lib/src1/bruker2dicom.cxx

   1 #include "bruker2dicom.h"
   2
   3 #ifndef PATH_MAX // If not defined yet : do it
   4         #define PATH_MAX 2048
   5 #endif
   6
   7
   8
   9 bool Bruker2Dicom::Execute()
  10 {
  11    // ----- Begin Processing -----
  12
  13    bool bigEndian = GDCM_NAME_SPACE::Util::IsCurrentProcessorBigEndian();
  14
  15    if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(InputDirName) )
  16    {
  17       std::cout << "KO : [" << InputDirName << "] is not a Directory." << std::endl;
  18       return 0;
  19    }
  20    else
  21    {
  22       if (verbose)
  23          std::cout << "OK : [" << InputDirName << "] is a Directory." << std::endl;
  24    }
  25
  26    std::string strDirNameOut(OutputDirName);
  27    bool res=CreateDirectory(strDirNameOut);
  28    if (!res) {
  29       std::cout << "[" << OutputDirName << "] Directory creation failure " << std::endl;
  30       exit (0);
  31    }
  32
  33    std::string strDirNamein(InputDirName);
  34    GDCM_NAME_SPACE::DirList dirList(strDirNamein, false, true); // DON'T get recursively the list of files
  35    std::string strDirNameout(OutputDirName);
  36
  37 /*
  38    if (listonly)
  39    {
  40       std::cout << "------------List of found files ------------" << std::endl;
  41       dirList.Print();
  42       std::cout << std::endl;
  43       return 1;
  44    }
  45 */
  46
  47 //
  48 // e.g : at level 0, in : B67d1.Bp1
  49 //
  50 //           1  2  3  4  5  6  AdjStatePerStudy  subject
  51 //
  52
  53    GDCM_NAME_SPACE::DirListType fileNames;
  54    fileNames = dirList.GetFilenames();
  55    bool canOpen;
  56    std::string outputFileName;
  57
  58   // BrukerDataSet br_subject;
  59    std::string subject;
  60    subject = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
  61              GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
  62              "subject";
  63    if (verbose)
  64         std::cout << " Subject : [" <<  subject << "]" << std::endl;
  65    canOpen =br_subject.LoadFile(subject);
  66
  67    if (!canOpen)
  68    {
  69       std::cout << "Hopeless! no 'subject' found" << std::endl;
  70       exit(0);  /// \TODO throw an exception !
  71    }
  72    else
  73    {
  74       br_subject.FillMap();
  75    }
  76    //br_subject.PrintSelf();
  77
  78   // get info for 'Study Description'
  79
  80   /*
  81          BrukerFieldData b_protocol_location=br_acqp.GetFieldData("ACQ_protocol_location");
  82          acqp_protocol_location = b_protocol_location.GetStringValue()[0];
  83          cleanString(acqp_protocol_location);
  84 */
  85          BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string");
  86          std::string subject_name = b_name.GetStringValue()[0];
  87          strPatientName = subject_name;
  88          cleanString(subject_name);
  89
  90          BrukerFieldData b_entry=br_subject.GetFieldData("SUBJECT_entry");
  91          std::string subject_entry = b_entry.GetStringValue()[0];
  92          //cleanString(subject_entry);
  93          subject_entry = subject_entry.substr(11, subject_entry.size()-11);
  94
  95          BrukerFieldData b_position=br_subject.GetFieldData("SUBJECT_position");
  96          std::string subject_position = b_position.GetStringValue()[0];
  97          //cleanString(subject_position);
  98          subject_position = subject_position.substr(9, subject_position.size()-9);
  99
 100          BrukerFieldData b_date=br_subject.GetFieldData("SUBJECT_date");
 101          std::string subject_date = b_date.GetStringValue()[0];
 102          strStudyTimeDate = subject_date;
 103          cleanString(subject_date);
 104
 105          BrukerFieldData b_study_name=br_subject.GetFieldData("SUBJECT_study_name");
 106          std::string subject_study_name = b_study_name.GetStringValue()[0];
 107          subject_study_name = subject_study_name.substr(1, subject_study_name.size()-2);
 108          cleanString(subject_date);
 109
 110    strStudyDescr = subject_name + "-" + subject_study_name + "-" + subject_entry + "-" + subject_position + "-" + subject_date;
 111
 112    char outputDirName[(unsigned int) PATH_MAX+2];
 113
 114    strStudyUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 115
 116    // -----------------------------------------------------
 117    // Iterate to ALL the objets(files/directories) found in the input directory
 118    // (this is level ZERO)
 119    // -----------------------------------------------------
 120
 121    GDCM_NAME_SPACE::DirListType::iterator it;
 122
 123    for (it = fileNames.begin();
 124          it != fileNames.end();
 125        ++it)
 126    {
 127       if ( GDCM_NAME_SPACE::DirList::IsDirectory(*it) )
 128       {
 129          if (verbose)
 130             std::cout << "[" << *it << "] is a directory" << std::endl;
 131
 132          //BrukerDataSet br_acqp;
 133          std::string strAcqp;
 134          strAcqp = (*it) +
 135                    GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 136                    "acqp";
 137
 138          br_acqp.LoadFile(strAcqp);
 139          br_acqp.FillMap();
 140
 141          std::string acqp_scan_name;
 142          std::string acqp_method;
 143          std::string acqp_protocol_location;
 144
 145          BrukerFieldData b_protocol_location=br_acqp.GetFieldData("ACQ_protocol_location");
 146          acqp_protocol_location = b_protocol_location.GetStringValue()[0];
 147          cleanString(acqp_protocol_location);
 148
 149          BrukerFieldData b_scan_name=br_acqp.GetFieldData("ACQ_scan_name");
 150          acqp_scan_name = b_scan_name.GetStringValue()[0];
 151          cleanString(acqp_scan_name);
 152
 153          BrukerFieldData b_method=br_acqp.GetFieldData("ACQ_method");
 154          acqp_method = b_method.GetStringValue()[0];
 155          cleanString(acqp_method);
 156
 157          BrukerFieldData b_list_size = br_acqp.GetFieldData("ACQ_O1_list_size");
 158          b_list_size.PrintSelf(); //JP
 159
 160          nbSlices =  b_list_size.GetIntValue()[0];
 161
 162          strSerieDescr = GDCM_NAME_SPACE::Util::GetName(*it)
 163                          + "-" + acqp_protocol_location
 164                          + "-" + acqp_scan_name
 165                          + "-" + acqp_method.c_str();
 166
 167          sprintf(outputDirName, "%s%c%s", OutputDirName.c_str(),
 168                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 169                           strSerieDescr.c_str() );
 170
 171          std::cout << " ================================================================================\n"
 172                    << " ========================= [" << GDCM_NAME_SPACE::Util::GetName(*it).c_str()
 173                    << acqp_protocol_location.c_str()
 174                    << acqp_scan_name.c_str()
 175                    << acqp_method.c_str()
 176                    << "]\n"
 177                    << " ================================================================================"
 178                    << std::endl;
 179
 180         if (verbose)
 181            printf ("outputDirName [%s]\n", outputDirName);
 182
 183         DealWithNiveau1(*it, outputDirName);
 184       }
 185    } // end of : for (GDCM_NAME_SPACE::DirListType::iterator it
 186 }
 187
 188
 189 // =====================================================================
 190
 191 void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string currentOutputDirName) {
 192 //
 193 // e.g. : at level 1, in B67d1.Bp1/6
 194 //
 195 // acqp  fid  imnd  pdata  pulseprogram  spnam0  spnam1
 196
 197    bool res = CreateDirectory(currentOutputDirName);
 198
 199    if (!res) {
 200       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 201       exit (0);
 202    }
 203    GDCM_NAME_SPACE::DirList dirList(level1Directory, false, true); // DON'T get recursively the list of files
 204    GDCM_NAME_SPACE::DirListType fileNames;
 205    fileNames = dirList.GetFilenames();
 206    // -----------------------------------------------------
 207    // Iterate to ALL the objets(files/directories) found in the input directory
 208    // -----------------------------------------------------
 209    GDCM_NAME_SPACE::DirListType::iterator it;
 210
 211    for (it = fileNames.begin();
 212         it != fileNames.end();
 213       ++it)
 214    {
 215       if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(*it) )
 216       {
 217          if (verbose)
 218             std::cout << "--- [" << *it << "] is a file" << std::endl;
 219       }
 220    }
 221
 222    char outputDirName[(unsigned int) PATH_MAX+2];
 223    //std::string firstName;
 224    bool canOpen;
 225    for (it = fileNames.begin();
 226         it != fileNames.end();
 227       ++it)
 228    {
 229       if ( GDCM_NAME_SPACE::DirList::IsDirectory(*it) )
 230       {
 231          // will be always "pdata" ...
 232          if (verbose)
 233             std::cout << "--- [" << *it << "] is a directory" << std::endl;
 234
 235               /* a recuperer :
 236               if (FileLine.startsWith("##$ACQ_size=")) {
 237               if (FileLine.startsWith("##$NI=")) {
 238               if (FileLine.startsWith("##$NR=")) {
 239               if (FileLine.startsWith("##$ACQ_obj_order=")) {
 240               if (FileLine.startsWith("##$ACQ_word_size=")) {
 241               if (FileLine.startsWith("##$BYTORDA=")) {
 242               if (FileLine.startsWith("##$PULPROG=")) {
 243               */
 244
 245          sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 246                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 247                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str());
 248          //br1.PrintSelf();
 249
 250           std::string strMethod;
 251           //std::string firstName = *(fileNames.begin());
 252
 253           strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin())) +
 254                       GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 255                       "method";
 256             // std::cout << "---strMethod (for method)=> [" << strMethod << "]" << std::endl;
 257           canOpen = br_method.LoadFile(strMethod);
 258           if (!canOpen)
 259           {
 260              strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
 261                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 262                          "imnd";
 263              //std::cout << "---strMethod (for imnd) => [" << strMethod << "]" << std::endl;
 264              canOpen = br_method.LoadFile(strMethod);
 265              if (!canOpen)
 266              {
 267                 std::cout << "Hopeless! neither 'method' nor 'imnd' found" << std::endl;
 268                 exit(0);  /// \TODO throw an exception !
 269              }
 270           }
 271           if (verbose)
 272              std::cout << "open => [" << strMethod << "] successfully" << std::endl;
 273           br_method.FillMap();
 274
 275           /* a recuperer :
 276              ##$PVM_Fov (dimension)
 277           */
 278   /*
 279           dans method (pour perfusion  seulement?) :
 280           ##$PVM_ObjOrderList=( 8 )
 281           0 2 4 6 1 3 5 7
 282           ##$PVM_NSPacks=2
 283           ##$PVM_SPackArrNSlices=( 2 )
 284           7 1
 285   */
 286          DealWithNiveau2(*it,outputDirName );
 287       }
 288    }
 289 }
 290
 291 // =====================================================================
 292
 293 void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string currentOutputDirName) {
 294
 295 // e.g. : at level 2 in B67d1.Bp1/6/pdata
 296 //
 297 // acqp  fid  imnd  pdata  pulseprogram  spnam0  spnam1
 298 //
 299
 300    bool res = CreateDirectory(currentOutputDirName);
 301
 302    if (!res) {
 303       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 304       exit (0);
 305    }
 306
 307    GDCM_NAME_SPACE::DirList dirList(level2Directory, false, true); // DON'T get recursively the list of files
 308
 309    GDCM_NAME_SPACE::DirListType fileNames;
 310    fileNames = dirList.GetFilenames();
 311
 312    char outputDirName[(unsigned int) PATH_MAX+2];
 313
 314    // -----------------------------------------------------
 315    // Iterate to ALL the objets(files/directories) found in the input directory
 316    // -----------------------------------------------------
 317    GDCM_NAME_SPACE::DirListType::iterator it;
 318    bool canOpen;
 319
 320    if (verbose)
 321    for (it = fileNames.begin();
 322         it != fileNames.end();
 323       ++it)
 324    {
 325       if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(*it) )
 326       {
 327          std::cout << "--- --- [" << *it << "] is a file" << std::endl;
 328       }
 329
 330    }
 331
 332    for (it = fileNames.begin();
 333          it != fileNames.end();
 334        ++it)
 335    {
 336       if ( GDCM_NAME_SPACE::DirList::IsDirectory(*it) )
 337       {
 338
 339          if (verbose)
 340             std::cout << "--- --- [" << *it << "] is a directory" << std::endl;
 341
 342         // sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 343         //                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 344         //                                GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
 345   // MUST be 'pdata'!
 346
 347 //
 348 // (interest of previous method :
 349 // If unaware user changed the pdata name, it goes on working
 350 //
 351           std::string str_isa;
 352           str_isa = (*it) +
 353                     GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 354                    "isa";
 355
 356           std::string str_isa_func_name;
 357           canOpen = br_isa.LoadFile(str_isa);
 358           if (!canOpen)
 359           {
 360              sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 361                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 362                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
 363           }
 364           else
 365           {
 366              br_isa.FillMap();
 367              BrukerFieldData b_isa_func_name = br_isa.GetFieldData("ISA_func_name");
 368
 369              str_isa_func_name = b_isa_func_name.GetStringValue()[0];
 370              cleanString(str_isa_func_name);
 371
 372              sprintf(outputDirName, "%s%c%s-%s", currentOutputDirName.c_str(),
 373                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 374                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str(),
 375              str_isa_func_name.c_str());
 376           }
 377           DealWithNiveau3(*it, outputDirName);
 378       }
 379    }
 380 }
 381
 382
 383 //
 384 // =====================================================================
 385 //
 386
 387 void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string currentOutputDirName){
 388
 389 //
 390 // e.g. at level 3, in
 391
 392    // just to be able to go on checking // JP
 393    if ( GDCM_NAME_SPACE::Util::GetName(level3Directory) != "1")
 394       return;
 395
 396    bool res = CreateDirectory(currentOutputDirName);
 397
 398    if (!res)
 399    {
 400       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 401       exit (0);
 402    }
 403
 404    GDCM_NAME_SPACE::DirList dirList(level3Directory, false, true); // DON'T get recursively the list of files
 405    GDCM_NAME_SPACE::DirListType::iterator it;
 406    GDCM_NAME_SPACE::DirListType fileNames;
 407    fileNames = dirList.GetFilenames();
 408
 409    char original2dseqName       [(unsigned int) PATH_MAX+2];
 410    char currentOutputMhdDirName [(unsigned int) PATH_MAX+2];
 411
 412    char outputMhdFileName       [(unsigned int) PATH_MAX+2];
 413    char output2dseqSliceFileName[(unsigned int) PATH_MAX+6]; // think about extra '.dcm'
 414    char output2dseqName         [(unsigned int) PATH_MAX+6];
 415    char output2dseqCartoName    [(unsigned int) PATH_MAX+6];
 416
 417    char copyFile[PATH_MAX + PATH_MAX + 5]; // Should be enough!
 418    bool canOpen;
 419
 420    //-------------- try d3proc;
 421    char char_d3proc[(unsigned int) PATH_MAX+2];
 422
 423    sprintf(char_d3proc,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"d3proc" );
 424
 425    if (verbose)
 426       std::cout << "--- => [" << char_d3proc << "]" << std::endl;
 427    std::string str_d3proc(char_d3proc);
 428    canOpen = br_d3proc.LoadFile(str_d3proc);
 429
 430    if (!canOpen)
 431    {
 432       std::cout << "Hopeless! no 'd3proc' found" << std::endl;
 433       exit(0);  /// \TODO throw an exception !
 434    }
 435
 436    canOpen = br_d3proc.FillMap();
 437    if (!canOpen)
 438    {
 439       std::cout << "Hopeless! FillMap failed on 'd3proc'" << std::endl;
 440       exit(0);  /// \TODO throw an exception !
 441    }
 442
 443    //-------------- end try d3proc;
 444
 445
 446  // -------------------try reco
 447
 448    char char_reco[(unsigned int) PATH_MAX+2];
 449
 450    sprintf(char_reco,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
 451     //str_d3proc = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
 452     //             GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 453     //             "d3proc";
 454    if (verbose)
 455       std::cout << "--- => [" << char_reco << "]" << std::endl;
 456    std::string str_reco(char_reco);
 457    canOpen = br_reco.LoadFile(str_reco);
 458
 459    if (!canOpen) // we try in directory ../1
 460    {
 461       if (verbose)
 462          std::cout << "[" << str_reco << "] not found " << std::endl;
 463       std::string lastDirName = GDCM_NAME_SPACE::Util::GetPath(level3Directory);
 464       //lastDirName = GDCM_NAME_SPACE::Util::GetPath(lastDirName);
 465       sprintf(char_reco,"%s%c1%c%s", lastDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
 466       str_reco=char_reco;
 467       canOpen = br_reco.LoadFile(str_reco);
 468       if (!canOpen)
 469       {
 470          std::cout << "Hopeless! cannot find 'reco' in [" << str_reco << "]"  << std::endl;
 471          exit(0);  /// \TODO throw an exception !
 472       }
 473    }
 474
 475    canOpen = br_reco.FillMap();
 476    if (!canOpen)
 477    {
 478       std::cout << "Hopeless! FillMap failed on [" << str_reco << "]" << std::endl;
 479       exit(0);  /// \TODO throw an exception !
 480    }
 481    //std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
 482    // br_reco.PrintSelf();
 483    // std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
 484
 485    // -------------------end try reco
 486
 487
 488    BrukerFieldData bX = br_d3proc.GetFieldData("IM_SIX");
 489    int NX = bX.GetIntValue()[0];
 490
 491    std::cout << "IM_SIX " << NX << std::endl;
 492    BrukerFieldData bY=br_d3proc.GetFieldData("IM_SIY");
 493    int NY = bY.GetIntValue()[0];
 494
 495    std::cout << "IM_SIY " << NY << std::endl;
 496    /// \todo : check if there are actually 3 dimensions or only 2
 497
 498    BrukerFieldData bZ= br_d3proc.GetFieldData("IM_SIZ");
 499    int nbFrames = bZ.GetIntValue()[0];
 500    std::cout << "IM_SIZ " << nbFrames << std::endl;
 501
 502         // WARNING DATTYPE is, either in {ip_short, ip_int, ip_char, ...}, or in {1, 2, 3, ...}
 503
 504    BrukerFieldData bDPT = br_d3proc.GetFieldData("DATTYPE");
 505
 506    std::string mhdDataPixelType;
 507    int pixelSize;
 508    getImhDataType(bDPT, mhdDataPixelType, pixelSize);
 509
 510    BrukerFieldData fov = br_method.GetFieldData("PVM_Fov");
 511    double fovX = fov.GetDoubleValue()[0];
 512    double fovY = fov.GetDoubleValue()[1];
 513    if (verbose)
 514       std::cout << "FOV (ds method) " << fovX << " " << fovY << std::endl;
 515
 516    /// \TODO probabely a more sophisticated accessor will be necessary :
 517    ///  (cf : non contiguous slices, overlapping, slice thickness, space between clices, etc)
 518    BrukerFieldData bsliceDistance = br_method.GetFieldData("PVM_SPackArrSliceDistance");
 519    double sliceDistance = bsliceDistance.GetDoubleValue()[0];
 520
 521    if (mhd)
 522    {
 523       sprintf(currentOutputMhdDirName, "%s%c%s", currentOutputDirName.c_str(),
 524                                GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "MhdFiles");
 525       res = CreateDirectory( currentOutputMhdDirName );
 526       if (!res) {
 527          std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 528          exit (0);
 529       }
 530
 531       if (verbose)
 532          std::cout << "Directory creation [" <<  currentOutputDirName << "]" << std::endl;
 533    }  // end if mhd
 534
 535    std::cout << "nbFrames " << nbFrames << std::endl;
 536    std::cout << "nbSlices " << nbSlices << std::endl;
 537    int k;
 538    int nbInstants = nbFrames/nbSlices;
 539    std::cout << "nbInstants (deduced )" << nbInstants << std::endl;
 540    int instantNb;
 541    int sliceNb;
 542    FILE *fp;  // for MHD files
 543
 544    sprintf( original2dseqName, "%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "2dseq");
 545
 546 /**/
 547   // \TODO : tenir compte du bazar precedent
 548
 549     // load 2dseq in memory
 550
 551    fp = fopen(original2dseqName, "rb");
 552    if (!fp)
 553    {
 554       std::cout << "Cannot open [" << original2dseqName << "] for reading" << std::endl;
 555       exit (0);
 556    }
 557
 558    unsigned char * buffer_2dseq = new unsigned char[NX*NY*pixelSize*nbSlices*nbInstants];
 559    ///\ TODO : find a safer way to be sure to read everything!
 560    size_t lgr = fread(buffer_2dseq, 1, NX*NY*pixelSize*nbSlices*nbInstants, fp);
 561
 562    // This one will be important!
 563    // ---------------------------
 564    imageSet = CreateImageSet ( );
 565
 566    strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 567    if (nbInstants==1) // creer un seul fichier .mhd  pour toutes les Slices! (images natives)
 568    {
 569        std::cout << "Single instant : do not split" << std::endl;
 570        if (mhd)
 571        {
 572              sprintf(outputMhdFileName, "%s%cMhdData_Toutes_les_Slices.mhd", currentOutputMhdDirName,
 573                                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 574              fp=fopen(outputMhdFileName, "w");
 575              if (!fp)
 576              {
 577                 std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 578                 exit(0);
 579              }
 580              else
 581              {
 582                fprintf(fp, "ObjectType = Image\n");
 583                fprintf(fp, "NDims = 3\n" );
 584                fprintf(fp, "BinaryData = True \n" );
 585                fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 586                fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices );
 587                fprintf(fp, "HeaderSize = %d\n", 0);
 588                fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
 589                fprintf(fp, "Position = 0 0 %d\n", 0 );
 590                fprintf(fp, "Offset = 0 0 0\n" );
 591                fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 592                fprintf(fp, "ElementNumberOfChannels = 1\n" );
 593                fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
 594                fprintf(fp, "ElementDataFile = %s\n", "../2dseq_toutes_les_Slices" );
 595                fclose(fp);
 596              }
 597              sprintf(output2dseqSliceFileName, "%s%c2dseq_toutes_les_Slices",
 598                                        currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 599              fp=fopen(output2dseqSliceFileName, "wb");
 600              if (!fp)
 601              {
 602                 std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 603              }
 604              else
 605              {
 606                 fwrite( buffer_2dseq, NX*NY*pixelSize, nbSlices, fp);
 607              }
 608              fclose(fp);
 609              strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 610        }  // end if mhd
 611        if (dicom)
 612        {
 613              sprintf(output2dseqSliceFileName, "%s%c2dseq_toutes_les_Slices.dcm",
 614                                        currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 615
 616             /* ----------- Write Dicom Image  ---------------*/
 617              MakeDicomImage(buffer_2dseq,
 618                NX,
 619                NY,
 620                nbFrames,
 621                pixelSize,
 622                fovX/NY, fovY/NY, sliceDistance,
 623                output2dseqSliceFileName,
 624                strPatientName,
 625                day,
 626                strStudyUID,
 627                strSerieUID,
 628                strStudyDescr,
 629                strSerieDescr,
 630                strStudyTimeDate,
 631                0,// index frame number
 632                GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
 633              );
 634        }  // end if dicom
 635    }  // end if nbInstants = 1
 636
 637    else  // more than ONE instant
 638    {
 639           // Interleaved !
 640           // it's (slice1,slide2, ...)t1 ; (slice1,slide2, ...)t2 ; ...
 641
 642          unsigned char * pixelsForCurrentSlice = new unsigned char[NX*NY*pixelSize*nbInstants];
 643
 644          k = 0;
 645          for (sliceNb=0; sliceNb<nbSlices; sliceNb++)
 646          {
 647             if (mhd)
 648             {
 649                sprintf(outputMhdFileName, "%s%cMhdData_%03d.mhd", currentOutputMhdDirName,
 650                                         GDCM_NAME_SPACE::GDCM_FILESEPARATOR, k  );
 651                if (verbose)
 652                   std::cout << "--- Output MHD file [" << outputMhdFileName << "]" << std::endl;
 653                fp=fopen(outputMhdFileName, "w");
 654                if (!fp)
 655                {
 656                    std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 657                    exit(0);
 658                }
 659                else
 660                {
 661             /* ----------- Write MHD Image  ---------------*/
 662                 //if (verbose)
 663                 //   std::cout << "Open sucessfully[" << outputMhdFileName << "] for writting" << std::endl;
 664                    fprintf(fp, "ObjectType = Image\n");
 665                    fprintf(fp, "NDims = 3\n" );
 666                    fprintf(fp, "BinaryData = True \n" );
 667                    fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 668                    fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbInstants);
 669                    fprintf(fp, "HeaderSize = %d\n", 0);
 670                    fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, 1.0 ); // slice distance : no meaning for temporal serie
 671                    fprintf(fp, "Position = 0 0 %d\n", sliceNb );
 672                    fprintf(fp, "Offset = 0 0 0\n" );
 673                    fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 674                    fprintf(fp, "ElementNumberOfChannels = 1\n" );
 675                    fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
 676                    fprintf(fp, "ElementDataFile = ..%c2dseq_Slice_%d\n", GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb );
 677                    fclose(fp);
 678                } // end write MHD
 679
 680                sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d",
 681                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,sliceNb);
 682                fp=fopen(output2dseqSliceFileName, "wb");
 683                if (!fp)
 684                {
 685                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 686                    exit (0);
 687                }
 688                int frameSize = NX*NY*pixelSize;
 689                for (instantNb=0; instantNb<nbInstants; instantNb++)
 690                {
 691 // std::cout << "------------SN " << sliceNb << " IN " << instantNb <<  " T " << nbSlices*instantNb + sliceNb << std::endl;
 692                     fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
 693                             frameSize,
 694                             1, fp);
 695                }
 696                fclose(fp);
 697 // std::cout << "end writting[" << output2dseqSliceFileName << "]" << std::endl;
 698             }  // end if mhd
 699
 700             if (dicom)
 701             {
 702                // desperate try !
 703                /*
 704                sprintf(output2dseqSliceFileName, "%sdummy_buffer",
 705                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 706                fp=fopen(output2dseqSliceFileName, "wb");
 707                if (!fp)
 708                {
 709                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 710                    exit (0);
 711                }
 712                int frameSize = NX*NY*pixelSize;
 713                for (instantNb=0; instantNb<nbInstants; instantNb++)
 714                {
 715 // std::cout << "------------SN " << sliceNb << " IN " << instantNb <<  " T " << nbSlices*instantNb + sliceNb << std::endl;
 716                     fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
 717                             frameSize,
 718                             1, fp);
 719                }
 720                fclose(fp);
 721
 722                fp=fopen(output2dseqSliceFileName, "rb");
 723                if (!fp)
 724                {
 725                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for reading" << std::endl;
 726                    exit (0);
 727                }
 728                fread( pixelsForCurrentSlice,
 729                             frameSize*nbInstants,
 730                             1, fp);
 731                fclose(fp);
 732               // end of desperate try !
 733                */
 734
 735                /* ----------- Write Dicom Image  ---------------*/
 736
 737                int frameSize = NX*NY*pixelSize;
 738                for (instantNb=0; instantNb<nbInstants; instantNb++)
 739                {
 740                   memcpy(pixelsForCurrentSlice + frameSize*instantNb, buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize, frameSize);
 741                }
 742
 743                int indOfFirsImageWithinImageSet =  nbSlices*instantNb;
 744                sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d.dcm",
 745                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb);
 746
 747                MakeDicomImage(
 748                   pixelsForCurrentSlice,
 749                   NX,
 750                   NY,
 751                   nbInstants,
 752                   pixelSize,
 753                   fovX/NY, fovY/NY, sliceDistance,
 754                   output2dseqSliceFileName,
 755                   strPatientName,
 756                   day,
 757                   strStudyUID,
 758                   strSerieUID,
 759                   strStudyDescr,
 760                   strSerieDescr,
 761                   strStudyTimeDate,
 762                   sliceNb*nbInstants,
 763                   GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
 764                );
 765                if (verbose)
 766                   std::cout << "--- Output DCM file [" << output2dseqSliceFileName << "]" << std::endl;
 767
 768             } // en if dicom
 769
 770         k++;
 771         }
 772         delete [] pixelsForCurrentSlice;
 773      }  // end nbInstants == 1
 774    delete [] buffer_2dseq;
 775 /**/
 776
 777
 778    // -----------------------------------------------------
 779    //  deal with MatLab-generated Carto file.
 780    // -----------------------------------------------------
 781
 782    dealWithCarto(fileNames,  NX,  NY,  nbSlices, fovX, fovY, sliceDistance,
 783                    copyFile, currentOutputDirName, outputMhdFileName, output2dseqCartoName);
 784 }
 785
 786
 787 // ===========================================================================================
 788
 789 void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX, int NY, int nbSlices,
 790                                  double fovX, double fovY, double sliceDistance,
 791                                  char *copyFile, std::string &currentOutputDirName,
 792                                  char *outputMhdFileName, char *output2dseqCartoName)
 793 {
 794    // -----------------------------------------------------
 795    //  deal with MatLab-generated Carto file.
 796    // -----------------------------------------------------
 797
 798    char *code[] ={ "ADC", "adc", "TTP", "ttp", "PEAK", "peak" , ""};  // add more carto file name identifiers if necessary; end with ""
 799    int icode;
 800    GDCM_NAME_SPACE::DirListType::iterator it;
 801    char file_name_ident[500];
 802    FILE *fp;
 803
 804    // Iterate to ALL the objets(files/directories) found in the input directory
 805    for (it = fileNames.begin();
 806         it != fileNames.end();
 807       ++it)
 808    {
 809       if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(*it) )
 810       {
 811          if (verbose)
 812             std::cout << "--- [" << *it << "] is a file" << std::endl;
 813
 814          icode = 0;
 815
 816          while (code[icode][0] != 0)
 817          {
 818             sprintf(file_name_ident, "2dseq_%s",code[icode]); // e.g  "2dseq_ADC"
 819             std::string::size_type loc = (*it).rfind(file_name_ident);
 820
 821             if ( loc != std::string::npos )
 822             {
 823
 824        ///\ TODO : find a safer way to be sure to read everything!
 825               unsigned char *buffer_carto = new unsigned char[NX*NY*sizeof(double)*nbSlices];
 826               fp = fopen ( (*it).c_str(), "rb");
 827               if (!fp){
 828                  std::cout << "Cannot open [" << *it << "] for reading" << std::endl;
 829
 830                }
 831                fread(buffer_carto, NX*NY*sizeof(double), nbSlices, fp);
 832
 833                std::cout << "Deal with Carto file :[" <<*it << "], computed length : "
 834                          << NX*NY*sizeof(double)*nbSlices << std::endl;
 835                   std::string lastFileName = GDCM_NAME_SPACE::Util::GetName((*it).c_str());
 836                if (mhd)
 837                {
 838                   // Copy the data file in the new directory
 839                   sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() ,
 840                             currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str());
 841                   system(copyFile);
 842                   sprintf(outputMhdFileName, "%s%c%s%s",
 843                                        currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".mhd" );
 844                   if (verbose)
 845                     std::cout << "--- Output Carto MHD file [" << outputMhdFileName << "]" << std::endl;
 846
 847                   FILE *fp;
 848                   fp=fopen(outputMhdFileName, "w");
 849                   if (!fp)
 850                   {
 851                      std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 852                   }
 853                   else
 854                   {
 855                      fprintf(fp, "ObjectType = Image\n");
 856                      fprintf(fp, "NDims = 3\n" );
 857                      fprintf(fp, "BinaryData = True \n" );
 858                      fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 859                      fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices);
 860                      fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
 861                      fprintf(fp, "HeaderSize = %d\n", 0 );
 862                      fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
 863                      fprintf(fp, "Position = 0 0 0\n" );
 864                      fprintf(fp, "Offset = 0 0 0\n" );
 865                      fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 866                      fprintf(fp, "ElementNumberOfChannels = 1\n" );
 867                      fprintf(fp, "ElementType = %s\n", "MET_DOUBLE" );
 868                      fprintf(fp, "ElementDataFile = %s\n", lastFileName.c_str() );
 869
 870                      fclose(fp);
 871                   }
 872                   if (verbose)
 873                      std::cout << "--- end write Carto MHD file [" << outputMhdFileName << "]" << std::endl;
 874                }  // end if mhd
 875
 876             // ----------- Write Dicom Image  ---------------
 877
 878                if (dicom)
 879                {
 880                   sprintf(output2dseqCartoName, "%s%c%s%s",
 881                                        currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".dcm" );
 882                   if (verbose)
 883                      std::cout << "--- end create name output2dseqCartoName file [" << output2dseqCartoName << "]" << std::endl;
 884
 885                   strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID(); //New SerieUID for each carto.
 886                   std::string strNewSerieDescr(strSerieDescr+ "_" +GDCM_NAME_SPACE::Util::GetName((*it).c_str()));
 887                   MakeDicomImage(buffer_carto,
 888                      NX,
 889                      NY,
 890                      nbSlices,
 891                      8, // pixelSize
 892                      fovX/NY, fovY/NY, sliceDistance,
 893                      output2dseqCartoName,
 894                      strPatientName,
 895                      day,
 896                      strStudyUID,
 897                      strSerieUID,
 898                      strStudyDescr,
 899                      strNewSerieDescr,
 900                      strStudyTimeDate,
 901                      0,
 902                      GDCM_NAME_SPACE::CREATED_IMAGE
 903                   );
 904                }  // end if dicom
 905
 906                delete [] buffer_carto;
 907                if (verbose)
 908                      std::cout << "--- End writing Carto DICOM file [" << output2dseqCartoName << "]" << std::endl;
 909                break; // don't check for more ident on same file name!
 910
 911             }
 912             icode++;
 913          }
 914       }
 915    } // end iterate on files
 916 }
 917
 918
 919 // ==========================================================================================================
 920
 921 bool Bruker2Dicom::CreateDirectory(std::string OutputDirName)
 922 {
 923    std::string systemCommand;
 924
 925    if (verbose)
 926       std::cout << "Check for output directory :[" << OutputDirName << "]."
 927                 <<std::endl;
 928    if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(OutputDirName) )    // dirout not found
 929    {
 930       std::string strDirNameout(OutputDirName);          // to please gcc 4
 931       systemCommand = "mkdir " + strDirNameout;        // create it!
 932       if (verbose)
 933          std::cout << systemCommand << std::endl;
 934       system (systemCommand.c_str());
 935       if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(OutputDirName) ) // be sure it worked
 936       {
 937          if (verbose)
 938             std::cout << "KO : not a dir : [" << OutputDirName << "] (creation failure ?)" << std::endl;
 939          return 0;
 940          /// \todo : THROW AN EXCEPTION
 941       }
 942       else
 943       {
 944          if (verbose)
 945            std::cout << "Directory [" << OutputDirName << "] created." << std::endl;
 946       }
 947    }
 948    else
 949    {
 950        if (verbose)
 951           std::cout << "Output Directory [" << OutputDirName << "] already exists; Used as is." << std::endl;
 952    }
 953
 954    return 1;
 955
 956 }
 957
 958
 959 // ===========================================================================================
 960
 961 /// \TODO move cleanString to 'crea' ?
 962
 963 void Bruker2Dicom::cleanString(std::string &s)
 964 {
 965    int l = s.size();
 966    if (s[l-1] == 0x0A || s[l-1] == 0x0D ) // CR or NL
 967    {
 968       l--;
 969       s = s.substr(0, l);
 970    }
 971    if (s[l-1] == ' ' ) // blank space
 972    {
 973       l--;
 974       s = s.substr(0, l);
 975    }
 976
 977    if (s[0] == '<')
 978       s= s.substr(1,l-2);
 979    std::string repChar("_");
 980    GDCM_NAME_SPACE::Util::ReplaceSpecChar(s, repChar);
 981 }
 982
 983
 984
 985 // ===========================================================================================
 986
 987
 988 void Bruker2Dicom::getImhDataType(BrukerFieldData &bDPT, std::string &mhdDataPixelType, int &pixelSize)
 989 {
 990    if(bDPT.GetDataType() == "string")
 991    {
 992          std::string brukerDataPixelType = bDPT.GetStringValue()[0];
 993          std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
 994          //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
 995
 996          if (brukerDataPixelType ==  "ip_short") {
 997             mhdDataPixelType = "MET_USHORT";
 998             pixelSize = 2;
 999          }
1000          if (brukerDataPixelType ==  "ip_int") {
1001             mhdDataPixelType = "MET_UINT";
1002             pixelSize = 4;
1003          }
1004          if (brukerDataPixelType ==  "ip_char") {
1005              mhdDataPixelType = "MET_UCHAR";
1006              pixelSize = 1;
1007          }
1008                   /// \TODO : finish the list
1009     /*
1010     case 0 : fp << "ElementType = MET_CHAR" << std::endl;
1011       break;
1012     case 1 : fp << "ElementType = MET_UCHAR" << std::endl;
1013       break;
1014     case 2 : fp << "ElementType = MET_SHORT" << std::endl;
1015       break;
1016     case 3 : fp << "ElementType = MET_USHORT" << std::endl;
1017       break;
1018     case 4 : fp << "ElementType = MET_INT" << std::endl;
1019       break;
1020     case 5 : fp << "ElementType = MET_UINT" << std::endl;
1021       break;
1022     case 6 : fp << "ElementType = MET_FLOAT" << std::endl;
1023       break;
1024     case 7 : fp << "ElementType = MET_DOUBLE" << std::endl;
1025     */
1026     }
1027     else
1028     {
1029          int brukerDataPixelType = bDPT.GetIntValue()[0];
1030          std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
1031          //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
1032
1033 // Cross your fingers !!!
1034
1035 // pb : found values : 2, 3, 5
1036
1037          if (brukerDataPixelType ==  2) {
1038             mhdDataPixelType = "MET_USHORT";
1039             pixelSize = 2;
1040          }
1041          if (brukerDataPixelType ==  3) {
1042             mhdDataPixelType = "MET_USHORT";
1043             pixelSize = 2;
1044          }
1045          if (brukerDataPixelType ==  1) {
1046             mhdDataPixelType = "MET_UCHAR";
1047             pixelSize = 1;
1048          }
1049     }
1050 }
1051
1052 // ===========================================================================================
1053
1054 std::vector<BrukerImage> Bruker2Dicom::CreateImageSet ( )
1055 {
1056          std::vector<BrukerImage> imageSet;
1057          br_acqp.SetLoopStructure();
1058          std::vector<int> tempVect                      = br_acqp.GetLoopStructure() ;
1059          std::map<std::string, BrukerFieldData> map     = br_acqp.GetBrukerHeaderMap();
1060          bool result                                    = br_acqp.ObjectVaryingProperties.init(map,tempVect);
1061
1062          br_acqp.SetImageLoopStructure();
1063          br_acqp.SetBrukerImageList();
1064          std::vector<std::vector<int> > brukerImageList = br_acqp.GetBrukerImageList();
1065
1066          BrukerImage image(br_acqp,br_reco);
1067          image.Init(br_acqp,br_reco,1);
1068
1069          for(int i=0;i<brukerImageList.size();i++)
1070          {
1071             image.Init(br_acqp,br_reco,i);
1072             imageSet.push_back(image);
1073          }
1074
1075  // Just for checking
1076  /*
1077
1078          std::vector<std::vector <double> > imageOrientation;
1079          std::vector <double> imagePosition;
1080          for(int i=0;i<brukerImageList.size();i++)
1081          {
1082            // fread(buffer_2dseq, NX*NY*pixelSize*nbSlices*nbInstants, 1, fp);
1083
1084            imagePosition = imageSet[i].getTranslationVectorRPS2XYZ();
1085            std::cout << "Position " << imagePosition[0] << " "
1086                      << imagePosition[1] << " "  << imagePosition[2] ;
1087            imageOrientation =  imageSet[i].getRotationMatrixRPS2XYZ();
1088            std::cout << "\t  Orientation " ;
1089            for(int i1=0; i1<3;i1++)for(int i2=0; i2<3;i2++)
1090               std::cout << imageOrientation[i1][i2] << " ";
1091
1092            //std::cout << "\t  Abs Time " << imageSet[i].getAbsoluteTimePosition();
1093            std::cout << "\t  Relat Time " << imageSet[i].getRelativeTimePosition();
1094
1095            std::cout << "\t [";
1096            for (int i3=0; i3<imageSet[i].getLoopStamp().size();i3++)
1097               std::cout << " " << imageSet[i].getLoopStamp()[i3];
1098            std::cout << "]" << std::endl;
1099          }
1100 */
1101    return imageSet;
1102 }
1103
1104
1105 // ===========================================================================================
1106
1107 void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels,
1108               int X,
1109               int Y,
1110               int nbFrames,
1111               int pixelSize,
1112               double spacingX, double spacingY, double sliceDistance,
1113               std::string dcmImageName,
1114               const std::string &patientName,
1115               const char *day,
1116               std::string &studyUID,
1117               std::string &serieUID,
1118               std::string &studyDescr,
1119               std::string &serieDescr,
1120               std::string &strStudyTimeDate,
1121               int imgNum,
1122               GDCM_NAME_SPACE::ImageContentType contentType
1123       )
1124 {
1125    std::ostringstream str;
1126
1127    GDCM_NAME_SPACE::File *file;
1128    file = GDCM_NAME_SPACE::File::New();
1129
1130   // Set the image size
1131    str.str("");
1132    str << X;
1133    file->InsertEntryString(str.str(),0x0028,0x0011,"US"); // Columns
1134    str.str("");
1135    str << Y;
1136    file->InsertEntryString(str.str(),0x0028,0x0010,"US"); // Rows
1137
1138    if (nbFrames != 1)
1139    {
1140       str.str("");
1141       str << nbFrames;
1142       file->InsertEntryString(str.str(),0x0028,0x0008,"IS"); // Number of Frames
1143    }
1144
1145   // Set the pixel type
1146   //      //8, 16, 32, 64 (for double ?)
1147    str.str("");
1148    str << pixelSize*8;
1149    file->InsertEntryString(str.str(),0x0028,0x0100,"US"); // Bits Allocated
1150
1151    file->InsertEntryString(str.str(),0x0028,0x0101,"US"); // Bits Stored
1152
1153    str.str("");
1154    str << pixelSize*8-1;
1155    file->InsertEntryString(str.str(),0x0028,0x0102,"US"); // High Bit
1156
1157   // Set the pixel representation // 0/1 , 0=unsigned
1158    file->InsertEntryString("1",0x0028,0x0103, "US"); // Pixel Representation
1159
1160   // Set the samples per pixel // 1:Grey level, 3:RGB
1161    file->InsertEntryString("1",0x0028,0x0002, "US"); // Samples per Pixel
1162
1163 //  0028 0030 DS 2 Pixel Spacing
1164    str.str("");
1165    str << spacingX << "\\" << spacingY;
1166    file->InsertEntryString(str.str(),0x0028,0x0030, "DS"); // Pixel Spacing
1167
1168  //   0018 0050 DS 1 Slice Thickness
1169    str.str("");
1170    str << sliceDistance;
1171    file->InsertEntryString(str.str(),0x0018,0x0050, "DS");
1172
1173   // 1.2.840.10008.5.1.4.1.1.4.1 : Enhanced MR Image Storage
1174  //  file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0002, 0x0002, "UI");  // [Media Storage SOP Class UID]
1175   // file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0008, 0x0016, "UI");  // [SOP Class UID]
1176
1177
1178 // OK : MR is NOT multiframe, but I want just a quick an dirty solution
1179 // 1.2.840.10008.5.1.4.1.1.4         MR Image Storage
1180    file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0002, 0x0002, "UI");  // [Media Storage SOP Class UID]
1181    file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0008, 0x0016, "UI");  // [SOP Class UID]
1182
1183   // if (strlen(patientName) != 0)
1184    file->InsertEntryString(patientName.c_str(),0x0010,0x0010, "PN"); // Patient's Name
1185
1186    file->InsertEntryString(studyUID, 0x0020, 0x000d, "UI");
1187    file->InsertEntryString(serieUID, 0x0020, 0x000e, "UI");
1188
1189 //  0008 0020 DA 1 Study Date
1190 //  0008 0030 TM 1 Study Time
1191
1192 /// \TODO split into 2 strings!
1193    file->InsertEntryString(strStudyTimeDate.substr(10,11).c_str(),0x0008,0x0020, "DA");
1194    file->InsertEntryString(strStudyTimeDate.substr(1,8).c_str(),0x0008,0x0030, "TM");
1195
1196    file->InsertEntryString(studyDescr,0x0008,0x1030, "LO");  // Study Description
1197    file->InsertEntryString(serieDescr,0x0008,0x103e, "LO");  // Series Description
1198
1199 //0008|0060 [CS] [Modality]
1200    file->InsertEntryString("MR",0x0008,0x0060, "CS");
1201
1202 // 0020 0037 DS 6 Image Orientation (Patient)
1203    char charImageOrientation[256];
1204
1205 /*
1206 std::cout << "try charImageOrientation  " <<
1207                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0] << " " <<
1208                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1] << " " <<
1209                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2] << " " <<
1210                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0] << " " <<
1211                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1] << " " <<
1212                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] << std::endl ;
1213 */
1214    sprintf(charImageOrientation,"%f\\%f\\%f \\ %f\\%f\\%f",
1215                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0],
1216                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1],
1217                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2],
1218                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0],
1219                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1],
1220                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] ) ;
1221
1222    file->InsertEntryString(charImageOrientation,0x0020,0x0037, "DS");
1223
1224
1225 // 0020 0032 DS 3 Image Position (Patient)
1226
1227    char charImagePosition[256];
1228    sprintf(charImagePosition,"%f\\%f\\%f",
1229                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[0],
1230                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[1],
1231                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[2]);
1232
1233    file->InsertEntryString(charImagePosition,0x0020,0x0032, "DS");  //0020 0032 DS 3 Image Position (Patient)
1234
1235
1236
1237 // 0020 0x1041 DS 1 Slice Location
1238 //        sprintf(charImagePosition,"%f",float(imgNum));
1239 //        file->InsertEntryString(charImagePosition,0x0020,0x1041, "DS");
1240 /*
1241   // Set Rescale Intercept
1242         str.str("");
1243         str << div;
1244         file->InsertEntryString(str.str(),0x0028,0x1052,"DS");
1245
1246   // Set Rescale Slope
1247         str.str("");
1248         str << mini;
1249         file->InsertEntryString(str.str(),0x0028,0x1053,"DS");
1250 */
1251
1252    GDCM_NAME_SPACE::FileHelper *fileH;
1253    fileH = GDCM_NAME_SPACE::FileHelper::New(file);
1254    fileH->SetContentType(contentType);
1255
1256    // cast is just to avoid warnings (*no* conversion is performed)
1257    //fileH->SetImageData((uint8_t *)img,int(maxX*maxY)*sizeof(uint16_t)); // troubles when maxX, mayY are *actually* float!
1258
1259 //std::cout << "--------------------------------  X*Y*nbFrames*pixelSize " << X << " " << Y << " " << nbFrames << " " << pixelSize << std::endl;
1260
1261    fileH->SetImageData((uint8_t *)tabPixels, X*Y*nbFrames*pixelSize);
1262    fileH->SetWriteModeToRaw();
1263    fileH->SetWriteTypeToDcmExplVR();
1264    if( !fileH->Write(dcmImageName))
1265       std::cout << "Failed for [" << dcmImageName << "]\n"
1266                 << "           File is unwrittable" << std::endl;
1267
1268    if (verbose)
1269       file->Print();
1270
1271    file->Delete();
1272    fileH->Delete();
1273 }
1274
1275