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 directory name -----
  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    // ----- Check output directory name -----
  31
  32    std::string strDirNameOut(OutputDirName);
  33    bool res=CreateDirectory(strDirNameOut);
  34    if (!res) {
  35       std::cout << "[" << OutputDirName << "] Directory creation failure " << std::endl;
  36       //exit (0);
  37       throw ( BrukerHopelessException ("Output directory creation failure "));
  38    }
  39
  40    std::string strDirNamein(InputDirName);
  41    GDCM_NAME_SPACE::DirList dirList(strDirNamein, false, true); // DON'T get recursively the list of files
  42    std::string strDirNameout(OutputDirName);
  43
  44 /*
  45    if (listonly)
  46    {
  47       std::cout << "------------List of found files ------------" << std::endl;
  48       dirList.Print();
  49       std::cout << std::endl;
  50       return 1;
  51    }
  52 */
  53
  54 //
  55 // e.g : at level 0, in : B67d1.Bp1
  56 //
  57 //           1  2  3  4  5  6  AdjStatePerStudy  subject
  58 //
  59
  60    GDCM_NAME_SPACE::DirListType fileNames;
  61    fileNames = dirList.GetFilenames();
  62    bool canOpen;
  63    std::string outputFileName;
  64
  65
  66   // BrukerDataSet br_subject;
  67    std::string subject;
  68    subject = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
  69              GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
  70              "subject";
  71    if (verbose)
  72         std::cout << " Subject : [" <<  subject << "]" << std::endl;
  73    canOpen =br_subject.LoadFile(subject);
  74
  75    if (!canOpen)
  76    {
  77       std::cout << "Hopeless! no 'subject' found" << std::endl;
  78       throw ( BrukerHopelessException ("Hopeless! no 'subject' found in root input directory "));
  79       //exit(0);  /// \TODO throw an exception !
  80    }
  81    else
  82    {
  83       br_subject.FillMap();
  84    }
  85    //br_subject.PrintSelf();
  86
  87   // get info for 'Study Description'
  88
  89     BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string");
  90     subject_name = b_name.GetStringValue()[0];
  91     strPatientName = subject_name;
  92     cleanString(subject_name);
  93
  94     // creation directory : 'nom du patient'
  95     std::string tempStringPatDir(OutputDirName);
  96     tempStringPatDir = tempStringPatDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + subject_name;
  97
  98     res=CreateDirectory(tempStringPatDir);
  99     if (!res) {
 100        std::cout << "[" << tempStringPatDir << "] Directory creation failure " << std::endl;
 101        throw ( BrukerHopelessException ("Patient directory creation failure "));
 102     }
 103
 104     BrukerFieldData b_entry=br_subject.GetFieldData("SUBJECT_entry");
 105     std::string subject_entry = b_entry.GetStringValue()[0];
 106     //cleanString(subject_entry);
 107     subject_entry = subject_entry.substr(11, subject_entry.size()-11);
 108
 109     BrukerFieldData b_position=br_subject.GetFieldData("SUBJECT_position");
 110     std::string subject_position = b_position.GetStringValue()[0];
 111     //cleanString(subject_position);
 112     subject_position = subject_position.substr(9, subject_position.size()-9);
 113
 114     BrukerFieldData b_date=br_subject.GetFieldData("SUBJECT_date");
 115     std::string subject_date = b_date.GetStringValue()[0];
 116     strStudyTimeDate = subject_date;
 117     cleanString(subject_date);
 118
 119     BrukerFieldData b_study_name=br_subject.GetFieldData("SUBJECT_study_name");
 120     std::string subject_study_name = b_study_name.GetStringValue()[0];
 121     subject_study_name = subject_study_name.substr(1, subject_study_name.size()-2);
 122     cleanString(subject_study_name);
 123
 124     // subject_name is already in 'Patient Name'
 125     strStudyDescr = /*subject_name + "." + */ subject_study_name + "." + subject_entry + "." + subject_position + "." + subject_date;
 126
 127     // creation directory : 'nom de la Study'
 128
 129     std::string tempStringStudyDir(OutputDirName);
 130     tempStringStudyDir = tempStringPatDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + strStudyDescr;
 131
 132     res=CreateDirectory(tempStringStudyDir);
 133     if (!res) {
 134        std::cout << "[" << tempStringStudyDir << "] Directory creation failure " << std::endl;
 135        throw ( BrukerHopelessException ("Study directory creation failure "));
 136     }
 137
 138    char outputDirName[(unsigned int) PATH_MAX+2];
 139
 140    strStudyUID    = GDCM_NAME_SPACE::Util::CreateUniqueUID();
 141    serieNumber    = 0;
 142    instanceNumber = 0;
 143    // -----------------------------------------------------
 144    // Iterate to ALL the objets(files/directories) found in the input directory
 145    // (this is level ZERO)
 146    // each Directory (name : 1, 2, 3, ...) will be a Dicom Serie
 147    // -----------------------------------------------------
 148
 149    GDCM_NAME_SPACE::DirListType::iterator it;
 150
 151    for (it = fileNames.begin();
 152          it != fileNames.end();
 153        ++it)
 154    {
 155       if ( boost::filesystem::is_directory(*it) )
 156       {
 157          if (verbose)
 158             std::cout << "[" << *it << "] is a directory" << std::endl;
 159
 160          //BrukerDataSet br_acqp;
 161          std::string strAcqp;
 162          strAcqp = (*it) +
 163                    GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 164                    "acqp";
 165
 166          br_acqp.LoadFile(strAcqp);
 167          br_acqp.FillMap();
 168
 169          std::string acqp_scan_name;
 170          std::string acqp_method;
 171          std::string acqp_protocol_location;
 172
 173          BrukerFieldData b_protocol_location=br_acqp.GetFieldData("ACQ_protocol_location");
 174          acqp_protocol_location = b_protocol_location.GetStringValue()[0];
 175          cleanString(acqp_protocol_location);
 176
 177          BrukerFieldData b_scan_name=br_acqp.GetFieldData("ACQ_scan_name");
 178          acqp_scan_name = b_scan_name.GetStringValue()[0];
 179          cleanString(acqp_scan_name);
 180
 181          BrukerFieldData b_method=br_acqp.GetFieldData("ACQ_method");
 182          acqp_method = b_method.GetStringValue()[0];
 183          cleanString(acqp_method);
 184
 185          BrukerFieldData b_list_size = br_acqp.GetFieldData("ACQ_O1_list_size");
 186          //b_list_size.PrintSelf(); //JP
 187
 188          nbSlices =  b_list_size.GetIntValue()[0];
 189
 190          strSerieDescr = GDCM_NAME_SPACE::Util::GetName(*it)
 191                        /*  + "." + acqp_protocol_location */ // always the same (in each acquisition)
 192                          + "." + acqp_scan_name
 193                          + "." + acqp_method.c_str();
 194
 195          sprintf(outputDirName, "%s%c%s", tempStringStudyDir.c_str(),                //OutputDirName.c_str(),
 196                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 197                           strSerieDescr.c_str() );
 198
 199          std::cout << " ================================================================================\n"
 200                    << " === [" << GDCM_NAME_SPACE::Util::GetName(*it) << "] -> [" << strSerieDescr << "]\n"
 201                    << " ================================================================================"
 202                    << std::endl;
 203
 204
 205         if (verbose)
 206            printf ("outputDirName [%s]\n", outputDirName);
 207         try {
 208            DealWithNiveau1(*it, outputDirName);
 209         }
 210         catch (BrukerHopelessException &e)
 211         {
 212          std::cout << "And Exception was thrown in DealWithNiveau1 (" << e.what() << ") " << std::endl;
 213          continue;
 214         }
 215       }
 216    } // end of : for (GDCM_NAME_SPACE::DirListType::iterator it
 217 }
 218
 219
 220 // =====================================================================
 221
 222 void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string currentOutputDirName) {
 223 //
 224 // e.g. : at level 1, in B67d1.Bp1/6
 225 //
 226 // acqp  fid  imnd  pdata  pulseprogram  spnam0  spnam1
 227
 228    bool res = CreateDirectory(currentOutputDirName);
 229
 230    if (!res) {
 231       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 232       throw ( BrukerHopelessException ("Level 1 output directory creation failure "));
 233      // exit (0);
 234    }
 235    GDCM_NAME_SPACE::DirList dirList(level1Directory, false, true); // DON'T get recursively the list of files
 236    GDCM_NAME_SPACE::DirListType fileNames;
 237    fileNames = dirList.GetFilenames();
 238    // -----------------------------------------------------
 239    // Iterate to ALL the objets(files/directories) found in the input directory
 240    // -----------------------------------------------------
 241    GDCM_NAME_SPACE::DirListType::iterator it;
 242
 243    for (it = fileNames.begin();
 244         it != fileNames.end();
 245       ++it)
 246    {
 247       if ( boost::filesystem::is_regular(*it) )
 248       //if ( ! boost::filesystem::is_directory(*it) )
 249       {
 250          if (verbose)
 251             std::cout << "--- [" << *it << "] is a file." << std::endl;
 252       }
 253    }
 254
 255    char outputDirName[(unsigned int) PATH_MAX+2];
 256    //std::string firstName;
 257    bool canOpen;
 258    for (it = fileNames.begin();
 259         it != fileNames.end();
 260       ++it)
 261    {
 262       if ( boost::filesystem::is_directory(*it) )
 263       {
 264          // will be always "pdata" ...
 265          if (verbose)
 266             std::cout << "--- [" << *it << "] is a directory" << std::endl;
 267
 268               /* a recuperer :
 269               if (FileLine.startsWith("##$ACQ_size=")) {
 270               if (FileLine.startsWith("##$NI=")) {
 271               if (FileLine.startsWith("##$NR=")) {
 272               if (FileLine.startsWith("##$ACQ_obj_order=")) {
 273               if (FileLine.startsWith("##$ACQ_word_size=")) {
 274               if (FileLine.startsWith("##$BYTORDA=")) {
 275               if (FileLine.startsWith("##$PULPROG=")) {
 276               */
 277
 278          sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 279                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 280                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str());
 281          //br1.PrintSelf();
 282
 283           std::string strMethod;
 284           //std::string firstName = *(fileNames.begin());
 285
 286           strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin())) +
 287                       GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 288                       "method";
 289             // std::cout << "---strMethod (for method)=> [" << strMethod << "]" << std::endl;
 290           canOpen = br_method.LoadFile(strMethod);
 291           if (!canOpen)
 292           {
 293              strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
 294                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 295                          "imnd";
 296              //std::cout << "---strMethod (for imnd) => [" << strMethod << "]" << std::endl;
 297              canOpen = br_method.LoadFile(strMethod);
 298              if (!canOpen)
 299              {
 300                 std::cout << "Hopeless! neither 'method' nor 'imnd' found in ["
 301                           << level1Directory  << "]; we skip it!" << std::endl;
 302                 continue;
 303                 //throw ( BrukerHopelessException ("Hopeless! neither 'method' nor 'imnd' found "));
 304                 //exit(0);  /// \TODO throw an exception !
 305              }
 306           }
 307           if (verbose)
 308              std::cout << "open => [" << strMethod << "] successfully" << std::endl;
 309           br_method.FillMap();
 310
 311           /* a recuperer :
 312              ##$PVM_Fov (dimension)
 313           */
 314   /*
 315           dans method (pour perfusion  seulement?) :
 316           ##$PVM_ObjOrderList=( 8 )
 317           0 2 4 6 1 3 5 7
 318           ##$PVM_NSPacks=2
 319           ##$PVM_SPackArrNSlices=( 2 )
 320           7 1
 321   */
 322          try {
 323             DealWithNiveau2(*it,outputDirName );
 324          }
 325          catch (BrukerHopelessException &e)
 326          {
 327             std::cout << "And Exception was thrown in DealWithNiveau2 (" << e.what() << ") " << std::endl;
 328             continue;
 329          }
 330       }
 331    }
 332 }
 333
 334 // =====================================================================
 335
 336 void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string currentOutputDirName) {
 337
 338 // e.g. : at level 2 in B67d1.Bp1/6/pdata
 339 //
 340 // acqp  fid  imnd  pdata  pulseprogram  spnam0  spnam1
 341 //
 342
 343    bool res = CreateDirectory(currentOutputDirName);
 344
 345    if (!res) {
 346       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 347       throw ( BrukerHopelessException ("Hopeless! Level2 output directory creation failure"));
 348       //exit (0);
 349    }
 350
 351    GDCM_NAME_SPACE::DirList dirList(level2Directory, false, true); // DON'T get recursively the list of files
 352
 353    GDCM_NAME_SPACE::DirListType fileNames;
 354    fileNames = dirList.GetFilenames();
 355
 356    char outputDirName[(unsigned int) PATH_MAX+2];
 357
 358    // -----------------------------------------------------
 359    // Iterate to ALL the objets(files/directories) found in the input directory
 360    // -----------------------------------------------------
 361    GDCM_NAME_SPACE::DirListType::iterator it;
 362    bool canOpen;
 363
 364    if (verbose)
 365    for (it = fileNames.begin();
 366         it != fileNames.end();
 367       ++it)
 368    {
 369       if ( ! boost::filesystem::is_directory(*it) )
 370       {
 371          std::cout << "--- --- [" << *it << "] is a file.." << std::endl;
 372       }
 373
 374    }
 375
 376    for (it = fileNames.begin();
 377          it != fileNames.end();
 378        ++it)
 379    {
 380       if ( boost::filesystem::is_directory(*it) )
 381       {
 382
 383          if (verbose)
 384             std::cout << "--- --- [" << *it << "] is a directory" << std::endl;
 385
 386         // sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 387         //                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 388         //                                GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
 389   // MUST be 'pdata'!
 390
 391 //
 392 // (interest of previous method :
 393 // If unaware user changed the pdata name, it goes on working
 394 //
 395           std::string str_isa;
 396           str_isa = (*it) +
 397                     GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 398                    "isa";
 399
 400           std::string str_isa_func_name;
 401           canOpen = br_isa.LoadFile(str_isa);
 402           if (!canOpen)
 403           {
 404              sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 405                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 406                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
 407           }
 408           else
 409           {
 410              br_isa.FillMap();
 411              BrukerFieldData b_isa_func_name = br_isa.GetFieldData("ISA_func_name");
 412
 413              str_isa_func_name = b_isa_func_name.GetStringValue()[0];
 414              cleanString(str_isa_func_name);
 415
 416              sprintf(outputDirName, "%s%c%s.%s", currentOutputDirName.c_str(),
 417                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 418                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str(),
 419              str_isa_func_name.c_str());
 420           }
 421           try {
 422              DealWithNiveau3(*it, outputDirName);
 423           }
 424           catch (BrukerHopelessException &e)
 425           {
 426              std::cout << "And Exception was thrown in DealWithNiveau3 (" << e.what() << "); "
 427                        << " We skip [" << level2Directory << "]" << std::endl;
 428              continue;
 429           }
 430           catch (BrukerInitException &e)
 431           {
 432              std::cout << "And Init Exception was thrown in DealWithNiveau3 (" << e.what() << "); "
 433                        << " We skip [" << level2Directory << "]" << std::endl;
 434              continue;
 435           }
 436       }
 437    }
 438 }
 439
 440
 441 //
 442 // =====================================================================
 443 //
 444
 445 void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string currentOutputDirName){
 446
 447 //
 448 // e.g. at level 3, in
 449
 450    // just to be able to go on checking // JP
 451    if ( GDCM_NAME_SPACE::Util::GetName(level3Directory) != "1")
 452       return;
 453
 454    bool res = CreateDirectory(currentOutputDirName);
 455
 456    if (!res)
 457    {
 458       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 459       throw ( BrukerHopelessException ("Hopeless! Level3 output directory creation failure"));
 460       //exit (0);
 461    }
 462
 463    GDCM_NAME_SPACE::DirList dirList(level3Directory, false, true); // DON'T get recursively the list of files
 464    GDCM_NAME_SPACE::DirListType::iterator it;
 465    GDCM_NAME_SPACE::DirListType fileNames;
 466    fileNames = dirList.GetFilenames();
 467
 468    char original2dseqName       [(unsigned int) PATH_MAX+2];
 469    char original2dseqName_XXX   [(unsigned int) PATH_MAX+2];
 470    char currentOutputMhdDirName [(unsigned int) PATH_MAX+2];
 471
 472    char outputMhdFileName       [(unsigned int) PATH_MAX+2];
 473    char output2dseqSliceFileName[(unsigned int) PATH_MAX+6]; // think about extra '.dcm'
 474    char output2dseqName         [(unsigned int) PATH_MAX+6];
 475    char output2dseqCartoName    [(unsigned int) PATH_MAX+6];
 476
 477    char copyFile[PATH_MAX + PATH_MAX + 5]; // Should be enough!
 478    bool canOpen;
 479
 480    //-------------- try d3proc;
 481    char char_d3proc[(unsigned int) PATH_MAX+2];
 482
 483    sprintf(char_d3proc,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"d3proc" );
 484
 485    if (verbose)
 486       std::cout << "d3proc: --- => [" << char_d3proc << "]" << std::endl;
 487    std::string str_d3proc(char_d3proc);
 488    canOpen = br_d3proc.LoadFile(str_d3proc);
 489
 490    if (!canOpen)
 491    {
 492       std::cout << "Hopeless! no 'd3proc' found" << std::endl;
 493       throw ( BrukerHopelessException ("Hopeless! no 'd3proc' found"));
 494       //exit(0);  /// \TODO throw an exception !
 495    }
 496
 497    canOpen = br_d3proc.FillMap();
 498    if (!canOpen)
 499    {
 500       std::cout << "Hopeless! FillMap failed on 'd3proc'" << std::endl;
 501       throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'd3proc'"));
 502       //exit(0);  /// \TODO throw an exception !
 503    }
 504
 505    //-------------- end try d3proc;
 506
 507
 508  // -------------------try reco
 509
 510    char char_reco[(unsigned int) PATH_MAX+2];
 511
 512    sprintf(char_reco,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
 513     //str_d3proc = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
 514     //             GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 515     //             "d3proc";
 516    if (verbose)
 517       std::cout << "reco --- => [" << char_reco << "]" << std::endl;
 518    std::string str_reco(char_reco);
 519    canOpen = br_reco.LoadFile(str_reco);
 520
 521    if (!canOpen) // we try in directory ../1
 522    {
 523       if (verbose)
 524          std::cout << "[" << str_reco << "] not found " << std::endl;
 525       std::string lastDirName = GDCM_NAME_SPACE::Util::GetPath(level3Directory);
 526       //lastDirName = GDCM_NAME_SPACE::Util::GetPath(lastDirName);
 527       sprintf(char_reco,"%s%c1%c%s", lastDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
 528       str_reco=char_reco;
 529       canOpen = br_reco.LoadFile(str_reco);
 530       if (!canOpen)
 531       {
 532          std::cout << "Hopeless! cannot find 'reco' in [" << str_reco << "]"  << std::endl;
 533          throw ( BrukerHopelessException ("Hopeless! cannot find 'reco'"));
 534          //exit(0);  /// \TODO throw an exception !
 535       }
 536    }
 537
 538    canOpen = br_reco.FillMap();
 539    if (!canOpen)
 540    {
 541       std::cout << "Hopeless! FillMap failed on [" << str_reco << "]" << std::endl;
 542       throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'reco'"));
 543       //exit(0);  /// \TODO throw an exception !
 544    }
 545    //std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
 546    // br_reco.PrintSelf();
 547    // std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
 548    // -------------------end try reco
 549
 550
 551    BrukerFieldData bX = br_d3proc.GetFieldData("IM_SIX");
 552    int NX = bX.GetIntValue()[0];
 553
 554    if (verbose)
 555       std::cout << "IM_SIX " << NX << std::endl;
 556    BrukerFieldData bY=br_d3proc.GetFieldData("IM_SIY");
 557    int NY = bY.GetIntValue()[0];
 558
 559    if (verbose)
 560          std::cout << "IM_SIY " << NY << std::endl;
 561    /// \todo : check if there are actually 3 dimensions or only 2
 562
 563    BrukerFieldData bZ= br_d3proc.GetFieldData("IM_SIZ");
 564    int nbFrames = bZ.GetIntValue()[0];
 565    if (verbose)
 566          std::cout << "IM_SIZ " << nbFrames << std::endl;
 567
 568         // WARNING DATTYPE is, either in {ip_short, ip_int, ip_char, ...}, or in {1, 2, 3, ...}
 569
 570    BrukerFieldData bDPT = br_d3proc.GetFieldData("DATTYPE");
 571
 572    std::string mhdDataPixelType;
 573    int pixelSize;
 574    getImhDataType(bDPT, mhdDataPixelType, pixelSize);
 575
 576    BrukerFieldData fov = br_method.GetFieldData("PVM_Fov");
 577    double fovX = fov.GetDoubleValue()[0];
 578    double fovY = fov.GetDoubleValue()[1];
 579    if (verbose)
 580       std::cout << "FOV (ds method) " << fovX << " " << fovY << std::endl;
 581
 582    BrukerFieldData spatResol = br_method.GetFieldData("PVM_SpatResol");
 583    double spatResolX = spatResol.GetDoubleValue()[0];
 584    double spatResolY = spatResol.GetDoubleValue()[1];
 585    if (verbose)
 586       std::cout << "SpatResol (ds method) " << spatResolX << " " << spatResolY << std::endl;
 587
 588
 589    /// \TODO probabely a more sophisticated accessor will be necessary :
 590    ///  (cf : non contiguous slices, overlapping, slice thickness, space between slices, etc)
 591    BrukerFieldData bsliceDistance = br_method.GetFieldData("PVM_SPackArrSliceDistance");
 592    double sliceDistance = bsliceDistance.GetDoubleValue()[0];
 593
 594    if (mhd)
 595    {
 596       sprintf(currentOutputMhdDirName, "%s%c%s", currentOutputDirName.c_str(),
 597                                GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "MhdFiles");
 598       res = CreateDirectory( currentOutputMhdDirName );
 599       if (!res) {
 600          std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 601          throw ( BrukerHopelessException ("Hopeless!FillMap failed on 'reco'"));
 602          //exit (0);
 603       }
 604
 605       if (verbose)
 606          std::cout << "Directory creation [" <<  currentOutputDirName << "]" << std::endl;
 607    }  // end if mhd
 608
 609    if (verbose)
 610          std::cout << "nbFrames " << nbFrames << std::endl;
 611    if (verbose)
 612          std::cout << "nbSlices " << nbSlices << std::endl;
 613    int k;
 614    int nbInstants = nbFrames/nbSlices;
 615    if (verbose)
 616          std::cout << "nbInstants (deduced )" << nbInstants << std::endl;
 617    int instantNb;
 618    int sliceNb;
 619    FILE *fp;  // for MHD files
 620
 621    sprintf( original2dseqName, "%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "2dseq");
 622
 623 /**/
 624   // \TODO : tenir compte du bazar precedent
 625
 626     // load 2dseq in memory
 627
 628    fp = fopen(original2dseqName, "rb");
 629    if (!fp)
 630    {
 631       // try 2dseq_Angio2D ?!?
 632
 633       sprintf( original2dseqName_XXX, "%s%s", original2dseqName, "_Angio2D");
 634       fp = fopen(original2dseqName_XXX, "rb");
 635       if (!fp)
 636       {
 637          std::cout << "Cannot open [" << original2dseqName << "] nor [" <<  original2dseqName_XXX << "] for reading" << std::endl;
 638          fclose(fp);
 639          throw ( BrukerHopelessException ("Hopeless! Cannot open '2dseq'"));
 640          //exit (0);
 641       }
 642    }
 643
 644    unsigned char *buffer_2dseq = new unsigned char[NX*NY*pixelSize*nbSlices*nbInstants];
 645    ///\ TODO : find a safer way to be sure to read everything!
 646    size_t lgr = fread(buffer_2dseq, 1, NX*NY*pixelSize*nbSlices*nbInstants, fp);
 647
 648    // This one will be important!
 649    // ---------------------------
 650    try {
 651       imageSet = CreateImageSet ( );
 652    }
 653    catch (BrukerInitException& e)
 654    {
 655       if (verbose)
 656          std::cout <<  "an Init Exception was thrown in CreateImageSet ( ); " << e.what()
 657                    <<  "catched in DealWithNiveau3" << std::endl;
 658       //return;
 659       throw (e);
 660    }
 661
 662    serieNumber++;
 663    strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 664    if (nbInstants==1) // creer un seul fichier .mhd  pour toutes les Slices! (images natives)
 665    {
 666        if (verbose)
 667           std::cout << "Single instant : do not split" << std::endl;
 668        if (mhd)
 669        {
 670              sprintf(outputMhdFileName, "%s%cMhdData_All_the_Slices.mhd", currentOutputMhdDirName,
 671                                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 672              fp=fopen(outputMhdFileName, "w");
 673              if (!fp)
 674              {
 675                 std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 676                 throw ( BrukerHopelessException ("Hopeless! Cannot open  mhd file for writting"));
 677                 //exit(0);
 678              }
 679              else
 680              {
 681                fprintf(fp, "ObjectType = Image\n");
 682                fprintf(fp, "NDims = 3\n" );
 683                fprintf(fp, "BinaryData = True \n" );
 684                fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 685                fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices );
 686                fprintf(fp, "HeaderSize = %d\n", 0);
 687                //fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
 688                fprintf(fp, "ElementSpacing = %lf %lf %lf\n", spatResolX, spatResolY, sliceDistance );
 689                fprintf(fp, "Position = 0 0 %d\n", 0 );
 690                fprintf(fp, "Offset = 0 0 0\n" );
 691                fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 692                fprintf(fp, "ElementNumberOfChannels = 1\n" );
 693                fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
 694                fprintf(fp, "ElementDataFile = %s\n", "../2dseq_All_the_Slices" );
 695                fclose(fp);
 696              }
 697              sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices",
 698                                        currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 699              fp=fopen(output2dseqSliceFileName, "wb");
 700              if (!fp)
 701              {
 702                 std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 703                 throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseq file for writting"));
 704              }
 705              else
 706              {
 707                 fwrite( buffer_2dseq, NX*NY*pixelSize, nbSlices, fp);
 708              }
 709              fclose(fp);
 710              serieNumber ++;
 711              strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 712        }  // end if mhd
 713        if (dicom)
 714        {
 715              sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices.dcm",
 716                                        currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 717
 718             /* ----------- Write Dicom Image  ---------------*/
 719              MakeDicomImage(buffer_2dseq,
 720                NX,
 721                NY,
 722                nbFrames,
 723                pixelSize,
 724                //fovX/NY, fovY/NY, sliceDistance,
 725                spatResolX, spatResolY, sliceDistance,
 726                output2dseqSliceFileName,
 727                subject_name,
 728                day,
 729                strStudyUID,
 730                strSerieUID,
 731                strStudyDescr,
 732                strSerieDescr,
 733                strStudyTimeDate,
 734                0,// index frame number
 735                GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
 736              );
 737        }  // end if dicom
 738    }  // end if nbInstants = 1
 739
 740    else  // more than ONE instant
 741    {
 742           // Interleaved !
 743           // it's (slice1,slide2, ...)t1 ; (slice1,slide2, ...)t2 ; ...
 744          unsigned char *pixelsForCurrentSlice = new unsigned char[NX*NY*pixelSize*nbInstants];
 745
 746          k = 0;
 747          for (sliceNb=0; sliceNb<nbSlices; sliceNb++)
 748          {
 749             if (mhd)
 750             {
 751                sprintf(outputMhdFileName, "%s%cMhdData_%03d.mhd", currentOutputMhdDirName,
 752                                         GDCM_NAME_SPACE::GDCM_FILESEPARATOR, k  );
 753                if (verbose)
 754                   std::cout << "--- Output MHD file [" << outputMhdFileName << "]" << std::endl;
 755                fp=fopen(outputMhdFileName, "w");
 756                if (!fp)
 757                {
 758                    std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 759                    throw ( BrukerHopelessException ("Hopeless! Cannot open  mhd file for writting"));
 760                    //exit(0);
 761                }
 762                else
 763                {
 764             /* ----------- Write MHD Image  ---------------*/
 765                 //if (verbose)
 766                 //   std::cout << "Open sucessfully[" << outputMhdFileName << "] for writting" << std::endl;
 767                    fprintf(fp, "ObjectType = Image\n");
 768                    fprintf(fp, "NDims = 3\n" );
 769                    fprintf(fp, "BinaryData = True \n" );
 770                    fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 771                    fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbInstants);
 772                    fprintf(fp, "HeaderSize = %d\n", 0);
 773                    //fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, 1.0 ); //
 774                    fprintf(fp, "ElementSpacing = %lf %lf %lf\n",spatResolX, spatResolY, 1.0 ); //slice distance : no meaning for temporal serie
 775                    fprintf(fp, "Position = 0 0 %d\n", sliceNb );
 776                    fprintf(fp, "Offset = 0 0 0\n" );
 777                    fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 778                    fprintf(fp, "ElementNumberOfChannels = 1\n" );
 779                    fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
 780                    fprintf(fp, "ElementDataFile = ..%c2dseq_Slice_%d\n", GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb );
 781                    fclose(fp);
 782                } // end write MHD
 783
 784                sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d",
 785                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,sliceNb);
 786                fp=fopen(output2dseqSliceFileName, "wb");
 787                if (!fp)
 788                {
 789                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 790                    throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseqSliceFile file for writting"));
 791                    //exit (0);
 792                }
 793                int frameSize = NX*NY*pixelSize;
 794                for (instantNb=0; instantNb<nbInstants; instantNb++)
 795                {
 796 // std::cout << "------------SN " << sliceNb << " IN " << instantNb <<  " T " << nbSlices*instantNb + sliceNb << std::endl;
 797                     fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
 798                             frameSize,
 799                             1, fp);
 800                }
 801                fclose(fp);
 802 // std::cout << "end writting[" << output2dseqSliceFileName << "]" << std::endl;
 803             }  // end if mhd
 804
 805             if (dicom)
 806             {
 807                // desperate try !
 808              /*
 809                sprintf(output2dseqSliceFileName, "%sdummy_buffer",
 810                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 811                fp=fopen(output2dseqSliceFileName, "wb");
 812                if (!fp)
 813                {
 814                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 815                    exit (0);
 816                }
 817                int frameSize = NX*NY*pixelSize;
 818                for (instantNb=0; instantNb<nbInstants; instantNb++)
 819                {
 820 // std::cout << "------------SN " << sliceNb << " IN " << instantNb <<  " T " << nbSlices*instantNb + sliceNb << std::endl;
 821                     fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
 822                             frameSize,
 823                             1, fp);
 824                }
 825                fclose(fp);
 826
 827                fp=fopen(output2dseqSliceFileName, "rb");
 828                if (!fp)
 829                {
 830                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for reading" << std::endl;
 831                    exit (0);
 832                }
 833                fread( pixelsForCurrentSlice,
 834                             frameSize*nbInstants,
 835                             1, fp);
 836                fclose(fp);
 837               // end of desperate try !
 838               */
 839
 840                /* ----------- Write Dicom Image  ---------------*/
 841
 842                int frameSize = NX*NY*pixelSize;
 843                for (instantNb=0; instantNb<nbInstants; instantNb++)
 844                {
 845                   memcpy(pixelsForCurrentSlice + frameSize*instantNb, buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize, frameSize);
 846                }
 847
 848                int indOfFirsImageWithinImageSet =  nbSlices*instantNb;
 849                sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d.dcm",
 850                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb);
 851
 852                MakeDicomImage(
 853                   pixelsForCurrentSlice,
 854                   NX,
 855                   NY,
 856                   nbInstants,
 857                   pixelSize,
 858                   spatResolX, spatResolY, sliceDistance,
 859                   //fovX/NY, fovY/NY, sliceDistance,
 860                   output2dseqSliceFileName,
 861                   subject_name,
 862                   day,
 863                   strStudyUID,
 864                   strSerieUID,
 865                   strStudyDescr,
 866                   strSerieDescr,
 867                   strStudyTimeDate,
 868                   sliceNb*nbInstants,
 869                   GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
 870                );
 871                if (verbose)
 872                   std::cout << "--- Output DCM file [" << output2dseqSliceFileName << "]" << std::endl;
 873
 874            } // en if dicom
 875
 876         k++;
 877         }
 878         delete [] pixelsForCurrentSlice;
 879      }  // end nbInstants == 1
 880    delete [] buffer_2dseq;
 881 /**/
 882
 883
 884    // -----------------------------------------------------
 885    //  deal with MatLab-generated Carto file.
 886    // -----------------------------------------------------
 887
 888    dealWithCarto(fileNames,  NX,  NY,  nbSlices, /*fovX, fovY,*/ spatResolX, spatResolY, sliceDistance,
 889                    copyFile, currentOutputDirName, outputMhdFileName, output2dseqCartoName);
 890 }
 891
 892
 893 // ===========================================================================================
 894
 895 void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX, int NY, int nbSlices,
 896                                  /*double fovX, double fovY, */
 897                                  double spatResolX, double spatResolY, double sliceDistance,
 898                                  char *copyFile, std::string &currentOutputDirName,
 899                                  char *outputMhdFileName, char *output2dseqCartoName)
 900 {
 901    // -----------------------------------------------------
 902    //  deal with MatLab-generated Carto file.
 903    // -----------------------------------------------------
 904
 905    char *code[] = { "ADC", "adc", "TTP", "ttp", "PEAK", "peak", "" };  // add more carto file name identifiers if necessary; end with ""
 906    char *separator[] =  { "_", ".", "-", "" }; //  add more, if necessary, to ckeck for 2dseq.ADC, 2dseq_ADC, 2dseq-ADC, etc; end with ""
 907    int icode;
 908    int iseparator;
 909    GDCM_NAME_SPACE::DirListType::iterator it;
 910    char file_name_ident[500];
 911    FILE *fp;
 912
 913    // Iterate to ALL the objets(files/directories) found in the input directory
 914    for (it = fileNames.begin();
 915         it != fileNames.end();
 916       ++it)
 917    {
 918       if ( boost::filesystem::is_regular(*it) )
 919       //if ( ! boost::filesystem::is_directory(*it) )
 920       {
 921          if (verbose)
 922             std::cout << "--- [" << *it << "] is a file..." << std::endl;
 923
 924          icode      = 0;
 925          while (code[icode][0] != 0)
 926          {
 927          iseparator = 0;
 928          while (separator[iseparator][0] != 0)
 929          {
 930             sprintf(file_name_ident, "2dseq%s%s",separator[iseparator],code[icode]); // e.g  "2dseq_ADC"
 931             //if (verbose)
 932             //   std::cout << "check name ["<<(*it) << "] for string [" << file_name_ident << "]" << std::endl;
 933             std::string::size_type loc = (*it).rfind(file_name_ident);
 934
 935             if ( loc != std::string::npos )
 936             {
 937
 938        ///\ TODO : find a safer way to be sure to read everything!
 939               unsigned char *buffer_carto = new unsigned char[NX*NY*sizeof(double)*nbSlices];
 940               fp = fopen ( (*it).c_str(), "rb");
 941               if (!fp){
 942                  std::cout << "Cannot open [" << *it << "] for reading" << std::endl;
 943                  throw ( BrukerHopelessException ("Level 1 Unable to open 'carto' file "));
 944                }
 945                fread(buffer_carto, NX*NY*sizeof(double), nbSlices, fp);
 946
 947                     // ?!?  sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() ,
 948                std::cout << "Deal with Carto file :[" <<*it << "], computed length : "
 949                          << NX*NY*sizeof(double)*nbSlices << std::endl;
 950                std::string lastFileName = GDCM_NAME_SPACE::Util::GetName((*it).c_str());
 951                if (mhd)
 952                {
 953                   // Copy the data file in the new directory
 954                   sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() ,
 955                             currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str());
 956                   system(copyFile);
 957                   sprintf(outputMhdFileName, "%s%c%s%s",
 958                                          currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".mhd" );
 959                   if (verbose)
 960                     std::cout << "--- Output Carto MHD file [" << outputMhdFileName << "]" << std::endl;
 961
 962                   FILE *fp;
 963                   fp=fopen(outputMhdFileName, "w");
 964                   if (!fp)
 965                   {
 966                      std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 967                   }
 968                   else
 969                   {
 970                      fprintf(fp, "ObjectType = Image\n");
 971                      fprintf(fp, "NDims = 3\n" );
 972                      fprintf(fp, "BinaryData = True \n" );
 973                      fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 974                      fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices);
 975                      fprintf(fp, "HeaderSize = %d\n", 0 );
 976                      fprintf(fp, "ElementSpacing = %lf %lf %lf\n",spatResolX, spatResolY, sliceDistance );
 977                      fprintf(fp, "Position = 0 0 0\n" );
 978                      fprintf(fp, "Offset = 0 0 0\n" );
 979                      fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 980                      fprintf(fp, "ElementNumberOfChannels = 1\n" );
 981                      fprintf(fp, "ElementType = %s\n", "MET_DOUBLE" );
 982                      fprintf(fp, "ElementDataFile = %s\n", lastFileName.c_str() );
 983
 984                      fclose(fp);
 985                   }
 986                   if (verbose)
 987                      std::cout << "--- end write Carto MHD file [" << outputMhdFileName << "]" << std::endl;
 988                }  // end if mhd
 989
 990             // ----------- Write Dicom Image  ---------------
 991
 992                if (dicom)
 993                {
 994                   sprintf(output2dseqCartoName, "%s%c%s%s",
 995                                        currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".dcm" );
 996                   if (verbose)
 997                      std::cout << "--- end create name output2dseqCartoName file [" << output2dseqCartoName << "]" << std::endl;
 998
 999                   strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID(); //New SerieUID for each carto.
1000                   std::string strNewSerieDescr(strSerieDescr+ "_" +GDCM_NAME_SPACE::Util::GetName((*it).c_str()));
1001                   MakeDicomImage(buffer_carto,
1002                      NX,
1003                      NY,
1004                      nbSlices,
1005                      8, // pixelSize
1006                      //fovX/NY, fovY/NY, sliceDistance,
1007                      spatResolX, spatResolY, sliceDistance,
1008                      output2dseqCartoName,
1009                      subject_name,
1010                      day,
1011                      strStudyUID,
1012                      strSerieUID,
1013                      strStudyDescr,
1014                      strNewSerieDescr,
1015                      strStudyTimeDate,
1016                      0,
1017                      GDCM_NAME_SPACE::CREATED_IMAGE
1018                   );
1019                }  // end if dicom
1020
1021                delete [] buffer_carto;
1022                if (verbose)
1023                   std::cout << "--- End writing Carto DICOM file [" << output2dseqCartoName << "]" << std::endl;
1024                break; // don't check for more ident on same file name!
1025
1026             }  // end deal with _ADC, -adc, etc
1027           iseparator ++;
1028           }  // end iterate speparators
1029           icode++;
1030           } // end iterate code
1031       } // end boost::filesystem::is_regular(*it)
1032    } // end iterate on all objects (files, dir, etc)
1033 } // end method
1034
1035
1036 // ==========================================================================================================
1037
1038 bool Bruker2Dicom::CreateDirectory(std::string OutputDirName)
1039 {
1040    std::string systemCommand;
1041
1042    if (verbose)
1043       std::cout << "Check for output directory :[" << OutputDirName << "]."
1044                 <<std::endl;
1045    if ( ! boost::filesystem::is_directory(OutputDirName) )    // dirout not found
1046    {
1047       std::string strDirNameout(OutputDirName);        // to please gcc 4
1048       systemCommand = "mkdir " + strDirNameout;        // create it!
1049       if (verbose)
1050          std::cout << systemCommand << std::endl;
1051       system (systemCommand.c_str());
1052       if ( ! boost::filesystem::is_directory(OutputDirName) ) // be sure it worked
1053       {
1054          if (verbose)
1055             std::cout << "KO : not a dir : [" << OutputDirName << "] (creation failure ?)" << std::endl;
1056          //return 0;
1057          throw ( BrukerHopelessException ("Level 1 output directory creation failure "));
1058       }
1059       else
1060       {
1061          if (verbose)
1062            std::cout << "Directory [" << OutputDirName << "] created." << std::endl;
1063       }
1064    }
1065    else
1066    {
1067        if (verbose)
1068             std::cout << "Output Directory [" << OutputDirName << "] already exists; Used as is." << std::endl;
1069    }
1070
1071    return 1;
1072
1073 }
1074
1075
1076 // ===========================================================================================
1077
1078 /// \TODO move cleanString to 'crea' ?
1079
1080 void Bruker2Dicom::cleanString(std::string &s)
1081 {
1082    int l = s.size();
1083    if (s[l-1] == 0x0A || s[l-1] == 0x0D ) // CR or NL
1084    {
1085       l--;
1086       s = s.substr(0, l);
1087    }
1088    if (s[l-1] == ' ' ) // blank space
1089    {
1090       l--;
1091       s = s.substr(0, l);
1092    }
1093
1094    if (s[0] == '<')
1095       s= s.substr(1,l-2);
1096    std::string repChar("_");
1097    GDCM_NAME_SPACE::Util::ReplaceSpecChar(s, repChar);
1098 }
1099
1100
1101
1102 // ===========================================================================================
1103
1104
1105 void Bruker2Dicom::getImhDataType(BrukerFieldData &bDPT, std::string &mhdDataPixelType, int &pixelSize)
1106 {
1107    if(bDPT.GetDataType() == "string")
1108    {
1109          std::string brukerDataPixelType = bDPT.GetStringValue()[0];
1110          if (verbose)
1111             std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
1112          //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
1113
1114          if (brukerDataPixelType ==  "ip_short") {
1115             mhdDataPixelType = "MET_USHORT";
1116             pixelSize = 2;
1117          }
1118          if (brukerDataPixelType ==  "ip_int") {
1119             mhdDataPixelType = "MET_UINT";
1120             pixelSize = 4;
1121          }
1122          if (brukerDataPixelType ==  "ip_char") {
1123              mhdDataPixelType = "MET_UCHAR";
1124              pixelSize = 1;
1125          }
1126                   /// \TODO : finish the list
1127     /*
1128     case 0 : fp << "ElementType = MET_CHAR" << std::endl;
1129       break;
1130     case 1 : fp << "ElementType = MET_UCHAR" << std::endl;
1131       break;
1132     case 2 : fp << "ElementType = MET_SHORT" << std::endl;
1133       break;
1134     case 3 : fp << "ElementType = MET_USHORT" << std::endl;
1135       break;
1136     case 4 : fp << "ElementType = MET_INT" << std::endl;
1137       break;
1138     case 5 : fp << "ElementType = MET_UINT" << std::endl;
1139       break;
1140     case 6 : fp << "ElementType = MET_FLOAT" << std::endl;
1141       break;
1142     case 7 : fp << "ElementType = MET_DOUBLE" << std::endl;
1143     */
1144     }
1145     else
1146     {
1147          int brukerDataPixelType = bDPT.GetIntValue()[0];
1148          if (verbose)
1149             std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
1150          //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
1151
1152 // Cross your fingers !!!
1153
1154 // pb : found values : 2, 3, 5
1155
1156          if (brukerDataPixelType ==  2) {
1157             mhdDataPixelType = "MET_USHORT";
1158             pixelSize = 2;
1159          }
1160          if (brukerDataPixelType ==  3) {
1161             mhdDataPixelType = "MET_USHORT";
1162             pixelSize = 2;
1163          }
1164          if (brukerDataPixelType ==  1) {
1165             mhdDataPixelType = "MET_UCHAR";
1166             pixelSize = 1;
1167          }
1168     }
1169 }
1170
1171 // ===========================================================================================
1172
1173 std::vector<BrukerImage> Bruker2Dicom::CreateImageSet ( )
1174 {
1175          std::vector<BrukerImage> imageSet;
1176          br_acqp.SetLoopStructure();
1177          std::vector<int> tempVect                      = br_acqp.GetLoopStructure() ;
1178          std::map<std::string, BrukerFieldData> map     = br_acqp.GetBrukerHeaderMap();
1179
1180          bool result                                    = br_acqp.ObjectVaryingProperties.init(map,tempVect);
1181
1182          if (result == false)
1183          {
1184             throw ( BrukerInitException  ("ObjectVaryingProperties.init() failure in Bruker2Dicom::CreateImageSet()") );
1185          }
1186
1187          br_acqp.SetImageLoopStructure();
1188          br_acqp.SetBrukerImageList();
1189          std::vector<std::vector<int> > brukerImageList = br_acqp.GetBrukerImageList();
1190
1191          BrukerImage image(br_acqp,br_reco);
1192          image.Init(br_acqp,br_reco,1);
1193
1194          for(int i=0;i<brukerImageList.size();i++)
1195          {
1196             image.Init(br_acqp,br_reco,i);
1197             imageSet.push_back(image);
1198          }
1199
1200  // Just for checking
1201  /*
1202
1203          std::vector<std::vector <double> > imageOrientation;
1204          std::vector <double> imagePosition;
1205          for(int i=0;i<brukerImageList.size();i++)
1206          {
1207            // fread(buffer_2dseq, NX*NY*pixelSize*nbSlices*nbInstants, 1, fp);
1208
1209            imagePosition = imageSet[i].getTranslationVectorRPS2XYZ();
1210            std::cout << "Position " << imagePosition[0] << " "
1211                      << imagePosition[1] << " "  << imagePosition[2] ;
1212            imageOrientation =  imageSet[i].getRotationMatrixRPS2XYZ();
1213            std::cout << "\t  Orientation " ;
1214            for(int i1=0; i1<3;i1++)for(int i2=0; i2<3;i2++)
1215               std::cout << imageOrientation[i1][i2] << " ";CreateImageSet
1216
1217            //std::cout << "\t  Abs Time " << imageSet[i].getAbsoluteTimePosition();
1218            std::cout << "\t  Relat Time " << imageSet[i].getRelativeTimePosition();
1219
1220            std::cout << "\t [";
1221            for (int i3=0; i3<imageSet[i].getLoopStamp().size();i3++)
1222               std::cout << " " << imageSet[i].getLoopStamp()[i3];
1223            std::cout << "]" << std::endl;
1224          }
1225 */
1226    return imageSet;
1227 }
1228
1229 // ===========================================================================================
1230
1231 void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels,
1232               int X,
1233               int Y,
1234               int nbFrames,
1235               int pixelSize,
1236               double spacingX, double spacingY, double sliceDistance,
1237               std::string dcmImageName,
1238               const std::string &patientName,
1239               const char *day,
1240               std::string &studyUID,
1241               std::string &serieUID,
1242               std::string &studyDescr,
1243               std::string &serieDescr,
1244               std::string &strStudyTimeDate,
1245               int imgNum,
1246               GDCM_NAME_SPACE::ImageContentType contentType
1247       )
1248 {
1249    std::ostringstream str;
1250
1251    GDCM_NAME_SPACE::File *file;
1252    file = GDCM_NAME_SPACE::File::New();
1253
1254   // Set the image size
1255    str.str("");
1256    str << X;
1257    file->InsertEntryString(str.str(),0x0028,0x0011,"US"); // Columns
1258    str.str("");
1259    str << Y;
1260    file->InsertEntryString(str.str(),0x0028,0x0010,"US"); // Rows
1261
1262    if (nbFrames != 1)
1263    {
1264       str.str("");
1265       str << nbFrames;
1266       file->InsertEntryString(str.str(),0x0028,0x0008,"IS"); // Number of Frames
1267    }
1268
1269   // Set the pixel type
1270   //      //8, 16, 32, 64 (for double ?)
1271    str.str("");
1272    str << pixelSize*8;
1273    file->InsertEntryString(str.str(),0x0028,0x0100,"US"); // Bits Allocated
1274
1275    file->InsertEntryString(str.str(),0x0028,0x0101,"US"); // Bits Stored
1276
1277    str.str("");
1278    str << pixelSize*8-1;
1279    file->InsertEntryString(str.str(),0x0028,0x0102,"US"); // High Bit
1280
1281   // Set the pixel representation // 0/1 , 0=unsigned
1282    file->InsertEntryString("1",0x0028,0x0103, "US"); // Pixel Representation
1283
1284   // Set the samples per pixel // 1:Grey level, 3:RGB
1285    file->InsertEntryString("1",0x0028,0x0002, "US"); // Samples per Pixel
1286
1287 //  0028 0030 DS 2 Pixel Spacing
1288    str.str("");
1289    str << spacingX << "\\" << spacingY;
1290    file->InsertEntryString(str.str(),0x0028,0x0030, "DS"); // Pixel Spacing
1291
1292  //   0018 0050 DS 1 Slice Thickness
1293    str.str("");
1294    str << sliceDistance;
1295    file->InsertEntryString(str.str(),0x0018,0x0050, "DS");
1296
1297 //    0020 0011 IS 1 Series Number
1298    str.str("");
1299    str << serieNumber;
1300    file->InsertEntryString(str.str(),0x0020,0x0011, "IS");
1301
1302 //    0020|0013 [IS]  [Instance Number]
1303    instanceNumber++;
1304    str.str("");
1305    str << instanceNumber;
1306    file->InsertEntryString(str.str(),0x0020,0x0013, "IS");
1307
1308
1309   // 1.2.840.10008.5.1.4.1.1.4.1 : Enhanced MR Image Storage
1310  //  file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0002, 0x0002, "UI");  // [Media Storage SOP Class UID]
1311   // file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0008, 0x0016, "UI");  // [SOP Class UID]
1312
1313
1314 // OK : MR is NOT multiframe, but I want just a quick an dirty solution
1315
1316 // 1.2.840.10008.5.1.4.1.1.4         MR Image Storage
1317    file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0002, 0x0002, "UI");  // [Media Storage SOP Class UID]
1318    file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0008, 0x0016, "UI");  // [SOP Class UID]
1319
1320   // if (strlen(patientName) != 0)
1321    file->InsertEntryString(patientName.c_str(),0x0010,0x0010, "PN"); // Patient's Name
1322
1323    file->InsertEntryString(studyUID, 0x0020, 0x000d, "UI");
1324    file->InsertEntryString(serieUID, 0x0020, 0x000e, "UI");
1325
1326 //  0008 0020 DA 1 Study Date
1327 //  0008 0030 TM 1 Study Time
1328
1329 /// \TODO split into 2 strings!
1330    file->InsertEntryString(strStudyTimeDate.substr(10,11).c_str(),0x0008,0x0020, "DA");
1331    file->InsertEntryString(strStudyTimeDate.substr(1,8).c_str(),  0x0008,0x0030, "TM");
1332
1333    file->InsertEntryString(studyDescr, 0x0008,0x1030, "LO");  // Study Description
1334    file->InsertEntryString(serieDescr, 0x0008,0x103e, "LO");  // Series Description
1335
1336 //0008|0060 [CS] [Modality]
1337    file->InsertEntryString("MR",0x0008,0x0060, "CS");
1338
1339 // 0020 0037 DS 6 Image Orientation (Patient)
1340    char charImageOrientation[256];
1341
1342 /*
1343 std::cout << "charImageOrientation  " <<
1344                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0] << " " <<
1345                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1] << " " <<
1346                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2] << " " <<
1347                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0] << " " <<
1348                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1] << " " <<
1349                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] << std::endl ;
1350 */
1351    sprintf(charImageOrientation,"%f\\%f\\%f \\ %f\\%f\\%f",
1352                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0],
1353                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1],
1354                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2],
1355                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0],
1356                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1],
1357                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] ) ;
1358
1359    file->InsertEntryString(charImageOrientation,0x0020,0x0037, "DS");
1360
1361
1362 // 0020 0032 DS 3 Image Position (Patient)
1363
1364    char charImagePosition[256];
1365    sprintf(charImagePosition,"%f\\%f\\%f",
1366                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[0],
1367                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[1],
1368                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[2]);
1369
1370    file->InsertEntryString(charImagePosition,0x0020,0x0032, "DS");  //0020 0032 DS 3 Image Position (Patient)
1371
1372
1373
1374 // 0020 0x1041 DS 1 Slice Location
1375 //        sprintf(charImagePosition,"%f",float(imgNum));
1376 //        file->InsertEntryString(charImagePosition,0x0020,0x1041, "DS");
1377 /*
1378   // Set Rescale Intercept
1379         str.str("");
1380         str << div;
1381         file->InsertEntryString(str.str(),0x0028,0x1052,"DS");
1382
1383   // Set Rescale Slope
1384         str.str("");
1385         str << mini;
1386         file->InsertEntryString(str.str(),0x0028,0x1053,"DS");
1387 */
1388
1389    GDCM_NAME_SPACE::FileHelper *fileH;
1390    fileH = GDCM_NAME_SPACE::FileHelper::New(file);
1391    fileH->SetContentType(contentType);
1392
1393    // cast is just to avoid warnings (*no* conversion is performed)
1394    //fileH->SetImageData((uint8_t *)img,int(maxX*maxY)*sizeof(uint16_t)); // troubles when maxX, mayY are *actually* float!
1395
1396 //std::cout << "--------------------------------  X*Y*nbFrames*pixelSize " << X << " " << Y << " " << nbFrames << " " << pixelSize << std::endl;
1397
1398    fileH->SetImageData((uint8_t *)tabPixels, X*Y*nbFrames*pixelSize);
1399    fileH->SetWriteModeToRaw();
1400    fileH->SetWriteTypeToDcmExplVR();
1401    if( !fileH->Write(dcmImageName)) {
1402       std::cout << "Failed for [" << dcmImageName << "]\n"
1403                 << "           File is unwrittable" << std::endl;
1404       file->Delete();
1405       fileH->Delete();
1406       throw ( BrukerHopelessException ("Level 1 Unable to write Dicom file "));
1407    }
1408    //if (verbose)
1409    //   file->Print();
1410
1411    file->Delete();
1412    fileH->Delete();
1413 }
1414
1415