lib/src1/bruker2dicom.cxx

   1 #include "bruker2dicom.h"
   2 #include <boost/filesystem/path.hpp>
   3 #include <boost/filesystem/operations.hpp>
   4
   5 #ifndef PATH_MAX // If not defined yet : do it
   6         #define PATH_MAX 2048
   7 #endif
   8
   9
  10
  11 bool Bruker2Dicom::Execute()
  12 {
  13    // ----- Check input values -----
  14
  15    bool bigEndian = GDCM_NAME_SPACE::Util::IsCurrentProcessorBigEndian();
  16
  17    //if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(InputDirName) )
  18    if ( ! boost::filesystem::is_directory(InputDirName) )
  19    {
  20       std::cout << "KO : [" << InputDirName << "] is not a Directory." << std::endl;
  21       return 0;
  22    }
  23    else
  24    {
  25       if (verbose)
  26          std::cout << "OK : [" << InputDirName << "] is a Directory." << std::endl;
  27    }
  28
  29    std::string strDirNameOut(OutputDirName);
  30    bool res=CreateDirectory(strDirNameOut);
  31    if (!res) {
  32       std::cout << "[" << OutputDirName << "] Directory creation failure " << std::endl;
  33       exit (0);
  34    }
  35
  36    std::string strDirNamein(InputDirName);
  37    GDCM_NAME_SPACE::DirList dirList(strDirNamein, false, true); // DON'T get recursively the list of files
  38    std::string strDirNameout(OutputDirName);
  39
  40 /*
  41    if (listonly)
  42    {
  43       std::cout << "------------List of found files ------------" << std::endl;
  44       dirList.Print();
  45       std::cout << std::endl;
  46       return 1;
  47    }
  48 */
  49
  50 //
  51 // e.g : at level 0, in : B67d1.Bp1
  52 //
  53 //           1  2  3  4  5  6  AdjStatePerStudy  subject
  54 //
  55
  56    GDCM_NAME_SPACE::DirListType fileNames;
  57    fileNames = dirList.GetFilenames();
  58    bool canOpen;
  59    std::string outputFileName;
  60
  61   // BrukerDataSet br_subject;
  62    std::string subject;
  63    subject = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
  64              GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
  65              "subject";
  66    if (verbose)
  67         std::cout << " Subject : [" <<  subject << "]" << std::endl;
  68    canOpen =br_subject.LoadFile(subject);
  69
  70    if (!canOpen)
  71    {
  72       std::cout << "Hopeless! no 'subject' found" << std::endl;
  73       exit(0);  /// \TODO throw an exception !
  74    }
  75    else
  76    {
  77       br_subject.FillMap();
  78    }
  79    //br_subject.PrintSelf();
  80
  81   // get info for 'Study Description'
  82
  83  /*
  84          BrukerFieldData b_protocol_location=br_acqp.GetFieldData("ACQ_protocol_location");
  85          acqp_protocol_location = b_protocol_location.GetStringValue()[0];
  86          cleanString(acqp_protocol_location);
  87 */
  88          BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string");
  89          std::string subject_name = b_name.GetStringValue()[0];
  90          strPatientName = subject_name;
  91          cleanString(subject_name);
  92
  93          BrukerFieldData b_entry=br_subject.GetFieldData("SUBJECT_entry");
  94          std::string subject_entry = b_entry.GetStringValue()[0];
  95          //cleanString(subject_entry);
  96          subject_entry = subject_entry.substr(11, subject_entry.size()-11);
  97
  98          BrukerFieldData b_position=br_subject.GetFieldData("SUBJECT_position");
  99          std::string subject_position = b_position.GetStringValue()[0];
 100          //cleanString(subject_position);
 101          subject_position = subject_position.substr(9, subject_position.size()-9);
 102
 103          BrukerFieldData b_date=br_subject.GetFieldData("SUBJECT_date");
 104          std::string subject_date = b_date.GetStringValue()[0];
 105          strStudyTimeDate = subject_date;
 106          cleanString(subject_date);
 107
 108          BrukerFieldData b_study_name=br_subject.GetFieldData("SUBJECT_study_name");
 109          std::string subject_study_name = b_study_name.GetStringValue()[0];
 110          subject_study_name = subject_study_name.substr(1, subject_study_name.size()-2);
 111          cleanString(subject_date);
 112
 113    strStudyDescr = subject_name + "." + subject_study_name + "." + subject_entry + "." + subject_position + "." + subject_date;
 114
 115    char outputDirName[(unsigned int) PATH_MAX+2];
 116
 117    strStudyUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 118
 119    // -----------------------------------------------------
 120    // Iterate to ALL the objets(files/directories) found in the input directory
 121    // (this is level ZERO)
 122    // each Directory (name : 1, 2, 3, ...) will be a Dicom Serie
 123    // -----------------------------------------------------
 124
 125    GDCM_NAME_SPACE::DirListType::iterator it;
 126
 127    for (it = fileNames.begin();
 128          it != fileNames.end();
 129        ++it)
 130    {
 131       if ( !boost::filesystem::is_regular(*it) ) // check twice !
 132       if ( boost::filesystem::is_directory(*it) )
 133       {
 134          if (verbose)
 135             std::cout << "[" << *it << "] is a directory" << std::endl;
 136
 137          //BrukerDataSet br_acqp;
 138          std::string strAcqp;
 139          strAcqp = (*it) +
 140                    GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 141                    "acqp";
 142
 143          br_acqp.LoadFile(strAcqp);
 144          br_acqp.FillMap();
 145
 146          std::string acqp_scan_name;
 147          std::string acqp_method;
 148          std::string acqp_protocol_location;
 149
 150          BrukerFieldData b_protocol_location=br_acqp.GetFieldData("ACQ_protocol_location");
 151          acqp_protocol_location = b_protocol_location.GetStringValue()[0];
 152          cleanString(acqp_protocol_location);
 153
 154          BrukerFieldData b_scan_name=br_acqp.GetFieldData("ACQ_scan_name");
 155          acqp_scan_name = b_scan_name.GetStringValue()[0];
 156          cleanString(acqp_scan_name);
 157
 158          BrukerFieldData b_method=br_acqp.GetFieldData("ACQ_method");
 159          acqp_method = b_method.GetStringValue()[0];
 160          cleanString(acqp_method);
 161
 162          BrukerFieldData b_list_size = br_acqp.GetFieldData("ACQ_O1_list_size");
 163          b_list_size.PrintSelf(); //JP
 164
 165          nbSlices =  b_list_size.GetIntValue()[0];
 166
 167          strSerieDescr = GDCM_NAME_SPACE::Util::GetName(*it)
 168                          + "." + acqp_protocol_location
 169                          + "." + acqp_scan_name
 170                          + "." + acqp_method.c_str();
 171
 172          sprintf(outputDirName, "%s%c%s", OutputDirName.c_str(),
 173                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 174                           strSerieDescr.c_str() );
 175
 176          std::cout << " ================================================================================\n"
 177                    << " === [" << GDCM_NAME_SPACE::Util::GetName(*it) << "] -> [" << strSerieDescr << "]\n"
 178                    << " ================================================================================"
 179                    << std::endl;
 180
 181 /*
 182          std::cout << " ================================================================================\n"
 183                    << " ========================= [" << GDCM_NAME_SPACE::Util::GetName(*it).c_str()
 184                    << acqp_protocol_location.c_str()
 185                    << acqp_scan_name.c_str()
 186                    << acqp_method.c_str()
 187                    << "]\n"
 188                    << " ================================================================================"
 189                    << std::endl;
 190 */
 191         if (verbose)
 192            printf ("outputDirName [%s]\n", outputDirName);
 193
 194         DealWithNiveau1(*it, outputDirName);
 195       }
 196    } // end of : for (GDCM_NAME_SPACE::DirListType::iterator it
 197 }
 198
 199
 200 // =====================================================================
 201
 202 void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string currentOutputDirName) {
 203 //
 204 // e.g. : at level 1, in B67d1.Bp1/6
 205 //
 206 // acqp  fid  imnd  pdata  pulseprogram  spnam0  spnam1
 207
 208    bool res = CreateDirectory(currentOutputDirName);
 209
 210    if (!res) {
 211       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 212       exit (0);
 213    }
 214    GDCM_NAME_SPACE::DirList dirList(level1Directory, false, true); // DON'T get recursively the list of files
 215    GDCM_NAME_SPACE::DirListType fileNames;
 216    fileNames = dirList.GetFilenames();
 217    // -----------------------------------------------------
 218    // Iterate to ALL the objets(files/directories) found in the input directory
 219    // -----------------------------------------------------
 220    GDCM_NAME_SPACE::DirListType::iterator it;
 221
 222    for (it = fileNames.begin();
 223         it != fileNames.end();
 224       ++it)
 225    {
 226       if ( boost::filesystem::is_regular(*it) )
 227       //if ( ! boost::filesystem::is_directory(*it) )
 228       {
 229          if (verbose)
 230             std::cout << "--- [" << *it << "] is a file" << std::endl;
 231       }
 232    }
 233
 234    char outputDirName[(unsigned int) PATH_MAX+2];
 235    //std::string firstName;
 236    bool canOpen;
 237    for (it = fileNames.begin();
 238         it != fileNames.end();
 239       ++it)
 240    {
 241       if ( !boost::filesystem::is_regular(*it) ) // check twice !
 242       if ( boost::filesystem::is_directory(*it) )
 243       {
 244          // will be always "pdata" ...
 245          if (verbose)
 246             std::cout << "--- [" << *it << "] is a directory" << std::endl;
 247
 248               /* a recuperer :
 249               if (FileLine.startsWith("##$ACQ_size=")) {
 250               if (FileLine.startsWith("##$NI=")) {
 251               if (FileLine.startsWith("##$NR=")) {
 252               if (FileLine.startsWith("##$ACQ_obj_order=")) {
 253               if (FileLine.startsWith("##$ACQ_word_size=")) {
 254               if (FileLine.startsWith("##$BYTORDA=")) {
 255               if (FileLine.startsWith("##$PULPROG=")) {
 256               */
 257
 258          sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 259                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 260                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str());
 261          //br1.PrintSelf();
 262
 263           std::string strMethod;
 264           //std::string firstName = *(fileNames.begin());
 265
 266           strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin())) +
 267                       GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 268                       "method";
 269             // std::cout << "---strMethod (for method)=> [" << strMethod << "]" << std::endl;
 270           canOpen = br_method.LoadFile(strMethod);
 271           if (!canOpen)
 272           {
 273              strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
 274                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 275                          "imnd";
 276              //std::cout << "---strMethod (for imnd) => [" << strMethod << "]" << std::endl;
 277              canOpen = br_method.LoadFile(strMethod);
 278              if (!canOpen)
 279              {
 280                 std::cout << "Hopeless! neither 'method' nor 'imnd' found" << std::endl;
 281                 exit(0);  /// \TODO throw an exception !
 282              }
 283           }
 284           if (verbose)
 285              std::cout << "open => [" << strMethod << "] successfully" << std::endl;
 286           br_method.FillMap();
 287
 288           /* a recuperer :
 289              ##$PVM_Fov (dimension)
 290           */
 291   /*
 292           dans method (pour perfusion  seulement?) :
 293           ##$PVM_ObjOrderList=( 8 )
 294           0 2 4 6 1 3 5 7
 295           ##$PVM_NSPacks=2
 296           ##$PVM_SPackArrNSlices=( 2 )
 297           7 1
 298   */
 299          DealWithNiveau2(*it,outputDirName );
 300       }
 301    }
 302 }
 303
 304 // =====================================================================
 305
 306 void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string currentOutputDirName) {
 307
 308 // e.g. : at level 2 in B67d1.Bp1/6/pdata
 309 //
 310 // acqp  fid  imnd  pdata  pulseprogram  spnam0  spnam1
 311 //
 312
 313    bool res = CreateDirectory(currentOutputDirName);
 314
 315    if (!res) {
 316       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 317       exit (0);
 318    }
 319
 320    GDCM_NAME_SPACE::DirList dirList(level2Directory, false, true); // DON'T get recursively the list of files
 321
 322    GDCM_NAME_SPACE::DirListType fileNames;
 323    fileNames = dirList.GetFilenames();
 324
 325    char outputDirName[(unsigned int) PATH_MAX+2];
 326
 327    // -----------------------------------------------------
 328    // Iterate to ALL the objets(files/directories) found in the input directory
 329    // -----------------------------------------------------
 330    GDCM_NAME_SPACE::DirListType::iterator it;
 331    bool canOpen;
 332
 333    if (verbose)
 334    for (it = fileNames.begin();
 335         it != fileNames.end();
 336       ++it)
 337    {
 338       if ( !boost::filesystem::is_regular(*it) )
 339       //if ( ! boost::filesystem::is_directory(*it) )
 340       {
 341          std::cout << "--- --- [" << *it << "] is a file" << std::endl;
 342       }
 343
 344    }
 345
 346    for (it = fileNames.begin();
 347          it != fileNames.end();
 348        ++it)
 349    {
 350       if ( !boost::filesystem::is_regular(*it) ) // check twice !
 351       if ( boost::filesystem::is_directory(*it) )
 352       {
 353
 354          if (verbose)
 355             std::cout << "--- --- [" << *it << "] is a directory" << std::endl;
 356
 357         // sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 358         //                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 359         //                                GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
 360   // MUST be 'pdata'!
 361
 362 //
 363 // (interest of previous method :
 364 // If unaware user changed the pdata name, it goes on working
 365 //
 366           std::string str_isa;
 367           str_isa = (*it) +
 368                     GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 369                    "isa";
 370
 371           std::string str_isa_func_name;
 372           canOpen = br_isa.LoadFile(str_isa);
 373           if (!canOpen)
 374           {
 375              sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 376                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 377                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
 378           }
 379           else
 380           {
 381              br_isa.FillMap();
 382              BrukerFieldData b_isa_func_name = br_isa.GetFieldData("ISA_func_name");
 383
 384              str_isa_func_name = b_isa_func_name.GetStringValue()[0];
 385              cleanString(str_isa_func_name);
 386
 387              sprintf(outputDirName, "%s%c%s.%s", currentOutputDirName.c_str(),
 388                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 389                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str(),
 390              str_isa_func_name.c_str());
 391           }
 392           DealWithNiveau3(*it, outputDirName);
 393       }
 394    }
 395 }
 396
 397
 398 //
 399 // =====================================================================
 400 //
 401
 402 void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string currentOutputDirName){
 403
 404 //
 405 // e.g. at level 3, in
 406
 407    // just to be able to go on checking // JP
 408    if ( GDCM_NAME_SPACE::Util::GetName(level3Directory) != "1")
 409       return;
 410
 411    bool res = CreateDirectory(currentOutputDirName);
 412
 413    if (!res)
 414    {
 415       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 416       exit (0);
 417    }
 418
 419    GDCM_NAME_SPACE::DirList dirList(level3Directory, false, true); // DON'T get recursively the list of files
 420    GDCM_NAME_SPACE::DirListType::iterator it;
 421    GDCM_NAME_SPACE::DirListType fileNames;
 422    fileNames = dirList.GetFilenames();
 423
 424    char original2dseqName       [(unsigned int) PATH_MAX+2];
 425    char currentOutputMhdDirName [(unsigned int) PATH_MAX+2];
 426
 427    char outputMhdFileName       [(unsigned int) PATH_MAX+2];
 428    char output2dseqSliceFileName[(unsigned int) PATH_MAX+6]; // think about extra '.dcm'
 429    char output2dseqName         [(unsigned int) PATH_MAX+6];
 430    char output2dseqCartoName    [(unsigned int) PATH_MAX+6];
 431
 432    char copyFile[PATH_MAX + PATH_MAX + 5]; // Should be enough!
 433    bool canOpen;
 434
 435    //-------------- try d3proc;
 436    char char_d3proc[(unsigned int) PATH_MAX+2];
 437
 438    sprintf(char_d3proc,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"d3proc" );
 439
 440    if (verbose)
 441       std::cout << "--- => [" << char_d3proc << "]" << std::endl;
 442    std::string str_d3proc(char_d3proc);
 443    canOpen = br_d3proc.LoadFile(str_d3proc);
 444
 445    if (!canOpen)
 446    {
 447       std::cout << "Hopeless! no 'd3proc' found" << std::endl;
 448       exit(0);  /// \TODO throw an exception !
 449    }
 450
 451    canOpen = br_d3proc.FillMap();
 452    if (!canOpen)
 453    {
 454       std::cout << "Hopeless! FillMap failed on 'd3proc'" << std::endl;
 455       exit(0);  /// \TODO throw an exception !
 456    }
 457
 458    //-------------- end try d3proc;
 459
 460
 461  // -------------------try reco
 462
 463    char char_reco[(unsigned int) PATH_MAX+2];
 464
 465    sprintf(char_reco,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
 466     //str_d3proc = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
 467     //             GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 468     //             "d3proc";
 469    if (verbose)
 470       std::cout << "--- => [" << char_reco << "]" << std::endl;
 471    std::string str_reco(char_reco);
 472    canOpen = br_reco.LoadFile(str_reco);
 473
 474    if (!canOpen) // we try in directory ../1
 475    {
 476       if (verbose)
 477          std::cout << "[" << str_reco << "] not found " << std::endl;
 478       std::string lastDirName = GDCM_NAME_SPACE::Util::GetPath(level3Directory);
 479       //lastDirName = GDCM_NAME_SPACE::Util::GetPath(lastDirName);
 480       sprintf(char_reco,"%s%c1%c%s", lastDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
 481       str_reco=char_reco;
 482       canOpen = br_reco.LoadFile(str_reco);
 483       if (!canOpen)
 484       {
 485          std::cout << "Hopeless! cannot find 'reco' in [" << str_reco << "]"  << std::endl;
 486          exit(0);  /// \TODO throw an exception !
 487       }
 488    }
 489
 490    canOpen = br_reco.FillMap();
 491    if (!canOpen)
 492    {
 493       std::cout << "Hopeless! FillMap failed on [" << str_reco << "]" << std::endl;
 494       exit(0);  /// \TODO throw an exception !
 495    }
 496    //std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
 497    // br_reco.PrintSelf();
 498    // std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
 499
 500    // -------------------end try reco
 501
 502
 503    BrukerFieldData bX = br_d3proc.GetFieldData("IM_SIX");
 504    int NX = bX.GetIntValue()[0];
 505
 506    std::cout << "IM_SIX " << NX << std::endl;
 507    BrukerFieldData bY=br_d3proc.GetFieldData("IM_SIY");
 508    int NY = bY.GetIntValue()[0];
 509
 510    std::cout << "IM_SIY " << NY << std::endl;
 511    /// \todo : check if there are actually 3 dimensions or only 2
 512
 513    BrukerFieldData bZ= br_d3proc.GetFieldData("IM_SIZ");
 514    int nbFrames = bZ.GetIntValue()[0];
 515    std::cout << "IM_SIZ " << nbFrames << std::endl;
 516
 517         // WARNING DATTYPE is, either in {ip_short, ip_int, ip_char, ...}, or in {1, 2, 3, ...}
 518
 519    BrukerFieldData bDPT = br_d3proc.GetFieldData("DATTYPE");
 520
 521    std::string mhdDataPixelType;
 522    int pixelSize;
 523    getImhDataType(bDPT, mhdDataPixelType, pixelSize);
 524
 525    BrukerFieldData fov = br_method.GetFieldData("PVM_Fov");
 526    double fovX = fov.GetDoubleValue()[0];
 527    double fovY = fov.GetDoubleValue()[1];
 528    if (verbose)
 529       std::cout << "FOV (ds method) " << fovX << " " << fovY << std::endl;
 530
 531    /// \TODO probabely a more sophisticated accessor will be necessary :
 532    ///  (cf : non contiguous slices, overlapping, slice thickness, space between clices, etc)
 533    BrukerFieldData bsliceDistance = br_method.GetFieldData("PVM_SPackArrSliceDistance");
 534    double sliceDistance = bsliceDistance.GetDoubleValue()[0];
 535
 536    if (mhd)
 537    {
 538       sprintf(currentOutputMhdDirName, "%s%c%s", currentOutputDirName.c_str(),
 539                                GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "MhdFiles");
 540       res = CreateDirectory( currentOutputMhdDirName );
 541       if (!res) {
 542          std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 543          exit (0);
 544       }
 545
 546       if (verbose)
 547          std::cout << "Directory creation [" <<  currentOutputDirName << "]" << std::endl;
 548    }  // end if mhd
 549
 550    std::cout << "nbFrames " << nbFrames << std::endl;
 551    std::cout << "nbSlices " << nbSlices << std::endl;
 552    int k;
 553    int nbInstants = nbFrames/nbSlices;
 554    std::cout << "nbInstants (deduced )" << nbInstants << std::endl;
 555    int instantNb;
 556    int sliceNb;
 557    FILE *fp;  // for MHD files
 558
 559    sprintf( original2dseqName, "%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "2dseq");
 560
 561 /**/
 562   // \TODO : tenir compte du bazar precedent
 563
 564     // load 2dseq in memory
 565
 566    fp = fopen(original2dseqName, "rb");
 567    if (!fp)
 568    {
 569       std::cout << "Cannot open [" << original2dseqName << "] for reading" << std::endl;
 570       exit (0);
 571    }
 572
 573    unsigned char *buffer_2dseq = new unsigned char[NX*NY*pixelSize*nbSlices*nbInstants];
 574    ///\ TODO : find a safer way to be sure to read everything!
 575    size_t lgr = fread(buffer_2dseq, 1, NX*NY*pixelSize*nbSlices*nbInstants, fp);
 576
 577    // This one will be important!
 578    // ---------------------------
 579    imageSet = CreateImageSet ( );
 580
 581    strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 582    if (nbInstants==1) // creer un seul fichier .mhd  pour toutes les Slices! (images natives)
 583    {
 584        std::cout << "Single instant : do not split" << std::endl;
 585        if (mhd)
 586        {
 587              sprintf(outputMhdFileName, "%s%cMhdData_All_the_Slices.mhd", currentOutputMhdDirName,
 588                                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 589              fp=fopen(outputMhdFileName, "w");
 590              if (!fp)
 591              {
 592                 std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 593                 exit(0);
 594              }
 595              else
 596              {
 597                fprintf(fp, "ObjectType = Image\n");
 598                fprintf(fp, "NDims = 3\n" );
 599                fprintf(fp, "BinaryData = True \n" );
 600                fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 601                fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices );
 602                fprintf(fp, "HeaderSize = %d\n", 0);
 603                fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
 604                fprintf(fp, "Position = 0 0 %d\n", 0 );
 605                fprintf(fp, "Offset = 0 0 0\n" );
 606                fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 607                fprintf(fp, "ElementNumberOfChannels = 1\n" );
 608                fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
 609                fprintf(fp, "ElementDataFile = %s\n", "../2dseq_All_the_Slices" );
 610                fclose(fp);
 611              }
 612              sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices",
 613                                        currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 614              fp=fopen(output2dseqSliceFileName, "wb");
 615              if (!fp)
 616              {
 617                 std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 618              }
 619              else
 620              {
 621                 fwrite( buffer_2dseq, NX*NY*pixelSize, nbSlices, fp);
 622              }
 623              fclose(fp);
 624              strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 625        }  // end if mhd
 626        if (dicom)
 627        {
 628              sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices.dcm",
 629                                        currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 630
 631             /* ----------- Write Dicom Image  ---------------*/
 632              MakeDicomImage(buffer_2dseq,
 633                NX,
 634                NY,
 635                nbFrames,
 636                pixelSize,
 637                fovX/NY, fovY/NY, sliceDistance,
 638                output2dseqSliceFileName,
 639                strPatientName,
 640                day,
 641                strStudyUID,
 642                strSerieUID,
 643                strStudyDescr,
 644                strSerieDescr,
 645                strStudyTimeDate,
 646                0,// index frame number
 647                GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
 648              );
 649        }  // end if dicom
 650    }  // end if nbInstants = 1
 651
 652    else  // more than ONE instant
 653    {
 654           // Interleaved !
 655           // it's (slice1,slide2, ...)t1 ; (slice1,slide2, ...)t2 ; ...
 656
 657          unsigned char *pixelsForCurrentSlice = new unsigned char[NX*NY*pixelSize*nbInstants];
 658
 659          k = 0;
 660          for (sliceNb=0; sliceNb<nbSlices; sliceNb++)
 661          {
 662             if (mhd)
 663             {
 664                sprintf(outputMhdFileName, "%s%cMhdData_%03d.mhd", currentOutputMhdDirName,
 665                                         GDCM_NAME_SPACE::GDCM_FILESEPARATOR, k  );
 666                if (verbose)
 667                   std::cout << "--- Output MHD file [" << outputMhdFileName << "]" << std::endl;
 668                fp=fopen(outputMhdFileName, "w");
 669                if (!fp)
 670                {
 671                    std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 672                    exit(0);
 673                }
 674                else
 675                {
 676             /* ----------- Write MHD Image  ---------------*/
 677                 //if (verbose)
 678                 //   std::cout << "Open sucessfully[" << outputMhdFileName << "] for writting" << std::endl;
 679                    fprintf(fp, "ObjectType = Image\n");
 680                    fprintf(fp, "NDims = 3\n" );
 681                    fprintf(fp, "BinaryData = True \n" );
 682                    fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 683                    fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbInstants);
 684                    fprintf(fp, "HeaderSize = %d\n", 0);
 685                    fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, 1.0 ); // slice distance : no meaning for temporal serie
 686                    fprintf(fp, "Position = 0 0 %d\n", sliceNb );
 687                    fprintf(fp, "Offset = 0 0 0\n" );
 688                    fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 689                    fprintf(fp, "ElementNumberOfChannels = 1\n" );
 690                    fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
 691                    fprintf(fp, "ElementDataFile = ..%c2dseq_Slice_%d\n", GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb );
 692                    fclose(fp);
 693                } // end write MHD
 694
 695                sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d",
 696                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,sliceNb);
 697                fp=fopen(output2dseqSliceFileName, "wb");
 698                if (!fp)
 699                {
 700                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 701                    exit (0);
 702                }
 703                int frameSize = NX*NY*pixelSize;
 704                for (instantNb=0; instantNb<nbInstants; instantNb++)
 705                {
 706 // std::cout << "------------SN " << sliceNb << " IN " << instantNb <<  " T " << nbSlices*instantNb + sliceNb << std::endl;
 707                     fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
 708                             frameSize,
 709                             1, fp);
 710                }
 711                fclose(fp);
 712 // std::cout << "end writting[" << output2dseqSliceFileName << "]" << std::endl;
 713             }  // end if mhd
 714
 715             if (dicom)
 716             {
 717                // desperate try !
 718                /*
 719                sprintf(output2dseqSliceFileName, "%sdummy_buffer",
 720                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 721                fp=fopen(output2dseqSliceFileName, "wb");
 722                if (!fp)
 723                {
 724                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 725                    exit (0);
 726                }
 727                int frameSize = NX*NY*pixelSize;
 728                for (instantNb=0; instantNb<nbInstants; instantNb++)
 729                {
 730 // std::cout << "------------SN " << sliceNb << " IN " << instantNb <<  " T " << nbSlices*instantNb + sliceNb << std::endl;
 731                     fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
 732                             frameSize,
 733                             1, fp);
 734                }
 735                fclose(fp);
 736
 737                fp=fopen(output2dseqSliceFileName, "rb");
 738                if (!fp)
 739                {
 740                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for reading" << std::endl;
 741                    exit (0);
 742                }
 743                fread( pixelsForCurrentSlice,
 744                             frameSize*nbInstants,
 745                             1, fp);
 746                fclose(fp);
 747               // end of desperate try !
 748                */
 749
 750                /* ----------- Write Dicom Image  ---------------*/
 751
 752                int frameSize = NX*NY*pixelSize;
 753                for (instantNb=0; instantNb<nbInstants; instantNb++)
 754                {
 755                   memcpy(pixelsForCurrentSlice + frameSize*instantNb, buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize, frameSize);
 756                }
 757
 758                int indOfFirsImageWithinImageSet =  nbSlices*instantNb;
 759                sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d.dcm",
 760                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb);
 761
 762                MakeDicomImage(
 763                   pixelsForCurrentSlice,
 764                   NX,
 765                   NY,
 766                   nbInstants,
 767                   pixelSize,
 768                   fovX/NY, fovY/NY, sliceDistance,
 769                   output2dseqSliceFileName,
 770                   strPatientName,
 771                   day,
 772                   strStudyUID,
 773                   strSerieUID,
 774                   strStudyDescr,
 775                   strSerieDescr,
 776                   strStudyTimeDate,
 777                   sliceNb*nbInstants,
 778                   GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
 779                );
 780                if (verbose)
 781                   std::cout << "--- Output DCM file [" << output2dseqSliceFileName << "]" << std::endl;
 782
 783             } // en if dicom
 784
 785         k++;
 786         }
 787         delete [] pixelsForCurrentSlice;
 788      }  // end nbInstants == 1
 789    delete [] buffer_2dseq;
 790 /**/
 791
 792
 793    // -----------------------------------------------------
 794    //  deal with MatLab-generated Carto file.
 795    // -----------------------------------------------------
 796
 797    dealWithCarto(fileNames,  NX,  NY,  nbSlices, fovX, fovY, sliceDistance,
 798                    copyFile, currentOutputDirName, outputMhdFileName, output2dseqCartoName);
 799 }
 800
 801
 802 // ===========================================================================================
 803
 804 void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX, int NY, int nbSlices,
 805                                  double fovX, double fovY, double sliceDistance,
 806                                  char *copyFile, std::string &currentOutputDirName,
 807                                  char *outputMhdFileName, char *output2dseqCartoName)
 808 {
 809    // -----------------------------------------------------
 810    //  deal with MatLab-generated Carto file.
 811    // -----------------------------------------------------
 812
 813    char *code[] ={ "ADC", "adc", "TTP", "ttp", "PEAK", "peak" , ""};  // add more carto file name identifiers if necessary; end with ""
 814    int icode;
 815    GDCM_NAME_SPACE::DirListType::iterator it;
 816    char file_name_ident[500];
 817    FILE *fp;
 818
 819    // Iterate to ALL the objets(files/directories) found in the input directory
 820    for (it = fileNames.begin();
 821         it != fileNames.end();
 822       ++it)
 823    {
 824       if ( boost::filesystem::is_regular(*it) )
 825       //if ( ! boost::filesystem::is_directory(*it) )
 826       {
 827          if (verbose)
 828             std::cout << "--- [" << *it << "] is a file" << std::endl;
 829
 830          icode = 0;
 831
 832          while (code[icode][0] != 0)
 833          {
 834             sprintf(file_name_ident, "2dseq_%s",code[icode]); // e.g  "2dseq_ADC"
 835             std::string::size_type loc = (*it).rfind(file_name_ident);
 836
 837             if ( loc != std::string::npos )
 838             {
 839
 840        ///\ TODO : find a safer way to be sure to read everything!
 841               unsigned char *buffer_carto = new unsigned char[NX*NY*sizeof(double)*nbSlices];
 842               fp = fopen ( (*it).c_str(), "rb");
 843               if (!fp){
 844                  std::cout << "Cannot open [" << *it << "] for reading" << std::endl;
 845
 846                }
 847                fread(buffer_carto, NX*NY*sizeof(double), nbSlices, fp);
 848
 849                std::cout << "Deal with Carto file :[" <<*it << "], computed length : "
 850                          << NX*NY*sizeof(double)*nbSlices << std::endl;
 851                   std::string lastFileName = GDCM_NAME_SPACE::Util::GetName((*it).c_str());
 852                if (mhd)
 853                {
 854                   // Copy the data file in the new directory
 855                   sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() ,
 856                             currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str());
 857                   system(copyFile);
 858                   sprintf(outputMhdFileName, "%s%c%s%s",
 859                                        currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".mhd" );
 860                   if (verbose)
 861                     std::cout << "--- Output Carto MHD file [" << outputMhdFileName << "]" << std::endl;
 862
 863                   FILE *fp;
 864                   fp=fopen(outputMhdFileName, "w");
 865                   if (!fp)
 866                   {
 867                      std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 868                   }
 869                   else
 870                   {
 871                      fprintf(fp, "ObjectType = Image\n");
 872                      fprintf(fp, "NDims = 3\n" );
 873                      fprintf(fp, "BinaryData = True \n" );
 874                      fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 875                      fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices);
 876                      fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
 877                      fprintf(fp, "HeaderSize = %d\n", 0 );
 878                      fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
 879                      fprintf(fp, "Position = 0 0 0\n" );
 880                      fprintf(fp, "Offset = 0 0 0\n" );
 881                      fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 882                      fprintf(fp, "ElementNumberOfChannels = 1\n" );
 883                      fprintf(fp, "ElementType = %s\n", "MET_DOUBLE" );
 884                      fprintf(fp, "ElementDataFile = %s\n", lastFileName.c_str() );
 885
 886                      fclose(fp);
 887                   }
 888                   if (verbose)
 889                      std::cout << "--- end write Carto MHD file [" << outputMhdFileName << "]" << std::endl;
 890                }  // end if mhd
 891
 892             // ----------- Write Dicom Image  ---------------
 893
 894                if (dicom)
 895                {
 896                   sprintf(output2dseqCartoName, "%s%c%s%s",
 897                                        currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".dcm" );
 898                   if (verbose)
 899                      std::cout << "--- end create name output2dseqCartoName file [" << output2dseqCartoName << "]" << std::endl;
 900
 901                   strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID(); //New SerieUID for each carto.
 902                   std::string strNewSerieDescr(strSerieDescr+ "_" +GDCM_NAME_SPACE::Util::GetName((*it).c_str()));
 903                   MakeDicomImage(buffer_carto,
 904                      NX,
 905                      NY,
 906                      nbSlices,
 907                      8, // pixelSize
 908                      fovX/NY, fovY/NY, sliceDistance,
 909                      output2dseqCartoName,
 910                      strPatientName,
 911                      day,
 912                      strStudyUID,
 913                      strSerieUID,
 914                      strStudyDescr,
 915                      strNewSerieDescr,
 916                      strStudyTimeDate,
 917                      0,
 918                      GDCM_NAME_SPACE::CREATED_IMAGE
 919                   );
 920                }  // end if dicom
 921
 922                delete [] buffer_carto;
 923                if (verbose)
 924                      std::cout << "--- End writing Carto DICOM file [" << output2dseqCartoName << "]" << std::endl;
 925                break; // don't check for more ident on same file name!
 926
 927             }
 928             icode++;
 929          }
 930       }
 931    } // end iterate on files
 932 }
 933
 934
 935 // ==========================================================================================================
 936
 937 bool Bruker2Dicom::CreateDirectory(std::string OutputDirName)
 938 {
 939    std::string systemCommand;
 940
 941    if (verbose)
 942       std::cout << "Check for output directory :[" << OutputDirName << "]."
 943                 <<std::endl;
 944    if ( ! boost::filesystem::is_directory(OutputDirName) )    // dirout not found
 945    {
 946       std::string strDirNameout(OutputDirName);        // to please gcc 4
 947       systemCommand = "mkdir " + strDirNameout;        // create it!
 948       if (verbose)
 949          std::cout << systemCommand << std::endl;
 950       system (systemCommand.c_str());
 951       if ( ! boost::filesystem::is_directory(OutputDirName) ) // be sure it worked
 952       {
 953          if (verbose)
 954             std::cout << "KO : not a dir : [" << OutputDirName << "] (creation failure ?)" << std::endl;
 955          return 0;
 956          /// \todo : THROW AN EXCEPTION
 957       }
 958       else
 959       {
 960          if (verbose)
 961            std::cout << "Directory [" << OutputDirName << "] created." << std::endl;
 962       }
 963    }
 964    else
 965    {
 966        if (verbose)
 967           std::cout << "Output Directory [" << OutputDirName << "] already exists; Used as is." << std::endl;
 968    }
 969
 970    return 1;
 971
 972 }
 973
 974
 975 // ===========================================================================================
 976
 977 /// \TODO move cleanString to 'crea' ?
 978
 979 void Bruker2Dicom::cleanString(std::string &s)
 980 {
 981    int l = s.size();
 982    if (s[l-1] == 0x0A || s[l-1] == 0x0D ) // CR or NL
 983    {
 984       l--;
 985       s = s.substr(0, l);
 986    }
 987    if (s[l-1] == ' ' ) // blank space
 988    {
 989       l--;
 990       s = s.substr(0, l);
 991    }
 992
 993    if (s[0] == '<')
 994       s= s.substr(1,l-2);
 995    std::string repChar("_");
 996    GDCM_NAME_SPACE::Util::ReplaceSpecChar(s, repChar);
 997 }
 998
 999
1000
1001 // ===========================================================================================
1002
1003
1004 void Bruker2Dicom::getImhDataType(BrukerFieldData &bDPT, std::string &mhdDataPixelType, int &pixelSize)
1005 {
1006    if(bDPT.GetDataType() == "string")
1007    {
1008          std::string brukerDataPixelType = bDPT.GetStringValue()[0];
1009          std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
1010          //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
1011
1012          if (brukerDataPixelType ==  "ip_short") {
1013             mhdDataPixelType = "MET_USHORT";
1014             pixelSize = 2;
1015          }
1016          if (brukerDataPixelType ==  "ip_int") {
1017             mhdDataPixelType = "MET_UINT";
1018             pixelSize = 4;
1019          }
1020          if (brukerDataPixelType ==  "ip_char") {
1021              mhdDataPixelType = "MET_UCHAR";
1022              pixelSize = 1;
1023          }
1024                   /// \TODO : finish the list
1025     /*
1026     case 0 : fp << "ElementType = MET_CHAR" << std::endl;
1027       break;
1028     case 1 : fp << "ElementType = MET_UCHAR" << std::endl;
1029       break;
1030     case 2 : fp << "ElementType = MET_SHORT" << std::endl;
1031       break;
1032     case 3 : fp << "ElementType = MET_USHORT" << std::endl;
1033       break;
1034     case 4 : fp << "ElementType = MET_INT" << std::endl;
1035       break;
1036     case 5 : fp << "ElementType = MET_UINT" << std::endl;
1037       break;
1038     case 6 : fp << "ElementType = MET_FLOAT" << std::endl;
1039       break;
1040     case 7 : fp << "ElementType = MET_DOUBLE" << std::endl;
1041     */
1042     }
1043     else
1044     {
1045          int brukerDataPixelType = bDPT.GetIntValue()[0];
1046          std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
1047          //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
1048
1049 // Cross your fingers !!!
1050
1051 // pb : found values : 2, 3, 5
1052
1053          if (brukerDataPixelType ==  2) {
1054             mhdDataPixelType = "MET_USHORT";
1055             pixelSize = 2;
1056          }
1057          if (brukerDataPixelType ==  3) {
1058             mhdDataPixelType = "MET_USHORT";
1059             pixelSize = 2;
1060          }
1061          if (brukerDataPixelType ==  1) {
1062             mhdDataPixelType = "MET_UCHAR";
1063             pixelSize = 1;
1064          }
1065     }
1066 }
1067
1068 // ===========================================================================================
1069
1070 std::vector<BrukerImage> Bruker2Dicom::CreateImageSet ( )
1071 {
1072          std::vector<BrukerImage> imageSet;
1073          br_acqp.SetLoopStructure();
1074          std::vector<int> tempVect                      = br_acqp.GetLoopStructure() ;
1075          std::map<std::string, BrukerFieldData> map     = br_acqp.GetBrukerHeaderMap();
1076          bool result                                    = br_acqp.ObjectVaryingProperties.init(map,tempVect);
1077
1078          br_acqp.SetImageLoopStructure();
1079          br_acqp.SetBrukerImageList();
1080          std::vector<std::vector<int> > brukerImageList = br_acqp.GetBrukerImageList();
1081
1082          BrukerImage image(br_acqp,br_reco);
1083          image.Init(br_acqp,br_reco,1);
1084
1085          for(int i=0;i<brukerImageList.size();i++)
1086          {
1087             image.Init(br_acqp,br_reco,i);
1088             imageSet.push_back(image);
1089          }
1090
1091  // Just for checking
1092  /*
1093
1094          std::vector<std::vector <double> > imageOrientation;
1095          std::vector <double> imagePosition;
1096          for(int i=0;i<brukerImageList.size();i++)
1097          {
1098            // fread(buffer_2dseq, NX*NY*pixelSize*nbSlices*nbInstants, 1, fp);
1099
1100            imagePosition = imageSet[i].getTranslationVectorRPS2XYZ();
1101            std::cout << "Position " << imagePosition[0] << " "
1102                      << imagePosition[1] << " "  << imagePosition[2] ;
1103            imageOrientation =  imageSet[i].getRotationMatrixRPS2XYZ();
1104            std::cout << "\t  Orientation " ;
1105            for(int i1=0; i1<3;i1++)for(int i2=0; i2<3;i2++)
1106               std::cout << imageOrientation[i1][i2] << " ";
1107
1108            //std::cout << "\t  Abs Time " << imageSet[i].getAbsoluteTimePosition();
1109            std::cout << "\t  Relat Time " << imageSet[i].getRelativeTimePosition();
1110
1111            std::cout << "\t [";
1112            for (int i3=0; i3<imageSet[i].getLoopStamp().size();i3++)
1113               std::cout << " " << imageSet[i].getLoopStamp()[i3];
1114            std::cout << "]" << std::endl;
1115          }
1116 */
1117    return imageSet;
1118 }
1119
1120
1121 // ===========================================================================================
1122
1123 void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels,
1124               int X,
1125               int Y,
1126               int nbFrames,
1127               int pixelSize,
1128               double spacingX, double spacingY, double sliceDistance,
1129               std::string dcmImageName,
1130               const std::string &patientName,
1131               const char *day,
1132               std::string &studyUID,
1133               std::string &serieUID,
1134               std::string &studyDescr,
1135               std::string &serieDescr,
1136               std::string &strStudyTimeDate,
1137               int imgNum,
1138               GDCM_NAME_SPACE::ImageContentType contentType
1139       )
1140 {
1141    std::ostringstream str;
1142
1143    GDCM_NAME_SPACE::File *file;
1144    file = GDCM_NAME_SPACE::File::New();
1145
1146   // Set the image size
1147    str.str("");
1148    str << X;
1149    file->InsertEntryString(str.str(),0x0028,0x0011,"US"); // Columns
1150    str.str("");
1151    str << Y;
1152    file->InsertEntryString(str.str(),0x0028,0x0010,"US"); // Rows
1153
1154    if (nbFrames != 1)
1155    {
1156       str.str("");
1157       str << nbFrames;
1158       file->InsertEntryString(str.str(),0x0028,0x0008,"IS"); // Number of Frames
1159    }
1160
1161   // Set the pixel type
1162   //      //8, 16, 32, 64 (for double ?)
1163    str.str("");
1164    str << pixelSize*8;
1165    file->InsertEntryString(str.str(),0x0028,0x0100,"US"); // Bits Allocated
1166
1167    file->InsertEntryString(str.str(),0x0028,0x0101,"US"); // Bits Stored
1168
1169    str.str("");
1170    str << pixelSize*8-1;
1171    file->InsertEntryString(str.str(),0x0028,0x0102,"US"); // High Bit
1172
1173   // Set the pixel representation // 0/1 , 0=unsigned
1174    file->InsertEntryString("1",0x0028,0x0103, "US"); // Pixel Representation
1175
1176   // Set the samples per pixel // 1:Grey level, 3:RGB
1177    file->InsertEntryString("1",0x0028,0x0002, "US"); // Samples per Pixel
1178
1179 //  0028 0030 DS 2 Pixel Spacing
1180    str.str("");
1181    str << spacingX << "\\" << spacingY;
1182    file->InsertEntryString(str.str(),0x0028,0x0030, "DS"); // Pixel Spacing
1183
1184  //   0018 0050 DS 1 Slice Thickness
1185    str.str("");
1186    str << sliceDistance;
1187    file->InsertEntryString(str.str(),0x0018,0x0050, "DS");
1188
1189   // 1.2.840.10008.5.1.4.1.1.4.1 : Enhanced MR Image Storage
1190  //  file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0002, 0x0002, "UI");  // [Media Storage SOP Class UID]
1191   // file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0008, 0x0016, "UI");  // [SOP Class UID]
1192
1193
1194 // OK : MR is NOT multiframe, but I want just a quick an dirty solution
1195 // 1.2.840.10008.5.1.4.1.1.4         MR Image Storage
1196    file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0002, 0x0002, "UI");  // [Media Storage SOP Class UID]
1197    file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0008, 0x0016, "UI");  // [SOP Class UID]
1198
1199   // if (strlen(patientName) != 0)
1200    file->InsertEntryString(patientName.c_str(),0x0010,0x0010, "PN"); // Patient's Name
1201
1202    file->InsertEntryString(studyUID, 0x0020, 0x000d, "UI");
1203    file->InsertEntryString(serieUID, 0x0020, 0x000e, "UI");
1204
1205 //  0008 0020 DA 1 Study Date
1206 //  0008 0030 TM 1 Study Time
1207
1208 /// \TODO split into 2 strings!
1209    file->InsertEntryString(strStudyTimeDate.substr(10,11).c_str(),0x0008,0x0020, "DA");
1210    file->InsertEntryString(strStudyTimeDate.substr(1,8).c_str(),0x0008,0x0030, "TM");
1211
1212    file->InsertEntryString(studyDescr,0x0008,0x1030, "LO");  // Study Description
1213    file->InsertEntryString(serieDescr,0x0008,0x103e, "LO");  // Series Description
1214
1215 //0008|0060 [CS] [Modality]
1216    file->InsertEntryString("MR",0x0008,0x0060, "CS");
1217
1218 // 0020 0037 DS 6 Image Orientation (Patient)
1219    char charImageOrientation[256];
1220
1221 /*
1222 std::cout << "try charImageOrientation  " <<
1223                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0] << " " <<
1224                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1] << " " <<
1225                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2] << " " <<
1226                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0] << " " <<
1227                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1] << " " <<
1228                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] << std::endl ;
1229 */
1230    sprintf(charImageOrientation,"%f\\%f\\%f \\ %f\\%f\\%f",
1231                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0],
1232                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1],
1233                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2],
1234                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0],
1235                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1],
1236                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] ) ;
1237
1238    file->InsertEntryString(charImageOrientation,0x0020,0x0037, "DS");
1239
1240
1241 // 0020 0032 DS 3 Image Position (Patient)
1242
1243    char charImagePosition[256];
1244    sprintf(charImagePosition,"%f\\%f\\%f",
1245                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[0],
1246                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[1],
1247                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[2]);
1248
1249    file->InsertEntryString(charImagePosition,0x0020,0x0032, "DS");  //0020 0032 DS 3 Image Position (Patient)
1250
1251
1252
1253 // 0020 0x1041 DS 1 Slice Location
1254 //        sprintf(charImagePosition,"%f",float(imgNum));
1255 //        file->InsertEntryString(charImagePosition,0x0020,0x1041, "DS");
1256 /*
1257   // Set Rescale Intercept
1258         str.str("");
1259         str << div;
1260         file->InsertEntryString(str.str(),0x0028,0x1052,"DS");
1261
1262   // Set Rescale Slope
1263         str.str("");
1264         str << mini;
1265         file->InsertEntryString(str.str(),0x0028,0x1053,"DS");
1266 */
1267
1268    GDCM_NAME_SPACE::FileHelper *fileH;
1269    fileH = GDCM_NAME_SPACE::FileHelper::New(file);
1270    fileH->SetContentType(contentType);
1271
1272    // cast is just to avoid warnings (*no* conversion is performed)
1273    //fileH->SetImageData((uint8_t *)img,int(maxX*maxY)*sizeof(uint16_t)); // troubles when maxX, mayY are *actually* float!
1274
1275 //std::cout << "--------------------------------  X*Y*nbFrames*pixelSize " << X << " " << Y << " " << nbFrames << " " << pixelSize << std::endl;
1276
1277    fileH->SetImageData((uint8_t *)tabPixels, X*Y*nbFrames*pixelSize);
1278    fileH->SetWriteModeToRaw();
1279    fileH->SetWriteTypeToDcmExplVR();
1280    if( !fileH->Write(dcmImageName))
1281       std::cout << "Failed for [" << dcmImageName << "]\n"
1282                 << "           File is unwrittable" << std::endl;
1283
1284    if (verbose)
1285       file->Print();
1286
1287    file->Delete();
1288    fileH->Delete();
1289 }
1290
1291