_position.GetStringValue()[0];
 111     //cleanString(subject_position);
 112     subject_position = subject_position.substr(9, subject_position.size()-9);
 113
 114     BrukerFieldData b_date=br_subject.GetFieldData("SUBJECT_date");
 115     std::string subject_date = b_date.GetStringValue()[0];
 116     strStudyTimeDate = subject_date;
 117     cleanString(subject_date);
 118
 119     BrukerFieldData b_study_name=br_subject.GetFieldData("SUBJECT_study_name");
 120     std::string subject_study_name = b_study_name.GetStringValue()[0];
 121     subject_study_name = subject_study_name.substr(1, subject_study_name.size()-2);
 122     cleanString(subject_study_name);
 123
 124     // subject_name is already in 'Patient Name'
 125     strStudyDescr = /*subject_name + "." + */ subject_study_name + "." + subject_entry + "." + subject_position + "." + subject_date;
 126
 127     // creation directory : 'nom de la Study'
 128
 129     std::string tempStringStudyDir(OutputDirName);
 130     tempStringStudyDir = tempStringPatDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + strStudyDescr;
 131
 132     res=CreateDirectory(tempStringStudyDir);
 133     if (!res) {
 134        std::cout << "[" << tempStringStudyDir << "] Directory creation failure " << std::endl;
 135        throw ( BrukerHopelessException ("Study directory creation failure "));
 136     }
 137
 138    char outputDirName[(unsigned int) PATH_MAX+2];
 139
 140    strStudyUID    = GDCM_NAME_SPACE::Util::CreateUniqueUID();
 141    serieNumber    = 0;
 142    instanceNumber = 0;
 143    // -----------------------------------------------------
 144    // Iterate to ALL the objets(files/directories) found in the input directory
 145    // (this is level ZERO)
 146    // each Directory (name : 1, 2, 3, ...) will be a Dicom Serie
 147    // -----------------------------------------------------
 148
 149    GDCM_NAME_SPACE::DirListType::iterator it;
 150
 151    for (it = fileNames.begin();
 152          it != fileNames.end();
 153        ++it)
 154    {
 155       if ( boost::filesystem::is_directory(*it) )
 156       {
 157          if (verbose)
 158             std::cout << "[" << *it << "] is a directory" << std::endl;
 159
 160          //BrukerDataSet br_acqp;
 161          std::string strAcqp;
 162          strAcqp = (*it) +
 163                    GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 164                    "acqp";
 165
 166          br_acqp.LoadFile(strAcqp);
 167          br_acqp.FillMap();
 168
 169          std::string acqp_scan_name;
 170          std::string acqp_method;
 171          std::string acqp_protocol_location;
 172
 173          BrukerFieldData b_protocol_location=br_acqp.GetFieldData("ACQ_protocol_location");
 174          acqp_protocol_location = b_protocol_location.GetStringValue()[0];
 175          cleanString(acqp_protocol_location);
 176
 177          BrukerFieldData b_scan_name=br_acqp.GetFieldData("ACQ_scan_name");
 178          acqp_scan_name = b_scan_name.GetStringValue()[0];
 179          cleanString(acqp_scan_name);
 180
 181          BrukerFieldData b_method=br_acqp.GetFieldData("ACQ_method");
 182          acqp_method = b_method.GetStringValue()[0];
 183          cleanString(acqp_method);
 184
 185          BrukerFieldData b_list_size = br_acqp.GetFieldData("ACQ_O1_list_size");
 186          //b_list_size.PrintSelf(); //JP
 187
 188          nbSlices =  b_list_size.GetIntValue()[0];
 189
 190          strSerieDescr = GDCM_NAME_SPACE::Util::GetName(*it)
 191                        /*  + "." + acqp_protocol_location */ // always the same (in each acquisition)
 192                          + "." + acqp_scan_name
 193                          + "." + acqp_method.c_str();
 194
 195          sprintf(outputDirName, "%s%c%s", tempStringStudyDir.c_str(),                //OutputDirName.c_str(),
 196                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 197                           strSerieDescr.c_str() );
 198
 199          std::cout << " ================================================================================\n"
 200                    << " === [" << GDCM_NAME_SPACE::Util::GetName(*it) << "] -> [" << strSerieDescr << "]\n"
 201                    << " ================================================================================"
 202                    << std::endl;
 203
 204
 205         if (verbose)
 206            printf ("outputDirName [%s]\n", outputDirName);
 207         try {
 208            DealWithNiveau1(*it, outputDirName);
 209         }
 210         catch (BrukerHopelessException &e)
 211         {
 212          std::cout << "And Exception was thrown in DealWithNiveau1 (" << e.what() << ") " << std::endl;
 213          continue;
 214         }
 215       }
 216    } // end of : for (GDCM_NAME_SPACE::DirListType::iterator it
 217 }
 218
 219
 220 // =====================================================================
 221
 222 void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string currentOutputDirName) {
 223 //
 224 // e.g. : at level 1, in B67d1.Bp1/6
 225 //
 226 // acqp  fid  imnd  pdata  pulseprogram  spnam0  spnam1
 227
 228    bool res = CreateDirectory(currentOutputDirName);
 229
 230    if (!res) {
 231       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 232       throw ( BrukerHopelessException ("Level 1 output directory creation failure "));
 233      // exit (0);
 234    }
 235    GDCM_NAME_SPACE::DirList dirList(level1Directory, false, true); // DON'T get recursively the list of files
 236    GDCM_NAME_SPACE::DirListType fileNames;
 237    fileNames = dirList.GetFilenames();
 238    // -----------------------------------------------------
 239    // Iterate to ALL the objets(files/directories) found in the input directory
 240    // -----------------------------------------------------
 241    GDCM_NAME_SPACE::DirListType::iterator it;
 242
 243    for (it = fileNames.begin();
 244         it != fileNames.end();
 245       ++it)
 246    {
 247       if ( boost::filesystem::is_regular(*it) )
 248       //if ( ! boost::filesystem::is_directory(*it) )
 249       {
 250          if (verbose)
 251             std::cout << "--- [" << *it << "] is a file." << std::endl;
 252       }
 253    }
 254
 255    char outputDirName[(unsigned int) PATH_MAX+2];
 256    //std::string firstName;
 257    bool canOpen;
 258    for (it = fileNames.begin();
 259         it != fileNames.end();
 260       ++it)
 261    {
 262       if ( boost::filesystem::is_directory(*it) )
 263       {
 264          // will be always "pdata" ...
 265          if (verbose)
 266             std::cout << "--- [" << *it << "] is a directory" << std::endl;
 267
 268               /* a recuperer :
 269               if (FileLine.startsWith("##$ACQ_size=")) {
 270               if (FileLine.startsWith("##$NI=")) {
 271               if (FileLine.startsWith("##$NR=")) {
 272               if (FileLine.startsWith("##$ACQ_obj_order=")) {
 273               if (FileLine.startsWith("##$ACQ_word_size=")) {
 274               if (FileLine.startsWith("##$BYTORDA=")) {
 275               if (FileLine.startsWith("##$PULPROG=")) {
 276               */
 277
 278          sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 279                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 280                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str());
 281          //br1.PrintSelf();
 282
 283           std::string strMethod;
 284           //std::string firstName = *(fileNames.begin());
 285
 286           strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin())) +
 287                       GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 288                       "method";
 289             // std::cout << "---strMethod (for method)=> [" << strMethod << "]" << std::endl;
 290           canOpen = br_method.LoadFile(strMethod);
 291           if (!canOpen)
 292           {
 293              strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
 294                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 295                          "imnd";
 296              //std::cout << "---strMethod (for imnd) => [" << strMethod << "]" << std::endl;
 297              canOpen = br_method.LoadFile(strMethod);
 298              if (!canOpen)
 299              {
 300                 std::cout << "Hopeless! neither 'method' nor 'imnd' found in ["
 301                           << level1Directory  << "]; we skip it!" << std::endl;
 302                 continue;
 303                 //throw ( BrukerHopelessException ("Hopeless! neither 'method' nor 'imnd' found "));
 304                 //exit(0);  /// \TODO throw an exception !
 305              }
 306           }
 307           if (verbose)
 308              std::cout << "open => [" << strMethod << "] successfully" << std::endl;
 309           br_method.FillMap();
 310
 311           /* a recuperer :
 312              ##$PVM_Fov (dimension)
 313           */
 314   /*
 315           dans method (pour perfusion  seulement?) :
 316           ##$PVM_ObjOrderList=( 8 )
 317           0 2 4 6 1 3 5 7
 318           ##$PVM_NSPacks=2
 319           ##$PVM_SPackArrNSlices=( 2 )
 320           7 1
 321   */
 322          try {
 323             DealWithNiveau2(*it,outputDirName );
 324          }
 325          catch (BrukerHopelessException &e)
 326          {
 327             std::cout << "And Exception was thrown in DealWithNiveau2 (" << e.what() << ") " << std::endl;
 328             continue;
 329          }
 330       }
 331    }
 332 }
 333
 334 // =====================================================================
 335
 336 void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string currentOutputDirName) {
 337
 338 // e.g. : at level 2 in B67d1.Bp1/6/pdata
 339 //
 340 // acqp  fid  imnd  pdata  pulseprogram  spnam0  spnam1
 341 //
 342
 343    bool res = CreateDirectory(currentOutputDirName);
 344
 345    if (!res) {
 346       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 347       throw ( BrukerHopelessException ("Hopeless! Level2 output directory creation failure"));
 348       //exit (0);
 349    }
 350
 351    GDCM_NAME_SPACE::DirList dirList(level2Directory, false, true); // DON'T get recursively the list of files
 352
 353    GDCM_NAME_SPACE::DirListType fileNames;
 354    fileNames = dirList.GetFilenames();
 355
 356    char outputDirName[(unsigned int) PATH_MAX+2];
 357
 358    // -----------------------------------------------------
 359    // Iterate to ALL the objets(files/directories) found in the input directory
 360    // -----------------------------------------------------
 361    GDCM_NAME_SPACE::DirListType::iterator it;
 362    bool canOpen;
 363
 364    if (verbose)
 365    for (it = fileNames.begin();
 366         it != fileNames.end();
 367       ++it)
 368    {
 369       if ( ! boost::filesystem::is_directory(*it) )
 370       {
 371          std::cout << "--- --- [" << *it << "] is a file.." << std::endl;
 372       }
 373
 374    }
 375
 376    for (it = fileNames.begin();
 377          it != fileNames.end();
 378        ++it)
 379    {
 380       if ( boost::filesystem::is_directory(*it) )
 381       {
 382
 383          if (verbose)
 384             std::cout << "--- --- [" << *it << "] is a directory" << std::endl;
 385
 386         // sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 387         //                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 388         //                                GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
 389   // MUST be 'pdata'!
 390
 391 //
 392 // (interest of previous method :
 393 // If unaware user changed the pdata name, it goes on working
 394 //
 395           std::string str_isa;
 396           str_isa = (*it) +
 397                     GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 398                    "isa";
 399
 400           std::string str_isa_func_name;
 401           canOpen = br_isa.LoadFile(str_isa);
 402           if (!canOpen)
 403           {
 404              sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 405                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 406                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
 407           }
 408           else
 409           {
 410              br_isa.FillMap();
 411              BrukerFieldData b_isa_func_name = br_isa.GetFieldData("ISA_func_name");
 412
 413              str_isa_func_name = b_isa_func_name.GetStringValue()[0];
 414              cleanString(str_isa_func_name);
 415
 416              sprintf(outputDirName, "%s%c%s.%s", currentOutputDirName.c_str(),
 417                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 418                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str(),
 419              str_isa_func_name.c_str());
 420           }
 421           try {
 422              DealWithNiveau3(*it, outputDirName);
 423           }
 424           catch (BrukerHopelessException &e)
 425           {
 426              std::cout << "And Exception was thrown in DealWithNiveau3 (" << e.what() << "); "
 427                        << " We skip [" << level2Directory << "]" << std::endl;
 428              continue;
 429           }
 430           catch (BrukerInitException &e)
 431           {
 432              std::cout << "And Init Exception was thrown in DealWithNiveau3 (" << e.what() << "); "
 433                        << " We skip [" << level2Directory << "]" << std::endl;
 434              continue;
 435           }
 436       }
 437    }
 438 }
 439
 440
 441 //
 442 // =====================================================================
 443 //
 444
 445 void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string currentOutputDirName){
 446
 447 //
 448 // e.g. at level 3, in
 449
 450    // just to be able to go on checking // JP
 451    if ( GDCM_NAME_SPACE::Util::GetName(level3Directory) != "1")
 452       return;
 453
 454    bool res = CreateDirectory(currentOutputDirName);
 455
 456    if (!res)
 457    {
 458       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 459       throw ( BrukerHopelessException ("Hopeless! Level3 output directory creation failure"));
 460       //exit (0);
 461    }
 462
 463    GDCM_NAME_SPACE::DirList dirList(level3Directory, false, true); // DON'T get recursively the list of files
 464    GDCM_NAME_SPACE::DirListType::iterator it;
 465    GDCM_NAME_SPACE::DirListType fileNames;
 466    fileNames = dirList.GetFilenames();
 467
 468    char original2dseqName       [(unsigned int) PATH_MAX+2];
 469    char original2dseqName_XXX   [(unsigned int) PATH_MAX+2];
 470    char currentOutputMhdDirName [(unsigned int) PATH_MAX+2];
 471
 472    char outputMhdFileName       [(unsigned int) PATH_MAX+2];
 473    char output2dseqSliceFileName[(unsigned int) PATH_MAX+6]; // think about extra '.dcm'
 474    char output2dseqName         [(unsigned int) PATH_MAX+6];
 475    char output2dseqCartoName    [(unsigned int) PATH_MAX+6];
 476
 477    char copyFile[PATH_MAX + PATH_MAX + 5]; // Should be enough!
 478    bool canOpen;
 479
 480    //-------------- try d3proc;
 481    char char_d3proc[(unsigned int) PATH_MAX+2];
 482
 483    sprintf(char_d3proc,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"d3proc" );
 484
 485    if (verbose)
 486       std::cout << "d3proc: --- => [" << char_d3proc << "]" << std::endl;
 487    std::string str_d3proc(char_d3proc);
 488    canOpen = br_d3proc.LoadFile(str_d3proc);
 489
 490    if (!canOpen)
 491    {
 492       std::cout << "Hopeless! no 'd3proc' found" << std::endl;
 493       throw ( BrukerHopelessException ("Hopeless! no 'd3proc' found"));
 494       //exit(0);  /// \TODO throw an exception !
 495    }
 496
 497    canOpen = br_d3proc.FillMap();
 498    if (!canOpen)
 499    {
 500       std::cout << "Hopeless! FillMap failed on 'd3proc'" << std::endl;
 501       throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'd3proc'"));
 502       //exit(0);  /// \TODO throw an exception !
 503    }
 504
 505    //-------------- end try d3proc;
 506
 507
 508  // -------------------try reco
 509
 510    char char_reco[(unsigned int) PATH_MAX+2];
 511
 512    sprintf(char_reco,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
 513     //str_d3proc = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
 514     //             GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 515     //             "d3proc";
 516    if (verbose)
 517       std::cout << "reco --- => [" << char_reco << "]" << std::endl;
 518    std::string str_reco(char_reco);
 519    canOpen = br_reco.LoadFile(str_reco);
 520
 521    if (!canOpen) // we try in directory ../1
 522    {
 523       if (verbose)
 524          std::cout << "[" << str_reco << "] not found " << std::endl;
 525       std::string lastDirName = GDCM_NAME_SPACE::Util::GetPath(level3Directory);
 526       //lastDirName = GDCM_NAME_SPACE::Util::GetPath(lastDirName);
 527       sprintf(char_reco,"%s%c1%c%s", lastDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
 528       str_reco=char_reco;
 529       canOpen = br_reco.LoadFile(str_reco);
 530       if (!canOpen)
 531       {
 532          std::cout << "Hopeless! cannot find 'reco' in [" << str_reco << "]"  << std::endl;
 533          throw ( BrukerHopelessException ("Hopeless! cannot find 'reco'"));
 534          //exit(0);  /// \TODO throw an exception !
 535       }
 536    }
 537
 538    canOpen = br_reco.FillMap();
 539    if (!canOpen)
 540    {
 541       std::cout << "Hopeless! FillMap failed on [" << str_reco << "]" << std::endl;
 542       throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'reco'"));
 543       //exit(0);  /// \TODO throw an exception !
 544    }
 545    //std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
 546    // br_reco.PrintSelf();
 547    // std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
 548
 549    // -------------------end try reco
 550
 551
 552    BrukerFieldData bX = br_d3proc.GetFieldData("IM_SIX");
 553    int NX = bX.GetIntValue()[0];
 554
 555    if (verbose)
 556       std::cout << "IM_SIX " << NX << std::endl;
 557    BrukerFieldData bY=br_d3proc.GetFieldData("IM_SIY");
 558    int NY = bY.GetIntValue()[0];
 559
 560    if (verbose)
 561          std::cout << "IM_SIY " << NY << std::endl;
 562    /// \todo : check if there are actually 3 dimensions or only 2
 563
 564    BrukerFieldData bZ= br_d3proc.GetFieldData("IM_SIZ");
 565    int nbFrames = bZ.GetIntValue()[0];
 566    if (verbose)
 567          std::cout << "IM_SIZ " << nbFrames << std::endl;
 568
 569         // WARNING DATTYPE is, either in {ip_short, ip_int, ip_char, ...}, or in {1, 2, 3, ...}
 570
 571    BrukerFieldData bDPT = br_d3proc.GetFieldData("DATTYPE");
 572
 573    std::string mhdDataPixelType;
 574    int pixelSize;
 575    getImhDataType(bDPT, mhdDataPixelType, pixelSize);
 576
 577    BrukerFieldData fov = br_method.GetFieldData("PVM_Fov");
 578    double fovX = fov.GetDoubleValue()[0];
 579    double fovY = fov.GetDoubleValue()[1];
 580    if (verbose)
 581       std::cout << "FOV (ds method) " << fovX << " " << fovY << std::endl;
 582
 583    BrukerFieldData spatResol = br_method.GetFieldData("PVM_SpatResol");
 584    double spatResolX = spatResol.GetDoubleValue()[0];
 585    double spatResolY = spatResol.GetDoubleValue()[1];
 586    if (verbose)
 587       std::cout << "SpatResol (ds method) " << spatResolX << " " << spatResolY << std::endl;
 588
 589
 590    /// \TODO probabely a more sophisticated accessor will be necessary :
 591    ///  (cf : non contiguous slices, overlapping, slice thickness, space between slices, etc)
 592    BrukerFieldData bsliceDistance = br_method.GetFieldData("PVM_SPackArrSliceDistance");
 593    double sliceDistance = bsliceDistance.GetDoubleValue()[0];
 594
 595    if (mhd)
 596    {
 597       sprintf(currentOutputMhdDirName, "%s%c%s", currentOutputDirName.c_str(),
 598                                GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "MhdFiles");
 599       res = CreateDirectory( currentOutputMhdDirName );
 600       if (!res) {
 601          std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 602          throw ( BrukerHopelessException ("Hopeless!FillMap failed on 'reco'"));
 603          //exit (0);
 604       }
 605
 606       if (verbose)
 607          std::cout << "Directory creation [" <<  currentOutputDirName << "]" << std::endl;
 608    }  // end if mhd
 609
 610    if (verbose)
 611          std::cout << "nbFrames " << nbFrames << std::endl;
 612    if (verbose)
 613          std::cout << "nbSlices " << nbSlices << std::endl;
 614    int k;
 615    int nbInstants = nbFrames/nbSlices;
 616    if (verbose)
 617          std::cout << "nbInstants (deduced )" << nbInstants << std::endl;
 618    int instantNb;
 619    int sliceNb;
 620    FILE *fp;  // for MHD files
 621
 622    sprintf( original2dseqName, "%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "2dseq");
 623
 624 /**/
 625   // \TODO : tenir compte du bazar precedent
 626
 627     // load 2dseq in memory
 628
 629    fp = fopen(original2dseqName, "rb");
 630    if (!fp)
 631    {
 632       // try 2dseq_Angio2D ?!?
 633
 634       sprintf( original2dseqName_XXX, "%s%s", original2dseqName, "_Angio2D");
 635       fp = fopen(original2dseqName_XXX, "rb");
 636       if (!fp)
 637       {
 638          std::cout << "Cannot open [" << original2dseqName << "] nor [" <<  original2dseqName_XXX << "] for reading" << std::endl;
 639          fclose(fp);
 640          throw ( BrukerHopelessException ("Hopeless! Cannot open '2dseq'"));
 641          //exit (0);
 642       }
 643    }
 644
 645    unsigned char *buffer_2dseq = new unsigned char[NX*NY*pixelSize*nbSlices*nbInstants];
 646    ///\ TODO : find a safer way to be sure to read everything!
 647    size_t lgr = fread(buffer_2dseq, 1, NX*NY*pixelSize*nbSlices*nbInstants, fp);
 648
 649    // This one will be important!
 650    // ---------------------------
 651    try {
 652       imageSet = CreateImageSet ( );
 653    }
 654    catch (BrukerInitException& e)
 655    {
 656       if (verbose)
 657          std::cout <<  "an Init Exception was thrown in CreateImageSet ( ); " << e.what()
 658                    <<  "catched in DealWithNiveau3" << std::endl;
 659       //return;
 660       throw (e);
 661    }
 662
 663    serieNumber++;
 664    strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 665    if (nbInstants==1) // creer un seul fichier .mhd  pour toutes les Slices! (images natives)
 666    {
 667        if (verbose)
 668           std::cout << "Single instant : do not split" << std::endl;
 669        if (mhd)
 670        {
 671              sprintf(outputMhdFileName, "%s%cMhdData_All_the_Slices.mhd", currentOutputMhdDirName,
 672                                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 673              fp=fopen(outputMhdFileName, "w");
 674              if (!fp)
 675              {
 676                 std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 677                 throw ( BrukerHopelessException ("Hopeless! Cannot open  mhd file for writting"));
 678                 //exit(0);
 679              }
 680              else
 681              {
 682                fprintf(fp, "ObjectType = Image\n");
 683                fprintf(fp, "NDims = 3\n" );
 684                fprintf(fp, "BinaryData = True \n" );
 685                fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 686                fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices );
 687                fprintf(fp, "HeaderSize = %d\n", 0);
 688                //fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
 689                fprintf(fp, "ElementSpacing = %lf %lf %lf\n", spatResolX, spatResolY, sliceDistance );
 690                fprintf(fp, "Position = 0 0 %d\n", 0 );
 691                fprintf(fp, "Offset = 0 0 0\n" );
 692                fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 693                fprintf(fp, "ElementNumberOfChannels = 1\n" );
 694                fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
 695                fprintf(fp, "ElementDataFile = %s\n", "../2dseq_All_the_Slices" );
 696                fclose(fp);
 697              }
 698              sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices",
 699                                        currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 700              fp=fopen(output2dseqSliceFileName, "wb");
 701              if (!fp)
 702              {
 703                 std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 704                 throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseq file for writting"));
 705              }
 706              else
 707              {
 708                 fwrite( buffer_2dseq, NX*NY*pixelSize, nbSlices, fp);
 709              }
 710              fclose(fp);
 711              serieNumber ++;
 712              strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 713        }  // end if mhd
 714        if (dicom)
 715        {
 716              sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices.dcm",
 717                                        currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 718
 719             /* ----------- Write Dicom Image  ---------------*/
 720              MakeDicomImage(buffer_2dseq,
 721                NX,
 722                NY,
 723                nbFrames,
 724                pixelSize,
 725                //fovX/NY, fovY/NY, sliceDistance,
 726                spatResolX, spatResolY, sliceDistance,
 727                output2dseqSliceFileName,
 728                strPatientName,
 729                day,
 730                strStudyUID,
 731                strSerieUID,
 732                strStudyDescr,
 733                strSerieDescr,
 734                strStudyTimeDate,
 735                0,// index frame number
 736                GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
 737              );
 738        }  // end if dicom
 739    }  // end if nbInstants = 1
 740
 741    else  // more than ONE instant
 742    {
 743           // Interleaved !
 744           // it's (slice1,slide2, ...)t1 ; (slice1,slide2, ...)t2 ; ...
 745
 746          unsigned char *pixelsForCurrentSlice = new unsigned char[NX*NY*pixelSize*nbInstants];
 747
 748          k = 0;
 749          for (sliceNb=0; sliceNb<nbSlices; sliceNb++)
 750          {
 751             if (mhd)
 752             {
 753                sprintf(outputMhdFileName, "%s%cMhdData_%03d.mhd", currentOutputMhdDirName,
 754                                         GDCM_NAME_SPACE::GDCM_FILESEPARATOR, k  );
 755                if (verbose)
 756                   std::cout << "--- Output MHD file [" << outputMhdFileName << "]" << std::endl;
 757                fp=fopen(outputMhdFileName, "w");
 758                if (!fp)
 759                {
 760                    std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 761                    throw ( BrukerHopelessException ("Hopeless! Cannot open  mhd file for writting"));
 762                    //exit(0);
 763                }
 764                else
 765                {
 766             /* ----------- Write MHD Image  ---------------*/
 767                 //if (verbose)
 768                 //   std::cout << "Open sucessfully[" << outputMhdFileName << "] for writting" << std::endl;
 769                    fprintf(fp, "ObjectType = Image\n");
 770                    fprintf(fp, "NDims = 3\n" );
 771                    fprintf(fp, "BinaryData = True \n" );
 772                    fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 773                    fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbInstants);
 774                    fprintf(fp, "HeaderSize = %d\n", 0);
 775                    //fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, 1.0 ); //
 776                    fprintf(fp, "ElementSpacing = %lf %lf %lf\n",spatResolX, spatResolY, 1.0 ); //slice distance : no meaning for temporal serie
 777                    fprintf(fp, "Position = 0 0 %d\n", sliceNb );
 778                    fprintf(fp, "Offset = 0 0 0\n" );
 779                    fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 780                    fprintf(fp, "ElementNumberOfChannels = 1\n" );
 781                    fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
 782                    fprintf(fp, "ElementDataFile = ..%c2dseq_Slice_%d\n", GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb );
 783                    fclose(fp);
 784                } // end write MHD
 785
 786                sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d",
 787                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,sliceNb);
 788                fp=fopen(output2dseqSliceFileName, "wb");
 789                if (!fp)
 790                {
 791                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 792                    throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseqSliceFile file for writting"));
 793                    //exit (0);
 794                }
 795                int frameSize = NX*NY*pixelSize;
 796                for (instantNb=0; instantNb<nbInstants; instantNb++)
 797                {
 798 // std::cout << "------------SN " << sliceNb << " IN " << instantNb <<  " T " << nbSlices*instantNb + sliceNb << std::endl;
 799                     fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
 800                             frameSize,
 801                             1, fp);
 802                }
 803                fclose(fp);
 804 // std::cout << "end writting[" << output2dseqSliceFileName << "]" << std::endl;
 805             }  // end if mhd
 806
 807             if (dicom)
 808             {
 809                // desperate try !
 810              /*
 811                sprintf(output2dseqSliceFileName, "%sdummy_buffer",
 812                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 813                fp=fopen(output2dseqSliceFileName, "wb");
 814                if (!fp)
 815                {
 816                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 817                    exit (0);
 818                }
 819                int frameSize = NX*NY*pixelSize;
 820                for (instantNb=0; instantNb<nbInstants; instantNb++)
 821                {
 822 // std::cout << "------------SN " << sliceNb << " IN " << instantNb <<  " T " << nbSlices*instantNb + sliceNb << std::endl;
 823                     fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
 824                             frameSize,
 825                             1, fp);
 826                }
 827                fclose(fp);
 828
 829                fp=fopen(output2dseqSliceFileName, "rb");
 830                if (!fp)
 831                {
 832                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for reading" << std::endl;
 833                    exit (0);
 834                }
 835                fread( pixelsForCurrentSlice,
 836                             frameSize*nbInstants,
 837                             1, fp);
 838                fclose(fp);
 839               // end of desperate try !
 840               */
 841
 842                /* ----------- Write Dicom Image  ---------------*/
 843
 844                int frameSize = NX*NY*pixelSize;
 845                for (instantNb=0; instantNb<nbInstants; instantNb++)
 846                {
 847                   memcpy(pixelsForCurrentSlice + frameSize*instantNb, buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize, frameSize);
 848                }
 849
 850                int indOfFirsImageWithinImageSet =  nbSlices*instantNb;
 851                sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d.dcm",
 852                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb);
 853
 854                MakeDicomImage(
 855                   pixelsForCurrentSlice,
 856                   NX,
 857                   NY,
 858                   nbInstants,
 859                   pixelSize,
 860                   spatResolX, spatResolY, sliceDistance,
 861                   //fovX/NY, fovY/NY, sliceDistance,
 862                   output2dseqSliceFileName,
 863                   strPatientName,
 864                   day,
 865                   strStudyUID,
 866                   strSerieUID,
 867                   strStudyDescr,
 868                   strSerieDescr,
 869                   strStudyTimeDate,
 870                   sliceNb*nbInstants,
 871                   GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
 872                );
 873                if (verbose)
 874                   std::cout << "--- Output DCM file [" << output2dseqSliceFileName << "]" << std::endl;
 875
 876            } // en if dicom
 877
 878         k++;
 879         }
 880         delete [] pixelsForCurrentSlice;
 881      }  // end nbInstants == 1
 882    delete [] buffer_2dseq;
 883 /**/
 884
 885
 886    // -----------------------------------------------------
 887    //  deal with MatLab-generated Carto file.
 888    // -----------------------------------------------------
 889
 890    dealWithCarto(fileNames,  NX,  NY,  nbSlices, /*fovX, fovY,*/ spatResolX, spatResolY, sliceDistance,
 891                    copyFile, currentOutputDirName, outputMhdFileName, output2dseqCartoName);
 892 }
 893
 894
 895 // ===========================================================================================
 896
 897 void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX, int NY, int nbSlices,
 898                                  /*double fovX, double fovY, */
 899                                  double spatResolX, double spatResolY, double sliceDistance,
 900                                  char *copyFile, std::string &currentOutputDirName,
 901                                  char *outputMhdFileName, char *output2dseqCartoName)
 902 {
 903    // -----------------------------------------------------
 904    //  deal with MatLab-generated Carto file.
 905    // -----------------------------------------------------
 906
 907    char *code[] = { "ADC", "adc", "TTP", "ttp", "PEAK", "peak", "" };  // add more carto file name identifiers if necessary; end with ""
 908    char *separator[] =  { "_", ".", "-", "" }; //  add more, if necessary, to ckeck for 2dseq.ADC, 2dseq_ADC, 2dseq-ADC, etc; end with ""
 909    int icode;
 910    int iseparator;
 911    GDCM_NAME_SPACE::DirListType::iterator it;
 912    char file_name_ident[500];
 913    FILE *fp;
 914
 915    // Iterate to ALL the objets(files/directories) found in the input directory
 916    for (it = fileNames.begin();
 917         it != fileNames.end();
 918       ++it)
 919    {
 920       if ( boost::filesystem::is_regular(*it) )
 921       //if ( ! boost::filesystem::is_directory(*it) )
 922       {
 923          if (verbose)
 924             std::cout << "--- [" << *it << "] is a file..." << std::endl;
 925
 926          icode      = 0;
 927          while (code[icode][0] != 0)
 928          {
 929          iseparator = 0;
 930          while (separator[iseparator][0] != 0)
 931          {
 932             sprintf(file_name_ident, "2dseq%s%s",separator[iseparator],code[icode]); // e.g  "2dseq_ADC"
 933             //if (verbose)
 934             //   std::cout << "check name ["<<(*it) << "] for string [" << file_name_ident << "]" << std::endl;
 935             std::string::size_type loc = (*it).rfind(file_name_ident);
 936
 937             if ( loc != std::string::npos )
 938             {
 939
 940        ///\ TODO : find a safer way to be sure to read everything!
 941               unsigned char *buffer_carto = new unsigned char[NX*NY*sizeof(double)*nbSlices];
 942               fp = fopen ( (*it).c_str(), "rb");
 943               if (!fp){
 944                  std::cout << "Cannot open [" << *it << "] for reading" << std::endl;
 945                  throw ( BrukerHopelessException ("Level 1 Unable to open 'carto' file "));
 946                }
 947                fread(buffer_carto, NX*NY*sizeof(double), nbSlices, fp);
 948
 949                     // ?!?  sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() ,
 950                std::cout << "Deal with Carto file :[" <<*it << "], computed length : "
 951                          << NX*NY*sizeof(double)*nbSlices << std::endl;
 952                std::string lastFileName = GDCM_NAME_SPACE::Util::GetName((*it).c_str());
 953                if (mhd)
 954                {
 955                   // Copy the data file in the new directory
 956                   sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() ,
 957                             currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str());
 958                   system(copyFile);
 959                   sprintf(outputMhdFileName, "%s%c%s%s",
 960                                          currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".mhd" );
 961                   if (verbose)
 962                     std::cout << "--- Output Carto MHD file [" << outputMhdFileName << "]" << std::endl;
 963
 964                   FILE *fp;
 965                   fp=fopen(outputMhdFileName, "w");
 966                   if (!fp)
 967                   {
 968                      std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 969                   }
 970                   else
 971                   {
 972                      fprintf(fp, "ObjectType = Image\n");
 973                      fprintf(fp, "NDims = 3\n" );
 974                      fprintf(fp, "BinaryData = True \n" );
 975                      fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 976                      fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices);
 977                      fprintf(fp, "HeaderSize = %d\n", 0 );
 978                      fprintf(fp, "ElementSpacing = %lf %lf %lf\n",spatResolX, spatResolY, sliceDistance );
 979                      fprintf(fp, "Position = 0 0 0\n" );
 980                      fprintf(fp, "Offset = 0 0 0\n" );
 981                      fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 982                      fprintf(fp, "ElementNumberOfChannels = 1\n" );
 983                      fprintf(fp, "ElementType = %s\n", "MET_DOUBLE" );
 984                      fprintf(fp, "ElementDataFile = %s\n", lastFileName.c_str() );
 985
 986                      fclose(fp);
 987                   }
 988                   if (verbose)
 989                      std::cout << "--- end write Carto MHD file [" << outputMhdFileName << "]" << std::endl;
 990                }  // end if mhd
 991
 992             // ----------- Write Dicom Image  ---------------
 993
 994                if (dicom)
 995                {
 996                   sprintf(output2dseqCartoName, "%s%c%s%s",
 997                                        currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".dcm" );
 998                   if (verbose)
 999                      std::cout << "--- end create name output2dseqCartoName file [" << output2dseqCartoName << "]" << std::endl;
1000
1001                   strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID(); //New SerieUID for each carto.
1002                   std::string strNewSerieDescr(strSerieDescr+ "_" +GDCM_NAME_SPACE::Util::GetName((*it).c_str()));
1003                   MakeDicomImage(buffer_carto,
1004                      NX,
1005                      NY,
1006                      nbSlices,
1007                      8, // pixelSize
1008                      //fovX/NY, fovY/NY, sliceDistance,
1009                      spatResolX, spatResolY, sliceDistance,
1010                      output2dseqCartoName,
1011                      strPatientName,
1012                      day,
1013                      strStudyUID,
1014                      strSerieUID,
1015                      strStudyDescr,
1016                      strNewSerieDescr,
1017                      strStudyTimeDate,
1018                      0,
1019                      GDCM_NAME_SPACE::CREATED_IMAGE
1020                   );
1021                }  // end if dicom
1022
1023                delete [] buffer_carto;
1024                if (verbose)
1025                   std::cout << "--- End writing Carto DICOM file [" << output2dseqCartoName << "]" << std::endl;
1026                break; // don't check for more ident on same file name!
1027
1028             }  // end deal with _ADC, -adc, etc
1029           iseparator ++;
1030           }  // end iterate speparators
1031           icode++;
1032           } // end iterate code
1033       } // end boost::filesystem::is_regular(*it)
1034    } // end iterate on all objects (files, dir, etc)
1035 } // end method
1036
1037
1038 // ==========================================================================================================
1039
1040 bool Bruker2Dicom::CreateDirectory(std::string OutputDirName)
1041 {
1042    std::string systemCommand;
1043
1044    if (verbose)
1045       std::cout << "Check for output directory :[" << OutputDirName << "]."
1046                 <<std::endl;
1047    if ( ! boost::filesystem::is_directory(OutputDirName) )    // dirout not found
1048    {
1049       std::string strDirNameout(OutputDirName);        // to please gcc 4
1050       systemCommand = "mkdir " + strDirNameout;        // create it!
1051       if (verbose)
1052          std::cout << systemCommand << std::endl;
1053       system (systemCommand.c_str());
1054       if ( ! boost::filesystem::is_directory(OutputDirName) ) // be sure it worked
1055       {
1056          if (verbose)
1057             std::cout << "KO : not a dir : [" << OutputDirName << "] (creation failure ?)" << std::endl;
1058          //return 0;
1059          throw ( BrukerHopelessException ("Level 1 output directory creation failure "));
1060       }
1061       else
1062       {
1063          if (verbose)
1064            std::cout << "Directory [" << OutputDirName << "] created." << std::endl;
1065       }
1066    }
1067    else
1068    {
1069        if (verbose)
1070             std::cout << "Output Directory [" << OutputDirName << "] already exists; Used as is." << std::endl;
1071    }
1072
1073    return 1;
1074
1075 }
1076
1077
1078 // ===========================================================================================
1079
1080 /// \TODO move cleanString to 'crea' ?
1081
1082 void Bruker2Dicom::cleanString(std::string &s)
1083 {
1084    int l = s.size();
1085    if (s[l-1] == 0x0A || s[l-1] == 0x0D ) // CR or NL
1086    {
1087       l--;
1088       s = s.substr(0, l);
1089    }
1090    if (s[l-1] == ' ' ) // blank space
1091    {
1092       l--;
1093       s = s.substr(0, l);
1094    }
1095
1096    if (s[0] == '<')
1097       s= s.substr(1,l-2);
1098    std::string repChar("_");
1099    GDCM_NAME_SPACE::Util::ReplaceSpecChar(s, repChar);
1100 }
1101
1102
1103
1104 // ===========================================================================================
1105
1106
1107 void Bruker2Dicom::getImhDataType(BrukerFieldData &bDPT, std::string &mhdDataPixelType, int &pixelSize)
1108 {
1109    if(bDPT.GetDataType() == "string")
1110    {
1111          std::string brukerDataPixelType = bDPT.GetStringValue()[0];
1112          if (verbose)
1113             std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
1114          //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
1115
1116          if (brukerDataPixelType ==  "ip_short") {
1117             mhdDataPixelType = "MET_USHORT";
1118             pixelSize = 2;
1119          }
1120          if (brukerDataPixelType ==  "ip_int") {
1121             mhdDataPixelType = "MET_UINT";
1122             pixelSize = 4;
1123          }
1124          if (brukerDataPixelType ==  "ip_char") {
1125              mhdDataPixelType = "MET_UCHAR";
1126              pixelSize = 1;
1127          }
1128                   /// \TODO : finish the list
1129     /*
1130     case 0 : fp << "ElementType = MET_CHAR" << std::endl;
1131       break;
1132     case 1 : fp << "ElementType = MET_UCHAR" << std::endl;
1133       break;
1134     case 2 : fp << "ElementType = MET_SHORT" << std::endl;
1135       break;
1136     case 3 : fp << "ElementType = MET_USHORT" << std::endl;
1137       break;
1138     case 4 : fp << "ElementType = MET_INT" << std::endl;
1139       break;
1140     case 5 : fp << "ElementType = MET_UINT" << std::endl;
1141       break;
1142     case 6 : fp << "ElementType = MET_FLOAT" << std::endl;
1143       break;
1144     case 7 : fp << "ElementType = MET_DOUBLE" << std::endl;
1145     */
1146     }
1147     else
1148     {
1149          int brukerDataPixelType = bDPT.GetIntValue()[0];
1150          if (verbose)
1151             std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
1152          //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
1153
1154 // Cross your fingers !!!
1155
1156 // pb : found values : 2, 3, 5
1157
1158          if (brukerDataPixelType ==  2) {
1159             mhdDataPixelType = "MET_USHORT";
1160             pixelSize = 2;
1161          }
1162          if (brukerDataPixelType ==  3) {
1163             mhdDataPixelType = "MET_USHORT";
1164             pixelSize = 2;
1165          }
1166          if (brukerDataPixelType ==  1) {
1167             mhdDataPixelType = "MET_UCHAR";
1168             pixelSize = 1;
1169          }
1170     }
1171 }
1172
1173 // ===========================================================================================
1174
1175 std::vector<BrukerImage> Bruker2Dicom::CreateImageSet ( )
1176 {
1177          std::vector<BrukerImage> imageSet;
1178          br_acqp.SetLoopStructure();
1179          std::vector<int> tempVect                      = br_acqp.GetLoopStructure() ;
1180          std::map<std::string, BrukerFieldData> map     = br_acqp.GetBrukerHeaderMap();
1181
1182          bool result                                    = br_acqp.ObjectVaryingProperties.init(map,tempVect);
1183
1184          if (result == false)
1185          {
1186             throw ( BrukerInitException  ("ObjectVaryingProperties.init() failure in Bruker2Dicom::CreateImageSet()") );
1187          }
1188
1189          br_acqp.SetImageLoopStructure();
1190          br_acqp.SetBrukerImageList();
1191          std::vector<std::vector<int> > brukerImageList = br_acqp.GetBrukerImageList();
1192
1193          BrukerImage image(br_acqp,br_reco);
1194          image.Init(br_acqp,br_reco,1);
1195
1196          for(int i=0;i<brukerImageList.size();i++)
1197          {
1198             image.Init(br_acqp,br_reco,i);
1199             imageSet.push_back(image);
1200          }
1201
1202  // Just for checking
1203  /*
1204
1205          std::vector<std::vector <double> > imageOrientation;
1206          std::vector <double> imagePosition;
1207          for(int i=0;i<brukerImageList.size();i++)
1208          {
1209            // fread(buffer_2dseq, NX*NY*pixelSize*nbSlices*nbInstants, 1, fp);
1210
1211            imagePosition = imageSet[i].getTranslationVectorRPS2XYZ();
1212            std::cout << "Position " << imagePosition[0] << " "
1213                      << imagePosition[1] << " "  << imagePosition[2] ;
1214            imageOrientation =  imageSet[i].getRotationMatrixRPS2XYZ();
1215            std::cout << "\t  Orientation " ;
1216            for(int i1=0; i1<3;i1++)for(int i2=0; i2<3;i2++)
1217               std::cout << imageOrientation[i1][i2] << " ";CreateImageSet
1218
1219            //std::cout << "\t  Abs Time " << imageSet[i].getAbsoluteTimePosition();
1220            std::cout << "\t  Relat Time " << imageSet[i].getRelativeTimePosition();
1221
1222            std::cout << "\t [";
1223            for (int i3=0; i3<imageSet[i].getLoopStamp().size();i3++)
1224               std::cout << " " << imageSet[i].getLoopStamp()[i3];
1225            std::cout << "]" << std::endl;
1226          }
1227 */
1228    return imageSet;
1229 }
1230
1231 // ===========================================================================================
1232
1233 void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels,
1234               int X,
1235               int Y,
1236               int nbFrames,
1237               int pixelSize,
1238               double spacingX, double spacingY, double sliceDistance,
1239               std::string dcmImageName,
1240               const std::string &patientName,
1241               const char *day,
1242               std::string &studyUID,
1243               std::string &serieUID,
1244               std::string &studyDescr,
1245               std::string &serieDescr,
1246               std::string &strStudyTimeDate,
1247               int imgNum,
1248               GDCM_NAME_SPACE::ImageContentType contentType
1249       )
1250 {
1251    std::ostringstream str;
1252
1253    GDCM_NAME_SPACE::File *file;
1254    file = GDCM_NAME_SPACE::File::New();
1255
1256   // Set the image size
1257    str.str("");
1258    str << X;
1259    file->InsertEntryString(str.str(),0x0028,0x0011,"US"); // Columns
1260    str.str("");
1261    str << Y;
1262    file->InsertEntryString(str.str(),0x0028,0x0010,"US"); // Rows
1263
1264    if (nbFrames != 1)
1265    {
1266       str.str("");
1267       str << nbFrames;
1268       file->InsertEntryString(str.str(),0x0028,0x0008,"IS"); // Number of Frames
1269    }
1270
1271   // Set the pixel type
1272   //      //8, 16, 32, 64 (for double ?)
1273    str.str("");
1274    str << pixelSize*8;
1275    file->InsertEntryString(str.str(),0x0028,0x0100,"US"); // Bits Allocated
1276
1277    file->InsertEntryString(str.str(),0x0028,0x0101,"US"); // Bits Stored
1278
1279    str.str("");
1280    str << pixelSize*8-1;
1281    file->InsertEntryString(str.str(),0x0028,0x0102,"US"); // High Bit
1282
1283   // Set the pixel representation // 0/1 , 0=unsigned
1284    file->InsertEntryString("1",0x0028,0x0103, "US"); // Pixel Representation
1285
1286   // Set the samples per pixel // 1:Grey level, 3:RGB
1287    file->InsertEntryString("1",0x0028,0x0002, "US"); // Samples per Pixel
1288
1289 //  0028 0030 DS 2 Pixel Spacing
1290    str.str("");
1291    str << spacingX << "\\" << spacingY;
1292    file->InsertEntryString(str.str(),0x0028,0x0030, "DS"); // Pixel Spacing
1293
1294  //   0018 0050 DS 1 Slice Thickness
1295    str.str("");
1296    str << sliceDistance;
1297    file->InsertEntryString(str.str(),0x0018,0x0050, "DS");
1298
1299 //    0020 0011 IS 1 Series Number
1300    str.str("");
1301    str << serieNumber;
1302    file->InsertEntryString(str.str(),0x0020,0x0011, "IS");
1303
1304 //    0020|0013 [IS]  [Instance Number]
1305    instanceNumber++;
1306    str.str("");
1307    str << instanceNumber;
1308    file->InsertEntryString(str.str(),0x0020,0x0013, "IS");
1309
1310
1311   // 1.2.840.10008.5.1.4.1.1.4.1 : Enhanced MR Image Storage
1312  //  file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0002, 0x0002, "UI");  // [Media Storage SOP Class UID]
1313   // file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0008, 0x0016, "UI");  // [SOP Class UID]
1314
1315
1316 // OK : MR is NOT multiframe, but I want just a quick an dirty solution
1317
1318 // 1.2.840.10008.5.1.4.1.1.4         MR Image Storage
1319    file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0002, 0x0002, "UI");  // [Media Storage SOP Class UID]
1320    file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0008, 0x0016, "UI");  // [SOP Class UID]
1321
1322   // if (strlen(patientName) != 0)
1323    file->InsertEntryString(patientName.c_str(),0x0010,0x0010, "PN"); // Patient's Name
1324
1325    file->InsertEntryString(studyUID, 0x0020, 0x000d, "UI");
1326    file->InsertEntryString(serieUID, 0x0020, 0x000e, "UI");
1327
1328 //  0008 0020 DA 1 Study Date
1329 //  0008 0030 TM 1 Study Time
1330
1331 /// \TODO split into 2 strings!
1332    file->InsertEntryString(strStudyTimeDate.substr(10,11).c_str(),0x0008,0x0020, "DA");
1333    file->InsertEntryString(strStudyTimeDate.substr(1,8).c_str(),  0x0008,0x0030, "TM");
1334
1335    file->InsertEntryString(studyDescr, 0x0008,0x1030, "LO");  // Study Description
1336    file->InsertEntryString(serieDescr, 0x0008,0x103e, "LO");  // Series Description
1337
1338 //0008|0060 [CS] [Modality]
1339    file->InsertEntryString("MR",0x0008,0x0060, "CS");
1340
1341 // 0020 0037 DS 6 Image Orientation (Patient)
1342    char charImageOrientation[256];
1343
1344 /*
1345 std::cout << "charImageOrientation  " <<
1346                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0] << " " <<
1347                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1] << " " <<
1348                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2] << " " <<
1349                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0] << " " <<
1350                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1] << " " <<
1351                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] << std::endl ;
1352 */
1353    sprintf(charImageOrientation,"%f\\%f\\%f \\ %f\\%f\\%f",
1354                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0],
1355                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1],
1356                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2],
1357                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0],
1358                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1],
1359                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] ) ;
1360
1361    file->InsertEntryString(charImageOrientation,0x0020,0x0037, "DS");
1362
1363
1364 // 0020 0032 DS 3 Image Position (Patient)
1365
1366    char charImagePosition[256];
1367    sprintf(charImagePosition,"%f\\%f\\%f",
1368                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[0],
1369                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[1],
1370                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[2]);
1371
1372    file->InsertEntryString(charImagePosition,0x0020,0x0032, "DS");  //0020 0032 DS 3 Image Position (Patient)
1373
1374
1375
1376 // 0020 0x1041 DS 1 Slice Location
1377 //        sprintf(charImagePosition,"%f",float(imgNum));
1378 //        file->InsertEntryString(charImagePosition,0x0020,0x1041, "DS");
1379 /*
1380   // Set Rescale Intercept
1381         str.str("");
1382         str << div;
1383         file->InsertEntryString(str.str(),0x0028,0x1052,"DS");
1384
1385   // Set Rescale Slope
1386         str.str("");
1387         str << mini;
1388         file->InsertEntryString(str.str(),0x0028,0x1053,"DS");
1389 */
1390
1391    GDCM_NAME_SPACE::FileHelper *fileH;
1392    fileH = GDCM_NAME_SPACE::FileHelper::New(file);
1393    fileH->SetContentType(contentType);
1394
1395    // cast is just to avoid warnings (*no* conversion is performed)
1396    //fileH->SetImageData((uint8_t *)img,int(maxX*maxY)*sizeof(uint16_t)); // troubles when maxX, mayY are *actually* float!
1397
1398 //std::cout << "--------------------------------  X*Y*nbFrames*pixelSize " << X << " " << Y << " " << nbFrames << " " << pixelSize << std::endl;
1399
1400    fileH->SetImageData((uint8_t *)tabPixels, X*Y*nbFrames*pixelSize);
1401    fileH->SetWriteModeToRaw();
1402    fileH->SetWriteTypeToDcmExplVR();
1403    if( !fileH->Write(dcmImageName)) {
1404       std::cout << "Failed for [" << dcmImageName << "]\n"
1405                 << "           File is unwrittable" << std::endl;
1406       file->Delete();
1407       fileH->Delete();
1408       throw ( BrukerHopelessException ("Level 1 Unable to write Dicom file "));
1409    }
1410    //if (verbose)
1411    //   file->Print();
1412
1413    file->Delete();
1414    fileH->Delete();
1415 }
1416
1417