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 bool Bruker2Dicom::Execute()
  11 {
  12    // ----- Check input directory name -----
  13
  14    bool bigEndian = GDCM_NAME_SPACE::Util::IsCurrentProcessorBigEndian();
  15
  16    //if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(InputDirName) )
  17    if ( ! boost::filesystem::is_directory(InputDirName) )
  18    {
  19       std::cout << "KO : [" << InputDirName << "] is not a Directory." << std::endl;
  20       return 0;
  21    }
  22    else
  23    {
  24       if (verbose)
  25          std::cout << "OK : [" << InputDirName << "] is a Directory." << std::endl;
  26    }
  27
  28    // ----- Check output directory name -----
  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 //
  39 // e.g : at level 0, in : B67d1.Bp1
  40 //
  41 //           1  2  3  4  5  6  AdjStatePerStudy  subject
  42 //
  43
  44    std::string strDirNamein(InputDirName);
  45
  46 /* */
  47    GDCM_NAME_SPACE::DirList dirList(strDirNamein, false, true); // DON'T get recursively the list of files
  48
  49    GDCM_NAME_SPACE::DirListType fileNames;
  50    fileNames = dirList.GetFilenames();
  51
  52    std::string path = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()));
  53
  54    std::string subject =  path +
  55                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
  56                           "subject";
  57
  58     std::string acqp = path +
  59                        GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
  60                        "acqp";
  61
  62     if ( boost::filesystem::is_regular(subject) )
  63        subjectFound = true;
  64     else
  65        subjectFound = false; // user passed only a 'serie', not a 'study
  66
  67     if ( boost::filesystem::is_regular(acqp) )
  68        acqpFound= true;
  69     else
  70        acqpFound = false; // user passed a 'non study' directory; Hope it's a 'set of studies' directory!
  71
  72    int type;
  73    if  (subjectFound )  type = 1; // user passed a 'study
  74    else if  (acqpFound) type = 2; // user passed a 'serie'
  75    else                 type = 3; // user passed a 'non study' directory; Hope it's a 'set of studies' directory!
  76  /* */
  77
  78    // 1 : if subjectFound                       : user passed a Single Study Directory
  79    // 2 : if NOT subjectFound and acqpFound     : user passed a Serie Directory
  80    // 3 : if NOT subjectFound and NOT acqpFound : user passed a 'non Study Directory' (Hope it's a set of Single Study Directories)
  81
  82    //int type = CheckUserDirectory(InputDirName);
  83
  84    switch (type)
  85    {
  86       case 1: {
  87          bool canOpen = br_subject.LoadFile(subject);
  88          if (!canOpen)
  89          {
  90             std::cout << "Hopeless! 'subject' found / cannot be open" << std::endl;
  91             throw ( BrukerHopelessException ("Hopeless! 'subject' found in root input directory / cannot be open"));
  92          }
  93          else
  94          {
  95             br_subject.FillMap();
  96
  97             // get info for 'Study Description'
  98             BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string");
  99             subject_name = b_name.GetStringValue()[0];
 100             strPatientName = subject_name;
 101             cleanString(subject_name);
 102             DealWithSingleStudyDirectory (fileNames);
 103          }
 104          break;
 105       }
 106
 107       case 2: {
 108          subject_name = "defaultPatName";
 109          strPatientName = subject_name;
 110          DealWithSingleStudyDirectory (fileNames);
 111          break;
 112       }
 113
 114       case 3: {
 115          std::cout << " User passed a 'non study' directory; Hope it's a *non recursive* 'set of studies' directory! (recursive not yet dealt with)" << std::endl;
 116          DealWithMultiStudyDirectory (fileNames);
 117          break;
 118       }
 119    }
 120 }
 121
 122 // ----------------------------------------------------------------------------------------------------------
 123
 124 void Bruker2Dicom::DealWithMultiStudyDirectory (GDCM_NAME_SPACE::DirListType &dirNames)
 125 {
 126    GDCM_NAME_SPACE::DirListType::iterator it;
 127
 128    for (it = dirNames.begin();
 129          it != dirNames.end();
 130        ++it)
 131    {
 132       if ( boost::filesystem::is_directory(*it) )
 133       {
 134          subjectFound = false;
 135          if (verbose)
 136             std::cout << "in 'DealWithMultiStudyDirectory' [" << *it << "] is a directory" << std::endl;
 137
 138          GDCM_NAME_SPACE::DirList dirList(*it, false, true); // DON'T get recursively the list of files
 139          GDCM_NAME_SPACE::DirListType fileNames;
 140          fileNames = dirList.GetFilenames();
 141
 142          std::string path = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()));
 143          std::string subject =  path +
 144                                 GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 145                                 "subject";
 146          if (! boost::filesystem::is_regular(subject) )
 147          {
 148             std::cout << "no [" << subject << "] file found" << std::endl;
 149             continue;
 150          }
 151
 152          bool canOpen = br_subject.LoadFile(subject);
 153          if (!canOpen)
 154          {
 155             std::cout << "Hopeless! 'subject' found / cannot be open" << std::endl;
 156             throw ( BrukerHopelessException ("Hopeless! 'subject' found in root input directory / cannot be open"));
 157          }
 158          else
 159          {
 160             br_subject.FillMap();
 161             subjectFound = true; // Hope so! (full checking needed!)
 162
 163             BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string");
 164             subject_name = b_name.GetStringValue()[0];
 165             strPatientName = subject_name;
 166             cleanString(subject_name);
 167             DealWithSingleStudyDirectory(fileNames);
 168          }
 169       }
 170       else
 171       {
 172          if (verbose)
 173             std::cout << "[" << *it << "] is NOT a directory; skipped!" << std::endl;
 174       }
 175    }
 176 }
 177
 178 // ----------------------------------------------------------------------------------------------------------
 179
 180 void Bruker2Dicom::DealWithSingleStudyDirectory (GDCM_NAME_SPACE::DirListType &fileNames)
 181 {
 182      bool res;
 183     // creation directory : 'nom du patient'
 184     std::string tempStringPatDir(OutputDirName);
 185     tempStringPatDir = tempStringPatDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + subject_name;
 186
 187     res=CreateDirectory(tempStringPatDir);
 188     if (!res) {
 189        std::cout << "[" << tempStringPatDir << "] Directory creation failure " << std::endl;
 190        throw ( BrukerHopelessException ("Patient directory creation failure "));
 191     }
 192
 193     if (subjectFound)
 194     {
 195        BrukerFieldData b_entry=br_subject.GetFieldData("SUBJECT_entry");
 196        subject_entry = b_entry.GetStringValue()[0];
 197        //cleanString(subject_entry);
 198        subject_entry = subject_entry.substr(11, subject_entry.size()-11);
 199
 200        BrukerFieldData b_position=br_subject.GetFieldData("SUBJECT_position");
 201        subject_position = b_position.GetStringValue()[0];
 202        //cleanString(subject_position);
 203        subject_position = subject_position.substr(9, subject_position.size()-9);
 204
 205        BrukerFieldData b_date=br_subject.GetFieldData("SUBJECT_date");
 206        subject_date = b_date.GetStringValue()[0];
 207        strStudyTimeDate = subject_date;
 208        cleanString(subject_date);
 209
 210        BrukerFieldData b_study_name=br_subject.GetFieldData("SUBJECT_study_name");
 211        subject_study_name = b_study_name.GetStringValue()[0];
 212        subject_study_name = subject_study_name.substr(1, subject_study_name.size()-2);
 213        cleanString(subject_study_name);
 214    }
 215    else  // Desperate trick when file 'subject' is missing
 216    {
 217       subject_entry      = "HeadFirst";            // Why not?
 218       subject_position   = "Supine";               // Why not?
 219       strStudyTimeDate   = "06_06_06_6_June_1666"; // Why not?
 220       subject_date       = "6_June_1666";          // Why not?
 221       subject_study_name = "defStudyName";         // Why not?
 222    }
 223     // subject_name is already in 'Patient Name'
 224     strStudyDescr = /*subject_name + "." + */ subject_study_name + "." + subject_entry + "." + subject_position + "." + subject_date;
 225
 226     // creation directory : 'nom de la Study'
 227
 228     std::string tempStringStudyDir(OutputDirName);
 229     tempStringStudyDir = tempStringPatDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + strStudyDescr;
 230
 231     res=CreateDirectory(tempStringStudyDir);
 232     if (!res) {
 233        std::cout << "[" << tempStringStudyDir << "] Directory creation failure " << std::endl;
 234        throw ( BrukerHopelessException ("Study directory creation failure "));
 235     }
 236
 237    char outputDirName[(unsigned int) PATH_MAX+2];
 238
 239    strStudyUID    = GDCM_NAME_SPACE::Util::CreateUniqueUID();
 240    serieNumber    = 0;
 241    instanceNumber = 0;
 242
 243    // -----------------------------------------------------
 244    // Iterate to ALL the objets(files/directories) found in the input directory
 245    // (this is level ZERO)
 246    // each Directory (name : 1, 2, 3, ...) will be a Dicom Serie
 247    // -----------------------------------------------------
 248
 249    /// \TODO better use directory iterator, from boost! // JPR
 250    GDCM_NAME_SPACE::DirListType::iterator it;
 251
 252    for (it = fileNames.begin();
 253          it != fileNames.end();
 254        ++it)
 255    {
 256       if ( boost::filesystem::is_directory(*it) )
 257       {
 258          if (verbose)
 259             std::cout << "[" << *it << "] is a directory" << std::endl;
 260
 261          //if((*it) == "AdjResult")  // avoid trouble with new version 'AdjResult' directory
 262          if(GDCM_NAME_SPACE::Util::GetName(*it) == "AdjResult")
 263             continue;
 264
 265          //BrukerDataSet br_acqp;
 266          std::string strAcqp;
 267          strAcqp = (*it) +
 268                    GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 269                    "acqp";
 270
 271          br_acqp.LoadFile(strAcqp);
 272          br_acqp.FillMap();
 273
 274 //std::cout << "out of br_acqp.FillMap " << std::endl;
 275          std::string acqp_scan_name;
 276          std::string acqp_method;
 277          std::string acqp_protocol_location;
 278
 279          BrukerFieldData b_protocol_location=br_acqp.GetFieldData("ACQ_protocol_location");
 280          acqp_protocol_location = b_protocol_location.GetStringValue()[0];
 281          cleanString(acqp_protocol_location);
 282
 283 //std::cout << "out of br_acqp.FillMap 1" << std::endl;
 284          BrukerFieldData b_scan_name=br_acqp.GetFieldData("ACQ_scan_name");
 285 //std::cout << "out of br_acqp.FillMap 11" << std::endl;
 286          acqp_scan_name = b_scan_name.GetStringValue()[0];
 287 //std::cout << "out of br_acqp.FillMap 12 [" << acqp_scan_name << "]" << std::endl;
 288          cleanString(acqp_scan_name);
 289 //std::cout << "out of br_acqp.FillMap 2" << std::endl;
 290          BrukerFieldData b_method=br_acqp.GetFieldData("ACQ_method");
 291          b_method.PrintSelf();
 292          acqp_method = b_method.GetStringValue()[0];
 293
 294          cleanString(acqp_method);
 295 //std::cout << "out of br_acqp.FillMap 3" << std::endl;
 296          BrukerFieldData b_list_size = br_acqp.GetFieldData("ACQ_O1_list_size");
 297 //std::cout << "out of br_acqp.FillMap 4" << std::endl;
 298          //b_list_size.PrintSelf(); //JP
 299
 300          nbSlices =  b_list_size.GetIntValue()[0];
 301 //std::cout << "out of br_acqp.FillMap 5" << std::endl;
 302          strSerieDescr = GDCM_NAME_SPACE::Util::GetName(*it)
 303                        /*  + "." + acqp_protocol_location */ // always the same (in each acquisition)
 304                          + "." + acqp_scan_name
 305                          + "." + acqp_method.c_str();
 306
 307          sprintf(outputDirName, "%s%c%s", tempStringStudyDir.c_str(),      //OutputDirName.c_str(),
 308                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 309                           strSerieDescr.c_str() );
 310
 311          std::cout << " ================================================================================\n"
 312                    << " === [" << GDCM_NAME_SPACE::Util::GetName(*it) << "] -> [" << strSerieDescr << "]\n"
 313                    << " ================================================================================"
 314                    << std::endl;
 315         std::string strOutputDirName(outputDirName);
 316         if (verbose)
 317            printf ("outputDirName [%s]\n", outputDirName);
 318         try {
 319            DealWithNiveau1(*it, strOutputDirName);
 320         }
 321         catch (BrukerHopelessException &e)
 322         {
 323          std::cout << "And Exception was thrown in DealWithNiveau1 (" << e.what() << ") " << std::endl;
 324          continue;
 325         }
 326       }
 327    } // end of : for (GDCM_NAME_SPACE::DirListType::iterator it
 328 }
 329
 330 // =====================================================================
 331
 332 void Bruker2Dicom::DealWithNiveau1(std::string &level1Directory, std::string &currentOutputDirName) {
 333 //
 334 // e.g. : at level 1, in B67d1.Bp1/6
 335 //
 336 // acqp  fid  imnd  pdata  pulseprogram  spnam0  spnam1
 337
 338    bool res = CreateDirectory(currentOutputDirName);
 339
 340    if (!res) {
 341       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 342       throw ( BrukerHopelessException ("Level 1 output directory creation failure "));
 343      // exit (0);
 344    }
 345    GDCM_NAME_SPACE::DirList dirList(level1Directory, false, true); // DON'T get recursively the list of files
 346    GDCM_NAME_SPACE::DirListType fileNames;
 347    fileNames = dirList.GetFilenames();
 348    // -----------------------------------------------------
 349    // Iterate to ALL the objets(files/directories) found in the input directory
 350    // -----------------------------------------------------
 351    GDCM_NAME_SPACE::DirListType::iterator it;
 352
 353    for (it = fileNames.begin();
 354         it != fileNames.end();
 355       ++it)
 356    {
 357       if ( boost::filesystem::is_regular(*it) )
 358       //if ( ! boost::filesystem::is_directory(*it) )
 359       {
 360          if (verbose)
 361             std::cout << "--- [" << *it << "] is a file." << std::endl;
 362       }
 363    }
 364
 365    char outputDirName[(unsigned int) PATH_MAX+2];
 366    //std::string firstName;
 367    bool canOpen;
 368    for (it = fileNames.begin();
 369         it != fileNames.end();
 370       ++it)
 371    {
 372       if ( boost::filesystem::is_directory(*it) )
 373       {
 374          // will be always "pdata" ...
 375          if (verbose)
 376             std::cout << "--- [" << *it << "] is a directory" << std::endl;
 377
 378               /* a recuperer :
 379               if (FileLine.startsWith("##$ACQ_size=")) {
 380               if (FileLine.startsWith("##$NI=")) {
 381               if (FileLine.startsWith("##$NR=")) {
 382               if (FileLine.startsWith("##$ACQ_obj_order=")) {
 383               if (FileLine.startsWith("##$ACQ_word_size=")) {
 384               if (FileLine.startsWith("##$BYTORDA=")) {
 385               if (FileLine.startsWith("##$PULPROG=")) {
 386               */
 387
 388          sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 389                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 390                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str());
 391          std::string strOutputDirName(outputDirName);
 392          //br1.PrintSelf();
 393
 394           std::string strMethod;
 395           //std::string firstName = *(fileNames.begin());
 396
 397           strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin())) +
 398                       GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 399                       "method";
 400             // std::cout << "---strMethod (for method)=> [" << strMethod << "]" << std::endl;
 401           canOpen = br_method.LoadFile(strMethod);
 402           if (!canOpen)
 403           {
 404              strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
 405                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 406                          "imnd";
 407              //std::cout << "---strMethod (for imnd) => [" << strMethod << "]" << std::endl;
 408              canOpen = br_method.LoadFile(strMethod);
 409              if (!canOpen)
 410              {
 411                 std::cout << "Hopeless! neither 'method' nor 'imnd' found in ["
 412                           << level1Directory  << "]; we skip it!" << std::endl;
 413                 continue;
 414                 //throw ( BrukerHopelessException ("Hopeless! neither 'method' nor 'imnd' found "));
 415                 //exit(0);  /// \TODO throw an exception !
 416              }
 417           }
 418           if (verbose)
 419              std::cout << "open => [" << strMethod << "] successfully" << std::endl;
 420           br_method.FillMap();
 421
 422           /* a recuperer :
 423              ##$PVM_Fov (dimension)  // ou plutot RECO_fov !
 424           */
 425   /*
 426           dans method (pour perfusion  seulement?) :
 427           ##$PVM_ObjOrderList=( 8 )
 428           0 2 4 6 1 3 5 7
 429           ##$PVM_NSPacks=2
 430           ##$PVM_SPackArrNSlices=( 2 )
 431           7 1
 432   */
 433          try {
 434             DealWithNiveau2(*it, strOutputDirName);
 435          }
 436          catch (BrukerHopelessException &e)
 437          {
 438             std::cout << "And Exception was thrown in DealWithNiveau2 (" << e.what() << ") " << std::endl;
 439             continue;
 440          }
 441       }
 442    }
 443 }
 444
 445 // =====================================================================
 446
 447 void Bruker2Dicom::DealWithNiveau2(std::string &level2Directory, std::string &currentOutputDirName) {
 448
 449 // e.g. : at level 2 in B67d1.Bp1/6/pdata
 450 //
 451 // acqp  fid  imnd  pdata  pulseprogram  spnam0  spnam1
 452 //
 453
 454    bool res = CreateDirectory(currentOutputDirName);
 455
 456    if (!res) {
 457       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 458       throw ( BrukerHopelessException ("Hopeless! Level2 output directory creation failure"));
 459       //exit (0);
 460    }
 461
 462    GDCM_NAME_SPACE::DirList dirList(level2Directory, false, true); // DON'T get recursively the list of files
 463
 464    GDCM_NAME_SPACE::DirListType fileNames;
 465    fileNames = dirList.GetFilenames();
 466
 467    char outputDirName[(unsigned int) PATH_MAX+2];
 468
 469    // -----------------------------------------------------
 470    // Iterate to ALL the objets(files/directories) found in the input directory
 471    // -----------------------------------------------------
 472    GDCM_NAME_SPACE::DirListType::iterator it;
 473    bool canOpen;
 474
 475    if (verbose)
 476    for (it = fileNames.begin();
 477         it != fileNames.end();
 478       ++it)
 479    {
 480       if ( ! boost::filesystem::is_directory(*it) )
 481       {
 482          std::cout << "--- --- [" << *it << "] is a file.." << std::endl;
 483       }
 484    }
 485
 486    for (it = fileNames.begin();
 487          it != fileNames.end();
 488        ++it)
 489    {
 490       if ( boost::filesystem::is_directory(*it) )
 491       {
 492
 493          if (verbose)
 494             std::cout << "--- --- [" << *it << "] is a directory" << std::endl;
 495
 496         // sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 497         //                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 498         //                                GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
 499   // MUST be 'pdata'!
 500
 501 //
 502 // (interest of previous method :
 503 // If unaware user changed the pdata name, it goes on working
 504 //
 505           std::string str_isa;
 506           str_isa = (*it) +
 507                     GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 508                    "isa";
 509
 510           std::string str_isa_func_name;
 511           canOpen = br_isa.LoadFile(str_isa);
 512           if (!canOpen)
 513           {
 514              sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 515                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 516                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
 517           }
 518           else
 519           {
 520              br_isa.FillMap();
 521              BrukerFieldData b_isa_func_name = br_isa.GetFieldData("ISA_func_name");
 522
 523              str_isa_func_name = b_isa_func_name.GetStringValue()[0];
 524              cleanString(str_isa_func_name);
 525
 526              sprintf(outputDirName, "%s%c%s.%s", currentOutputDirName.c_str(),
 527                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 528                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str(),
 529              str_isa_func_name.c_str());
 530           }
 531           std::string strOutputDirName(outputDirName);
 532           try {
 533              DealWithNiveau3(*it, strOutputDirName);
 534           }
 535           catch (BrukerHopelessException &e)
 536           {
 537              std::cout << "And Exception was thrown in DealWithNiveau3 (" << e.what() << "); "
 538                        << " We skip [" << level2Directory << "]" << std::endl;
 539              continue;
 540           }
 541           catch (BrukerInitException &e)
 542           {
 543              std::cout << "And Init Exception was thrown in DealWithNiveau3 (" << e.what() << "); "
 544                        << " We skip [" << level2Directory << "]" << std::endl;
 545              continue;
 546           }
 547       }
 548    }
 549 }
 550
 551 //
 552 // =====================================================================
 553 //
 554
 555 void Bruker2Dicom::DealWithNiveau3(std::string &level3Directory, std::string &currentOutputDirName){
 556
 557 //
 558 // e.g. at level 3, in
 559
 560    // just to be able to go on checking // JP
 561    if ( GDCM_NAME_SPACE::Util::GetName(level3Directory) != "1")
 562       return;
 563
 564    bool res = CreateDirectory(currentOutputDirName);
 565
 566    if (!res)
 567    {
 568       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 569       throw ( BrukerHopelessException ("Hopeless! Level3 output directory creation failure"));
 570       //exit (0);
 571    }
 572
 573    GDCM_NAME_SPACE::DirList dirList(level3Directory, false, true); // DON'T get recursively the list of files
 574    GDCM_NAME_SPACE::DirListType::iterator it;
 575    GDCM_NAME_SPACE::DirListType fileNames;
 576    fileNames = dirList.GetFilenames();
 577
 578    char original2dseqName       [(unsigned int) PATH_MAX+2];
 579    char original2dseqName_XXX   [(unsigned int) PATH_MAX+2];
 580    char currentOutputMhdDirName [(unsigned int) PATH_MAX+2];
 581
 582    char outputMhdFileName       [(unsigned int) PATH_MAX+2];
 583    char output2dseqSliceFileName[(unsigned int) PATH_MAX+6]; // think about extra '.dcm'
 584    char output2dseqName         [(unsigned int) PATH_MAX+6];
 585    char output2dseqCartoName    [(unsigned int) PATH_MAX+6];
 586
 587    char copyFile[PATH_MAX + PATH_MAX + 5]; // Should be enough!
 588    bool canOpen;
 589
 590    //-------------- try d3proc;
 591    char char_d3proc[(unsigned int) PATH_MAX+2];
 592
 593    sprintf(char_d3proc,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"d3proc" );
 594
 595    if (verbose)
 596       std::cout << "d3proc: --- => [" << char_d3proc << "]" << std::endl;
 597    std::string str_d3proc(char_d3proc);
 598    canOpen = br_d3proc.LoadFile(str_d3proc);
 599
 600    if (!canOpen)
 601    {
 602       std::cout << "Hopeless! no 'd3proc' found" << std::endl;
 603       throw ( BrukerHopelessException ("Hopeless! no 'd3proc' found"));
 604       //exit(0);  /// \TODO throw an exception !
 605    }
 606
 607    canOpen = br_d3proc.FillMap();
 608    if (!canOpen)
 609    {
 610       std::cout << "Hopeless! FillMap failed on 'd3proc'" << std::endl;
 611       throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'd3proc'"));
 612       //exit(0);  /// \TODO throw an exception !
 613    }
 614
 615    //-------------- end try d3proc;
 616
 617
 618  // -------------------try reco
 619
 620    char char_reco[(unsigned int) PATH_MAX+2];
 621
 622    sprintf(char_reco,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
 623     //str_d3proc = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
 624     //             GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 625     //             "d3proc";
 626    if (verbose)
 627       std::cout << "reco: --- => [" << char_reco << "]" << std::endl;
 628
 629    std::string str_reco(char_reco);
 630    canOpen = br_reco.LoadFile(str_reco);
 631
 632    if (!canOpen) // we try in directory ../1
 633    {
 634       if (verbose)
 635          std::cout << "[" << str_reco << "] not found " << std::endl;
 636       std::string lastDirName = GDCM_NAME_SPACE::Util::GetPath(level3Directory);
 637       //lastDirName = GDCM_NAME_SPACE::Util::GetPath(lastDirName);
 638       sprintf(char_reco,"%s%c1%c%s", lastDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
 639       //str_reco=char_reco;
 640       canOpen = br_reco.LoadFile(str_reco);
 641       if (!canOpen)
 642       {
 643          std::cout << "Hopeless! cannot find 'reco' in [" << str_reco << "]"  << std::endl;
 644          throw ( BrukerHopelessException ("Hopeless! cannot find 'reco'"));
 645          //exit(0);  /// \TODO throw an exception !
 646       }
 647    } else {
 648       if (verbose)
 649          std::cout << "[" << str_reco << "] successfully Loaded " << std::endl;
 650    }
 651
 652    canOpen = br_reco.FillMap();
 653    if (!canOpen)
 654    {
 655       std::cout << "Hopeless! FillMap failed on [" << str_reco << "]" << std::endl;
 656       throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'reco'"));
 657       //exit(0);  /// \TODO throw an exception !
 658    } else {
 659       if (verbose)
 660          std::cout << "[" << str_reco << "] successfully Mapped" << std::endl;
 661    }
 662
 663    //std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
 664    // br_reco.PrintSelf();
 665    // std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
 666    // -------------------end try reco
 667
 668
 669    BrukerFieldData bX = br_d3proc.GetFieldData("IM_SIX");
 670    int NX = bX.GetIntValue()[0];
 671
 672    if (verbose)
 673       std::cout << "IM_SIX " << NX << std::endl;
 674    BrukerFieldData bY=br_d3proc.GetFieldData("IM_SIY");
 675    int NY = bY.GetIntValue()[0];
 676
 677    if (verbose)
 678          std::cout << "IM_SIY " << NY << std::endl;
 679    /// \todo : check if there are actually 3 dimensions or only 2
 680
 681    BrukerFieldData bZ= br_d3proc.GetFieldData("IM_SIZ");
 682    int nbFrames = bZ.GetIntValue()[0];
 683    if (verbose)
 684          std::cout << "IM_SIZ " << nbFrames << std::endl;
 685
 686         // WARNING DATTYPE is, either in {ip_short, ip_int, ip_char, ...}, or in {1, 2, 3, ...}
 687
 688    BrukerFieldData bDPT = br_d3proc.GetFieldData("DATTYPE");
 689
 690    std::string mhdDataPixelType;
 691    int pixelSize;
 692    getImhDataType(bDPT, mhdDataPixelType, pixelSize);
 693
 694
 695  /*
 696
 697  // See mail Denis :
 698  // En regle generale il vaut mieux que l'on passe par RECO_*
 699  // pour extraire les parametres de l'image
 700  //
 701
 702    BrukerFieldData fov = br_method.GetFieldData("PVM_Fov");
 703    double fovX = fov.GetDoubleValue()[0];
 704    double fovY = fov.GetDoubleValue()[1];
 705    if (verbose)
 706       std::cout << "FOV (ds method) " << fovX << " " << fovY << std::endl;
 707
 708    BrukerFieldData spatResol = br_method.GetFieldData("PVM_SpatResol");
 709    double spatResolX = spatResol.GetDoubleValue()[0];
 710    double spatResolY = spatResol.GetDoubleValue()[1];
 711    if (verbose)
 712       std::cout << "SpatResol (ds method) " << spatResolX << " " << spatResolY << std::endl;
 713
 714 */
 715
 716 /* ------  */
 717 // Better we use 'get' accessors from BrukerImage class, as Denis wrote them
 718
 719    BrukerFieldData fov = br_reco.GetFieldData("RECO_fov");
 720    double fovX = fov.GetDoubleValue()[0];
 721    double fovY = fov.GetDoubleValue()[1];
 722    if (verbose)
 723       std::cout << "FOV (ds reco) " << fovX << " " << fovY << std::endl;
 724
 725    BrukerFieldData size = br_reco.GetFieldData("RECO_size");
 726    double sizeX = size.GetDoubleValue()[0];
 727    double sizeY = size.GetDoubleValue()[1];
 728
 729    if (verbose)
 730       std::cout << "SIZE (ds reco) " << sizeX << " " << sizeY << std::endl;
 731
 732    double spatResolX = fovX / sizeX;
 733    double spatResolY = fovY / sizeY;
 734
 735    if (verbose)
 736       std::cout << "spatResol (ds reco : fov/size) " << spatResolX << " " << spatResolY << std::endl;
 737
 738 /* ------  */
 739
 740    /// \TODO probabely a more sophisticated accessor will be necessary :
 741    ///  (cf : non contiguous slices, overlapping, slice thickness, space between slices, etc)
 742
 743    BrukerFieldData bsliceDistance = br_method.GetFieldData("PVM_SPackArrSliceDistance");
 744    double sliceDistance = bsliceDistance.GetDoubleValue()[0];
 745
 746    if (verbose)
 747       std::cout << "SPackArrSliceDistance (ds method) " << sliceDistance << std::endl;
 748
 749 // ----------------------------------------------------------------------------------------
 750
 751    if (mhd)
 752    {
 753       sprintf(currentOutputMhdDirName, "%s%c%s", currentOutputDirName.c_str(),
 754                                GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "MhdFiles");
 755
 756       std::string strCurrentOutputMhdDirName(currentOutputMhdDirName);
 757       res = CreateDirectory( strCurrentOutputMhdDirName );
 758       if (!res) {
 759          std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 760          throw ( BrukerHopelessException ("Hopeless!FillMap failed on 'reco'"));
 761          //exit (0);
 762       }
 763
 764       if (verbose)
 765          std::cout << "Directory creation [" <<  currentOutputDirName << "]" << std::endl;
 766    }  // end if mhd
 767
 768    if (verbose)
 769          std::cout << "nbFrames " << nbFrames << std::endl;
 770    if (verbose)
 771          std::cout << "nbSlices " << nbSlices << std::endl;
 772    int k;
 773    int nbInstants = nbFrames/nbSlices;
 774    if (verbose)
 775          std::cout << "nbInstants (deduced)" << nbInstants << std::endl;
 776    int instantNb;
 777    int sliceNb;
 778    FILE *fp;  // for MHD files
 779
 780    sprintf( original2dseqName, "%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "2dseq");
 781
 782 /**/
 783   // \TODO : tenir compte du bazar precedent
 784
 785     // load 2dseq in memory
 786
 787    fp = fopen(original2dseqName, "rb");
 788    if (!fp)
 789    {
 790       // try 2dseq_Angio2D ?!?
 791
 792       sprintf( original2dseqName_XXX, "%s%s", original2dseqName, "_Angio2D");
 793       fp = fopen(original2dseqName_XXX, "rb");
 794       if (!fp)
 795       {
 796          std::cout << "Cannot open [" << original2dseqName << "] nor [" <<  original2dseqName_XXX << "] for reading" << std::endl;
 797          fclose(fp);
 798          throw ( BrukerHopelessException ("Hopeless! Cannot open '2dseq'"));
 799          //exit (0);
 800       }
 801    }
 802
 803    unsigned char *buffer_2dseq = new unsigned char[NX*NY*pixelSize*nbSlices*nbInstants];
 804    ///\ TODO : find a safer way to be sure to read everything!
 805    size_t lgr = fread(buffer_2dseq, 1, NX*NY*pixelSize*nbSlices*nbInstants, fp);
 806
 807    // This one will be important!
 808    // ---------------------------
 809    try {
 810       imageSet = CreateImageSet ( );
 811    }
 812    catch (BrukerInitException& e)
 813    {
 814       if (verbose)
 815          std::cout <<  "an Init Exception was thrown in CreateImageSet ( ); " << e.what()
 816                    <<  "catched in DealWithNiveau3" << std::endl;
 817       //return;
 818       throw (e);
 819    }
 820
 821    serieNumber++;
 822    strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 823    if (nbInstants==1) // creer un seul fichier .mhd  pour toutes les Slices! (images natives)
 824    {
 825        if (verbose)
 826           std::cout << "Single instant : do not split" << std::endl;
 827        if (mhd)
 828        {
 829              sprintf(outputMhdFileName, "%s%cMhdData_All_the_Slices.mhd", currentOutputMhdDirName,
 830                                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 831              fp=fopen(outputMhdFileName, "w");
 832              if (!fp)
 833              {
 834                 std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 835                 throw ( BrukerHopelessException ("Hopeless! Cannot open  mhd file for writting"));
 836                 //exit(0);
 837              }
 838              else
 839              {
 840                fprintf(fp, "ObjectType = Image\n");
 841                fprintf(fp, "NDims = 3\n" );
 842                fprintf(fp, "BinaryData = True \n" );
 843                fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 844                fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices );
 845                fprintf(fp, "HeaderSize = %d\n", 0);
 846                //fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
 847                fprintf(fp, "ElementSpacing = %lf %lf %lf\n", spatResolX, spatResolY, sliceDistance );
 848                fprintf(fp, "Position = 0 0 %d\n", 0 );
 849                fprintf(fp, "Offset = 0 0 0\n" );
 850                fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 851                fprintf(fp, "ElementNumberOfChannels = 1\n" );
 852                fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
 853                fprintf(fp, "ElementDataFile = %s\n", "../2dseq_All_the_Slices" );
 854                fclose(fp);
 855              }
 856              sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices",
 857                                        currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 858              fp=fopen(output2dseqSliceFileName, "wb");
 859              if (!fp)
 860              {
 861                 std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 862                 throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseq file for writting"));
 863              }
 864              else
 865              {
 866                 fwrite( buffer_2dseq, NX*NY*pixelSize, nbSlices, fp);
 867              }
 868              fclose(fp);
 869              serieNumber ++;
 870              strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 871        }  // end if mhd
 872        if (dicom)
 873        {
 874              sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices.dcm",
 875                                        currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 876
 877             /* ----------- Write Dicom Image  ---------------*/
 878              MakeDicomImage(buffer_2dseq,
 879                NX,
 880                NY,
 881                nbFrames,
 882                pixelSize,
 883                //fovX/NY, fovY/NY, sliceDistance,
 884                spatResolX, spatResolY, sliceDistance,
 885                output2dseqSliceFileName,
 886                subject_name,
 887                day,
 888                strStudyUID,
 889                strSerieUID,
 890                strStudyDescr,
 891                strSerieDescr,
 892                strStudyTimeDate,
 893                0,// index frame number
 894                GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
 895              );
 896        }  // end if dicom
 897    }  // end if nbInstants = 1
 898
 899    else  // more than ONE instant
 900    {
 901           // Interleaved !
 902           // it's (slice1,slide2, ...)t1 ; (slice1,slide2, ...)t2 ; ...
 903          unsigned char *pixelsForCurrentSlice = new unsigned char[NX*NY*pixelSize*nbInstants];
 904
 905          k = 0;
 906          for (sliceNb=0; sliceNb<nbSlices; sliceNb++)
 907          {
 908             if (mhd)
 909             {
 910                sprintf(outputMhdFileName, "%s%cMhdData_%03d.mhd", currentOutputMhdDirName,
 911                                         GDCM_NAME_SPACE::GDCM_FILESEPARATOR, k  );
 912                if (verbose)
 913                   std::cout << "--- Output MHD file [" << outputMhdFileName << "]" << std::endl;
 914                fp=fopen(outputMhdFileName, "w");
 915                if (!fp)
 916                {
 917                    std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 918                    throw ( BrukerHopelessException ("Hopeless! Cannot open  mhd file for writting"));
 919                    //exit(0);
 920                }
 921                else
 922                {
 923             /* ----------- Write MHD Image  ---------------*/
 924                 //if (verbose)
 925                 //   std::cout << "Open sucessfully[" << outputMhdFileName << "] for writting" << std::endl;
 926                    fprintf(fp, "ObjectType = Image\n");
 927                    fprintf(fp, "NDims = 3\n" );
 928                    fprintf(fp, "BinaryData = True \n" );
 929                    fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 930                    fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbInstants);
 931                    fprintf(fp, "HeaderSize = %d\n", 0);
 932                    //fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, 1.0 ); //
 933                    fprintf(fp, "ElementSpacing = %lf %lf %lf\n",spatResolX, spatResolY, 1.0 ); //slice distance : no meaning for temporal serie
 934                    fprintf(fp, "Position = 0 0 %d\n", sliceNb );
 935                    fprintf(fp, "Offset = 0 0 0\n" );
 936                    fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 937                    fprintf(fp, "ElementNumberOfChannels = 1\n" );
 938                    fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
 939                    fprintf(fp, "ElementDataFile = ..%c2dseq_Slice_%d\n", GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb );
 940                    fclose(fp);
 941                } // end write MHD
 942
 943                sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d",
 944                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,sliceNb);
 945                fp=fopen(output2dseqSliceFileName, "wb");
 946                if (!fp)
 947                {
 948                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 949                    throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseqSliceFile file for writting"));
 950                    //exit (0);
 951                }
 952                int frameSize = NX*NY*pixelSize;
 953                for (instantNb=0; instantNb<nbInstants; instantNb++)
 954                {
 955 // std::cout << "------------SN " << sliceNb << " IN " << instantNb <<  " T " << nbSlices*instantNb + sliceNb << std::endl;
 956                     fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
 957                             frameSize,
 958                             1, fp);
 959                }
 960                fclose(fp);
 961
 962 // std::cout << "end writting[" << output2dseqSliceFileName << "]" << std::endl;
 963             }  // end if mhd
 964
 965             if (dicom)
 966             {
 967                // desperate try !
 968              /*
 969                sprintf(output2dseqSliceFileName, "%sdummy_buffer",
 970                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 971                fp=fopen(output2dseqSliceFileName, "wb");
 972                if (!fp)
 973                {
 974                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 975                    exit (0);
 976                }
 977                int frameSize = NX*NY*pixelSize;
 978                for (instantNb=0; instantNb<nbInstants; instantNb++)
 979                {
 980 // std::cout << "------------SN " << sliceNb << " IN " << instantNb <<  " T " << nbSlices*instantNb + sliceNb << std::endl;
 981                     fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
 982                             frameSize,
 983                             1, fp);
 984                }
 985                fclose(fp);
 986
 987                fp=fopen(output2dseqSliceFileName, "rb");
 988                if (!fp)
 989                {
 990                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for reading" << std::endl;
 991                    exit (0);
 992                }
 993                fread( pixelsForCurrentSlice,
 994                             frameSize*nbInstants,
 995                             1, fp);
 996                fclose(fp);
 997               // end of desperate try !
 998               */
 999
1000                /* ----------- Write Dicom Image  ---------------*/
1001
1002                int frameSize = NX*NY*pixelSize;
1003                for (instantNb=0; instantNb<nbInstants; instantNb++)
1004                {
1005                   memcpy(pixelsForCurrentSlice + frameSize*instantNb, buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize, frameSize);
1006                }
1007
1008                int indOfFirsImageWithinImageSet =  nbSlices*instantNb;
1009                sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d.dcm",
1010                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb);
1011
1012                MakeDicomImage(
1013                   pixelsForCurrentSlice,
1014                   NX,
1015                   NY,
1016                   nbInstants,
1017                   pixelSize,
1018                   spatResolX, spatResolY, sliceDistance,
1019                   //fovX/NY, fovY/NY, sliceDistance,
1020                   output2dseqSliceFileName,
1021                   subject_name,
1022                   day,
1023                   strStudyUID,
1024                   strSerieUID,
1025                   strStudyDescr,
1026                   strSerieDescr,
1027                   strStudyTimeDate,
1028                   sliceNb*nbInstants,
1029                   GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
1030                );
1031                if (verbose)
1032                   std::cout << "--- Output DCM file [" << output2dseqSliceFileName << "]" << std::endl;
1033
1034            } // en if dicom
1035
1036         k++;
1037         }
1038         delete [] pixelsForCurrentSlice;
1039      }  // end nbInstants == 1
1040    delete [] buffer_2dseq;
1041 /**/
1042
1043
1044    // -----------------------------------------------------
1045    //  deal with MatLab-generated Carto file.
1046    // -----------------------------------------------------
1047
1048    dealWithCarto(fileNames,  NX,  NY,  nbSlices, /*fovX, fovY,*/ spatResolX, spatResolY, sliceDistance,
1049                    copyFile, currentOutputDirName, outputMhdFileName, output2dseqCartoName);
1050 }
1051
1052 // ===========================================================================================
1053
1054 void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX, int NY, int nbSlices,
1055                                  /*double fovX, double fovY, */
1056                                  double spatResolX, double spatResolY, double sliceDistance,
1057                                  char *copyFile, std::string &currentOutputDirName,
1058                                  char *outputMhdFileName, char *output2dseqCartoName)
1059 {
1060    // -----------------------------------------------------
1061    //  deal with MatLab-generated Carto file.
1062    // -----------------------------------------------------
1063
1064    const char *code[] = { "ADC", "adc", "TTP", "ttp", "PEAK", "peak", "" };  // add more carto file name identifiers if necessary; end with ""
1065    const char *separator[] =  { "_", ".", "-", "" }; //  add more, if necessary, to ckeck for 2dseq.ADC, 2dseq_ADC, 2dseq-ADC, etc; end with ""
1066    int icode;
1067    int iseparator;
1068    GDCM_NAME_SPACE::DirListType::iterator it;
1069    char file_name_ident[500];
1070    FILE *fp;
1071
1072    // Iterate to ALL the objets(files/directories) found in the input directory
1073    for (it = fileNames.begin();
1074         it != fileNames.end();
1075       ++it)
1076    {
1077       if ( boost::filesystem::is_regular(*it) )
1078       //if ( ! boost::filesystem::is_directory(*it) )
1079       {
1080          if (verbose)
1081             std::cout << "--- [" << *it << "] is a file..." << std::endl;
1082
1083          icode      = 0;
1084          while (code[icode][0] != 0)
1085          {
1086          iseparator = 0;
1087          while (separator[iseparator][0] != 0)
1088          {
1089             sprintf(file_name_ident, "2dseq%s%s",separator[iseparator],code[icode]); // e.g  "2dseq_ADC"
1090             //if (verbose)
1091             //   std::cout << "check name ["<<(*it) << "] for string [" << file_name_ident << "]" << std::endl;
1092             std::string::size_type loc = (*it).rfind(file_name_ident);
1093
1094             if ( loc != std::string::npos )
1095             {
1096
1097        ///\ TODO : find a safer way to be sure to read everything!
1098               unsigned char *buffer_carto = new unsigned char[NX*NY*sizeof(double)*nbSlices];
1099               fp = fopen ( (*it).c_str(), "rb");
1100               if (!fp){
1101                  std::cout << "Cannot open [" << *it << "] for reading" << std::endl;
1102                  throw ( BrukerHopelessException ("Level 1 Unable to open 'carto' file "));
1103                }
1104                fread(buffer_carto, NX*NY*sizeof(double), nbSlices, fp);
1105
1106                     // ?!?  sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() ,
1107                std::cout << "Deal with Carto file :[" <<*it << "], computed length : "
1108                          << NX*NY*sizeof(double)*nbSlices << std::endl;
1109                std::string lastFileName = GDCM_NAME_SPACE::Util::GetName((*it).c_str());
1110                if (mhd)
1111                {
1112                   // Copy the data file in the new directory
1113                   sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() ,
1114                             currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str());
1115                   system(copyFile);
1116                   sprintf(outputMhdFileName, "%s%c%s%s",
1117                                          currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".mhd" );
1118                   if (verbose)
1119                     std::cout << "--- Output Carto MHD file [" << outputMhdFileName << "]" << std::endl;
1120
1121                   FILE *fp;
1122                   fp=fopen(outputMhdFileName, "w");
1123                   if (!fp)
1124                   {
1125                      std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
1126                   }
1127                   else
1128                   {
1129                      fprintf(fp, "ObjectType = Image\n");
1130                      fprintf(fp, "NDims = 3\n" );
1131                      fprintf(fp, "BinaryData = True \n" );
1132                      fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
1133                      fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices);
1134                      fprintf(fp, "HeaderSize = %d\n", 0 );
1135                      fprintf(fp, "ElementSpacing = %lf %lf %lf\n",spatResolX, spatResolY, sliceDistance );
1136                      fprintf(fp, "Position = 0 0 0\n" );
1137                      fprintf(fp, "Offset = 0 0 0\n" );
1138                      fprintf(fp, "CenterOfRotation = 0 0 0\n" );
1139                      fprintf(fp, "ElementNumberOfChannels = 1\n" );
1140                      fprintf(fp, "ElementType = %s\n", "MET_DOUBLE" );
1141                      fprintf(fp, "ElementDataFile = %s\n", lastFileName.c_str() );
1142
1143                      fclose(fp);
1144                   }
1145                   if (verbose)
1146                      std::cout << "--- end write Carto MHD file [" << outputMhdFileName << "]" << std::endl;
1147                }  // end if mhd
1148
1149             // ----------- Write Dicom Image  ---------------
1150
1151                if (dicom)
1152                {
1153                   sprintf(output2dseqCartoName, "%s%c%s%s",
1154                                        currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".dcm" );
1155                   if (verbose)
1156                      std::cout << "--- end create name output2dseqCartoName file [" << output2dseqCartoName << "]" << std::endl;
1157
1158                   strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID(); //New SerieUID for each carto.
1159                   std::string strNewSerieDescr(strSerieDescr+ "_" +GDCM_NAME_SPACE::Util::GetName((*it).c_str()));
1160                   MakeDicomImage(buffer_carto,
1161                      NX,
1162                      NY,
1163                      nbSlices,
1164                      8, // pixelSize
1165                      //fovX/NY, fovY/NY, sliceDistance,
1166                      spatResolX, spatResolY, sliceDistance,
1167                      output2dseqCartoName,
1168                      subject_name,
1169                      day,
1170                      strStudyUID,
1171                      strSerieUID,
1172                      strStudyDescr,
1173                      strNewSerieDescr,
1174                      strStudyTimeDate,
1175                      0,
1176                      GDCM_NAME_SPACE::CREATED_IMAGE
1177                   );
1178                }  // end if dicom
1179
1180                delete [] buffer_carto;
1181                if (verbose)
1182                   std::cout << "--- End writing Carto DICOM file [" << output2dseqCartoName << "]" << std::endl;
1183                break; // don't check for more ident on same file name!
1184
1185             }  // end deal with _ADC, -adc, etc
1186           iseparator ++;
1187           }  // end iterate speparators
1188           icode++;
1189           } // end iterate code
1190       } // end boost::filesystem::is_regular(*it)
1191    } // end iterate on all objects (files, dir, etc)
1192 } // end method
1193
1194 // ==========================================================================================================
1195
1196 int Bruker2Dicom::CheckUserDirectory(std::string &userDirName)
1197 {
1198    GDCM_NAME_SPACE::DirList dirList(userDirName, false, true); // DON'T get recursively the list of files
1199
1200    GDCM_NAME_SPACE::DirListType fileNames;
1201    fileNames = dirList.GetFilenames();
1202
1203    std::string path = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()));
1204
1205    std::string subject =  path +
1206                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
1207                           "subject";
1208
1209     std::string acqp = path +
1210                        GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
1211                        "acqp";
1212
1213     if ( boost::filesystem::is_regular(subject) )
1214        subjectFound = true; // user passed a 'study
1215     else
1216        subjectFound = false; // user didnt' pass a 'study
1217
1218     if ( boost::filesystem::is_regular(acqp) )
1219        acqpFound= true; // user passes a 'serie', not a 'study'
1220     else
1221        acqpFound = false; // user passed a 'non study' directory; Hope it's a 'set of studies' directory!
1222
1223    int type;
1224    if  (subjectFound )  type = 1; // user passed a 'study
1225    else if  (acqpFound) type = 2; // user passed a 'serie'
1226    else                 type = 3; // user passed a 'non study' directory; Hope it's a 'set of studies' directory!
1227
1228    return type;
1229 }
1230
1231 // ==========================================================================================================
1232
1233 bool Bruker2Dicom::CreateDirectory(std::string &OutputDirName)
1234 {
1235    std::string systemCommand;
1236
1237    if (verbose)
1238       std::cout << "Check for output directory :[" << OutputDirName << "]."
1239                 <<std::endl;
1240    if ( ! boost::filesystem::is_directory(OutputDirName) )    // dirout not found
1241    {
1242       systemCommand = "mkdir " + OutputDirName;        // create it!
1243       if (verbose)
1244          std::cout << systemCommand << std::endl;
1245       system (systemCommand.c_str());
1246       if ( ! boost::filesystem::is_directory(OutputDirName) ) // be sure it worked
1247       {
1248          if (verbose)
1249             std::cout << "KO : not a dir : [" << OutputDirName << "] (creation failure ?)" << std::endl;
1250          //return 0;
1251          throw ( BrukerHopelessException ("Level 1 output directory creation failure "));
1252       }
1253       else
1254       {
1255          if (verbose)
1256            std::cout << "Directory [" << OutputDirName << "] created." << std::endl;
1257       }
1258    }
1259    else
1260    {
1261        if (verbose)
1262             std::cout << "Output Directory [" << OutputDirName << "] already exists; Used as is." << std::endl;
1263    }
1264    return 1;
1265 }
1266
1267 // ===========================================================================================
1268
1269 /// \TODO move cleanString to 'crea' ?
1270
1271 void Bruker2Dicom::cleanString(std::string &s)
1272 {
1273    int l = s.size();
1274    if (s[l-1] == 0x0A || s[l-1] == 0x0D ) // CR or NL
1275    {
1276       l--;
1277       s = s.substr(0, l);
1278    }
1279    if (s[l-1] == ' ' ) // blank space
1280    {
1281       l--;
1282       s = s.substr(0, l);
1283    }
1284
1285    if (s[0] == '<')
1286       s= s.substr(1,l-2);
1287    std::string repChar("_");
1288    GDCM_NAME_SPACE::Util::ReplaceSpecChar(s, repChar);
1289 }
1290
1291 // ===========================================================================================
1292
1293 void Bruker2Dicom::getImhDataType(BrukerFieldData &bDPT, std::string &mhdDataPixelType, int &pixelSize)
1294 {
1295    if(bDPT.GetDataType() == "string")
1296    {
1297          std::string brukerDataPixelType = bDPT.GetStringValue()[0];
1298          if (verbose)
1299             std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
1300          //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
1301
1302          if (brukerDataPixelType ==  "ip_short") {
1303             mhdDataPixelType = "MET_USHORT";
1304             pixelSize = 2;
1305          }
1306          if (brukerDataPixelType ==  "ip_int") {
1307             mhdDataPixelType = "MET_UINT";
1308             pixelSize = 4;
1309          }
1310          if (brukerDataPixelType ==  "ip_char") {
1311              mhdDataPixelType = "MET_UCHAR";
1312              pixelSize = 1;
1313          }
1314                   /// \TODO : finish the list
1315     /*
1316     case 0 : fp << "ElementType = MET_CHAR" << std::endl;
1317       break;
1318     case 1 : fp << "ElementType = MET_UCHAR" << std::endl;
1319       break;
1320     case 2 : fp << "ElementType = MET_SHORT" << std::endl;
1321       break;
1322     case 3 : fp << "ElementType = MET_USHORT" << std::endl;
1323       break;
1324     case 4 : fp << "ElementType = MET_INT" << std::endl;
1325       break;
1326     case 5 : fp << "ElementType = MET_UINT" << std::endl;
1327       break;
1328     case 6 : fp << "ElementType = MET_FLOAT" << std::endl;
1329       break;
1330     case 7 : fp << "ElementType = MET_DOUBLE" << std::endl;
1331     */
1332     }
1333     else
1334     {
1335          int brukerDataPixelType = bDPT.GetIntValue()[0];
1336          if (verbose)
1337             std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
1338          //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
1339
1340 // Cross your fingers !!!
1341
1342 // pb : found values : 2, 3, 5
1343
1344          if (brukerDataPixelType ==  2) {
1345             mhdDataPixelType = "MET_USHORT";
1346             pixelSize = 2;
1347          }
1348          if (brukerDataPixelType ==  3) {
1349             mhdDataPixelType = "MET_USHORT";
1350             pixelSize = 2;
1351          }
1352          if (brukerDataPixelType ==  1) {
1353             mhdDataPixelType = "MET_UCHAR";
1354             pixelSize = 1;
1355          }
1356     }
1357 }
1358
1359 // ===========================================================================================
1360
1361 std::vector<BrukerImage> Bruker2Dicom::CreateImageSet ( )
1362 {
1363          std::vector<BrukerImage> imageSet;
1364          br_acqp.SetLoopStructure();
1365          std::vector<int> tempVect                      = br_acqp.GetLoopStructure() ;
1366          std::map<std::string, BrukerFieldData> map     = br_acqp.GetBrukerHeaderMap();
1367
1368          bool result                                    = br_acqp.ObjectVaryingProperties.init(map,tempVect);
1369
1370          if (result == false)
1371          {
1372             throw ( BrukerInitException  ("ObjectVaryingProperties.init() failure in Bruker2Dicom::CreateImageSet()") );
1373          }
1374
1375          br_acqp.SetImageLoopStructure();
1376          br_acqp.SetBrukerImageList();
1377          std::vector<std::vector<int> > brukerImageList = br_acqp.GetBrukerImageList();
1378
1379          BrukerImage image(br_acqp,br_reco);
1380          image.Init(br_acqp,br_reco,1);
1381
1382          for(int i=0;i<brukerImageList.size();i++)
1383          {
1384             image.Init(br_acqp,br_reco,i);
1385             imageSet.push_back(image);
1386          }
1387
1388  // Just for checking
1389  /*
1390
1391          std::vector<std::vector <double> > imageOrientation;
1392          std::vector <double> imagePosition;
1393          for(int i=0;i<brukerImageList.size();i++)
1394          {
1395            // fread(buffer_2dseq, NX*NY*pixelSize*nbSlices*nbInstants, 1, fp);
1396
1397            imagePosition = imageSet[i].getTranslationVectorRPS2XYZ();
1398            std::cout << "Position " << imagePosition[0] << " "
1399                      << imagePosition[1] << " "  << imagePosition[2] ;
1400            imageOrientation =  imageSet[i].getRotationMatrixRPS2XYZ();
1401            std::cout << "\t  Orientation " ;
1402            for(int i1=0; i1<3;i1++)for(int i2=0; i2<3;i2++)
1403               std::cout << imageOrientation[i1][i2] << " ";CreateImageSet
1404
1405            //std::cout << "\t  Abs Time " << imageSet[i].getAbsoluteTimePosition();
1406            std::cout << "\t  Relat Time " << imageSet[i].getRelativeTimePosition();
1407
1408            std::cout << "\t [";
1409            for (int i3=0; i3<imageSet[i].getLoopStamp().size();i3++)
1410               std::cout << " " << imageSet[i].getLoopStamp()[i3];
1411            std::cout << "]" << std::endl;
1412          }
1413 */
1414    return imageSet;
1415 }
1416
1417 // ===========================================================================================
1418
1419 void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels,
1420               int X,
1421               int Y,
1422               int nbFrames,
1423               int pixelSize,
1424               double spacingX, double spacingY, double sliceDistance,
1425               std::string dcmImageName,
1426               const std::string &patientName,
1427               const char *day,
1428               std::string &studyUID,
1429               std::string &serieUID,
1430               std::string &studyDescr,
1431               std::string &serieDescr,
1432               std::string &strStudyTimeDate,
1433               int imgNum,
1434               GDCM_NAME_SPACE::ImageContentType contentType
1435       )
1436 {
1437    std::ostringstream str;
1438
1439    GDCM_NAME_SPACE::File *file;
1440    file = GDCM_NAME_SPACE::File::New();
1441
1442   // Set the image size
1443    str.str("");
1444    str << X;
1445    file->InsertEntryString(str.str(),0x0028,0x0011,"US"); // Columns
1446    str.str("");
1447    str << Y;
1448    file->InsertEntryString(str.str(),0x0028,0x0010,"US"); // Rows
1449
1450    if (nbFrames != 1)
1451    {
1452       str.str("");
1453       str << nbFrames;
1454       file->InsertEntryString(str.str(),0x0028,0x0008,"IS"); // Number of Frames
1455    }
1456
1457   // Set the pixel type
1458   //      //8, 16, 32, 64 (for double ?)
1459    str.str("");
1460    str << pixelSize*8;
1461    file->InsertEntryString(str.str(),0x0028,0x0100,"US"); // Bits Allocated
1462
1463    file->InsertEntryString(str.str(),0x0028,0x0101,"US"); // Bits Stored
1464
1465    str.str("");
1466    str << pixelSize*8-1;
1467    file->InsertEntryString(str.str(),0x0028,0x0102,"US"); // High Bit
1468
1469   // Set the pixel representation // 0/1 , 0=unsigned
1470    file->InsertEntryString("1",0x0028,0x0103, "US"); // Pixel Representation
1471
1472   // Set the samples per pixel // 1:Grey level, 3:RGB
1473    file->InsertEntryString("1",0x0028,0x0002, "US"); // Samples per Pixel
1474
1475 //  0028 0030 DS 2 Pixel Spacing
1476    str.str("");
1477    str << spacingX << "\\" << spacingY;
1478    file->InsertEntryString(str.str(),0x0028,0x0030, "DS"); // Pixel Spacing
1479
1480  //   0018 0050 DS 1 Slice Thickness
1481    str.str("");
1482    str << sliceDistance;
1483    file->InsertEntryString(str.str(),0x0018,0x0050, "DS");
1484
1485 //    0020 0011 IS 1 Series Number
1486    str.str("");
1487    str << serieNumber;
1488    file->InsertEntryString(str.str(),0x0020,0x0011, "IS");
1489
1490 //    0020|0013 [IS]  [Instance Number]
1491    instanceNumber++;
1492    str.str("");
1493    str << instanceNumber;
1494    file->InsertEntryString(str.str(),0x0020,0x0013, "IS");
1495
1496   // 1.2.840.10008.5.1.4.1.1.4.1 : Enhanced MR Image Storage
1497  //  file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0002, 0x0002, "UI");  // [Media Storage SOP Class UID]
1498   // file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0008, 0x0016, "UI");  // [SOP Class UID]
1499
1500 // OK : MR is NOT multiframe, but I want just a quick an dirty solution
1501
1502 // 1.2.840.10008.5.1.4.1.1.4         MR Image Storage
1503    file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0002, 0x0002, "UI");  // [Media Storage SOP Class UID]
1504    file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0008, 0x0016, "UI");  // [SOP Class UID]
1505
1506   // if (strlen(patientName) != 0)
1507    file->InsertEntryString(patientName.c_str(),0x0010,0x0010, "PN"); // Patient's Name
1508    file->InsertEntryString(patientName.c_str(),0x0010,0x0020, "LO"); // Patient's ID
1509
1510    file->InsertEntryString(studyUID, 0x0020, 0x000d, "UI");
1511    file->InsertEntryString(serieUID, 0x0020, 0x000e, "UI");
1512
1513 //  0008 0020 DA 1 Study Date
1514 //  0008 0030 TM 1 Study Time
1515
1516 /// \TODO split into 2 strings!
1517    file->InsertEntryString(strStudyTimeDate.substr(10,11).c_str(),0x0008,0x0020, "DA");
1518    file->InsertEntryString(strStudyTimeDate.substr(1,8).c_str(),  0x0008,0x0030, "TM");
1519
1520    file->InsertEntryString(studyDescr, 0x0008,0x1030, "LO");  // Study Description
1521    file->InsertEntryString(serieDescr, 0x0008,0x103e, "LO");  // Series Description
1522
1523 //0008|0060 [CS] [Modality]
1524    file->InsertEntryString("MR",0x0008,0x0060, "CS");
1525
1526 // 0020 0037 DS 6 Image Orientation (Patient)
1527    char charImageOrientation[256];
1528
1529 /*
1530 std::cout << "charImageOrientation  " <<
1531                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0] << " " <<
1532                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1] << " " <<
1533                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2] << " " <<
1534                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0] << " " <<
1535                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1] << " " <<
1536                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] << std::endl ;
1537 */
1538    sprintf(charImageOrientation,"%f\\%f\\%f \\ %f\\%f\\%f",
1539                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0],
1540                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1],
1541                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2],
1542                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0],
1543                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1],
1544                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] ) ;
1545
1546    file->InsertEntryString(charImageOrientation,0x0020,0x0037, "DS");
1547
1548 // 0020 0032 DS 3 Image Position (Patient)
1549
1550    char charImagePosition[256];
1551    sprintf(charImagePosition,"%f\\%f\\%f",
1552                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[0],
1553                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[1],
1554                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[2]);
1555
1556    file->InsertEntryString(charImagePosition,0x0020,0x0032, "DS");  //0020 0032 DS 3 Image Position (Patient)
1557
1558
1559    // Private creator
1560    /*
1561
1562 0029|0010 [LO]   [Private Creator] [CREATIS HEADER ]
1563 0029|0011 [LO]   [Private Creator] [CREATIS for BRUKER to DICOM]
1564 0029|1031 [LO]   [] [4.0.7571167 ]
1565 0029|1032 [UL]   [] [1440000] =0x(15f900)
1566
1567 > $$ Thu Jul 30 17:29:46 2009 CEST (UT+2h)  mwiart
1568 > $$ /opt/PV4.0/data/mwiart/nmr/dha80.Uw1/4/method
1569 > ##$Method=DtiEpi
1570 > ##$PVM_DwNDiffDir=3             % 3 directions
1571 > ##$PVM_DwNDiffExpEach=2         % 2 valeurs de b par direction
1572 > ##$PVM_DwAoImages=1             % 1 image pour b=0
1573 > ##$PVM_DwBvalEach=( 2 )         % Valeurs de b
1574 > 1500.000000 3000.000000
1575 >
1576 > $$ Wed Dec  2 09:56:01 2009 UTC (UT+0h)  mwiart
1577 > $$ /opt/Pv5.0/data/mwiart/nmr/ECI7.Wx1/4/method
1578 > ##$Method=DtiEpi
1579 > ##$PVM_DwNDiffDir=3             % 3 directions
1580 > ##$PVM_DwNDiffExpEach=2         % 2 valeurs de b par direction
1581 > ##$PVM_DwAoImages=1             % 1 image pour b=0
1582 > ##$PVM_DwBvalEach=( 2 )         % Valeurs de b
1583 > 1500 3000
1584 >
1585 > $$ Wed Dec  2 10:14:27 2009 UTC (UT+0h)  mwiart
1586 > $$ /opt/Pv5.0/data/mwiart/nmr/ECI7.Wx1/5/method
1587 > ##$Method=DtiStandard
1588 > ##$PVM_DwNDiffDir=1             % 1 direction
1589 > ##$PVM_DwNDiffExpEach=2         % 2 valeurs de b
1590 > ##$PVM_DwAoImages=0             % 0 image pour b=0
1591 > ##$PVM_DwBvalEach=( 2 )         % Valeurs de b
1592 > 138 1600
1593 >
1594    */
1595
1596    file->InsertEntryString("CREATIS HEADER", 0x0029,0x0010, "LO");
1597    file->InsertEntryString("CREATIS FOR BRUKER-TO-DICOM", 0x0029,0x0011, "LO");
1598
1599    BrukerFieldData brf_method            = br_method.GetFieldData("Method");
1600    const std::vector<std::string> method = brf_method.GetStringValue();
1601
1602   // std::string method = br_method.GetFieldData("Method").GetStringValue();
1603    file->InsertEntryString(method[0], 0x0029,0x0100, "LO");
1604
1605    std::cout << " method[" << method[0]  << "]" << std::endl;
1606    if (method[0] == "DtiEpi" || method[0] == "DtiStandard")
1607    {
1608      // const std::vector<int> NDiffDir       = br_method.GetFieldData("PVM_DwNDiffDir").GetIntValue();
1609       BrukerFieldData brf_NDiffDir    = br_method.GetFieldData("PVM_DwNDiffDir");
1610       const std::vector<int> NDiffDir = brf_NDiffDir.GetIntValue();
1611
1612       //const std::vector<int> NDiffExpEach   = br_method.GetFieldData("PVM_DwNDiffExpEach").GetIntValue();
1613       BrukerFieldData brf_NDiffExpEach      = br_method.GetFieldData("PVM_DwNDiffExpEach");
1614       const std::vector<int> NDiffExpEach   =brf_NDiffExpEach.GetIntValue();
1615
1616 //      const std::vector<int> AoImages     = br_method.GetFieldData("PVM_DwAoImages").GetIntValue();
1617       BrukerFieldData brf_AoImages        = br_method.GetFieldData("PVM_DwAoImages");
1618       const std::vector<int> AoImages     = brf_AoImages.GetIntValue();
1619
1620       BrukerFieldData brf_DwBvalEach       = br_method.GetFieldData("PVM_DwBvalEach");
1621       const std::vector<double> DwBvalEach = brf_DwBvalEach.GetDoubleValue();
1622
1623  std::cout << "nb directions : " <<  NDiffDir[0] << " nb valeurs de b par direction : " << NDiffExpEach[0]
1624            << " nb images for b=0 : " << AoImages[0] << std::endl;
1625
1626        str.str("");
1627        str << NDiffDir[0];
1628        file->InsertEntryString(str.str(),0x0029,0x0101,"US"); // directions
1629        str.str("");
1630        str << NDiffExpEach[0];
1631        file->InsertEntryString(str.str(),0x0029,0x0102,"US"); // valeurs de b par direction
1632        str.str("");
1633        str << AoImages[0];
1634        file->InsertEntryString(str.str(),0x0029,0x0103,"US"); // image pour b=0
1635
1636        str.str("");
1637        for (unsigned int i=0; i<NDiffExpEach[0]; i++) {
1638           str << DwBvalEach[i];
1639           if (i!=AoImages[0])
1640              str << "\\";
1641       }
1642       file->InsertEntryString(str.str(),0x0029,0x0104,"DS"); // Valeurs de b
1643    }
1644
1645 // 0020 0x1041 DS 1 Slice Location
1646 //        sprintf(charImagePosition,"%f",float(imgNum));
1647 //        file->InsertEntryString(charImagePosition,0x0020,0x1041, "DS");
1648 /*
1649   // Set Rescale Intercept
1650         str.str("");
1651         str << div;
1652         file->InsertEntryString(str.str(),0x0028,0x1052,"DS");
1653
1654   // Set Rescale Slope
1655         str.str("");
1656         str << mini;
1657         file->InsertEntryString(str.str(),0x0028,0x1053,"DS");
1658 */
1659
1660    GDCM_NAME_SPACE::FileHelper *fileH;
1661    fileH = GDCM_NAME_SPACE::FileHelper::New(file);
1662    fileH->SetContentType(contentType);
1663
1664    // cast is just to avoid warnings (*no* conversion is performed)
1665    //fileH->SetImageData((uint8_t *)img,int(maxX*maxY)*sizeof(uint16_t)); // troubles when maxX, mayY are *actually* float!
1666
1667 //std::cout << "--------------------------------  X*Y*nbFrames*pixelSize " << X << " " << Y << " " << nbFrames << " " << pixelSize << std::endl;
1668
1669    fileH->SetImageData((uint8_t *)tabPixels, X*Y*nbFrames*pixelSize);
1670    fileH->SetWriteModeToRaw();
1671    fileH->SetWriteTypeToDcmExplVR();
1672    if( !fileH->Write(dcmImageName)) {
1673       std::cout << "Failed for [" << dcmImageName << "]\n"
1674                 << "           File is unwrittable" << std::endl;
1675       file->Delete();
1676       fileH->Delete();
1677       throw ( BrukerHopelessException ("Level 1 Unable to write Dicom file "));
1678    }
1679    //if (verbose)
1680    //   file->Print();
1681
1682    file->Delete();
1683    fileH->Delete();
1684 }