lib/src1/bruker2dicom.cxx

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