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 bool Bruker2Dicom::Execute()
  11 {
  12    // ----- Check input directory name -----
  13
  14    bool bigEndian = GDCM_NAME_SPACE::Util::IsCurrentProcessorBigEndian();
  15
  16    //if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(InputDirName) )
  17    if ( ! boost::filesystem::is_directory(InputDirName) )
  18    {
  19       std::cout << "KO : [" << InputDirName << "] is not a Directory." << std::endl;
  20       return 0;
  21    }
  22    else
  23    {
  24       if (verbose)
  25          std::cout << "OK : [" << InputDirName << "] is a Directory." << std::endl;
  26    }
  27
  28    // ----- Check output directory name -----
  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   // BrukerDataSet br_subject;
  64    std::string subject;
  65    subject = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
  66              GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
  67              "subject";
  68    if (verbose)
  69         std::cout << " Subject : [" <<  subject << "]" << std::endl;
  70
  71    bool subjectFound;
  72    canOpen =br_subject.LoadFile(subject);
  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
  78       std::cout << "Not too much hope! no 'subject' found (Desperate try will be performed -default values- )" << std::endl;
  79       subjectFound = false;
  80    }
  81    else
  82    {
  83       br_subject.FillMap();
  84       subjectFound = true;
  85    }
  86    //br_subject.PrintSelf();
  87
  88   // get info for 'Study Description'
  89
  90     if (subjectFound)
  91     {
  92        BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string");
  93        subject_name = b_name.GetStringValue()[0];
  94        strPatientName = subject_name;
  95        cleanString(subject_name);
  96      }
  97      else
  98         subject_name ="defaultPatName";
  99
 100     // creation directory : 'nom du patient'
 101     std::string tempStringPatDir(OutputDirName);
 102     tempStringPatDir = tempStringPatDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + subject_name;
 103
 104     res=CreateDirectory(tempStringPatDir);
 105     if (!res) {
 106        std::cout << "[" << tempStringPatDir << "] Directory creation failure " << std::endl;
 107        throw ( BrukerHopelessException ("Patient directory creation failure "));
 108     }
 109
 110     std::string subject_entry;
 111     std::string subject_position;
 112     std::string subject_date;
 113     std::string subject_study_name;
 114
 115     if (subjectFound)
 116     {
 117        BrukerFieldData b_entry=br_subject.GetFieldData("SUBJECT_entry");
 118        subject_entry = b_entry.GetStringValue()[0];
 119        //cleanString(subject_entry);
 120        subject_entry = subject_entry.substr(11, subject_entry.size()-11);
 121
 122        BrukerFieldData b_position=br_subject.GetFieldData("SUBJECT_position");
 123        subject_position = b_position.GetStringValue()[0];
 124        //cleanString(subject_position);
 125        subject_position = subject_position.substr(9, subject_position.size()-9);
 126
 127        BrukerFieldData b_date=br_subject.GetFieldData("SUBJECT_date");
 128        subject_date = b_date.GetStringValue()[0];
 129        strStudyTimeDate = subject_date;
 130        cleanString(subject_date);
 131
 132        BrukerFieldData b_study_name=br_subject.GetFieldData("SUBJECT_study_name");
 133        subject_study_name = b_study_name.GetStringValue()[0];
 134        subject_study_name = subject_study_name.substr(1, subject_study_name.size()-2);
 135        cleanString(subject_study_name);
 136    }
 137    else  // Desperate trick when file 'subject' is missing
 138    {
 139       subject_entry      = "HeadFirst";            // Why not?
 140       subject_position   = "Supine";               // Why not?
 141       strStudyTimeDate   = "06_06_06_6_June_1666"; // Why not?
 142       subject_date       = "6_June_1666";          // Why not?
 143       subject_study_name = "defStudyName";         // Why not?
 144    }
 145     // subject_name is already in 'Patient Name'
 146     strStudyDescr = /*subject_name + "." + */ subject_study_name + "." + subject_entry + "." + subject_position + "." + subject_date;
 147
 148     // creation directory : 'nom de la Study'
 149
 150     std::string tempStringStudyDir(OutputDirName);
 151     tempStringStudyDir = tempStringPatDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + strStudyDescr;
 152
 153     res=CreateDirectory(tempStringStudyDir);
 154     if (!res) {
 155        std::cout << "[" << tempStringStudyDir << "] Directory creation failure " << std::endl;
 156        throw ( BrukerHopelessException ("Study directory creation failure "));
 157     }
 158
 159    char outputDirName[(unsigned int) PATH_MAX+2];
 160
 161    strStudyUID    = GDCM_NAME_SPACE::Util::CreateUniqueUID();
 162    serieNumber    = 0;
 163    instanceNumber = 0;
 164
 165    // -----------------------------------------------------
 166    // Iterate to ALL the objets(files/directories) found in the input directory
 167    // (this is level ZERO)
 168    // each Directory (name : 1, 2, 3, ...) will be a Dicom Serie
 169    // -----------------------------------------------------
 170
 171    GDCM_NAME_SPACE::DirListType::iterator it;
 172
 173    for (it = fileNames.begin();
 174          it != fileNames.end();
 175        ++it)
 176    {
 177       if ( boost::filesystem::is_directory(*it) )
 178       {
 179          if (verbose)
 180             std::cout << "[" << *it << "] is a directory" << std::endl;
 181
 182          //BrukerDataSet br_acqp;
 183          std::string strAcqp;
 184          strAcqp = (*it) +
 185                    GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 186                    "acqp";
 187
 188          br_acqp.LoadFile(strAcqp);
 189          br_acqp.FillMap();
 190
 191 //std::cout << "out of br_acqp.FillMap " << std::endl;
 192          std::string acqp_scan_name;
 193          std::string acqp_method;
 194          std::string acqp_protocol_location;
 195
 196          BrukerFieldData b_protocol_location=br_acqp.GetFieldData("ACQ_protocol_location");
 197          acqp_protocol_location = b_protocol_location.GetStringValue()[0];
 198          cleanString(acqp_protocol_location);
 199
 200 //std::cout << "out of br_acqp.FillMap 1" << std::endl;
 201          BrukerFieldData b_scan_name=br_acqp.GetFieldData("ACQ_scan_name");
 202 //std::cout << "out of br_acqp.FillMap 11" << std::endl;
 203          acqp_scan_name = b_scan_name.GetStringValue()[0];
 204 //std::cout << "out of br_acqp.FillMap 12 [" << acqp_scan_name << "]" << std::endl;
 205          cleanString(acqp_scan_name);
 206 //std::cout << "out of br_acqp.FillMap 2" << std::endl;
 207          BrukerFieldData b_method=br_acqp.GetFieldData("ACQ_method");
 208          b_method.PrintSelf();
 209          acqp_method = b_method.GetStringValue()[0];
 210
 211          cleanString(acqp_method);
 212 //std::cout << "out of br_acqp.FillMap 3" << std::endl;
 213          BrukerFieldData b_list_size = br_acqp.GetFieldData("ACQ_O1_list_size");
 214 //std::cout << "out of br_acqp.FillMap 4" << std::endl;
 215          //b_list_size.PrintSelf(); //JP
 216
 217          nbSlices =  b_list_size.GetIntValue()[0];
 218 //std::cout << "out of br_acqp.FillMap 5" << std::endl;
 219          strSerieDescr = GDCM_NAME_SPACE::Util::GetName(*it)
 220                        /*  + "." + acqp_protocol_location */ // always the same (in each acquisition)
 221                          + "." + acqp_scan_name
 222                          + "." + acqp_method.c_str();
 223
 224          sprintf(outputDirName, "%s%c%s", tempStringStudyDir.c_str(),                //OutputDirName.c_str(),
 225                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 226                           strSerieDescr.c_str() );
 227
 228          std::cout << " ================================================================================\n"
 229                    << " === [" << GDCM_NAME_SPACE::Util::GetName(*it) << "] -> [" << strSerieDescr << "]\n"
 230                    << " ================================================================================"
 231                    << std::endl;
 232
 233         if (verbose)
 234            printf ("outputDirName [%s]\n", outputDirName);
 235         try {
 236            DealWithNiveau1(*it, outputDirName);
 237         }
 238         catch (BrukerHopelessException &e)
 239         {
 240          std::cout << "And Exception was thrown in DealWithNiveau1 (" << e.what() << ") " << std::endl;
 241          continue;
 242         }
 243       }
 244    } // end of : for (GDCM_NAME_SPACE::DirListType::iterator it
 245 }
 246
 247 // =====================================================================
 248
 249 void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string currentOutputDirName) {
 250 //
 251 // e.g. : at level 1, in B67d1.Bp1/6
 252 //
 253 // acqp  fid  imnd  pdata  pulseprogram  spnam0  spnam1
 254
 255    bool res = CreateDirectory(currentOutputDirName);
 256
 257    if (!res) {
 258       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 259       throw ( BrukerHopelessException ("Level 1 output directory creation failure "));
 260      // exit (0);
 261    }
 262    GDCM_NAME_SPACE::DirList dirList(level1Directory, false, true); // DON'T get recursively the list of files
 263    GDCM_NAME_SPACE::DirListType fileNames;
 264    fileNames = dirList.GetFilenames();
 265    // -----------------------------------------------------
 266    // Iterate to ALL the objets(files/directories) found in the input directory
 267    // -----------------------------------------------------
 268    GDCM_NAME_SPACE::DirListType::iterator it;
 269
 270    for (it = fileNames.begin();
 271         it != fileNames.end();
 272       ++it)
 273    {
 274       if ( boost::filesystem::is_regular(*it) )
 275       //if ( ! boost::filesystem::is_directory(*it) )
 276       {
 277          if (verbose)
 278             std::cout << "--- [" << *it << "] is a file." << std::endl;
 279       }
 280    }
 281
 282    char outputDirName[(unsigned int) PATH_MAX+2];
 283    //std::string firstName;
 284    bool canOpen;
 285    for (it = fileNames.begin();
 286         it != fileNames.end();
 287       ++it)
 288    {
 289       if ( boost::filesystem::is_directory(*it) )
 290       {
 291          // will be always "pdata" ...
 292          if (verbose)
 293             std::cout << "--- [" << *it << "] is a directory" << std::endl;
 294
 295               /* a recuperer :
 296               if (FileLine.startsWith("##$ACQ_size=")) {
 297               if (FileLine.startsWith("##$NI=")) {
 298               if (FileLine.startsWith("##$NR=")) {
 299               if (FileLine.startsWith("##$ACQ_obj_order=")) {
 300               if (FileLine.startsWith("##$ACQ_word_size=")) {
 301               if (FileLine.startsWith("##$BYTORDA=")) {
 302               if (FileLine.startsWith("##$PULPROG=")) {
 303               */
 304
 305          sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 306                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 307                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str());
 308          //br1.PrintSelf();
 309
 310           std::string strMethod;
 311           //std::string firstName = *(fileNames.begin());
 312
 313           strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin())) +
 314                       GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 315                       "method";
 316             // std::cout << "---strMethod (for method)=> [" << strMethod << "]" << std::endl;
 317           canOpen = br_method.LoadFile(strMethod);
 318           if (!canOpen)
 319           {
 320              strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
 321                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 322                          "imnd";
 323              //std::cout << "---strMethod (for imnd) => [" << strMethod << "]" << std::endl;
 324              canOpen = br_method.LoadFile(strMethod);
 325              if (!canOpen)
 326              {
 327                 std::cout << "Hopeless! neither 'method' nor 'imnd' found in ["
 328                           << level1Directory  << "]; we skip it!" << std::endl;
 329                 continue;
 330                 //throw ( BrukerHopelessException ("Hopeless! neither 'method' nor 'imnd' found "));
 331                 //exit(0);  /// \TODO throw an exception !
 332              }
 333           }
 334           if (verbose)
 335              std::cout << "open => [" << strMethod << "] successfully" << std::endl;
 336           br_method.FillMap();
 337
 338           /* a recuperer :
 339              ##$PVM_Fov (dimension)  // ou plutot RECO_fov !
 340           */
 341   /*
 342           dans method (pour perfusion  seulement?) :
 343           ##$PVM_ObjOrderList=( 8 )
 344           0 2 4 6 1 3 5 7
 345           ##$PVM_NSPacks=2
 346           ##$PVM_SPackArrNSlices=( 2 )
 347           7 1
 348   */
 349          try {
 350             DealWithNiveau2(*it, outputDirName);
 351          }
 352          catch (BrukerHopelessException &e)
 353          {
 354             std::cout << "And Exception was thrown in DealWithNiveau2 (" << e.what() << ") " << std::endl;
 355             continue;
 356          }
 357       }
 358    }
 359 }
 360
 361 // =====================================================================
 362
 363 void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string currentOutputDirName) {
 364
 365 // e.g. : at level 2 in B67d1.Bp1/6/pdata
 366 //
 367 // acqp  fid  imnd  pdata  pulseprogram  spnam0  spnam1
 368 //
 369
 370    bool res = CreateDirectory(currentOutputDirName);
 371
 372    if (!res) {
 373       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 374       throw ( BrukerHopelessException ("Hopeless! Level2 output directory creation failure"));
 375       //exit (0);
 376    }
 377
 378    GDCM_NAME_SPACE::DirList dirList(level2Directory, false, true); // DON'T get recursively the list of files
 379
 380    GDCM_NAME_SPACE::DirListType fileNames;
 381    fileNames = dirList.GetFilenames();
 382
 383    char outputDirName[(unsigned int) PATH_MAX+2];
 384
 385    // -----------------------------------------------------
 386    // Iterate to ALL the objets(files/directories) found in the input directory
 387    // -----------------------------------------------------
 388    GDCM_NAME_SPACE::DirListType::iterator it;
 389    bool canOpen;
 390
 391    if (verbose)
 392    for (it = fileNames.begin();
 393         it != fileNames.end();
 394       ++it)
 395    {
 396       if ( ! boost::filesystem::is_directory(*it) )
 397       {
 398          std::cout << "--- --- [" << *it << "] is a file.." << std::endl;
 399       }
 400    }
 401
 402    for (it = fileNames.begin();
 403          it != fileNames.end();
 404        ++it)
 405    {
 406       if ( boost::filesystem::is_directory(*it) )
 407       {
 408
 409          if (verbose)
 410             std::cout << "--- --- [" << *it << "] is a directory" << std::endl;
 411
 412         // sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 413         //                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 414         //                                GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
 415   // MUST be 'pdata'!
 416
 417 //
 418 // (interest of previous method :
 419 // If unaware user changed the pdata name, it goes on working
 420 //
 421           std::string str_isa;
 422           str_isa = (*it) +
 423                     GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 424                    "isa";
 425
 426           std::string str_isa_func_name;
 427           canOpen = br_isa.LoadFile(str_isa);
 428           if (!canOpen)
 429           {
 430              sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 431                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 432                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
 433           }
 434           else
 435           {
 436              br_isa.FillMap();
 437              BrukerFieldData b_isa_func_name = br_isa.GetFieldData("ISA_func_name");
 438
 439              str_isa_func_name = b_isa_func_name.GetStringValue()[0];
 440              cleanString(str_isa_func_name);
 441
 442              sprintf(outputDirName, "%s%c%s.%s", currentOutputDirName.c_str(),
 443                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 444                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str(),
 445              str_isa_func_name.c_str());
 446           }
 447           try {
 448              DealWithNiveau3(*it, outputDirName);
 449           }
 450           catch (BrukerHopelessException &e)
 451           {
 452              std::cout << "And Exception was thrown in DealWithNiveau3 (" << e.what() << "); "
 453                        << " We skip [" << level2Directory << "]" << std::endl;
 454              continue;
 455           }
 456           catch (BrukerInitException &e)
 457           {
 458              std::cout << "And Init Exception was thrown in DealWithNiveau3 (" << e.what() << "); "
 459                        << " We skip [" << level2Directory << "]" << std::endl;
 460              continue;
 461           }
 462       }
 463    }
 464 }
 465
 466 //
 467 // =====================================================================
 468 //
 469
 470 void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string currentOutputDirName){
 471
 472 //
 473 // e.g. at level 3, in
 474
 475    // just to be able to go on checking // JP
 476    if ( GDCM_NAME_SPACE::Util::GetName(level3Directory) != "1")
 477       return;
 478
 479    bool res = CreateDirectory(currentOutputDirName);
 480
 481    if (!res)
 482    {
 483       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 484       throw ( BrukerHopelessException ("Hopeless! Level3 output directory creation failure"));
 485       //exit (0);
 486    }
 487
 488    GDCM_NAME_SPACE::DirList dirList(level3Directory, false, true); // DON'T get recursively the list of files
 489    GDCM_NAME_SPACE::DirListType::iterator it;
 490    GDCM_NAME_SPACE::DirListType fileNames;
 491    fileNames = dirList.GetFilenames();
 492
 493    char original2dseqName       [(unsigned int) PATH_MAX+2];
 494    char original2dseqName_XXX   [(unsigned int) PATH_MAX+2];
 495    char currentOutputMhdDirName [(unsigned int) PATH_MAX+2];
 496
 497    char outputMhdFileName       [(unsigned int) PATH_MAX+2];
 498    char output2dseqSliceFileName[(unsigned int) PATH_MAX+6]; // think about extra '.dcm'
 499    char output2dseqName         [(unsigned int) PATH_MAX+6];
 500    char output2dseqCartoName    [(unsigned int) PATH_MAX+6];
 501
 502    char copyFile[PATH_MAX + PATH_MAX + 5]; // Should be enough!
 503    bool canOpen;
 504
 505    //-------------- try d3proc;
 506    char char_d3proc[(unsigned int) PATH_MAX+2];
 507
 508    sprintf(char_d3proc,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"d3proc" );
 509
 510    if (verbose)
 511       std::cout << "d3proc: --- => [" << char_d3proc << "]" << std::endl;
 512    std::string str_d3proc(char_d3proc);
 513    canOpen = br_d3proc.LoadFile(str_d3proc);
 514
 515    if (!canOpen)
 516    {
 517       std::cout << "Hopeless! no 'd3proc' found" << std::endl;
 518       throw ( BrukerHopelessException ("Hopeless! no 'd3proc' found"));
 519       //exit(0);  /// \TODO throw an exception !
 520    }
 521
 522    canOpen = br_d3proc.FillMap();
 523    if (!canOpen)
 524    {
 525       std::cout << "Hopeless! FillMap failed on 'd3proc'" << std::endl;
 526       throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'd3proc'"));
 527       //exit(0);  /// \TODO throw an exception !
 528    }
 529
 530    //-------------- end try d3proc;
 531
 532
 533  // -------------------try reco
 534
 535    char char_reco[(unsigned int) PATH_MAX+2];
 536
 537    sprintf(char_reco,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
 538     //str_d3proc = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
 539     //             GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 540     //             "d3proc";
 541    if (verbose)
 542       std::cout << "reco: --- => [" << char_reco << "]" << std::endl;
 543
 544    std::string str_reco(char_reco);
 545    canOpen = br_reco.LoadFile(str_reco);
 546
 547    if (!canOpen) // we try in directory ../1
 548    {
 549       if (verbose)
 550          std::cout << "[" << str_reco << "] not found " << std::endl;
 551       std::string lastDirName = GDCM_NAME_SPACE::Util::GetPath(level3Directory);
 552       //lastDirName = GDCM_NAME_SPACE::Util::GetPath(lastDirName);
 553       sprintf(char_reco,"%s%c1%c%s", lastDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
 554       //str_reco=char_reco;
 555       canOpen = br_reco.LoadFile(str_reco);
 556       if (!canOpen)
 557       {
 558          std::cout << "Hopeless! cannot find 'reco' in [" << str_reco << "]"  << std::endl;
 559          throw ( BrukerHopelessException ("Hopeless! cannot find 'reco'"));
 560          //exit(0);  /// \TODO throw an exception !
 561       }
 562    } else {
 563       if (verbose)
 564          std::cout << "[" << str_reco << "] successfully Loaded " << std::endl;
 565    }
 566
 567    canOpen = br_reco.FillMap();
 568    if (!canOpen)
 569    {
 570       std::cout << "Hopeless! FillMap failed on [" << str_reco << "]" << std::endl;
 571       throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'reco'"));
 572       //exit(0);  /// \TODO throw an exception !
 573    } else {
 574       if (verbose)
 575          std::cout << "[" << str_reco << "] successfully Mapped" << std::endl;
 576    }
 577
 578    //std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
 579    // br_reco.PrintSelf();
 580    // std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
 581    // -------------------end try reco
 582
 583
 584    BrukerFieldData bX = br_d3proc.GetFieldData("IM_SIX");
 585    int NX = bX.GetIntValue()[0];
 586
 587    if (verbose)
 588       std::cout << "IM_SIX " << NX << std::endl;
 589    BrukerFieldData bY=br_d3proc.GetFieldData("IM_SIY");
 590    int NY = bY.GetIntValue()[0];
 591
 592    if (verbose)
 593          std::cout << "IM_SIY " << NY << std::endl;
 594    /// \todo : check if there are actually 3 dimensions or only 2
 595
 596    BrukerFieldData bZ= br_d3proc.GetFieldData("IM_SIZ");
 597    int nbFrames = bZ.GetIntValue()[0];
 598    if (verbose)
 599          std::cout << "IM_SIZ " << nbFrames << std::endl;
 600
 601         // WARNING DATTYPE is, either in {ip_short, ip_int, ip_char, ...}, or in {1, 2, 3, ...}
 602
 603    BrukerFieldData bDPT = br_d3proc.GetFieldData("DATTYPE");
 604
 605    std::string mhdDataPixelType;
 606    int pixelSize;
 607    getImhDataType(bDPT, mhdDataPixelType, pixelSize);
 608
 609
 610  /*
 611
 612  // See mail Denis :
 613  // En regle generale il vaut mieux que l'on passe par RECO_*
 614  // pour extraire les parametres de l'image
 615  //
 616
 617    BrukerFieldData fov = br_method.GetFieldData("PVM_Fov");
 618    double fovX = fov.GetDoubleValue()[0];
 619    double fovY = fov.GetDoubleValue()[1];
 620    if (verbose)
 621       std::cout << "FOV (ds method) " << fovX << " " << fovY << std::endl;
 622
 623    BrukerFieldData spatResol = br_method.GetFieldData("PVM_SpatResol");
 624    double spatResolX = spatResol.GetDoubleValue()[0];
 625    double spatResolY = spatResol.GetDoubleValue()[1];
 626    if (verbose)
 627       std::cout << "SpatResol (ds method) " << spatResolX << " " << spatResolY << std::endl;
 628
 629 */
 630
 631 /* ------  */
 632 // Better we use 'get' accessors from BrukerImage class, as Denis wrote them
 633
 634    BrukerFieldData fov = br_reco.GetFieldData("RECO_fov");
 635    double fovX = fov.GetDoubleValue()[0];
 636    double fovY = fov.GetDoubleValue()[1];
 637    if (verbose)
 638       std::cout << "FOV (ds reco) " << fovX << " " << fovY << std::endl;
 639
 640    BrukerFieldData size = br_reco.GetFieldData("RECO_size");
 641    double sizeX = size.GetDoubleValue()[0];
 642    double sizeY = size.GetDoubleValue()[1];
 643
 644    if (verbose)
 645       std::cout << "SIZE (ds reco) " << sizeX << " " << sizeY << std::endl;
 646
 647    double spatResolX = fovX / sizeX;
 648    double spatResolY = fovY / sizeY;
 649
 650    if (verbose)
 651       std::cout << "spatResol (ds reco : fov/size) " << spatResolX << " " << spatResolY << std::endl;
 652
 653 /* ------  */
 654
 655    /// \TODO probabely a more sophisticated accessor will be necessary :
 656    ///  (cf : non contiguous slices, overlapping, slice thickness, space between slices, etc)
 657
 658    BrukerFieldData bsliceDistance = br_method.GetFieldData("PVM_SPackArrSliceDistance");
 659    double sliceDistance = bsliceDistance.GetDoubleValue()[0];
 660
 661    if (verbose)
 662       std::cout << "SPackArrSliceDistance (ds method) " << sliceDistance << std::endl;
 663
 664 // ----------------------------------------------------------------------------------------
 665
 666    if (mhd)
 667    {
 668       sprintf(currentOutputMhdDirName, "%s%c%s", currentOutputDirName.c_str(),
 669                                GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "MhdFiles");
 670       res = CreateDirectory( currentOutputMhdDirName );
 671       if (!res) {
 672          std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 673          throw ( BrukerHopelessException ("Hopeless!FillMap failed on 'reco'"));
 674          //exit (0);
 675       }
 676
 677       if (verbose)
 678          std::cout << "Directory creation [" <<  currentOutputDirName << "]" << std::endl;
 679    }  // end if mhd
 680
 681    if (verbose)
 682          std::cout << "nbFrames " << nbFrames << std::endl;
 683    if (verbose)
 684          std::cout << "nbSlices " << nbSlices << std::endl;
 685    int k;
 686    int nbInstants = nbFrames/nbSlices;
 687    if (verbose)
 688          std::cout << "nbInstants (deduced)" << nbInstants << std::endl;
 689    int instantNb;
 690    int sliceNb;
 691    FILE *fp;  // for MHD files
 692
 693    sprintf( original2dseqName, "%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "2dseq");
 694
 695 /**/
 696   // \TODO : tenir compte du bazar precedent
 697
 698     // load 2dseq in memory
 699
 700    fp = fopen(original2dseqName, "rb");
 701    if (!fp)
 702    {
 703       // try 2dseq_Angio2D ?!?
 704
 705       sprintf( original2dseqName_XXX, "%s%s", original2dseqName, "_Angio2D");
 706       fp = fopen(original2dseqName_XXX, "rb");
 707       if (!fp)
 708       {
 709          std::cout << "Cannot open [" << original2dseqName << "] nor [" <<  original2dseqName_XXX << "] for reading" << std::endl;
 710          fclose(fp);
 711          throw ( BrukerHopelessException ("Hopeless! Cannot open '2dseq'"));
 712          //exit (0);
 713       }
 714    }
 715
 716    unsigned char *buffer_2dseq = new unsigned char[NX*NY*pixelSize*nbSlices*nbInstants];
 717    ///\ TODO : find a safer way to be sure to read everything!
 718    size_t lgr = fread(buffer_2dseq, 1, NX*NY*pixelSize*nbSlices*nbInstants, fp);
 719
 720    // This one will be important!
 721    // ---------------------------
 722    try {
 723       imageSet = CreateImageSet ( );
 724    }
 725    catch (BrukerInitException& e)
 726    {
 727       if (verbose)
 728          std::cout <<  "an Init Exception was thrown in CreateImageSet ( ); " << e.what()
 729                    <<  "catched in DealWithNiveau3" << std::endl;
 730       //return;
 731       throw (e);
 732    }
 733
 734    serieNumber++;
 735    strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 736    if (nbInstants==1) // creer un seul fichier .mhd  pour toutes les Slices! (images natives)
 737    {
 738        if (verbose)
 739           std::cout << "Single instant : do not split" << std::endl;
 740        if (mhd)
 741        {
 742              sprintf(outputMhdFileName, "%s%cMhdData_All_the_Slices.mhd", currentOutputMhdDirName,
 743                                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 744              fp=fopen(outputMhdFileName, "w");
 745              if (!fp)
 746              {
 747                 std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 748                 throw ( BrukerHopelessException ("Hopeless! Cannot open  mhd file for writting"));
 749                 //exit(0);
 750              }
 751              else
 752              {
 753                fprintf(fp, "ObjectType = Image\n");
 754                fprintf(fp, "NDims = 3\n" );
 755                fprintf(fp, "BinaryData = True \n" );
 756                fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 757                fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices );
 758                fprintf(fp, "HeaderSize = %d\n", 0);
 759                //fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
 760                fprintf(fp, "ElementSpacing = %lf %lf %lf\n", spatResolX, spatResolY, sliceDistance );
 761                fprintf(fp, "Position = 0 0 %d\n", 0 );
 762                fprintf(fp, "Offset = 0 0 0\n" );
 763                fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 764                fprintf(fp, "ElementNumberOfChannels = 1\n" );
 765                fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
 766                fprintf(fp, "ElementDataFile = %s\n", "../2dseq_All_the_Slices" );
 767                fclose(fp);
 768              }
 769              sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices",
 770                                        currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 771              fp=fopen(output2dseqSliceFileName, "wb");
 772              if (!fp)
 773              {
 774                 std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 775                 throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseq file for writting"));
 776              }
 777              else
 778              {
 779                 fwrite( buffer_2dseq, NX*NY*pixelSize, nbSlices, fp);
 780              }
 781              fclose(fp);
 782              serieNumber ++;
 783              strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 784        }  // end if mhd
 785        if (dicom)
 786        {
 787              sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices.dcm",
 788                                        currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 789
 790             /* ----------- Write Dicom Image  ---------------*/
 791              MakeDicomImage(buffer_2dseq,
 792                NX,
 793                NY,
 794                nbFrames,
 795                pixelSize,
 796                //fovX/NY, fovY/NY, sliceDistance,
 797                spatResolX, spatResolY, sliceDistance,
 798                output2dseqSliceFileName,
 799                subject_name,
 800                day,
 801                strStudyUID,
 802                strSerieUID,
 803                strStudyDescr,
 804                strSerieDescr,
 805                strStudyTimeDate,
 806                0,// index frame number
 807                GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
 808              );
 809        }  // end if dicom
 810    }  // end if nbInstants = 1
 811
 812    else  // more than ONE instant
 813    {
 814           // Interleaved !
 815           // it's (slice1,slide2, ...)t1 ; (slice1,slide2, ...)t2 ; ...
 816          unsigned char *pixelsForCurrentSlice = new unsigned char[NX*NY*pixelSize*nbInstants];
 817
 818          k = 0;
 819          for (sliceNb=0; sliceNb<nbSlices; sliceNb++)
 820          {
 821             if (mhd)
 822             {
 823                sprintf(outputMhdFileName, "%s%cMhdData_%03d.mhd", currentOutputMhdDirName,
 824                                         GDCM_NAME_SPACE::GDCM_FILESEPARATOR, k  );
 825                if (verbose)
 826                   std::cout << "--- Output MHD file [" << outputMhdFileName << "]" << std::endl;
 827                fp=fopen(outputMhdFileName, "w");
 828                if (!fp)
 829                {
 830                    std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 831                    throw ( BrukerHopelessException ("Hopeless! Cannot open  mhd file for writting"));
 832                    //exit(0);
 833                }
 834                else
 835                {
 836             /* ----------- Write MHD Image  ---------------*/
 837                 //if (verbose)
 838                 //   std::cout << "Open sucessfully[" << outputMhdFileName << "] for writting" << std::endl;
 839                    fprintf(fp, "ObjectType = Image\n");
 840                    fprintf(fp, "NDims = 3\n" );
 841                    fprintf(fp, "BinaryData = True \n" );
 842                    fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 843                    fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbInstants);
 844                    fprintf(fp, "HeaderSize = %d\n", 0);
 845                    //fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, 1.0 ); //
 846                    fprintf(fp, "ElementSpacing = %lf %lf %lf\n",spatResolX, spatResolY, 1.0 ); //slice distance : no meaning for temporal serie
 847                    fprintf(fp, "Position = 0 0 %d\n", sliceNb );
 848                    fprintf(fp, "Offset = 0 0 0\n" );
 849                    fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 850                    fprintf(fp, "ElementNumberOfChannels = 1\n" );
 851                    fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
 852                    fprintf(fp, "ElementDataFile = ..%c2dseq_Slice_%d\n", GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb );
 853                    fclose(fp);
 854                } // end write MHD
 855
 856                sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d",
 857                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,sliceNb);
 858                fp=fopen(output2dseqSliceFileName, "wb");
 859                if (!fp)
 860                {
 861                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 862                    throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseqSliceFile file for writting"));
 863                    //exit (0);
 864                }
 865                int frameSize = NX*NY*pixelSize;
 866                for (instantNb=0; instantNb<nbInstants; instantNb++)
 867                {
 868 // std::cout << "------------SN " << sliceNb << " IN " << instantNb <<  " T " << nbSlices*instantNb + sliceNb << std::endl;
 869                     fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
 870                             frameSize,
 871                             1, fp);
 872                }
 873                fclose(fp);
 874 // std::cout << "end writting[" << output2dseqSliceFileName << "]" << std::endl;
 875             }  // end if mhd
 876
 877             if (dicom)
 878             {
 879                // desperate try !
 880              /*
 881                sprintf(output2dseqSliceFileName, "%sdummy_buffer",
 882                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 883                fp=fopen(output2dseqSliceFileName, "wb");
 884                if (!fp)
 885                {
 886                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 887                    exit (0);
 888                }
 889                int frameSize = NX*NY*pixelSize;
 890                for (instantNb=0; instantNb<nbInstants; instantNb++)
 891                {
 892 // std::cout << "------------SN " << sliceNb << " IN " << instantNb <<  " T " << nbSlices*instantNb + sliceNb << std::endl;
 893                     fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
 894                             frameSize,
 895                             1, fp);
 896                }
 897                fclose(fp);
 898
 899                fp=fopen(output2dseqSliceFileName, "rb");
 900                if (!fp)
 901                {
 902                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for reading" << std::endl;
 903                    exit (0);
 904                }
 905                fread( pixelsForCurrentSlice,
 906                             frameSize*nbInstants,
 907                             1, fp);
 908                fclose(fp);
 909               // end of desperate try !
 910               */
 911
 912                /* ----------- Write Dicom Image  ---------------*/
 913
 914                int frameSize = NX*NY*pixelSize;
 915                for (instantNb=0; instantNb<nbInstants; instantNb++)
 916                {
 917                   memcpy(pixelsForCurrentSlice + frameSize*instantNb, buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize, frameSize);
 918                }
 919
 920                int indOfFirsImageWithinImageSet =  nbSlices*instantNb;
 921                sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d.dcm",
 922                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb);
 923
 924                MakeDicomImage(
 925                   pixelsForCurrentSlice,
 926                   NX,
 927                   NY,
 928                   nbInstants,
 929                   pixelSize,
 930                   spatResolX, spatResolY, sliceDistance,
 931                   //fovX/NY, fovY/NY, sliceDistance,
 932                   output2dseqSliceFileName,
 933                   subject_name,
 934                   day,
 935                   strStudyUID,
 936                   strSerieUID,
 937                   strStudyDescr,
 938                   strSerieDescr,
 939                   strStudyTimeDate,
 940                   sliceNb*nbInstants,
 941                   GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
 942                );
 943                if (verbose)
 944                   std::cout << "--- Output DCM file [" << output2dseqSliceFileName << "]" << std::endl;
 945
 946            } // en if dicom
 947
 948         k++;
 949         }
 950         delete [] pixelsForCurrentSlice;
 951      }  // end nbInstants == 1
 952    delete [] buffer_2dseq;
 953 /**/
 954
 955
 956    // -----------------------------------------------------
 957    //  deal with MatLab-generated Carto file.
 958    // -----------------------------------------------------
 959
 960    dealWithCarto(fileNames,  NX,  NY,  nbSlices, /*fovX, fovY,*/ spatResolX, spatResolY, sliceDistance,
 961                    copyFile, currentOutputDirName, outputMhdFileName, output2dseqCartoName);
 962 }
 963
 964
 965 // ===========================================================================================
 966
 967 void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX, int NY, int nbSlices,
 968                                  /*double fovX, double fovY, */
 969                                  double spatResolX, double spatResolY, double sliceDistance,
 970                                  char *copyFile, std::string &currentOutputDirName,
 971                                  char *outputMhdFileName, char *output2dseqCartoName)
 972 {
 973    // -----------------------------------------------------
 974    //  deal with MatLab-generated Carto file.
 975    // -----------------------------------------------------
 976
 977    const char *code[] = { "ADC", "adc", "TTP", "ttp", "PEAK", "peak", "" };  // add more carto file name identifiers if necessary; end with ""
 978    const char *separator[] =  { "_", ".", "-", "" }; //  add more, if necessary, to ckeck for 2dseq.ADC, 2dseq_ADC, 2dseq-ADC, etc; end with ""
 979    int icode;
 980    int iseparator;
 981    GDCM_NAME_SPACE::DirListType::iterator it;
 982    char file_name_ident[500];
 983    FILE *fp;
 984
 985    // Iterate to ALL the objets(files/directories) found in the input directory
 986    for (it = fileNames.begin();
 987         it != fileNames.end();
 988       ++it)
 989    {
 990       if ( boost::filesystem::is_regular(*it) )
 991       //if ( ! boost::filesystem::is_directory(*it) )
 992       {
 993          if (verbose)
 994             std::cout << "--- [" << *it << "] is a file..." << std::endl;
 995
 996          icode      = 0;
 997          while (code[icode][0] != 0)
 998          {
 999          iseparator = 0;
1000          while (separator[iseparator][0] != 0)
1001          {
1002             sprintf(file_name_ident, "2dseq%s%s",separator[iseparator],code[icode]); // e.g  "2dseq_ADC"
1003             //if (verbose)
1004             //   std::cout << "check name ["<<(*it) << "] for string [" << file_name_ident << "]" << std::endl;
1005             std::string::size_type loc = (*it).rfind(file_name_ident);
1006
1007             if ( loc != std::string::npos )
1008             {
1009
1010        ///\ TODO : find a safer way to be sure to read everything!
1011               unsigned char *buffer_carto = new unsigned char[NX*NY*sizeof(double)*nbSlices];
1012               fp = fopen ( (*it).c_str(), "rb");
1013               if (!fp){
1014                  std::cout << "Cannot open [" << *it << "] for reading" << std::endl;
1015                  throw ( BrukerHopelessException ("Level 1 Unable to open 'carto' file "));
1016                }
1017                fread(buffer_carto, NX*NY*sizeof(double), nbSlices, fp);
1018
1019                     // ?!?  sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() ,
1020                std::cout << "Deal with Carto file :[" <<*it << "], computed length : "
1021                          << NX*NY*sizeof(double)*nbSlices << std::endl;
1022                std::string lastFileName = GDCM_NAME_SPACE::Util::GetName((*it).c_str());
1023                if (mhd)
1024                {
1025                   // Copy the data file in the new directory
1026                   sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() ,
1027                             currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str());
1028                   system(copyFile);
1029                   sprintf(outputMhdFileName, "%s%c%s%s",
1030                                          currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".mhd" );
1031                   if (verbose)
1032                     std::cout << "--- Output Carto MHD file [" << outputMhdFileName << "]" << std::endl;
1033
1034                   FILE *fp;
1035                   fp=fopen(outputMhdFileName, "w");
1036                   if (!fp)
1037                   {
1038                      std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
1039                   }
1040                   else
1041                   {
1042                      fprintf(fp, "ObjectType = Image\n");
1043                      fprintf(fp, "NDims = 3\n" );
1044                      fprintf(fp, "BinaryData = True \n" );
1045                      fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
1046                      fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices);
1047                      fprintf(fp, "HeaderSize = %d\n", 0 );
1048                      fprintf(fp, "ElementSpacing = %lf %lf %lf\n",spatResolX, spatResolY, sliceDistance );
1049                      fprintf(fp, "Position = 0 0 0\n" );
1050                      fprintf(fp, "Offset = 0 0 0\n" );
1051                      fprintf(fp, "CenterOfRotation = 0 0 0\n" );
1052                      fprintf(fp, "ElementNumberOfChannels = 1\n" );
1053                      fprintf(fp, "ElementType = %s\n", "MET_DOUBLE" );
1054                      fprintf(fp, "ElementDataFile = %s\n", lastFileName.c_str() );
1055
1056                      fclose(fp);
1057                   }
1058                   if (verbose)
1059                      std::cout << "--- end write Carto MHD file [" << outputMhdFileName << "]" << std::endl;
1060                }  // end if mhd
1061
1062             // ----------- Write Dicom Image  ---------------
1063
1064                if (dicom)
1065                {
1066                   sprintf(output2dseqCartoName, "%s%c%s%s",
1067                                        currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".dcm" );
1068                   if (verbose)
1069                      std::cout << "--- end create name output2dseqCartoName file [" << output2dseqCartoName << "]" << std::endl;
1070
1071                   strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID(); //New SerieUID for each carto.
1072                   std::string strNewSerieDescr(strSerieDescr+ "_" +GDCM_NAME_SPACE::Util::GetName((*it).c_str()));
1073                   MakeDicomImage(buffer_carto,
1074                      NX,
1075                      NY,
1076                      nbSlices,
1077                      8, // pixelSize
1078                      //fovX/NY, fovY/NY, sliceDistance,
1079                      spatResolX, spatResolY, sliceDistance,
1080                      output2dseqCartoName,
1081                      subject_name,
1082                      day,
1083                      strStudyUID,
1084                      strSerieUID,
1085                      strStudyDescr,
1086                      strNewSerieDescr,
1087                      strStudyTimeDate,
1088                      0,
1089                      GDCM_NAME_SPACE::CREATED_IMAGE
1090                   );
1091                }  // end if dicom
1092
1093                delete [] buffer_carto;
1094                if (verbose)
1095                   std::cout << "--- End writing Carto DICOM file [" << output2dseqCartoName << "]" << std::endl;
1096                break; // don't check for more ident on same file name!
1097
1098             }  // end deal with _ADC, -adc, etc
1099           iseparator ++;
1100           }  // end iterate speparators
1101           icode++;
1102           } // end iterate code
1103       } // end boost::filesystem::is_regular(*it)
1104    } // end iterate on all objects (files, dir, etc)
1105 } // end method
1106
1107
1108 // ==========================================================================================================
1109
1110 bool Bruker2Dicom::CreateDirectory(std::string OutputDirName)
1111 {
1112    std::string systemCommand;
1113
1114    if (verbose)
1115       std::cout << "Check for output directory :[" << OutputDirName << "]."
1116                 <<std::endl;
1117    if ( ! boost::filesystem::is_directory(OutputDirName) )    // dirout not found
1118    {
1119       std::string strDirNameout(OutputDirName);        // to please gcc 4
1120       systemCommand = "mkdir " + strDirNameout;        // create it!
1121       if (verbose)
1122          std::cout << systemCommand << std::endl;
1123       system (systemCommand.c_str());
1124       if ( ! boost::filesystem::is_directory(OutputDirName) ) // be sure it worked
1125       {
1126          if (verbose)
1127             std::cout << "KO : not a dir : [" << OutputDirName << "] (creation failure ?)" << std::endl;
1128          //return 0;
1129          throw ( BrukerHopelessException ("Level 1 output directory creation failure "));
1130       }
1131       else
1132       {
1133          if (verbose)
1134            std::cout << "Directory [" << OutputDirName << "] created." << std::endl;
1135       }
1136    }
1137    else
1138    {
1139        if (verbose)
1140             std::cout << "Output Directory [" << OutputDirName << "] already exists; Used as is." << std::endl;
1141    }
1142
1143    return 1;
1144
1145 }
1146
1147
1148 // ===========================================================================================
1149
1150 /// \TODO move cleanString to 'crea' ?
1151
1152 void Bruker2Dicom::cleanString(std::string &s)
1153 {
1154    int l = s.size();
1155    if (s[l-1] == 0x0A || s[l-1] == 0x0D ) // CR or NL
1156    {
1157       l--;
1158       s = s.substr(0, l);
1159    }
1160    if (s[l-1] == ' ' ) // blank space
1161    {
1162       l--;
1163       s = s.substr(0, l);
1164    }
1165
1166    if (s[0] == '<')
1167       s= s.substr(1,l-2);
1168    std::string repChar("_");
1169    GDCM_NAME_SPACE::Util::ReplaceSpecChar(s, repChar);
1170 }
1171
1172
1173
1174 // ===========================================================================================
1175
1176
1177 void Bruker2Dicom::getImhDataType(BrukerFieldData &bDPT, std::string &mhdDataPixelType, int &pixelSize)
1178 {
1179    if(bDPT.GetDataType() == "string")
1180    {
1181          std::string brukerDataPixelType = bDPT.GetStringValue()[0];
1182          if (verbose)
1183             std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
1184          //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
1185
1186          if (brukerDataPixelType ==  "ip_short") {
1187             mhdDataPixelType = "MET_USHORT";
1188             pixelSize = 2;
1189          }
1190          if (brukerDataPixelType ==  "ip_int") {
1191             mhdDataPixelType = "MET_UINT";
1192             pixelSize = 4;
1193          }
1194          if (brukerDataPixelType ==  "ip_char") {
1195              mhdDataPixelType = "MET_UCHAR";
1196              pixelSize = 1;
1197          }
1198                   /// \TODO : finish the list
1199     /*
1200     case 0 : fp << "ElementType = MET_CHAR" << std::endl;
1201       break;
1202     case 1 : fp << "ElementType = MET_UCHAR" << std::endl;
1203       break;
1204     case 2 : fp << "ElementType = MET_SHORT" << std::endl;
1205       break;
1206     case 3 : fp << "ElementType = MET_USHORT" << std::endl;
1207       break;
1208     case 4 : fp << "ElementType = MET_INT" << std::endl;
1209       break;
1210     case 5 : fp << "ElementType = MET_UINT" << std::endl;
1211       break;
1212     case 6 : fp << "ElementType = MET_FLOAT" << std::endl;
1213       break;
1214     case 7 : fp << "ElementType = MET_DOUBLE" << std::endl;
1215     */
1216     }
1217     else
1218     {
1219          int brukerDataPixelType = bDPT.GetIntValue()[0];
1220          if (verbose)
1221             std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
1222          //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
1223
1224 // Cross your fingers !!!
1225
1226 // pb : found values : 2, 3, 5
1227
1228          if (brukerDataPixelType ==  2) {
1229             mhdDataPixelType = "MET_USHORT";
1230             pixelSize = 2;
1231          }
1232          if (brukerDataPixelType ==  3) {
1233             mhdDataPixelType = "MET_USHORT";
1234             pixelSize = 2;
1235          }
1236          if (brukerDataPixelType ==  1) {
1237             mhdDataPixelType = "MET_UCHAR";
1238             pixelSize = 1;
1239          }
1240     }
1241 }
1242
1243 // ===========================================================================================
1244
1245 std::vector<BrukerImage> Bruker2Dicom::CreateImageSet ( )
1246 {
1247          std::vector<BrukerImage> imageSet;
1248          br_acqp.SetLoopStructure();
1249          std::vector<int> tempVect                      = br_acqp.GetLoopStructure() ;
1250          std::map<std::string, BrukerFieldData> map     = br_acqp.GetBrukerHeaderMap();
1251
1252          bool result                                    = br_acqp.ObjectVaryingProperties.init(map,tempVect);
1253
1254          if (result == false)
1255          {
1256             throw ( BrukerInitException  ("ObjectVaryingProperties.init() failure in Bruker2Dicom::CreateImageSet()") );
1257          }
1258
1259          br_acqp.SetImageLoopStructure();
1260          br_acqp.SetBrukerImageList();
1261          std::vector<std::vector<int> > brukerImageList = br_acqp.GetBrukerImageList();
1262
1263          BrukerImage image(br_acqp,br_reco);
1264          image.Init(br_acqp,br_reco,1);
1265
1266          for(int i=0;i<brukerImageList.size();i++)
1267          {
1268             image.Init(br_acqp,br_reco,i);
1269             imageSet.push_back(image);
1270          }
1271
1272  // Just for checking
1273  /*
1274
1275          std::vector<std::vector <double> > imageOrientation;
1276          std::vector <double> imagePosition;
1277          for(int i=0;i<brukerImageList.size();i++)
1278          {
1279            // fread(buffer_2dseq, NX*NY*pixelSize*nbSlices*nbInstants, 1, fp);
1280
1281            imagePosition = imageSet[i].getTranslationVectorRPS2XYZ();
1282            std::cout << "Position " << imagePosition[0] << " "
1283                      << imagePosition[1] << " "  << imagePosition[2] ;
1284            imageOrientation =  imageSet[i].getRotationMatrixRPS2XYZ();
1285            std::cout << "\t  Orientation " ;
1286            for(int i1=0; i1<3;i1++)for(int i2=0; i2<3;i2++)
1287               std::cout << imageOrientation[i1][i2] << " ";CreateImageSet
1288
1289            //std::cout << "\t  Abs Time " << imageSet[i].getAbsoluteTimePosition();
1290            std::cout << "\t  Relat Time " << imageSet[i].getRelativeTimePosition();
1291
1292            std::cout << "\t [";
1293            for (int i3=0; i3<imageSet[i].getLoopStamp().size();i3++)
1294               std::cout << " " << imageSet[i].getLoopStamp()[i3];
1295            std::cout << "]" << std::endl;
1296          }
1297 */
1298    return imageSet;
1299 }
1300
1301 // ===========================================================================================
1302
1303 void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels,
1304               int X,
1305               int Y,
1306               int nbFrames,
1307               int pixelSize,
1308               double spacingX, double spacingY, double sliceDistance,
1309               std::string dcmImageName,
1310               const std::string &patientName,
1311               const char *day,
1312               std::string &studyUID,
1313               std::string &serieUID,
1314               std::string &studyDescr,
1315               std::string &serieDescr,
1316               std::string &strStudyTimeDate,
1317               int imgNum,
1318               GDCM_NAME_SPACE::ImageContentType contentType
1319       )
1320 {
1321    std::ostringstream str;
1322
1323    GDCM_NAME_SPACE::File *file;
1324    file = GDCM_NAME_SPACE::File::New();
1325
1326   // Set the image size
1327    str.str("");
1328    str << X;
1329    file->InsertEntryString(str.str(),0x0028,0x0011,"US"); // Columns
1330    str.str("");
1331    str << Y;
1332    file->InsertEntryString(str.str(),0x0028,0x0010,"US"); // Rows
1333
1334    if (nbFrames != 1)
1335    {
1336       str.str("");
1337       str << nbFrames;
1338       file->InsertEntryString(str.str(),0x0028,0x0008,"IS"); // Number of Frames
1339    }
1340
1341   // Set the pixel type
1342   //      //8, 16, 32, 64 (for double ?)
1343    str.str("");
1344    str << pixelSize*8;
1345    file->InsertEntryString(str.str(),0x0028,0x0100,"US"); // Bits Allocated
1346
1347    file->InsertEntryString(str.str(),0x0028,0x0101,"US"); // Bits Stored
1348
1349    str.str("");
1350    str << pixelSize*8-1;
1351    file->InsertEntryString(str.str(),0x0028,0x0102,"US"); // High Bit
1352
1353   // Set the pixel representation // 0/1 , 0=unsigned
1354    file->InsertEntryString("1",0x0028,0x0103, "US"); // Pixel Representation
1355
1356   // Set the samples per pixel // 1:Grey level, 3:RGB
1357    file->InsertEntryString("1",0x0028,0x0002, "US"); // Samples per Pixel
1358
1359 //  0028 0030 DS 2 Pixel Spacing
1360    str.str("");
1361    str << spacingX << "\\" << spacingY;
1362    file->InsertEntryString(str.str(),0x0028,0x0030, "DS"); // Pixel Spacing
1363
1364  //   0018 0050 DS 1 Slice Thickness
1365    str.str("");
1366    str << sliceDistance;
1367    file->InsertEntryString(str.str(),0x0018,0x0050, "DS");
1368
1369 //    0020 0011 IS 1 Series Number
1370    str.str("");
1371    str << serieNumber;
1372    file->InsertEntryString(str.str(),0x0020,0x0011, "IS");
1373
1374 //    0020|0013 [IS]  [Instance Number]
1375    instanceNumber++;
1376    str.str("");
1377    str << instanceNumber;
1378    file->InsertEntryString(str.str(),0x0020,0x0013, "IS");
1379
1380
1381   // 1.2.840.10008.5.1.4.1.1.4.1 : Enhanced MR Image Storage
1382  //  file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0002, 0x0002, "UI");  // [Media Storage SOP Class UID]
1383   // file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0008, 0x0016, "UI");  // [SOP Class UID]
1384
1385
1386 // OK : MR is NOT multiframe, but I want just a quick an dirty solution
1387
1388 // 1.2.840.10008.5.1.4.1.1.4         MR Image Storage
1389    file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0002, 0x0002, "UI");  // [Media Storage SOP Class UID]
1390    file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0008, 0x0016, "UI");  // [SOP Class UID]
1391
1392   // if (strlen(patientName) != 0)
1393    file->InsertEntryString(patientName.c_str(),0x0010,0x0010, "PN"); // Patient's Name
1394    file->InsertEntryString(patientName.c_str(),0x0010,0x0020, "LO"); // Patient's ID
1395
1396    file->InsertEntryString(studyUID, 0x0020, 0x000d, "UI");
1397    file->InsertEntryString(serieUID, 0x0020, 0x000e, "UI");
1398
1399 //  0008 0020 DA 1 Study Date
1400 //  0008 0030 TM 1 Study Time
1401
1402 /// \TODO split into 2 strings!
1403    file->InsertEntryString(strStudyTimeDate.substr(10,11).c_str(),0x0008,0x0020, "DA");
1404    file->InsertEntryString(strStudyTimeDate.substr(1,8).c_str(),  0x0008,0x0030, "TM");
1405
1406    file->InsertEntryString(studyDescr, 0x0008,0x1030, "LO");  // Study Description
1407    file->InsertEntryString(serieDescr, 0x0008,0x103e, "LO");  // Series Description
1408
1409 //0008|0060 [CS] [Modality]
1410    file->InsertEntryString("MR",0x0008,0x0060, "CS");
1411
1412 // 0020 0037 DS 6 Image Orientation (Patient)
1413    char charImageOrientation[256];
1414
1415 /*
1416 std::cout << "charImageOrientation  " <<
1417                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0] << " " <<
1418                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1] << " " <<
1419                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2] << " " <<
1420                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0] << " " <<
1421                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1] << " " <<
1422                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] << std::endl ;
1423 */
1424    sprintf(charImageOrientation,"%f\\%f\\%f \\ %f\\%f\\%f",
1425                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0],
1426                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1],
1427                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2],
1428                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0],
1429                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1],
1430                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] ) ;
1431
1432    file->InsertEntryString(charImageOrientation,0x0020,0x0037, "DS");
1433
1434
1435 // 0020 0032 DS 3 Image Position (Patient)
1436
1437    char charImagePosition[256];
1438    sprintf(charImagePosition,"%f\\%f\\%f",
1439                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[0],
1440                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[1],
1441                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[2]);
1442
1443    file->InsertEntryString(charImagePosition,0x0020,0x0032, "DS");  //0020 0032 DS 3 Image Position (Patient)
1444
1445
1446
1447 // 0020 0x1041 DS 1 Slice Location
1448 //        sprintf(charImagePosition,"%f",float(imgNum));
1449 //        file->InsertEntryString(charImagePosition,0x0020,0x1041, "DS");
1450 /*
1451   // Set Rescale Intercept
1452         str.str("");
1453         str << div;
1454         file->InsertEntryString(str.str(),0x0028,0x1052,"DS");
1455
1456   // Set Rescale Slope
1457         str.str("");
1458         str << mini;
1459         file->InsertEntryString(str.str(),0x0028,0x1053,"DS");
1460 */
1461
1462    GDCM_NAME_SPACE::FileHelper *fileH;
1463    fileH = GDCM_NAME_SPACE::FileHelper::New(file);
1464    fileH->SetContentType(contentType);
1465
1466    // cast is just to avoid warnings (*no* conversion is performed)
1467    //fileH->SetImageData((uint8_t *)img,int(maxX*maxY)*sizeof(uint16_t)); // troubles when maxX, mayY are *actually* float!
1468
1469 //std::cout << "--------------------------------  X*Y*nbFrames*pixelSize " << X << " " << Y << " " << nbFrames << " " << pixelSize << std::endl;
1470
1471    fileH->SetImageData((uint8_t *)tabPixels, X*Y*nbFrames*pixelSize);
1472    fileH->SetWriteModeToRaw();
1473    fileH->SetWriteTypeToDcmExplVR();
1474    if( !fileH->Write(dcmImageName)) {
1475       std::cout << "Failed for [" << dcmImageName << "]\n"
1476                 << "           File is unwrittable" << std::endl;
1477       file->Delete();
1478       fileH->Delete();
1479       throw ( BrukerHopelessException ("Level 1 Unable to write Dicom file "));
1480    }
1481    //if (verbose)
1482    //   file->Print();
1483
1484    file->Delete();
1485    fileH->Delete();
1486 }
1487
1488