lib/src1/bruker2dicom.cxx

   1 #include "bruker2dicom.h"
   2 #include <boost/filesystem/path.hpp>
   3 #include <boost/filesystem/operations.hpp>
   4 #include "brukerexception.h"
   5
   6 #ifndef PATH_MAX // If not defined yet : do it
   7    #define PATH_MAX 2048
   8 #endif
   9
  10
  11
  12 bool Bruker2Dicom::Execute()
  13 {
  14    // ----- Check input values -----
  15
  16    bool bigEndian = GDCM_NAME_SPACE::Util::IsCurrentProcessorBigEndian();
  17
  18    //if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(InputDirName) )
  19    if ( ! boost::filesystem::is_directory(InputDirName) )
  20    {
  21       std::cout << "KO : [" << InputDirName << "] is not a Directory." << std::endl;
  22       return 0;
  23    }
  24    else
  25    {
  26       if (verbose)
  27          std::cout << "OK : [" << InputDirName << "] is a Directory." << std::endl;
  28    }
  29
  30    std::string strDirNameOut(OutputDirName);
  31    bool res=CreateDirectory(strDirNameOut);
  32    if (!res) {
  33       std::cout << "[" << OutputDirName << "] Directory creation failure " << std::endl;
  34       //exit (0);
  35       throw ( BrukerHopelessException ("Output directory creation failure "));
  36    }
  37
  38    std::string strDirNamein(InputDirName);
  39    GDCM_NAME_SPACE::DirList dirList(strDirNamein, false, true); // DON'T get recursively the list of files
  40    std::string strDirNameout(OutputDirName);
  41
  42 /*
  43    if (listonly)
  44    {
  45       std::cout << "------------List of found files ------------" << std::endl;
  46       dirList.Print();
  47       std::cout << std::endl;
  48       return 1;
  49    }
  50 */
  51
  52 //
  53 // e.g : at level 0, in : B67d1.Bp1
  54 //
  55 //           1  2  3  4  5  6  AdjStatePerStudy  subject
  56 //
  57
  58    GDCM_NAME_SPACE::DirListType fileNames;
  59    fileNames = dirList.GetFilenames();
  60    bool canOpen;
  61    std::string outputFileName;
  62
  63
  64   // BrukerDataSet br_subject;
  65    std::string subject;
  66    subject = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
  67              GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
  68              "subject";
  69    if (verbose)
  70         std::cout << " Subject : [" <<  subject << "]" << std::endl;
  71    canOpen =br_subject.LoadFile(subject);
  72
  73    if (!canOpen)
  74    {
  75       std::cout << "Hopeless! no 'subject' found" << std::endl;
  76       throw ( BrukerHopelessException ("Hopeless! no 'subject' found in root input directory "));
  77       //exit(0);  /// \TODO throw an exception !
  78    }
  79    else
  80    {
  81       br_subject.FillMap();
  82    }
  83    //br_subject.PrintSelf();
  84
  85   // get info for 'Study Description'
  86
  87          BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string");
  88          std::string subject_name = b_name.GetStringValue()[0];
  89          strPatientName = subject_name;
  90          cleanString(subject_name);
  91
  92          BrukerFieldData b_entry=br_subject.GetFieldData("SUBJECT_entry");
  93          std::string subject_entry = b_entry.GetStringValue()[0];
  94          //cleanString(subject_entry);
  95          subject_entry = subject_entry.substr(11, subject_entry.size()-11);
  96
  97          BrukerFieldData b_position=br_subject.GetFieldData("SUBJECT_position");
  98          std::string subject_position = b_position.GetStringValue()[0];
  99          //cleanString(subject_position);
 100          subject_position = subject_position.substr(9, subject_position.size()-9);
 101
 102          BrukerFieldData b_date=br_subject.GetFieldData("SUBJECT_date");
 103          std::string subject_date = b_date.GetStringValue()[0];
 104          strStudyTimeDate = subject_date;
 105          cleanString(subject_date);
 106
 107          BrukerFieldData b_study_name=br_subject.GetFieldData("SUBJECT_study_name");
 108          std::string subject_study_name = b_study_name.GetStringValue()[0];
 109          subject_study_name = subject_study_name.substr(1, subject_study_name.size()-2);
 110          cleanString(subject_date);
 111
 112    // subject_name is already in 'Patient Name'
 113    strStudyDescr = /*subject_name + "." + */ subject_study_name + "." + subject_entry + "." + subject_position + "." + subject_date;
 114
 115    char outputDirName[(unsigned int) PATH_MAX+2];
 116
 117    strStudyUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 118    serieNumber = 0;
 119    // -----------------------------------------------------
 120    // Iterate to ALL the objets(files/directories) found in the input directory
 121    // (this is level ZERO)
 122    // each Directory (name : 1, 2, 3, ...) will be a Dicom Serie
 123    // -----------------------------------------------------
 124
 125    GDCM_NAME_SPACE::DirListType::iterator it;
 126
 127    for (it = fileNames.begin();
 128          it != fileNames.end();
 129        ++it)
 130    {
 131       if ( boost::filesystem::is_directory(*it) )
 132       {
 133          if (verbose)
 134             std::cout << "[" << *it << "] is a directory" << std::endl;
 135
 136          //BrukerDataSet br_acqp;
 137          std::string strAcqp;
 138          strAcqp = (*it) +
 139                    GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 140                    "acqp";
 141
 142          br_acqp.LoadFile(strAcqp);
 143          br_acqp.FillMap();
 144
 145          std::string acqp_scan_name;
 146          std::string acqp_method;
 147          std::string acqp_protocol_location;
 148
 149          BrukerFieldData b_protocol_location=br_acqp.GetFieldData("ACQ_protocol_location");
 150          acqp_protocol_location = b_protocol_location.GetStringValue()[0];
 151          cleanString(acqp_protocol_location);
 152
 153          BrukerFieldData b_scan_name=br_acqp.GetFieldData("ACQ_scan_name");
 154          acqp_scan_name = b_scan_name.GetStringValue()[0];
 155          cleanString(acqp_scan_name);
 156
 157          BrukerFieldData b_method=br_acqp.GetFieldData("ACQ_method");
 158          acqp_method = b_method.GetStringValue()[0];
 159          cleanString(acqp_method);
 160
 161          BrukerFieldData b_list_size = br_acqp.GetFieldData("ACQ_O1_list_size");
 162          //b_list_size.PrintSelf(); //JP
 163
 164          nbSlices =  b_list_size.GetIntValue()[0];
 165
 166          strSerieDescr = GDCM_NAME_SPACE::Util::GetName(*it)
 167                        /*  + "." + acqp_protocol_location */ // always the same (in each acquisition)
 168                          + "." + acqp_scan_name
 169                          + "." + acqp_method.c_str();
 170
 171          sprintf(outputDirName, "%s%c%s", OutputDirName.c_str(),
 172                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 173                           strSerieDescr.c_str() );
 174
 175          std::cout << " ================================================================================\n"
 176                    << " === [" << GDCM_NAME_SPACE::Util::GetName(*it) << "] -> [" << strSerieDescr << "]\n"
 177                    << " ================================================================================"
 178                    << std::endl;
 179
 180
 181         if (verbose)
 182            printf ("outputDirName [%s]\n", outputDirName);
 183
 184         DealWithNiveau1(*it, outputDirName);
 185       }
 186    } // end of : for (GDCM_NAME_SPACE::DirListType::iterator it
 187 }
 188
 189
 190 // =====================================================================
 191
 192 void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string currentOutputDirName) {
 193 //
 194 // e.g. : at level 1, in B67d1.Bp1/6
 195 //
 196 // acqp  fid  imnd  pdata  pulseprogram  spnam0  spnam1
 197
 198    bool res = CreateDirectory(currentOutputDirName);
 199
 200    if (!res) {
 201       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 202       throw ( BrukerHopelessException ("Level 1 output directory creation failure "));
 203      // exit (0);
 204    }
 205    GDCM_NAME_SPACE::DirList dirList(level1Directory, false, true); // DON'T get recursively the list of files
 206    GDCM_NAME_SPACE::DirListType fileNames;
 207    fileNames = dirList.GetFilenames();
 208    // -----------------------------------------------------
 209    // Iterate to ALL the objets(files/directories) found in the input directory
 210    // -----------------------------------------------------
 211    GDCM_NAME_SPACE::DirListType::iterator it;
 212
 213    for (it = fileNames.begin();
 214         it != fileNames.end();
 215       ++it)
 216    {
 217       if ( boost::filesystem::is_regular(*it) )
 218       //if ( ! boost::filesystem::is_directory(*it) )
 219       {
 220          if (verbose)
 221             std::cout << "--- [" << *it << "] is a file." << std::endl;
 222       }
 223    }
 224
 225    char outputDirName[(unsigned int) PATH_MAX+2];
 226    //std::string firstName;
 227    bool canOpen;
 228    for (it = fileNames.begin();
 229         it != fileNames.end();
 230       ++it)
 231    {
 232       if ( boost::filesystem::is_directory(*it) )
 233       {
 234          // will be always "pdata" ...
 235          if (verbose)
 236             std::cout << "--- [" << *it << "] is a directory" << std::endl;
 237
 238               /* a recuperer :
 239               if (FileLine.startsWith("##$ACQ_size=")) {
 240               if (FileLine.startsWith("##$NI=")) {
 241               if (FileLine.startsWith("##$NR=")) {
 242               if (FileLine.startsWith("##$ACQ_obj_order=")) {
 243               if (FileLine.startsWith("##$ACQ_word_size=")) {
 244               if (FileLine.startsWith("##$BYTORDA=")) {
 245               if (FileLine.startsWith("##$PULPROG=")) {
 246               */
 247
 248          sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 249                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 250                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str());
 251          //br1.PrintSelf();
 252
 253           std::string strMethod;
 254           //std::string firstName = *(fileNames.begin());
 255
 256           strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin())) +
 257                       GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 258                       "method";
 259             // std::cout << "---strMethod (for method)=> [" << strMethod << "]" << std::endl;
 260           canOpen = br_method.LoadFile(strMethod);
 261           if (!canOpen)
 262           {
 263              strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
 264                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 265                          "imnd";
 266              //std::cout << "---strMethod (for imnd) => [" << strMethod << "]" << std::endl;
 267              canOpen = br_method.LoadFile(strMethod);
 268              if (!canOpen)
 269              {
 270                 std::cout << "Hopeless! neither 'method' nor 'imnd' found" << std::endl;
 271                 throw ( BrukerHopelessException ("Hopeless! neither 'method' nor 'imnd' found "));
 272                 //exit(0);  /// \TODO throw an exception !
 273              }
 274           }
 275           if (verbose)
 276              std::cout << "open => [" << strMethod << "] successfully" << std::endl;
 277           br_method.FillMap();
 278
 279           /* a recuperer :
 280              ##$PVM_Fov (dimension)
 281           */
 282   /*
 283           dans method (pour perfusion  seulement?) :
 284           ##$PVM_ObjOrderList=( 8 )
 285           0 2 4 6 1 3 5 7
 286           ##$PVM_NSPacks=2
 287           ##$PVM_SPackArrNSlices=( 2 )
 288           7 1
 289   */
 290          DealWithNiveau2(*it,outputDirName );
 291       }
 292    }
 293 }
 294
 295 // =====================================================================
 296
 297 void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string currentOutputDirName) {
 298
 299 // e.g. : at level 2 in B67d1.Bp1/6/pdata
 300 //
 301 // acqp  fid  imnd  pdata  pulseprogram  spnam0  spnam1
 302 //
 303
 304    bool res = CreateDirectory(currentOutputDirName);
 305
 306    if (!res) {
 307       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 308       throw ( BrukerHopelessException ("Hopeless! Level2 output directory creation failure"));
 309       //exit (0);
 310    }
 311
 312    GDCM_NAME_SPACE::DirList dirList(level2Directory, false, true); // DON'T get recursively the list of files
 313
 314    GDCM_NAME_SPACE::DirListType fileNames;
 315    fileNames = dirList.GetFilenames();
 316
 317    char outputDirName[(unsigned int) PATH_MAX+2];
 318
 319    // -----------------------------------------------------
 320    // Iterate to ALL the objets(files/directories) found in the input directory
 321    // -----------------------------------------------------
 322    GDCM_NAME_SPACE::DirListType::iterator it;
 323    bool canOpen;
 324
 325    if (verbose)
 326    for (it = fileNames.begin();
 327         it != fileNames.end();
 328       ++it)
 329    {
 330       if ( ! boost::filesystem::is_directory(*it) )
 331       {
 332          std::cout << "--- --- [" << *it << "] is a file.." << std::endl;
 333       }
 334
 335    }
 336
 337    for (it = fileNames.begin();
 338          it != fileNames.end();
 339        ++it)
 340    {
 341       if ( boost::filesystem::is_directory(*it) )
 342       {
 343
 344          if (verbose)
 345             std::cout << "--- --- [" << *it << "] is a directory" << std::endl;
 346
 347         // sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 348         //                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 349         //                                GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
 350   // MUST be 'pdata'!
 351
 352 //
 353 // (interest of previous method :
 354 // If unaware user changed the pdata name, it goes on working
 355 //
 356           std::string str_isa;
 357           str_isa = (*it) +
 358                     GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 359                    "isa";
 360
 361           std::string str_isa_func_name;
 362           canOpen = br_isa.LoadFile(str_isa);
 363           if (!canOpen)
 364           {
 365              sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 366                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 367                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
 368           }
 369           else
 370           {
 371              br_isa.FillMap();
 372              BrukerFieldData b_isa_func_name = br_isa.GetFieldData("ISA_func_name");
 373
 374              str_isa_func_name = b_isa_func_name.GetStringValue()[0];
 375              cleanString(str_isa_func_name);
 376
 377              sprintf(outputDirName, "%s%c%s.%s", currentOutputDirName.c_str(),
 378                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 379                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str(),
 380              str_isa_func_name.c_str());
 381           }
 382           DealWithNiveau3(*it, outputDirName);
 383       }
 384    }
 385 }
 386
 387
 388 //
 389 // =====================================================================
 390 //
 391
 392 void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string currentOutputDirName){
 393
 394 //
 395 // e.g. at level 3, in
 396
 397    // just to be able to go on checking // JP
 398    if ( GDCM_NAME_SPACE::Util::GetName(level3Directory) != "1")
 399       return;
 400
 401    bool res = CreateDirectory(currentOutputDirName);
 402
 403    if (!res)
 404    {
 405       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 406       throw ( BrukerHopelessException ("Hopeless! Level3 output directory creation failure"));
 407       //exit (0);
 408    }
 409
 410    GDCM_NAME_SPACE::DirList dirList(level3Directory, false, true); // DON'T get recursively the list of files
 411    GDCM_NAME_SPACE::DirListType::iterator it;
 412    GDCM_NAME_SPACE::DirListType fileNames;
 413    fileNames = dirList.GetFilenames();
 414
 415    char original2dseqName       [(unsigned int) PATH_MAX+2];
 416    char currentOutputMhdDirName [(unsigned int) PATH_MAX+2];
 417
 418    char outputMhdFileName       [(unsigned int) PATH_MAX+2];
 419    char output2dseqSliceFileName[(unsigned int) PATH_MAX+6]; // think about extra '.dcm'
 420    char output2dseqName         [(unsigned int) PATH_MAX+6];
 421    char output2dseqCartoName    [(unsigned int) PATH_MAX+6];
 422
 423    char copyFile[PATH_MAX + PATH_MAX + 5]; // Should be enough!
 424    bool canOpen;
 425
 426    //-------------- try d3proc;
 427    char char_d3proc[(unsigned int) PATH_MAX+2];
 428
 429    sprintf(char_d3proc,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"d3proc" );
 430
 431    if (verbose)
 432       std::cout << "d3proc: --- => [" << char_d3proc << "]" << std::endl;
 433    std::string str_d3proc(char_d3proc);
 434    canOpen = br_d3proc.LoadFile(str_d3proc);
 435
 436    if (!canOpen)
 437    {
 438       std::cout << "Hopeless! no 'd3proc' found" << std::endl;
 439       throw ( BrukerHopelessException ("Hopeless! no 'd3proc' found"));
 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       throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'd3proc'"));
 448       //exit(0);  /// \TODO throw an exception !
 449    }
 450
 451    //-------------- end try d3proc;
 452
 453
 454  // -------------------try reco
 455
 456    char char_reco[(unsigned int) PATH_MAX+2];
 457
 458    sprintf(char_reco,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
 459     //str_d3proc = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
 460     //             GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 461     //             "d3proc";
 462    if (verbose)
 463       std::cout << "reco --- => [" << char_reco << "]" << std::endl;
 464    std::string str_reco(char_reco);
 465    canOpen = br_reco.LoadFile(str_reco);
 466
 467    if (!canOpen) // we try in directory ../1
 468    {
 469       if (verbose)
 470          std::cout << "[" << str_reco << "] not found " << std::endl;
 471       std::string lastDirName = GDCM_NAME_SPACE::Util::GetPath(level3Directory);
 472       //lastDirName = GDCM_NAME_SPACE::Util::GetPath(lastDirName);
 473       sprintf(char_reco,"%s%c1%c%s", lastDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
 474       str_reco=char_reco;
 475       canOpen = br_reco.LoadFile(str_reco);
 476       if (!canOpen)
 477       {
 478          std::cout << "Hopeless! cannot find 'reco' in [" << str_reco << "]"  << std::endl;
 479          throw ( BrukerHopelessException ("Hopeless! cannot find 'reco'"));
 480          //exit(0);  /// \TODO throw an exception !
 481       }
 482    }
 483
 484    canOpen = br_reco.FillMap();
 485    if (!canOpen)
 486    {
 487       std::cout << "Hopeless! FillMap failed on [" << str_reco << "]" << std::endl;
 488       throw ( BrukerHopelessException ("Hopeless!FillMap failed on 'reco'"));
 489       //exit(0);  /// \TODO throw an exception !
 490    }
 491    //std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
 492    // br_reco.PrintSelf();
 493    // std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
 494
 495    // -------------------end try reco
 496
 497
 498    BrukerFieldData bX = br_d3proc.GetFieldData("IM_SIX");
 499    int NX = bX.GetIntValue()[0];
 500
 501    if (verbose)
 502       std::cout << "IM_SIX " << NX << std::endl;
 503    BrukerFieldData bY=br_d3proc.GetFieldData("IM_SIY");
 504    int NY = bY.GetIntValue()[0];
 505
 506    if (verbose)
 507          std::cout << "IM_SIY " << NY << std::endl;
 508    /// \todo : check if there are actually 3 dimensions or only 2
 509
 510    BrukerFieldData bZ= br_d3proc.GetFieldData("IM_SIZ");
 511    int nbFrames = bZ.GetIntValue()[0];
 512    if (verbose)
 513          std::cout << "IM_SIZ " << nbFrames << std::endl;
 514
 515         // WARNING DATTYPE is, either in {ip_short, ip_int, ip_char, ...}, or in {1, 2, 3, ...}
 516
 517    BrukerFieldData bDPT = br_d3proc.GetFieldData("DATTYPE");
 518
 519    std::string mhdDataPixelType;
 520    int pixelSize;
 521    getImhDataType(bDPT, mhdDataPixelType, pixelSize);
 522
 523    BrukerFieldData fov = br_method.GetFieldData("PVM_Fov");
 524    double fovX = fov.GetDoubleValue()[0];
 525    double fovY = fov.GetDoubleValue()[1];
 526    if (verbose)
 527       std::cout << "FOV (ds method) " << fovX << " " << fovY << std::endl;
 528
 529    /// \TODO probabely a more sophisticated accessor will be necessary :
 530    ///  (cf : non contiguous slices, overlapping, slice thickness, space between slices, etc)
 531    BrukerFieldData bsliceDistance = br_method.GetFieldData("PVM_SPackArrSliceDistance");
 532    double sliceDistance = bsliceDistance.GetDoubleValue()[0];
 533
 534    if (mhd)
 535    {
 536       sprintf(currentOutputMhdDirName, "%s%c%s", currentOutputDirName.c_str(),
 537                                GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "MhdFiles");
 538       res = CreateDirectory( currentOutputMhdDirName );
 539       if (!res) {
 540          std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 541          throw ( BrukerHopelessException ("Hopeless!FillMap failed on 'reco'"));
 542          //exit (0);
 543       }
 544
 545       if (verbose)
 546          std::cout << "Directory creation [" <<  currentOutputDirName << "]" << std::endl;
 547    }  // end if mhd
 548
 549    if (verbose)
 550          std::cout << "nbFrames " << nbFrames << std::endl;
 551    if (verbose)
 552          std::cout << "nbSlices " << nbSlices << std::endl;
 553    int k;
 554    int nbInstants = nbFrames/nbSlices;
 555    if (verbose)
 556          std::cout << "nbInstants (deduced )" << nbInstants << std::endl;
 557    int instantNb;
 558    int sliceNb;
 559    FILE *fp;  // for MHD files
 560
 561    sprintf( original2dseqName, "%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "2dseq");
 562
 563 /**/
 564   // \TODO : tenir compte du bazar precedent
 565
 566     // load 2dseq in memory
 567
 568    fp = fopen(original2dseqName, "rb");
 569    if (!fp)
 570    {
 571       std::cout << "Cannot open [" << original2dseqName << "] for reading" << std::endl;
 572       throw ( BrukerHopelessException ("Hopeless! Cannot open '2dseq'"));
 573       //exit (0);
 574    }
 575
 576    unsigned char *buffer_2dseq = new unsigned char[NX*NY*pixelSize*nbSlices*nbInstants];
 577    ///\ TODO : find a safer way to be sure to read everything!
 578    size_t lgr = fread(buffer_2dseq, 1, NX*NY*pixelSize*nbSlices*nbInstants, fp);
 579
 580    // This one will be important!
 581    // ---------------------------
 582    try {
 583       imageSet = CreateImageSet ( );
 584    }
 585    catch (BrukerInitException& e)
 586    {
 587       std::cout <<  "Exception " << e.what() << std::endl;
 588       return;
 589    }
 590
 591    serieNumber++;
 592    strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 593    if (nbInstants==1) // creer un seul fichier .mhd  pour toutes les Slices! (images natives)
 594    {
 595        if (verbose)
 596           std::cout << "Single instant : do not split" << std::endl;
 597        if (mhd)
 598        {
 599              sprintf(outputMhdFileName, "%s%cMhdData_All_the_Slices.mhd", currentOutputMhdDirName,
 600                                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 601              fp=fopen(outputMhdFileName, "w");
 602              if (!fp)
 603              {
 604                 std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 605                 throw ( BrukerHopelessException ("Hopeless! Cannot open  mhd file for writting"));
 606                 //exit(0);
 607              }
 608              else
 609              {
 610                fprintf(fp, "ObjectType = Image\n");
 611                fprintf(fp, "NDims = 3\n" );
 612                fprintf(fp, "BinaryData = True \n" );
 613                fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 614                fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices );
 615                fprintf(fp, "HeaderSize = %d\n", 0);
 616                fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
 617                fprintf(fp, "Position = 0 0 %d\n", 0 );
 618                fprintf(fp, "Offset = 0 0 0\n" );
 619                fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 620                fprintf(fp, "ElementNumberOfChannels = 1\n" );
 621                fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
 622                fprintf(fp, "ElementDataFile = %s\n", "../2dseq_All_the_Slices" );
 623                fclose(fp);
 624              }
 625              sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices",
 626                                        currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 627              fp=fopen(output2dseqSliceFileName, "wb");
 628              if (!fp)
 629              {
 630                 std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 631                 throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseq file for writting"));
 632              }
 633              else
 634              {
 635                 fwrite( buffer_2dseq, NX*NY*pixelSize, nbSlices, fp);
 636              }
 637              fclose(fp);
 638              serieNumber ++;
 639              strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 640        }  // end if mhd
 641        if (dicom)
 642        {
 643              sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices.dcm",
 644                                        currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 645
 646             /* ----------- Write Dicom Image  ---------------*/
 647              MakeDicomImage(buffer_2dseq,
 648                NX,
 649                NY,
 650                nbFrames,
 651                pixelSize,
 652                fovX/NY, fovY/NY, sliceDistance,
 653                output2dseqSliceFileName,
 654                strPatientName,
 655                day,
 656                strStudyUID,
 657                strSerieUID,
 658                strStudyDescr,
 659                strSerieDescr,
 660                strStudyTimeDate,
 661                0,// index frame number
 662                GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
 663              );
 664        }  // end if dicom
 665    }  // end if nbInstants = 1
 666
 667    else  // more than ONE instant
 668    {
 669           // Interleaved !
 670           // it's (slice1,slide2, ...)t1 ; (slice1,slide2, ...)t2 ; ...
 671
 672          unsigned char *pixelsForCurrentSlice = new unsigned char[NX*NY*pixelSize*nbInstants];
 673
 674          k = 0;
 675          for (sliceNb=0; sliceNb<nbSlices; sliceNb++)
 676          {
 677             if (mhd)
 678             {
 679                sprintf(outputMhdFileName, "%s%cMhdData_%03d.mhd", currentOutputMhdDirName,
 680                                         GDCM_NAME_SPACE::GDCM_FILESEPARATOR, k  );
 681                if (verbose)
 682                   std::cout << "--- Output MHD file [" << outputMhdFileName << "]" << std::endl;
 683                fp=fopen(outputMhdFileName, "w");
 684                if (!fp)
 685                {
 686                    std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 687                    throw ( BrukerHopelessException ("Hopeless! Cannot open  mhd file for writting"));
 688                    //exit(0);
 689                }
 690                else
 691                {
 692             /* ----------- Write MHD Image  ---------------*/
 693                 //if (verbose)
 694                 //   std::cout << "Open sucessfully[" << outputMhdFileName << "] for writting" << std::endl;
 695                    fprintf(fp, "ObjectType = Image\n");
 696                    fprintf(fp, "NDims = 3\n" );
 697                    fprintf(fp, "BinaryData = True \n" );
 698                    fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 699                    fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbInstants);
 700                    fprintf(fp, "HeaderSize = %d\n", 0);
 701                    fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, 1.0 ); // slice distance : no meaning for temporal serie
 702                    fprintf(fp, "Position = 0 0 %d\n", sliceNb );
 703                    fprintf(fp, "Offset = 0 0 0\n" );
 704                    fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 705                    fprintf(fp, "ElementNumberOfChannels = 1\n" );
 706                    fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
 707                    fprintf(fp, "ElementDataFile = ..%c2dseq_Slice_%d\n", GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb );
 708                    fclose(fp);
 709                } // end write MHD
 710
 711                sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d",
 712                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,sliceNb);
 713                fp=fopen(output2dseqSliceFileName, "wb");
 714                if (!fp)
 715                {
 716                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 717                    throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseqSliceFile file for writting"));
 718                    //exit (0);
 719                }
 720                int frameSize = NX*NY*pixelSize;
 721                for (instantNb=0; instantNb<nbInstants; instantNb++)
 722                {
 723 // std::cout << "------------SN " << sliceNb << " IN " << instantNb <<  " T " << nbSlices*instantNb + sliceNb << std::endl;
 724                     fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
 725                             frameSize,
 726                             1, fp);
 727                }
 728                fclose(fp);
 729 // std::cout << "end writting[" << output2dseqSliceFileName << "]" << std::endl;
 730             }  // end if mhd
 731
 732             if (dicom)
 733             {
 734                // desperate try !
 735              /*
 736                sprintf(output2dseqSliceFileName, "%sdummy_buffer",
 737                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 738                fp=fopen(output2dseqSliceFileName, "wb");
 739                if (!fp)
 740                {
 741                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 742                    exit (0);
 743                }
 744                int frameSize = NX*NY*pixelSize;
 745                for (instantNb=0; instantNb<nbInstants; instantNb++)
 746                {
 747 // std::cout << "------------SN " << sliceNb << " IN " << instantNb <<  " T " << nbSlices*instantNb + sliceNb << std::endl;
 748                     fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
 749                             frameSize,
 750                             1, fp);
 751                }
 752                fclose(fp);
 753
 754                fp=fopen(output2dseqSliceFileName, "rb");
 755                if (!fp)
 756                {
 757                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for reading" << std::endl;
 758                    exit (0);
 759                }
 760                fread( pixelsForCurrentSlice,
 761                             frameSize*nbInstants,
 762                             1, fp);
 763                fclose(fp);
 764               // end of desperate try !
 765               */
 766
 767                /* ----------- Write Dicom Image  ---------------*/
 768
 769                int frameSize = NX*NY*pixelSize;
 770                for (instantNb=0; instantNb<nbInstants; instantNb++)
 771                {
 772                   memcpy(pixelsForCurrentSlice + frameSize*instantNb, buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize, frameSize);
 773                }
 774
 775                int indOfFirsImageWithinImageSet =  nbSlices*instantNb;
 776                sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d.dcm",
 777                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb);
 778
 779                MakeDicomImage(
 780                   pixelsForCurrentSlice,
 781                   NX,
 782                   NY,
 783                   nbInstants,
 784                   pixelSize,
 785                   fovX/NY, fovY/NY, sliceDistance,
 786                   output2dseqSliceFileName,
 787                   strPatientName,
 788                   day,
 789                   strStudyUID,
 790                   strSerieUID,
 791                   strStudyDescr,
 792                   strSerieDescr,
 793                   strStudyTimeDate,
 794                   sliceNb*nbInstants,
 795                   GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
 796                );
 797                if (verbose)
 798                   std::cout << "--- Output DCM file [" << output2dseqSliceFileName << "]" << std::endl;
 799
 800            } // en if dicom
 801
 802         k++;
 803         }
 804         delete [] pixelsForCurrentSlice;
 805      }  // end nbInstants == 1
 806    delete [] buffer_2dseq;
 807 /**/
 808
 809
 810    // -----------------------------------------------------
 811    //  deal with MatLab-generated Carto file.
 812    // -----------------------------------------------------
 813
 814    dealWithCarto(fileNames,  NX,  NY,  nbSlices, fovX, fovY, sliceDistance,
 815                    copyFile, currentOutputDirName, outputMhdFileName, output2dseqCartoName);
 816 }
 817
 818
 819 // ===========================================================================================
 820
 821 void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX, int NY, int nbSlices,
 822                                  double fovX, double fovY, double sliceDistance,
 823                                  char *copyFile, std::string &currentOutputDirName,
 824                                  char *outputMhdFileName, char *output2dseqCartoName)
 825 {
 826    // -----------------------------------------------------
 827    //  deal with MatLab-generated Carto file.
 828    // -----------------------------------------------------
 829
 830    char *code[] ={ "ADC", "adc", "TTP", "ttp", "PEAK", "peak" , ""};  // add more carto file name identifiers if necessary; end with ""
 831    int icode;
 832    GDCM_NAME_SPACE::DirListType::iterator it;
 833    char file_name_ident[500];
 834    FILE *fp;
 835
 836    // Iterate to ALL the objets(files/directories) found in the input directory
 837    for (it = fileNames.begin();
 838         it != fileNames.end();
 839       ++it)
 840    {
 841       if ( boost::filesystem::is_regular(*it) )
 842       //if ( ! boost::filesystem::is_directory(*it) )
 843       {
 844          if (verbose)
 845             std::cout << "--- [" << *it << "] is a file..." << std::endl;
 846
 847          icode = 0;
 848
 849          while (code[icode][0] != 0)
 850          {
 851             sprintf(file_name_ident, "2dseq.%s",code[icode]); // e.g  "2dseq_ADC"
 852             std::string::size_type loc = (*it).rfind(file_name_ident);
 853
 854             if ( loc != std::string::npos )
 855             {
 856
 857        ///\ TODO : find a safer way to be sure to read everything!
 858               unsigned char *buffer_carto = new unsigned char[NX*NY*sizeof(double)*nbSlices];
 859               fp = fopen ( (*it).c_str(), "rb");
 860               if (!fp){
 861                  std::cout << "Cannot open [" << *it << "] for reading" << std::endl;
 862
 863                }
 864                fread(buffer_carto, NX*NY*sizeof(double), nbSlices, fp);
 865
 866                std::cout << "Deal with Carto file :[" <<*it << "], computed length : "
 867                          << NX*NY*sizeof(double)*nbSlices << std::endl;
 868                   std::string lastFileName = GDCM_NAME_SPACE::Util::GetName((*it).c_str());
 869                if (mhd)
 870                {
 871                   // Copy the data file in the new directory
 872                   sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() ,
 873                             currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str());
 874                   system(copyFile);
 875                   sprintf(outputMhdFileName, "%s%c%s%s",
 876                                        currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".mhd" );
 877                   if (verbose)
 878                     std::cout << "--- Output Carto MHD file [" << outputMhdFileName << "]" << std::endl;
 879
 880                   FILE *fp;
 881                   fp=fopen(outputMhdFileName, "w");
 882                   if (!fp)
 883                   {
 884                      std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 885                   }
 886                   else
 887                   {
 888                      fprintf(fp, "ObjectType = Image\n");
 889                      fprintf(fp, "NDims = 3\n" );
 890                      fprintf(fp, "BinaryData = True \n" );
 891                      fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 892                      fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices);
 893                      fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
 894                      fprintf(fp, "HeaderSize = %d\n", 0 );
 895                      fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
 896                      fprintf(fp, "Position = 0 0 0\n" );
 897                      fprintf(fp, "Offset = 0 0 0\n" );
 898                      fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 899                      fprintf(fp, "ElementNumberOfChannels = 1\n" );
 900                      fprintf(fp, "ElementType = %s\n", "MET_DOUBLE" );
 901                      fprintf(fp, "ElementDataFile = %s\n", lastFileName.c_str() );
 902
 903                      fclose(fp);
 904                   }
 905                   if (verbose)
 906                      std::cout << "--- end write Carto MHD file [" << outputMhdFileName << "]" << std::endl;
 907                }  // end if mhd
 908
 909             // ----------- Write Dicom Image  ---------------
 910
 911                if (dicom)
 912                {
 913                   sprintf(output2dseqCartoName, "%s%c%s%s",
 914                                        currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".dcm" );
 915                   if (verbose)
 916                      std::cout << "--- end create name output2dseqCartoName file [" << output2dseqCartoName << "]" << std::endl;
 917
 918                   strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID(); //New SerieUID for each carto.
 919                   std::string strNewSerieDescr(strSerieDescr+ "_" +GDCM_NAME_SPACE::Util::GetName((*it).c_str()));
 920                   MakeDicomImage(buffer_carto,
 921                      NX,
 922                      NY,
 923                      nbSlices,
 924                      8, // pixelSize
 925                      fovX/NY, fovY/NY, sliceDistance,
 926                      output2dseqCartoName,
 927                      strPatientName,
 928                      day,
 929                      strStudyUID,
 930                      strSerieUID,
 931                      strStudyDescr,
 932                      strNewSerieDescr,
 933                      strStudyTimeDate,
 934                      0,
 935                      GDCM_NAME_SPACE::CREATED_IMAGE
 936                   );
 937                }  // end if dicom
 938
 939                delete [] buffer_carto;
 940                if (verbose)
 941                   std::cout << "--- End writing Carto DICOM file [" << output2dseqCartoName << "]" << std::endl;
 942                break; // don't check for more ident on same file name!
 943
 944             }
 945             icode++;
 946          }
 947       }
 948    } // end iterate on files
 949 }
 950
 951
 952 // ==========================================================================================================
 953
 954 bool Bruker2Dicom::CreateDirectory(std::string OutputDirName)
 955 {
 956    std::string systemCommand;
 957
 958    if (verbose)
 959       std::cout << "Check for output directory :[" << OutputDirName << "]."
 960                 <<std::endl;
 961    if ( ! boost::filesystem::is_directory(OutputDirName) )    // dirout not found
 962    {
 963       std::string strDirNameout(OutputDirName);        // to please gcc 4
 964       systemCommand = "mkdir " + strDirNameout;        // create it!
 965       if (verbose)
 966          std::cout << systemCommand << std::endl;
 967       system (systemCommand.c_str());
 968       if ( ! boost::filesystem::is_directory(OutputDirName) ) // be sure it worked
 969       {
 970          if (verbose)
 971             std::cout << "KO : not a dir : [" << OutputDirName << "] (creation failure ?)" << std::endl;
 972          return 0;
 973          /// \todo : THROW AN EXCEPTION
 974       }
 975       else
 976       {
 977          if (verbose)
 978            std::cout << "Directory [" << OutputDirName << "] created." << std::endl;
 979       }
 980    }
 981    else
 982    {
 983        if (verbose)
 984           std::cout << "Output Directory [" << OutputDirName << "] already exists; Used as is." << std::endl;
 985    }
 986
 987    return 1;
 988
 989 }
 990
 991
 992 // ===========================================================================================
 993
 994 /// \TODO move cleanString to 'crea' ?
 995
 996 void Bruker2Dicom::cleanString(std::string &s)
 997 {
 998    int l = s.size();
 999    if (s[l-1] == 0x0A || s[l-1] == 0x0D ) // CR or NL
1000    {
1001       l--;
1002       s = s.substr(0, l);
1003    }
1004    if (s[l-1] == ' ' ) // blank space
1005    {
1006       l--;
1007       s = s.substr(0, l);
1008    }
1009
1010    if (s[0] == '<')
1011       s= s.substr(1,l-2);
1012    std::string repChar("_");
1013    GDCM_NAME_SPACE::Util::ReplaceSpecChar(s, repChar);
1014 }
1015
1016
1017
1018 // ===========================================================================================
1019
1020
1021 void Bruker2Dicom::getImhDataType(BrukerFieldData &bDPT, std::string &mhdDataPixelType, int &pixelSize)
1022 {
1023    if(bDPT.GetDataType() == "string")
1024    {
1025          std::string brukerDataPixelType = bDPT.GetStringValue()[0];
1026          if (verbose)
1027             std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
1028          //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
1029
1030          if (brukerDataPixelType ==  "ip_short") {
1031             mhdDataPixelType = "MET_USHORT";
1032             pixelSize = 2;
1033          }
1034          if (brukerDataPixelType ==  "ip_int") {
1035             mhdDataPixelType = "MET_UINT";
1036             pixelSize = 4;
1037          }
1038          if (brukerDataPixelType ==  "ip_char") {
1039              mhdDataPixelType = "MET_UCHAR";
1040              pixelSize = 1;
1041          }
1042                   /// \TODO : finish the list
1043     /*
1044     case 0 : fp << "ElementType = MET_CHAR" << std::endl;
1045       break;
1046     case 1 : fp << "ElementType = MET_UCHAR" << std::endl;
1047       break;
1048     case 2 : fp << "ElementType = MET_SHORT" << std::endl;
1049       break;
1050     case 3 : fp << "ElementType = MET_USHORT" << std::endl;
1051       break;
1052     case 4 : fp << "ElementType = MET_INT" << std::endl;
1053       break;
1054     case 5 : fp << "ElementType = MET_UINT" << std::endl;
1055       break;
1056     case 6 : fp << "ElementType = MET_FLOAT" << std::endl;
1057       break;
1058     case 7 : fp << "ElementType = MET_DOUBLE" << std::endl;
1059     */
1060     }
1061     else
1062     {
1063          int brukerDataPixelType = bDPT.GetIntValue()[0];
1064          if (verbose)
1065             std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
1066          //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
1067
1068 // Cross your fingers !!!
1069
1070 // pb : found values : 2, 3, 5
1071
1072          if (brukerDataPixelType ==  2) {
1073             mhdDataPixelType = "MET_USHORT";
1074             pixelSize = 2;
1075          }
1076          if (brukerDataPixelType ==  3) {
1077             mhdDataPixelType = "MET_USHORT";
1078             pixelSize = 2;
1079          }
1080          if (brukerDataPixelType ==  1) {
1081             mhdDataPixelType = "MET_UCHAR";
1082             pixelSize = 1;
1083          }
1084     }
1085 }
1086
1087 // ===========================================================================================
1088
1089 std::vector<BrukerImage> Bruker2Dicom::CreateImageSet ( )
1090 {
1091          std::vector<BrukerImage> imageSet;
1092          br_acqp.SetLoopStructure();
1093          std::vector<int> tempVect                      = br_acqp.GetLoopStructure() ;
1094          std::map<std::string, BrukerFieldData> map     = br_acqp.GetBrukerHeaderMap();
1095          bool result                                    = br_acqp.ObjectVaryingProperties.init(map,tempVect);
1096
1097          if (result == false)
1098          {
1099             throw ( BrukerInitException  ("Bruker2Dicom::CreateImageSet failure ") );
1100          }
1101
1102          br_acqp.SetImageLoopStructure();
1103          br_acqp.SetBrukerImageList();
1104          std::vector<std::vector<int> > brukerImageList = br_acqp.GetBrukerImageList();
1105
1106          BrukerImage image(br_acqp,br_reco);
1107          image.Init(br_acqp,br_reco,1);
1108
1109          for(int i=0;i<brukerImageList.size();i++)
1110          {
1111             image.Init(br_acqp,br_reco,i);
1112             imageSet.push_back(image);
1113          }
1114
1115  // Just for checking
1116  /*
1117
1118          std::vector<std::vector <double> > imageOrientation;
1119          std::vector <double> imagePosition;
1120          for(int i=0;i<brukerImageList.size();i++)
1121          {
1122            // fread(buffer_2dseq, NX*NY*pixelSize*nbSlices*nbInstants, 1, fp);
1123
1124            imagePosition = imageSet[i].getTranslationVectorRPS2XYZ();
1125            std::cout << "Position " << imagePosition[0] << " "
1126                      << imagePosition[1] << " "  << imagePosition[2] ;
1127            imageOrientation =  imageSet[i].getRotationMatrixRPS2XYZ();
1128            std::cout << "\t  Orientation " ;
1129            for(int i1=0; i1<3;i1++)for(int i2=0; i2<3;i2++)
1130               std::cout << imageOrientation[i1][i2] << " ";
1131
1132            //std::cout << "\t  Abs Time " << imageSet[i].getAbsoluteTimePosition();
1133            std::cout << "\t  Relat Time " << imageSet[i].getRelativeTimePosition();
1134
1135            std::cout << "\t [";
1136            for (int i3=0; i3<imageSet[i].getLoopStamp().size();i3++)
1137               std::cout << " " << imageSet[i].getLoopStamp()[i3];
1138            std::cout << "]" << std::endl;
1139          }
1140 */
1141    return imageSet;
1142 }
1143
1144 // ===========================================================================================
1145
1146 void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels,
1147               int X,
1148               int Y,
1149               int nbFrames,
1150               int pixelSize,
1151               double spacingX, double spacingY, double sliceDistance,
1152               std::string dcmImageName,
1153               const std::string &patientName,
1154               const char *day,
1155               std::string &studyUID,
1156               std::string &serieUID,
1157               std::string &studyDescr,
1158               std::string &serieDescr,
1159               std::string &strStudyTimeDate,
1160               int imgNum,
1161               GDCM_NAME_SPACE::ImageContentType contentType
1162       )
1163 {
1164    std::ostringstream str;
1165
1166    GDCM_NAME_SPACE::File *file;
1167    file = GDCM_NAME_SPACE::File::New();
1168
1169   // Set the image size
1170    str.str("");
1171    str << X;
1172    file->InsertEntryString(str.str(),0x0028,0x0011,"US"); // Columns
1173    str.str("");
1174    str << Y;
1175    file->InsertEntryString(str.str(),0x0028,0x0010,"US"); // Rows
1176
1177    if (nbFrames != 1)
1178    {
1179       str.str("");
1180       str << nbFrames;
1181       file->InsertEntryString(str.str(),0x0028,0x0008,"IS"); // Number of Frames
1182    }
1183
1184   // Set the pixel type
1185   //      //8, 16, 32, 64 (for double ?)
1186    str.str("");
1187    str << pixelSize*8;
1188    file->InsertEntryString(str.str(),0x0028,0x0100,"US"); // Bits Allocated
1189
1190    file->InsertEntryString(str.str(),0x0028,0x0101,"US"); // Bits Stored
1191
1192    str.str("");
1193    str << pixelSize*8-1;
1194    file->InsertEntryString(str.str(),0x0028,0x0102,"US"); // High Bit
1195
1196   // Set the pixel representation // 0/1 , 0=unsigned
1197    file->InsertEntryString("1",0x0028,0x0103, "US"); // Pixel Representation
1198
1199   // Set the samples per pixel // 1:Grey level, 3:RGB
1200    file->InsertEntryString("1",0x0028,0x0002, "US"); // Samples per Pixel
1201
1202 //  0028 0030 DS 2 Pixel Spacing
1203    str.str("");
1204    str << spacingX << "\\" << spacingY;
1205    file->InsertEntryString(str.str(),0x0028,0x0030, "DS"); // Pixel Spacing
1206
1207  //   0018 0050 DS 1 Slice Thickness
1208    str.str("");
1209    str << sliceDistance;
1210    file->InsertEntryString(str.str(),0x0018,0x0050, "DS");
1211
1212   // 1.2.840.10008.5.1.4.1.1.4.1 : Enhanced MR Image Storage
1213  //  file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0002, 0x0002, "UI");  // [Media Storage SOP Class UID]
1214   // file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0008, 0x0016, "UI");  // [SOP Class UID]
1215
1216
1217 // OK : MR is NOT multiframe, but I want just a quick an dirty solution
1218 // 1.2.840.10008.5.1.4.1.1.4         MR Image Storage
1219    file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0002, 0x0002, "UI");  // [Media Storage SOP Class UID]
1220    file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0008, 0x0016, "UI");  // [SOP Class UID]
1221
1222   // if (strlen(patientName) != 0)
1223    file->InsertEntryString(patientName.c_str(),0x0010,0x0010, "PN"); // Patient's Name
1224
1225    file->InsertEntryString(studyUID, 0x0020, 0x000d, "UI");
1226    file->InsertEntryString(serieUID, 0x0020, 0x000e, "UI");
1227
1228 //  0008 0020 DA 1 Study Date
1229 //  0008 0030 TM 1 Study Time
1230
1231 /// \TODO split into 2 strings!
1232    file->InsertEntryString(strStudyTimeDate.substr(10,11).c_str(),0x0008,0x0020, "DA");
1233    file->InsertEntryString(strStudyTimeDate.substr(1,8).c_str(),0x0008,0x0030, "TM");
1234
1235    file->InsertEntryString(studyDescr,0x0008,0x1030, "LO");  // Study Description
1236    file->InsertEntryString(serieDescr,0x0008,0x103e, "LO");  // Series Description
1237
1238 //0008|0060 [CS] [Modality]
1239    file->InsertEntryString("MR",0x0008,0x0060, "CS");
1240
1241 // 0020 0037 DS 6 Image Orientation (Patient)
1242    char charImageOrientation[256];
1243
1244 /*
1245 std::cout << "charImageOrientation  " <<
1246                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0] << " " <<
1247                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1] << " " <<
1248                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2] << " " <<
1249                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0] << " " <<
1250                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1] << " " <<
1251                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] << std::endl ;
1252 */
1253    sprintf(charImageOrientation,"%f\\%f\\%f \\ %f\\%f\\%f",
1254                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0],
1255                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1],
1256                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2],
1257                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0],
1258                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1],
1259                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] ) ;
1260
1261    file->InsertEntryString(charImageOrientation,0x0020,0x0037, "DS");
1262
1263
1264 // 0020 0032 DS 3 Image Position (Patient)
1265
1266    char charImagePosition[256];
1267    sprintf(charImagePosition,"%f\\%f\\%f",
1268                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[0],
1269                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[1],
1270                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[2]);
1271
1272    file->InsertEntryString(charImagePosition,0x0020,0x0032, "DS");  //0020 0032 DS 3 Image Position (Patient)
1273
1274
1275
1276 // 0020 0x1041 DS 1 Slice Location
1277 //        sprintf(charImagePosition,"%f",float(imgNum));
1278 //        file->InsertEntryString(charImagePosition,0x0020,0x1041, "DS");
1279 /*
1280   // Set Rescale Intercept
1281         str.str("");
1282         str << div;
1283         file->InsertEntryString(str.str(),0x0028,0x1052,"DS");
1284
1285   // Set Rescale Slope
1286         str.str("");
1287         str << mini;
1288         file->InsertEntryString(str.str(),0x0028,0x1053,"DS");
1289 */
1290
1291    GDCM_NAME_SPACE::FileHelper *fileH;
1292    fileH = GDCM_NAME_SPACE::FileHelper::New(file);
1293    fileH->SetContentType(contentType);
1294
1295    // cast is just to avoid warnings (*no* conversion is performed)
1296    //fileH->SetImageData((uint8_t *)img,int(maxX*maxY)*sizeof(uint16_t)); // troubles when maxX, mayY are *actually* float!
1297
1298 //std::cout << "--------------------------------  X*Y*nbFrames*pixelSize " << X << " " << Y << " " << nbFrames << " " << pixelSize << std::endl;
1299
1300    fileH->SetImageData((uint8_t *)tabPixels, X*Y*nbFrames*pixelSize);
1301    fileH->SetWriteModeToRaw();
1302    fileH->SetWriteTypeToDcmExplVR();
1303    if( !fileH->Write(dcmImageName))
1304       std::cout << "Failed for [" << dcmImageName << "]\n"
1305                 << "           File is unwrittable" << std::endl;
1306
1307    if (verbose)
1308       file->Print();
1309
1310    file->Delete();
1311    fileH->Delete();
1312 }
1313
1314