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