lib/src1/bruker2dicom.cxx

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