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