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
  74    bool subjectFound;
  75    canOpen =br_subject.LoadFile(subject);
  76    if (!canOpen)
  77    {
  78       //std::cout << "Hopeless! no 'subject' found" << std::endl;
  79       //throw ( BrukerHopelessException ("Hopeless! no 'subject' found in root input directory "));
  80
  81       std::cout << "Not too much hope! no 'subject' found (Desperate try will be performed -default values- )" << std::endl;
  82       subjectFound = false;
  83    }
  84    else
  85    {
  86       br_subject.FillMap();
  87       subjectFound = true;
  88    }
  89    //br_subject.PrintSelf();
  90
  91   // get info for 'Study Description'
  92
  93     if (subjectFound)
  94     {
  95        BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string");
  96        subject_name = b_name.GetStringValue()[0];
  97        strPatientName = subject_name;
  98        cleanString(subject_name);
  99      }
 100      else
 101         subject_name ="defaultPatName";
 102
 103     // creation directory : 'nom du patient'
 104     std::string tempStringPatDir(OutputDirName);
 105     tempStringPatDir = tempStringPatDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + subject_name;
 106
 107     res=CreateDirectory(tempStringPatDir);
 108     if (!res) {
 109        std::cout << "[" << tempStringPatDir << "] Directory creation failure " << std::endl;
 110        throw ( BrukerHopelessException ("Patient directory creation failure "));
 111     }
 112
 113     std::string subject_entry;
 114     std::string subject_position;
 115     std::string subject_date;
 116     std::string subject_study_name;
 117
 118     if (subjectFound)
 119     {
 120        BrukerFieldData b_entry=br_subject.GetFieldData("SUBJECT_entry");
 121        subject_entry = b_entry.GetStringValue()[0];
 122        //cleanString(subject_entry);
 123        subject_entry = subject_entry.substr(11, subject_entry.size()-11);
 124
 125        BrukerFieldData b_position=br_subject.GetFieldData("SUBJECT_position");
 126        subject_position = b_position.GetStringValue()[0];
 127        //cleanString(subject_position);
 128        subject_position = subject_position.substr(9, subject_position.size()-9);
 129
 130        BrukerFieldData b_date=br_subject.GetFieldData("SUBJECT_date");
 131        subject_date = b_date.GetStringValue()[0];
 132        strStudyTimeDate = subject_date;
 133        cleanString(subject_date);
 134
 135        BrukerFieldData b_study_name=br_subject.GetFieldData("SUBJECT_study_name");
 136        subject_study_name = b_study_name.GetStringValue()[0];
 137        subject_study_name = subject_study_name.substr(1, subject_study_name.size()-2);
 138        cleanString(subject_study_name);
 139    }
 140    else  // Desperate trick when file 'subject' is missing
 141    {
 142       subject_entry      = "HeadFirst";            // Why not?
 143       subject_position   = "Supine";               // Why not?
 144       strStudyTimeDate   = "06_06_06_6_June_1666"; // Why not?
 145       subject_date       = "6_June_1666";          // Why not?
 146       subject_study_name = "defStudyName";         // Why not?
 147    }
 148     // subject_name is already in 'Patient Name'
 149     strStudyDescr = /*subject_name + "." + */ subject_study_name + "." + subject_entry + "." + subject_position + "." + subject_date;
 150
 151     // creation directory : 'nom de la Study'
 152
 153     std::string tempStringStudyDir(OutputDirName);
 154     tempStringStudyDir = tempStringPatDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + strStudyDescr;
 155
 156     res=CreateDirectory(tempStringStudyDir);
 157     if (!res) {
 158        std::cout << "[" << tempStringStudyDir << "] Directory creation failure " << std::endl;
 159        throw ( BrukerHopelessException ("Study directory creation failure "));
 160     }
 161
 162    char outputDirName[(unsigned int) PATH_MAX+2];
 163
 164    strStudyUID    = GDCM_NAME_SPACE::Util::CreateUniqueUID();
 165    serieNumber    = 0;
 166    instanceNumber = 0;
 167
 168    // -----------------------------------------------------
 169    // Iterate to ALL the objets(files/directories) found in the input directory
 170    // (this is level ZERO)
 171    // each Directory (name : 1, 2, 3, ...) will be a Dicom Serie
 172    // -----------------------------------------------------
 173
 174    GDCM_NAME_SPACE::DirListType::iterator it;
 175
 176    for (it = fileNames.begin();
 177          it != fileNames.end();
 178        ++it)
 179    {
 180       if ( boost::filesystem::is_directory(*it) )
 181       {
 182          if (verbose)
 183             std::cout << "[" << *it << "] is a directory" << std::endl;
 184
 185          //BrukerDataSet br_acqp;
 186          std::string strAcqp;
 187          strAcqp = (*it) +
 188                    GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 189                    "acqp";
 190
 191          br_acqp.LoadFile(strAcqp);
 192          br_acqp.FillMap();
 193
 194 //std::cout << "out of br_acqp.FillMap " << std::endl;
 195          std::string acqp_scan_name;
 196          std::string acqp_method;
 197          std::string acqp_protocol_location;
 198
 199          BrukerFieldData b_protocol_location=br_acqp.GetFieldData("ACQ_protocol_location");
 200          acqp_protocol_location = b_protocol_location.GetStringValue()[0];
 201          cleanString(acqp_protocol_location);
 202
 203 //std::cout << "out of br_acqp.FillMap 1" << std::endl;
 204          BrukerFieldData b_scan_name=br_acqp.GetFieldData("ACQ_scan_name");
 205 //std::cout << "out of br_acqp.FillMap 11" << std::endl;
 206          acqp_scan_name = b_scan_name.GetStringValue()[0];
 207 //std::cout << "out of br_acqp.FillMap 12 [" << acqp_scan_name << "]" << std::endl;
 208          cleanString(acqp_scan_name);
 209 //std::cout << "out of br_acqp.FillMap 2" << std::endl;
 210          BrukerFieldData b_method=br_acqp.GetFieldData("ACQ_method");
 211          b_method.PrintSelf();
 212          acqp_method = b_method.GetStringValue()[0];
 213
 214          cleanString(acqp_method);
 215 //std::cout << "out of br_acqp.FillMap 3" << std::endl;
 216          BrukerFieldData b_list_size = br_acqp.GetFieldData("ACQ_O1_list_size");
 217 //std::cout << "out of br_acqp.FillMap 4" << std::endl;
 218          //b_list_size.PrintSelf(); //JP
 219
 220          nbSlices =  b_list_size.GetIntValue()[0];
 221 //std::cout << "out of br_acqp.FillMap 5" << std::endl;
 222          strSerieDescr = GDCM_NAME_SPACE::Util::GetName(*it)
 223                        /*  + "." + acqp_protocol_location */ // always the same (in each acquisition)
 224                          + "." + acqp_scan_name
 225                          + "." + acqp_method.c_str();
 226
 227          sprintf(outputDirName, "%s%c%s", tempStringStudyDir.c_str(),                //OutputDirName.c_str(),
 228                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 229                           strSerieDescr.c_str() );
 230
 231          std::cout << " ================================================================================\n"
 232                    << " === [" << GDCM_NAME_SPACE::Util::GetName(*it) << "] -> [" << strSerieDescr << "]\n"
 233                    << " ================================================================================"
 234                    << std::endl;
 235
 236
 237         if (verbose)
 238            printf ("outputDirName [%s]\n", outputDirName);
 239         try {
 240            DealWithNiveau1(*it, outputDirName);
 241         }
 242         catch (BrukerHopelessException &e)
 243         {
 244          std::cout << "And Exception was thrown in DealWithNiveau1 (" << e.what() << ") " << std::endl;
 245          continue;
 246         }
 247       }
 248    } // end of : for (GDCM_NAME_SPACE::DirListType::iterator it
 249 }
 250
 251 // =====================================================================
 252
 253 void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string currentOutputDirName) {
 254 //
 255 // e.g. : at level 1, in B67d1.Bp1/6
 256 //
 257 // acqp  fid  imnd  pdata  pulseprogram  spnam0  spnam1
 258
 259    bool res = CreateDirectory(currentOutputDirName);
 260
 261    if (!res) {
 262       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 263       throw ( BrukerHopelessException ("Level 1 output directory creation failure "));
 264      // exit (0);
 265    }
 266    GDCM_NAME_SPACE::DirList dirList(level1Directory, false, true); // DON'T get recursively the list of files
 267    GDCM_NAME_SPACE::DirListType fileNames;
 268    fileNames = dirList.GetFilenames();
 269    // -----------------------------------------------------
 270    // Iterate to ALL the objets(files/directories) found in the input directory
 271    // -----------------------------------------------------
 272    GDCM_NAME_SPACE::DirListType::iterator it;
 273
 274    for (it = fileNames.begin();
 275         it != fileNames.end();
 276       ++it)
 277    {
 278       if ( boost::filesystem::is_regular(*it) )
 279       //if ( ! boost::filesystem::is_directory(*it) )
 280       {
 281          if (verbose)
 282             std::cout << "--- [" << *it << "] is a file." << std::endl;
 283       }
 284    }
 285
 286    char outputDirName[(unsigned int) PATH_MAX+2];
 287    //std::string firstName;
 288    bool canOpen;
 289    for (it = fileNames.begin();
 290         it != fileNames.end();
 291       ++it)
 292    {
 293       if ( boost::filesystem::is_directory(*it) )
 294       {
 295          // will be always "pdata" ...
 296          if (verbose)
 297             std::cout << "--- [" << *it << "] is a directory" << std::endl;
 298
 299               /* a recuperer :
 300               if (FileLine.startsWith("##$ACQ_size=")) {
 301               if (FileLine.startsWith("##$NI=")) {
 302               if (FileLine.startsWith("##$NR=")) {
 303               if (FileLine.startsWith("##$ACQ_obj_order=")) {
 304               if (FileLine.startsWith("##$ACQ_word_size=")) {
 305               if (FileLine.startsWith("##$BYTORDA=")) {
 306               if (FileLine.startsWith("##$PULPROG=")) {
 307               */
 308
 309          sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 310                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 311                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str());
 312          //br1.PrintSelf();
 313
 314           std::string strMethod;
 315           //std::string firstName = *(fileNames.begin());
 316
 317           strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin())) +
 318                       GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 319                       "method";
 320             // std::cout << "---strMethod (for method)=> [" << strMethod << "]" << std::endl;
 321           canOpen = br_method.LoadFile(strMethod);
 322           if (!canOpen)
 323           {
 324              strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
 325                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 326                          "imnd";
 327              //std::cout << "---strMethod (for imnd) => [" << strMethod << "]" << std::endl;
 328              canOpen = br_method.LoadFile(strMethod);
 329              if (!canOpen)
 330              {
 331                 std::cout << "Hopeless! neither 'method' nor 'imnd' found in ["
 332                           << level1Directory  << "]; we skip it!" << std::endl;
 333                 continue;
 334                 //throw ( BrukerHopelessException ("Hopeless! neither 'method' nor 'imnd' found "));
 335                 //exit(0);  /// \TODO throw an exception !
 336              }
 337           }
 338           if (verbose)
 339              std::cout << "open => [" << strMethod << "] successfully" << std::endl;
 340           br_method.FillMap();
 341
 342           /* a recuperer :
 343              ##$PVM_Fov (dimension)  // ou plutot RECO_fov !
 344           */
 345   /*
 346           dans method (pour perfusion  seulement?) :
 347           ##$PVM_ObjOrderList=( 8 )
 348           0 2 4 6 1 3 5 7
 349           ##$PVM_NSPacks=2
 350           ##$PVM_SPackArrNSlices=( 2 )
 351           7 1
 352   */
 353          try {
 354             DealWithNiveau2(*it, outputDirName);
 355          }
 356          catch (BrukerHopelessException &e)
 357          {
 358             std::cout << "And Exception was thrown in DealWithNiveau2 (" << e.what() << ") " << std::endl;
 359             continue;
 360          }
 361       }
 362    }
 363 }
 364
 365 // =====================================================================
 366
 367 void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string currentOutputDirName) {
 368
 369 // e.g. : at level 2 in B67d1.Bp1/6/pdata
 370 //
 371 // acqp  fid  imnd  pdata  pulseprogram  spnam0  spnam1
 372 //
 373
 374    bool res = CreateDirectory(currentOutputDirName);
 375
 376    if (!res) {
 377       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 378       throw ( BrukerHopelessException ("Hopeless! Level2 output directory creation failure"));
 379       //exit (0);
 380    }
 381
 382    GDCM_NAME_SPACE::DirList dirList(level2Directory, false, true); // DON'T get recursively the list of files
 383
 384    GDCM_NAME_SPACE::DirListType fileNames;
 385    fileNames = dirList.GetFilenames();
 386
 387    char outputDirName[(unsigned int) PATH_MAX+2];
 388
 389    // -----------------------------------------------------
 390    // Iterate to ALL the objets(files/directories) found in the input directory
 391    // -----------------------------------------------------
 392    GDCM_NAME_SPACE::DirListType::iterator it;
 393    bool canOpen;
 394
 395    if (verbose)
 396    for (it = fileNames.begin();
 397         it != fileNames.end();
 398       ++it)
 399    {
 400       if ( ! boost::filesystem::is_directory(*it) )
 401       {
 402          std::cout << "--- --- [" << *it << "] is a file.." << std::endl;
 403       }
 404
 405    }
 406
 407    for (it = fileNames.begin();
 408          it != fileNames.end();
 409        ++it)
 410    {
 411       if ( boost::filesystem::is_directory(*it) )
 412       {
 413
 414          if (verbose)
 415             std::cout << "--- --- [" << *it << "] is a directory" << std::endl;
 416
 417         // sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 418         //                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 419         //                                GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
 420   // MUST be 'pdata'!
 421
 422 //
 423 // (interest of previous method :
 424 // If unaware user changed the pdata name, it goes on working
 425 //
 426           std::string str_isa;
 427           str_isa = (*it) +
 428                     GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 429                    "isa";
 430
 431           std::string str_isa_func_name;
 432           canOpen = br_isa.LoadFile(str_isa);
 433           if (!canOpen)
 434           {
 435              sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 436                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 437                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
 438           }
 439           else
 440           {
 441              br_isa.FillMap();
 442              BrukerFieldData b_isa_func_name = br_isa.GetFieldData("ISA_func_name");
 443
 444              str_isa_func_name = b_isa_func_name.GetStringValue()[0];
 445              cleanString(str_isa_func_name);
 446
 447              sprintf(outputDirName, "%s%c%s.%s", currentOutputDirName.c_str(),
 448                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 449                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str(),
 450              str_isa_func_name.c_str());
 451           }
 452           try {
 453              DealWithNiveau3(*it, outputDirName);
 454           }
 455           catch (BrukerHopelessException &e)
 456           {
 457              std::cout << "And Exception was thrown in DealWithNiveau3 (" << e.what() << "); "
 458                        << " We skip [" << level2Directory << "]" << std::endl;
 459              continue;
 460           }
 461           catch (BrukerInitException &e)
 462           {
 463              std::cout << "And Init Exception was thrown in DealWithNiveau3 (" << e.what() << "); "
 464                        << " We skip [" << level2Directory << "]" << std::endl;
 465              continue;
 466           }
 467       }
 468    }
 469 }
 470
 471
 472 //
 473 // =====================================================================
 474 //
 475
 476 void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string currentOutputDirName){
 477
 478 //
 479 // e.g. at level 3, in
 480
 481    // just to be able to go on checking // JP
 482    if ( GDCM_NAME_SPACE::Util::GetName(level3Directory) != "1")
 483       return;
 484
 485    bool res = CreateDirectory(currentOutputDirName);
 486
 487    if (!res)
 488    {
 489       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 490       throw ( BrukerHopelessException ("Hopeless! Level3 output directory creation failure"));
 491       //exit (0);
 492    }
 493
 494    GDCM_NAME_SPACE::DirList dirList(level3Directory, false, true); // DON'T get recursively the list of files
 495    GDCM_NAME_SPACE::DirListType::iterator it;
 496    GDCM_NAME_SPACE::DirListType fileNames;
 497    fileNames = dirList.GetFilenames();
 498
 499    char original2dseqName       [(unsigned int) PATH_MAX+2];
 500    char original2dseqName_XXX   [(unsigned int) PATH_MAX+2];
 501    char currentOutputMhdDirName [(unsigned int) PATH_MAX+2];
 502
 503    char outputMhdFileName       [(unsigned int) PATH_MAX+2];
 504    char output2dseqSliceFileName[(unsigned int) PATH_MAX+6]; // think about extra '.dcm'
 505    char output2dseqName         [(unsigned int) PATH_MAX+6];
 506    char output2dseqCartoName    [(unsigned int) PATH_MAX+6];
 507
 508    char copyFile[PATH_MAX + PATH_MAX + 5]; // Should be enough!
 509    bool canOpen;
 510
 511    //-------------- try d3proc;
 512    char char_d3proc[(unsigned int) PATH_MAX+2];
 513
 514    sprintf(char_d3proc,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"d3proc" );
 515
 516    if (verbose)
 517       std::cout << "d3proc: --- => [" << char_d3proc << "]" << std::endl;
 518    std::string str_d3proc(char_d3proc);
 519    canOpen = br_d3proc.LoadFile(str_d3proc);
 520
 521    if (!canOpen)
 522    {
 523       std::cout << "Hopeless! no 'd3proc' found" << std::endl;
 524       throw ( BrukerHopelessException ("Hopeless! no 'd3proc' found"));
 525       //exit(0);  /// \TODO throw an exception !
 526    }
 527
 528    canOpen = br_d3proc.FillMap();
 529    if (!canOpen)
 530    {
 531       std::cout << "Hopeless! FillMap failed on 'd3proc'" << std::endl;
 532       throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'd3proc'"));
 533       //exit(0);  /// \TODO throw an exception !
 534    }
 535
 536    //-------------- end try d3proc;
 537
 538
 539  // -------------------try reco
 540
 541    char char_reco[(unsigned int) PATH_MAX+2];
 542
 543    sprintf(char_reco,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
 544     //str_d3proc = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
 545     //             GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 546     //             "d3proc";
 547    if (verbose)
 548       std::cout << "reco --- => [" << char_reco << "]" << std::endl;
 549    std::string str_reco(char_reco);
 550    canOpen = br_reco.LoadFile(str_reco);
 551
 552    if (!canOpen) // we try in directory ../1
 553    {
 554       if (verbose)
 555          std::cout << "[" << str_reco << "] not found " << std::endl;
 556       std::string lastDirName = GDCM_NAME_SPACE::Util::GetPath(level3Directory);
 557       //lastDirName = GDCM_NAME_SPACE::Util::GetPath(lastDirName);
 558       sprintf(char_reco,"%s%c1%c%s", lastDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
 559       str_reco=char_reco;
 560       canOpen = br_reco.LoadFile(str_reco);
 561       if (!canOpen)
 562       {
 563          std::cout << "Hopeless! cannot find 'reco' in [" << str_reco << "]"  << std::endl;
 564          throw ( BrukerHopelessException ("Hopeless! cannot find 'reco'"));
 565          //exit(0);  /// \TODO throw an exception !
 566       }
 567    }
 568
 569    canOpen = br_reco.FillMap();
 570    if (!canOpen)
 571    {
 572       std::cout << "Hopeless! FillMap failed on [" << str_reco << "]" << std::endl;
 573       throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'reco'"));
 574       //exit(0);  /// \TODO throw an exception !
 575    }
 576    //std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
 577    // br_reco.PrintSelf();
 578    // std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
 579    // -------------------end try reco
 580
 581
 582    BrukerFieldData bX = br_d3proc.GetFieldData("IM_SIX");
 583    int NX = bX.GetIntValue()[0];
 584
 585    if (verbose)
 586       std::cout << "IM_SIX " << NX << std::endl;
 587    BrukerFieldData bY=br_d3proc.GetFieldData("IM_SIY");
 588    int NY = bY.GetIntValue()[0];
 589
 590    if (verbose)
 591          std::cout << "IM_SIY " << NY << std::endl;
 592    /// \todo : check if there are actually 3 dimensions or only 2
 593
 594    BrukerFieldData bZ= br_d3proc.GetFieldData("IM_SIZ");
 595    int nbFrames = bZ.GetIntValue()[0];
 596    if (verbose)
 597          std::cout << "IM_SIZ " << nbFrames << std::endl;
 598
 599         // WARNING DATTYPE is, either in {ip_short, ip_int, ip_char, ...}, or in {1, 2, 3, ...}
 600
 601    BrukerFieldData bDPT = br_d3proc.GetFieldData("DATTYPE");
 602
 603    std::string mhdDataPixelType;
 604    int pixelSize;
 605    getImhDataType(bDPT, mhdDataPixelType, pixelSize);
 606
 607
 608  /*
 609
 610  // See mail Denis :
 611  // En regle generale il vaut mieux que l'on passe par RECO_*
 612  // pour extraire les parametres de l'image
 613  //
 614
 615    BrukerFieldData fov = br_method.GetFieldData("PVM_Fov");
 616    double fovX = fov.GetDoubleValue()[0];
 617    double fovY = fov.GetDoubleValue()[1];
 618    if (verbose)
 619       std::cout << "FOV (ds method) " << fovX << " " << fovY << std::endl;
 620
 621    BrukerFieldData spatResol = br_method.GetFieldData("PVM_SpatResol");
 622    double spatResolX = spatResol.GetDoubleValue()[0];
 623    double spatResolY = spatResol.GetDoubleValue()[1];
 624    if (verbose)
 625       std::cout << "SpatResol (ds method) " << spatResolX << " " << spatResolY << std::endl;
 626    BrukerFieldData bsliceDistance = br_method.GetFieldData("PVM_SPackArrSliceDistance");
 627
 628    double sliceDistance = bsliceDistance.GetDoubleValue()[0];
 629 */
 630
 631 // Better we use 'get' accessors from BrukerImage class, as Denis wrote them
 632
 633    BrukerFieldData fov = br_reco.GetFieldData("RECO_Fov");
 634    double fovX = fov.GetDoubleValue()[0];
 635    double fovY = fov.GetDoubleValue()[1];
 636    if (verbose)
 637       std::cout << "FOV (ds method) " << fovX << " " << fovY << std::endl;
 638
 639    BrukerFieldData spatResol = br_reco.GetFieldData("RECO_SpatResol");
 640    double spatResolX = spatResol.GetDoubleValue()[0];
 641    double spatResolY = spatResol.GetDoubleValue()[1];
 642    if (verbose)
 643       std::cout << "SpatResol (ds method) " << spatResolX << " " << spatResolY << std::endl;
 644
 645    /// \TODO probabely a more sophisticated accessor will be necessary :
 646    ///  (cf : non contiguous slices, overlapping, slice thickness, space between slices, etc)
 647
 648    BrukerFieldData bsliceDistance = br_method.GetFieldData("RECO_SPackArrSliceDistance");
 649    double sliceDistance = bsliceDistance.GetDoubleValue()[0];
 650
 651 // ----------------------------------------------------------------------------------------
 652
 653    if (mhd)
 654    {
 655       sprintf(currentOutputMhdDirName, "%s%c%s", currentOutputDirName.c_str(),
 656                                GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "MhdFiles");
 657       res = CreateDirectory( currentOutputMhdDirName );
 658       if (!res) {
 659          std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 660          throw ( BrukerHopelessException ("Hopeless!FillMap failed on 'reco'"));
 661          //exit (0);
 662       }
 663
 664       if (verbose)
 665          std::cout << "Directory creation [" <<  currentOutputDirName << "]" << std::endl;
 666    }  // end if mhd
 667
 668    if (verbose)
 669          std::cout << "nbFrames " << nbFrames << std::endl;
 670    if (verbose)
 671          std::cout << "nbSlices " << nbSlices << std::endl;
 672    int k;
 673    int nbInstants = nbFrames/nbSlices;
 674    if (verbose)
 675          std::cout << "nbInstants (deduced )" << nbInstants << std::endl;
 676    int instantNb;
 677    int sliceNb;
 678    FILE *fp;  // for MHD files
 679
 680    sprintf( original2dseqName, "%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "2dseq");
 681
 682 /**/
 683   // \TODO : tenir compte du bazar precedent
 684
 685     // load 2dseq in memory
 686
 687    fp = fopen(original2dseqName, "rb");
 688    if (!fp)
 689    {
 690       // try 2dseq_Angio2D ?!?
 691
 692       sprintf( original2dseqName_XXX, "%s%s", original2dseqName, "_Angio2D");
 693       fp = fopen(original2dseqName_XXX, "rb");
 694       if (!fp)
 695       {
 696          std::cout << "Cannot open [" << original2dseqName << "] nor [" <<  original2dseqName_XXX << "] for reading" << std::endl;
 697          fclose(fp);
 698          throw ( BrukerHopelessException ("Hopeless! Cannot open '2dseq'"));
 699          //exit (0);
 700       }
 701    }
 702
 703    unsigned char *buffer_2dseq = new unsigned char[NX*NY*pixelSize*nbSlices*nbInstants];
 704    ///\ TODO : find a safer way to be sure to read everything!
 705    size_t lgr = fread(buffer_2dseq, 1, NX*NY*pixelSize*nbSlices*nbInstants, fp);
 706
 707    // This one will be important!
 708    // ---------------------------
 709    try {
 710       imageSet = CreateImageSet ( );
 711    }
 712    catch (BrukerInitException& e)
 713    {
 714       if (verbose)
 715          std::cout <<  "an Init Exception was thrown in CreateImageSet ( ); " << e.what()
 716                    <<  "catched in DealWithNiveau3" << std::endl;
 717       //return;
 718       throw (e);
 719    }
 720
 721    serieNumber++;
 722    strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 723    if (nbInstants==1) // creer un seul fichier .mhd  pour toutes les Slices! (images natives)
 724    {
 725        if (verbose)
 726           std::cout << "Single instant : do not split" << std::endl;
 727        if (mhd)
 728        {
 729              sprintf(outputMhdFileName, "%s%cMhdData_All_the_Slices.mhd", currentOutputMhdDirName,
 730                                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 731              fp=fopen(outputMhdFileName, "w");
 732              if (!fp)
 733              {
 734                 std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 735                 throw ( BrukerHopelessException ("Hopeless! Cannot open  mhd file for writting"));
 736                 //exit(0);
 737              }
 738              else
 739              {
 740                fprintf(fp, "ObjectType = Image\n");
 741                fprintf(fp, "NDims = 3\n" );
 742                fprintf(fp, "BinaryData = True \n" );
 743                fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 744                fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices );
 745                fprintf(fp, "HeaderSize = %d\n", 0);
 746                //fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
 747                fprintf(fp, "ElementSpacing = %lf %lf %lf\n", spatResolX, spatResolY, sliceDistance );
 748                fprintf(fp, "Position = 0 0 %d\n", 0 );
 749                fprintf(fp, "Offset = 0 0 0\n" );
 750                fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 751                fprintf(fp, "ElementNumberOfChannels = 1\n" );
 752                fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
 753                fprintf(fp, "ElementDataFile = %s\n", "../2dseq_All_the_Slices" );
 754                fclose(fp);
 755              }
 756              sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices",
 757                                        currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 758              fp=fopen(output2dseqSliceFileName, "wb");
 759              if (!fp)
 760              {
 761                 std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 762                 throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseq file for writting"));
 763              }
 764              else
 765              {
 766                 fwrite( buffer_2dseq, NX*NY*pixelSize, nbSlices, fp);
 767              }
 768              fclose(fp);
 769              serieNumber ++;
 770              strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 771        }  // end if mhd
 772        if (dicom)
 773        {
 774              sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices.dcm",
 775                                        currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 776
 777             /* ----------- Write Dicom Image  ---------------*/
 778              MakeDicomImage(buffer_2dseq,
 779                NX,
 780                NY,
 781                nbFrames,
 782                pixelSize,
 783                //fovX/NY, fovY/NY, sliceDistance,
 784                spatResolX, spatResolY, sliceDistance,
 785                output2dseqSliceFileName,
 786                subject_name,
 787                day,
 788                strStudyUID,
 789                strSerieUID,
 790                strStudyDescr,
 791                strSerieDescr,
 792                strStudyTimeDate,
 793                0,// index frame number
 794                GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
 795              );
 796        }  // end if dicom
 797    }  // end if nbInstants = 1
 798
 799    else  // more than ONE instant
 800    {
 801           // Interleaved !
 802           // it's (slice1,slide2, ...)t1 ; (slice1,slide2, ...)t2 ; ...
 803          unsigned char *pixelsForCurrentSlice = new unsigned char[NX*NY*pixelSize*nbInstants];
 804
 805          k = 0;
 806          for (sliceNb=0; sliceNb<nbSlices; sliceNb++)
 807          {
 808             if (mhd)
 809             {
 810                sprintf(outputMhdFileName, "%s%cMhdData_%03d.mhd", currentOutputMhdDirName,
 811                                         GDCM_NAME_SPACE::GDCM_FILESEPARATOR, k  );
 812                if (verbose)
 813                   std::cout << "--- Output MHD file [" << outputMhdFileName << "]" << std::endl;
 814                fp=fopen(outputMhdFileName, "w");
 815                if (!fp)
 816                {
 817                    std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 818                    throw ( BrukerHopelessException ("Hopeless! Cannot open  mhd file for writting"));
 819                    //exit(0);
 820                }
 821                else
 822                {
 823             /* ----------- Write MHD Image  ---------------*/
 824                 //if (verbose)
 825                 //   std::cout << "Open sucessfully[" << outputMhdFileName << "] for writting" << std::endl;
 826                    fprintf(fp, "ObjectType = Image\n");
 827                    fprintf(fp, "NDims = 3\n" );
 828                    fprintf(fp, "BinaryData = True \n" );
 829                    fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 830                    fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbInstants);
 831                    fprintf(fp, "HeaderSize = %d\n", 0);
 832                    //fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, 1.0 ); //
 833                    fprintf(fp, "ElementSpacing = %lf %lf %lf\n",spatResolX, spatResolY, 1.0 ); //slice distance : no meaning for temporal serie
 834                    fprintf(fp, "Position = 0 0 %d\n", sliceNb );
 835                    fprintf(fp, "Offset = 0 0 0\n" );
 836                    fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 837                    fprintf(fp, "ElementNumberOfChannels = 1\n" );
 838                    fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
 839                    fprintf(fp, "ElementDataFile = ..%c2dseq_Slice_%d\n", GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb );
 840                    fclose(fp);
 841                } // end write MHD
 842
 843                sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d",
 844                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,sliceNb);
 845                fp=fopen(output2dseqSliceFileName, "wb");
 846                if (!fp)
 847                {
 848                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 849                    throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseqSliceFile file for writting"));
 850                    //exit (0);
 851                }
 852                int frameSize = NX*NY*pixelSize;
 853                for (instantNb=0; instantNb<nbInstants; instantNb++)
 854                {
 855 // std::cout << "------------SN " << sliceNb << " IN " << instantNb <<  " T " << nbSlices*instantNb + sliceNb << std::endl;
 856                     fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
 857                             frameSize,
 858                             1, fp);
 859                }
 860                fclose(fp);
 861 // std::cout << "end writting[" << output2dseqSliceFileName << "]" << std::endl;
 862             }  // end if mhd
 863
 864             if (dicom)
 865             {
 866                // desperate try !
 867              /*
 868                sprintf(output2dseqSliceFileName, "%sdummy_buffer",
 869                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 870                fp=fopen(output2dseqSliceFileName, "wb");
 871                if (!fp)
 872                {
 873                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 874                    exit (0);
 875                }
 876                int frameSize = NX*NY*pixelSize;
 877                for (instantNb=0; instantNb<nbInstants; instantNb++)
 878                {
 879 // std::cout << "------------SN " << sliceNb << " IN " << instantNb <<  " T " << nbSlices*instantNb + sliceNb << std::endl;
 880                     fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
 881                             frameSize,
 882                             1, fp);
 883                }
 884                fclose(fp);
 885
 886                fp=fopen(output2dseqSliceFileName, "rb");
 887                if (!fp)
 888                {
 889                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for reading" << std::endl;
 890                    exit (0);
 891                }
 892                fread( pixelsForCurrentSlice,
 893                             frameSize*nbInstants,
 894                             1, fp);
 895                fclose(fp);
 896               // end of desperate try !
 897               */
 898
 899                /* ----------- Write Dicom Image  ---------------*/
 900
 901                int frameSize = NX*NY*pixelSize;
 902                for (instantNb=0; instantNb<nbInstants; instantNb++)
 903                {
 904                   memcpy(pixelsForCurrentSlice + frameSize*instantNb, buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize, frameSize);
 905                }
 906
 907                int indOfFirsImageWithinImageSet =  nbSlices*instantNb;
 908                sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d.dcm",
 909                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb);
 910
 911                MakeDicomImage(
 912                   pixelsForCurrentSlice,
 913                   NX,
 914                   NY,
 915                   nbInstants,
 916                   pixelSize,
 917                   spatResolX, spatResolY, sliceDistance,
 918                   //fovX/NY, fovY/NY, sliceDistance,
 919                   output2dseqSliceFileName,
 920                   subject_name,
 921                   day,
 922                   strStudyUID,
 923                   strSerieUID,
 924                   strStudyDescr,
 925                   strSerieDescr,
 926                   strStudyTimeDate,
 927                   sliceNb*nbInstants,
 928                   GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
 929                );
 930                if (verbose)
 931                   std::cout << "--- Output DCM file [" << output2dseqSliceFileName << "]" << std::endl;
 932
 933            } // en if dicom
 934
 935         k++;
 936         }
 937         delete [] pixelsForCurrentSlice;
 938      }  // end nbInstants == 1
 939    delete [] buffer_2dseq;
 940 /**/
 941
 942
 943    // -----------------------------------------------------
 944    //  deal with MatLab-generated Carto file.
 945    // -----------------------------------------------------
 946
 947    dealWithCarto(fileNames,  NX,  NY,  nbSlices, /*fovX, fovY,*/ spatResolX, spatResolY, sliceDistance,
 948                    copyFile, currentOutputDirName, outputMhdFileName, output2dseqCartoName);
 949 }
 950
 951
 952 // ===========================================================================================
 953
 954 void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX, int NY, int nbSlices,
 955                                  /*double fovX, double fovY, */
 956                                  double spatResolX, double spatResolY, double sliceDistance,
 957                                  char *copyFile, std::string &currentOutputDirName,
 958                                  char *outputMhdFileName, char *output2dseqCartoName)
 959 {
 960    // -----------------------------------------------------
 961    //  deal with MatLab-generated Carto file.
 962    // -----------------------------------------------------
 963
 964    char *code[] = { "ADC", "adc", "TTP", "ttp", "PEAK", "peak", "" };  // add more carto file name identifiers if necessary; end with ""
 965    char *separator[] =  { "_", ".", "-", "" }; //  add more, if necessary, to ckeck for 2dseq.ADC, 2dseq_ADC, 2dseq-ADC, etc; end with ""
 966    int icode;
 967    int iseparator;
 968    GDCM_NAME_SPACE::DirListType::iterator it;
 969    char file_name_ident[500];
 970    FILE *fp;
 971
 972    // Iterate to ALL the objets(files/directories) found in the input directory
 973    for (it = fileNames.begin();
 974         it != fileNames.end();
 975       ++it)
 976    {
 977       if ( boost::filesystem::is_regular(*it) )
 978       //if ( ! boost::filesystem::is_directory(*it) )
 979       {
 980          if (verbose)
 981             std::cout << "--- [" << *it << "] is a file..." << std::endl;
 982
 983          icode      = 0;
 984          while (code[icode][0] != 0)
 985          {
 986          iseparator = 0;
 987          while (separator[iseparator][0] != 0)
 988          {
 989             sprintf(file_name_ident, "2dseq%s%s",separator[iseparator],code[icode]); // e.g  "2dseq_ADC"
 990             //if (verbose)
 991             //   std::cout << "check name ["<<(*it) << "] for string [" << file_name_ident << "]" << std::endl;
 992             std::string::size_type loc = (*it).rfind(file_name_ident);
 993
 994             if ( loc != std::string::npos )
 995             {
 996
 997        ///\ TODO : find a safer way to be sure to read everything!
 998               unsigned char *buffer_carto = new unsigned char[NX*NY*sizeof(double)*nbSlices];
 999               fp = fopen ( (*it).c_str(), "rb");
1000               if (!fp){
1001                  std::cout << "Cannot open [" << *it << "] for reading" << std::endl;
1002                  throw ( BrukerHopelessException ("Level 1 Unable to open 'carto' file "));
1003                }
1004                fread(buffer_carto, NX*NY*sizeof(double), nbSlices, fp);
1005
1006                     // ?!?  sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() ,
1007                std::cout << "Deal with Carto file :[" <<*it << "], computed length : "
1008                          << NX*NY*sizeof(double)*nbSlices << std::endl;
1009                std::string lastFileName = GDCM_NAME_SPACE::Util::GetName((*it).c_str());
1010                if (mhd)
1011                {
1012                   // Copy the data file in the new directory
1013                   sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() ,
1014                             currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str());
1015                   system(copyFile);
1016                   sprintf(outputMhdFileName, "%s%c%s%s",
1017                                          currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".mhd" );
1018                   if (verbose)
1019                     std::cout << "--- Output Carto MHD file [" << outputMhdFileName << "]" << std::endl;
1020
1021                   FILE *fp;
1022                   fp=fopen(outputMhdFileName, "w");
1023                   if (!fp)
1024                   {
1025                      std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
1026                   }
1027                   else
1028                   {
1029                      fprintf(fp, "ObjectType = Image\n");
1030                      fprintf(fp, "NDims = 3\n" );
1031                      fprintf(fp, "BinaryData = True \n" );
1032                      fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
1033                      fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices);
1034                      fprintf(fp, "HeaderSize = %d\n", 0 );
1035                      fprintf(fp, "ElementSpacing = %lf %lf %lf\n",spatResolX, spatResolY, sliceDistance );
1036                      fprintf(fp, "Position = 0 0 0\n" );
1037                      fprintf(fp, "Offset = 0 0 0\n" );
1038                      fprintf(fp, "CenterOfRotation = 0 0 0\n" );
1039                      fprintf(fp, "ElementNumberOfChannels = 1\n" );
1040                      fprintf(fp, "ElementType = %s\n", "MET_DOUBLE" );
1041                      fprintf(fp, "ElementDataFile = %s\n", lastFileName.c_str() );
1042
1043                      fclose(fp);
1044                   }
1045                   if (verbose)
1046                      std::cout << "--- end write Carto MHD file [" << outputMhdFileName << "]" << std::endl;
1047                }  // end if mhd
1048
1049             // ----------- Write Dicom Image  ---------------
1050
1051                if (dicom)
1052                {
1053                   sprintf(output2dseqCartoName, "%s%c%s%s",
1054                                        currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".dcm" );
1055                   if (verbose)
1056                      std::cout << "--- end create name output2dseqCartoName file [" << output2dseqCartoName << "]" << std::endl;
1057
1058                   strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID(); //New SerieUID for each carto.
1059                   std::string strNewSerieDescr(strSerieDescr+ "_" +GDCM_NAME_SPACE::Util::GetName((*it).c_str()));
1060                   MakeDicomImage(buffer_carto,
1061                      NX,
1062                      NY,
1063                      nbSlices,
1064                      8, // pixelSize
1065                      //fovX/NY, fovY/NY, sliceDistance,
1066                      spatResolX, spatResolY, sliceDistance,
1067                      output2dseqCartoName,
1068                      subject_name,
1069                      day,
1070                      strStudyUID,
1071                      strSerieUID,
1072                      strStudyDescr,
1073                      strNewSerieDescr,
1074                      strStudyTimeDate,
1075                      0,
1076                      GDCM_NAME_SPACE::CREATED_IMAGE
1077                   );
1078                }  // end if dicom
1079
1080                delete [] buffer_carto;
1081                if (verbose)
1082                   std::cout << "--- End writing Carto DICOM file [" << output2dseqCartoName << "]" << std::endl;
1083                break; // don't check for more ident on same file name!
1084
1085             }  // end deal with _ADC, -adc, etc
1086           iseparator ++;
1087           }  // end iterate speparators
1088           icode++;
1089           } // end iterate code
1090       } // end boost::filesystem::is_regular(*it)
1091    } // end iterate on all objects (files, dir, etc)
1092 } // end method
1093
1094
1095 // ==========================================================================================================
1096
1097 bool Bruker2Dicom::CreateDirectory(std::string OutputDirName)
1098 {
1099    std::string systemCommand;
1100
1101    if (verbose)
1102       std::cout << "Check for output directory :[" << OutputDirName << "]."
1103                 <<std::endl;
1104    if ( ! boost::filesystem::is_directory(OutputDirName) )    // dirout not found
1105    {
1106       std::string strDirNameout(OutputDirName);        // to please gcc 4
1107       systemCommand = "mkdir " + strDirNameout;        // create it!
1108       if (verbose)
1109          std::cout << systemCommand << std::endl;
1110       system (systemCommand.c_str());
1111       if ( ! boost::filesystem::is_directory(OutputDirName) ) // be sure it worked
1112       {
1113          if (verbose)
1114             std::cout << "KO : not a dir : [" << OutputDirName << "] (creation failure ?)" << std::endl;
1115          //return 0;
1116          throw ( BrukerHopelessException ("Level 1 output directory creation failure "));
1117       }
1118       else
1119       {
1120          if (verbose)
1121            std::cout << "Directory [" << OutputDirName << "] created." << std::endl;
1122       }
1123    }
1124    else
1125    {
1126        if (verbose)
1127             std::cout << "Output Directory [" << OutputDirName << "] already exists; Used as is." << std::endl;
1128    }
1129
1130    return 1;
1131
1132 }
1133
1134
1135 // ===========================================================================================
1136
1137 /// \TODO move cleanString to 'crea' ?
1138
1139 void Bruker2Dicom::cleanString(std::string &s)
1140 {
1141    int l = s.size();
1142    if (s[l-1] == 0x0A || s[l-1] == 0x0D ) // CR or NL
1143    {
1144       l--;
1145       s = s.substr(0, l);
1146    }
1147    if (s[l-1] == ' ' ) // blank space
1148    {
1149       l--;
1150       s = s.substr(0, l);
1151    }
1152
1153    if (s[0] == '<')
1154       s= s.substr(1,l-2);
1155    std::string repChar("_");
1156    GDCM_NAME_SPACE::Util::ReplaceSpecChar(s, repChar);
1157 }
1158
1159
1160
1161 // ===========================================================================================
1162
1163
1164 void Bruker2Dicom::getImhDataType(BrukerFieldData &bDPT, std::string &mhdDataPixelType, int &pixelSize)
1165 {
1166    if(bDPT.GetDataType() == "string")
1167    {
1168          std::string brukerDataPixelType = bDPT.GetStringValue()[0];
1169          if (verbose)
1170             std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
1171          //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
1172
1173          if (brukerDataPixelType ==  "ip_short") {
1174             mhdDataPixelType = "MET_USHORT";
1175             pixelSize = 2;
1176          }
1177          if (brukerDataPixelType ==  "ip_int") {
1178             mhdDataPixelType = "MET_UINT";
1179             pixelSize = 4;
1180          }
1181          if (brukerDataPixelType ==  "ip_char") {
1182              mhdDataPixelType = "MET_UCHAR";
1183              pixelSize = 1;
1184          }
1185                   /// \TODO : finish the list
1186     /*
1187     case 0 : fp << "ElementType = MET_CHAR" << std::endl;
1188       break;
1189     case 1 : fp << "ElementType = MET_UCHAR" << std::endl;
1190       break;
1191     case 2 : fp << "ElementType = MET_SHORT" << std::endl;
1192       break;
1193     case 3 : fp << "ElementType = MET_USHORT" << std::endl;
1194       break;
1195     case 4 : fp << "ElementType = MET_INT" << std::endl;
1196       break;
1197     case 5 : fp << "ElementType = MET_UINT" << std::endl;
1198       break;
1199     case 6 : fp << "ElementType = MET_FLOAT" << std::endl;
1200       break;
1201     case 7 : fp << "ElementType = MET_DOUBLE" << std::endl;
1202     */
1203     }
1204     else
1205     {
1206          int brukerDataPixelType = bDPT.GetIntValue()[0];
1207          if (verbose)
1208             std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
1209          //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
1210
1211 // Cross your fingers !!!
1212
1213 // pb : found values : 2, 3, 5
1214
1215          if (brukerDataPixelType ==  2) {
1216             mhdDataPixelType = "MET_USHORT";
1217             pixelSize = 2;
1218          }
1219          if (brukerDataPixelType ==  3) {
1220             mhdDataPixelType = "MET_USHORT";
1221             pixelSize = 2;
1222          }
1223          if (brukerDataPixelType ==  1) {
1224             mhdDataPixelType = "MET_UCHAR";
1225             pixelSize = 1;
1226          }
1227     }
1228 }
1229
1230 // ===========================================================================================
1231
1232 std::vector<BrukerImage> Bruker2Dicom::CreateImageSet ( )
1233 {
1234          std::vector<BrukerImage> imageSet;
1235          br_acqp.SetLoopStructure();
1236          std::vector<int> tempVect                      = br_acqp.GetLoopStructure() ;
1237          std::map<std::string, BrukerFieldData> map     = br_acqp.GetBrukerHeaderMap();
1238
1239          bool result                                    = br_acqp.ObjectVaryingProperties.init(map,tempVect);
1240
1241          if (result == false)
1242          {
1243             throw ( BrukerInitException  ("ObjectVaryingProperties.init() failure in Bruker2Dicom::CreateImageSet()") );
1244          }
1245
1246          br_acqp.SetImageLoopStructure();
1247          br_acqp.SetBrukerImageList();
1248          std::vector<std::vector<int> > brukerImageList = br_acqp.GetBrukerImageList();
1249
1250          BrukerImage image(br_acqp,br_reco);
1251          image.Init(br_acqp,br_reco,1);
1252
1253          for(int i=0;i<brukerImageList.size();i++)
1254          {
1255             image.Init(br_acqp,br_reco,i);
1256             imageSet.push_back(image);
1257          }
1258
1259  // Just for checking
1260  /*
1261
1262          std::vector<std::vector <double> > imageOrientation;
1263          std::vector <double> imagePosition;
1264          for(int i=0;i<brukerImageList.size();i++)
1265          {
1266            // fread(buffer_2dseq, NX*NY*pixelSize*nbSlices*nbInstants, 1, fp);
1267
1268            imagePosition = imageSet[i].getTranslationVectorRPS2XYZ();
1269            std::cout << "Position " << imagePosition[0] << " "
1270                      << imagePosition[1] << " "  << imagePosition[2] ;
1271            imageOrientation =  imageSet[i].getRotationMatrixRPS2XYZ();
1272            std::cout << "\t  Orientation " ;
1273            for(int i1=0; i1<3;i1++)for(int i2=0; i2<3;i2++)
1274               std::cout << imageOrientation[i1][i2] << " ";CreateImageSet
1275
1276            //std::cout << "\t  Abs Time " << imageSet[i].getAbsoluteTimePosition();
1277            std::cout << "\t  Relat Time " << imageSet[i].getRelativeTimePosition();
1278
1279            std::cout << "\t [";
1280            for (int i3=0; i3<imageSet[i].getLoopStamp().size();i3++)
1281               std::cout << " " << imageSet[i].getLoopStamp()[i3];
1282            std::cout << "]" << std::endl;
1283          }
1284 */
1285    return imageSet;
1286 }
1287
1288 // ===========================================================================================
1289
1290 void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels,
1291               int X,
1292               int Y,
1293               int nbFrames,
1294               int pixelSize,
1295               double spacingX, double spacingY, double sliceDistance,
1296               std::string dcmImageName,
1297               const std::string &patientName,
1298               const char *day,
1299               std::string &studyUID,
1300               std::string &serieUID,
1301               std::string &studyDescr,
1302               std::string &serieDescr,
1303               std::string &strStudyTimeDate,
1304               int imgNum,
1305               GDCM_NAME_SPACE::ImageContentType contentType
1306       )
1307 {
1308    std::ostringstream str;
1309
1310    GDCM_NAME_SPACE::File *file;
1311    file = GDCM_NAME_SPACE::File::New();
1312
1313   // Set the image size
1314    str.str("");
1315    str << X;
1316    file->InsertEntryString(str.str(),0x0028,0x0011,"US"); // Columns
1317    str.str("");
1318    str << Y;
1319    file->InsertEntryString(str.str(),0x0028,0x0010,"US"); // Rows
1320
1321    if (nbFrames != 1)
1322    {
1323       str.str("");
1324       str << nbFrames;
1325       file->InsertEntryString(str.str(),0x0028,0x0008,"IS"); // Number of Frames
1326    }
1327
1328   // Set the pixel type
1329   //      //8, 16, 32, 64 (for double ?)
1330    str.str("");
1331    str << pixelSize*8;
1332    file->InsertEntryString(str.str(),0x0028,0x0100,"US"); // Bits Allocated
1333
1334    file->InsertEntryString(str.str(),0x0028,0x0101,"US"); // Bits Stored
1335
1336    str.str("");
1337    str << pixelSize*8-1;
1338    file->InsertEntryString(str.str(),0x0028,0x0102,"US"); // High Bit
1339
1340   // Set the pixel representation // 0/1 , 0=unsigned
1341    file->InsertEntryString("1",0x0028,0x0103, "US"); // Pixel Representation
1342
1343   // Set the samples per pixel // 1:Grey level, 3:RGB
1344    file->InsertEntryString("1",0x0028,0x0002, "US"); // Samples per Pixel
1345
1346 //  0028 0030 DS 2 Pixel Spacing
1347    str.str("");
1348    str << spacingX << "\\" << spacingY;
1349    file->InsertEntryString(str.str(),0x0028,0x0030, "DS"); // Pixel Spacing
1350
1351  //   0018 0050 DS 1 Slice Thickness
1352    str.str("");
1353    str << sliceDistance;
1354    file->InsertEntryString(str.str(),0x0018,0x0050, "DS");
1355
1356 //    0020 0011 IS 1 Series Number
1357    str.str("");
1358    str << serieNumber;
1359    file->InsertEntryString(str.str(),0x0020,0x0011, "IS");
1360
1361 //    0020|0013 [IS]  [Instance Number]
1362    instanceNumber++;
1363    str.str("");
1364    str << instanceNumber;
1365    file->InsertEntryString(str.str(),0x0020,0x0013, "IS");
1366
1367
1368   // 1.2.840.10008.5.1.4.1.1.4.1 : Enhanced MR Image Storage
1369  //  file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0002, 0x0002, "UI");  // [Media Storage SOP Class UID]
1370   // file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0008, 0x0016, "UI");  // [SOP Class UID]
1371
1372
1373 // OK : MR is NOT multiframe, but I want just a quick an dirty solution
1374
1375 // 1.2.840.10008.5.1.4.1.1.4         MR Image Storage
1376    file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0002, 0x0002, "UI");  // [Media Storage SOP Class UID]
1377    file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0008, 0x0016, "UI");  // [SOP Class UID]
1378
1379   // if (strlen(patientName) != 0)
1380    file->InsertEntryString(patientName.c_str(),0x0010,0x0010, "PN"); // Patient's Name
1381
1382    file->InsertEntryString(studyUID, 0x0020, 0x000d, "UI");
1383    file->InsertEntryString(serieUID, 0x0020, 0x000e, "UI");
1384
1385 //  0008 0020 DA 1 Study Date
1386 //  0008 0030 TM 1 Study Time
1387
1388 /// \TODO split into 2 strings!
1389    file->InsertEntryString(strStudyTimeDate.substr(10,11).c_str(),0x0008,0x0020, "DA");
1390    file->InsertEntryString(strStudyTimeDate.substr(1,8).c_str(),  0x0008,0x0030, "TM");
1391
1392    file->InsertEntryString(studyDescr, 0x0008,0x1030, "LO");  // Study Description
1393    file->InsertEntryString(serieDescr, 0x0008,0x103e, "LO");  // Series Description
1394
1395 //0008|0060 [CS] [Modality]
1396    file->InsertEntryString("MR",0x0008,0x0060, "CS");
1397
1398 // 0020 0037 DS 6 Image Orientation (Patient)
1399    char charImageOrientation[256];
1400
1401 /*
1402 std::cout << "charImageOrientation  " <<
1403                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0] << " " <<
1404                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1] << " " <<
1405                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2] << " " <<
1406                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0] << " " <<
1407                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1] << " " <<
1408                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] << std::endl ;
1409 */
1410    sprintf(charImageOrientation,"%f\\%f\\%f \\ %f\\%f\\%f",
1411                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0],
1412                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1],
1413                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2],
1414                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0],
1415                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1],
1416                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] ) ;
1417
1418    file->InsertEntryString(charImageOrientation,0x0020,0x0037, "DS");
1419
1420
1421 // 0020 0032 DS 3 Image Position (Patient)
1422
1423    char charImagePosition[256];
1424    sprintf(charImagePosition,"%f\\%f\\%f",
1425                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[0],
1426                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[1],
1427                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[2]);
1428
1429    file->InsertEntryString(charImagePosition,0x0020,0x0032, "DS");  //0020 0032 DS 3 Image Position (Patient)
1430
1431
1432
1433 // 0020 0x1041 DS 1 Slice Location
1434 //        sprintf(charImagePosition,"%f",float(imgNum));
1435 //        file->InsertEntryString(charImagePosition,0x0020,0x1041, "DS");
1436 /*
1437   // Set Rescale Intercept
1438         str.str("");
1439         str << div;
1440         file->InsertEntryString(str.str(),0x0028,0x1052,"DS");
1441
1442   // Set Rescale Slope
1443         str.str("");
1444         str << mini;
1445         file->InsertEntryString(str.str(),0x0028,0x1053,"DS");
1446 */
1447
1448    GDCM_NAME_SPACE::FileHelper *fileH;
1449    fileH = GDCM_NAME_SPACE::FileHelper::New(file);
1450    fileH->SetContentType(contentType);
1451
1452    // cast is just to avoid warnings (*no* conversion is performed)
1453    //fileH->SetImageData((uint8_t *)img,int(maxX*maxY)*sizeof(uint16_t)); // troubles when maxX, mayY are *actually* float!
1454
1455 //std::cout << "--------------------------------  X*Y*nbFrames*pixelSize " << X << " " << Y << " " << nbFrames << " " << pixelSize << std::endl;
1456
1457    fileH->SetImageData((uint8_t *)tabPixels, X*Y*nbFrames*pixelSize);
1458    fileH->SetWriteModeToRaw();
1459    fileH->SetWriteTypeToDcmExplVR();
1460    if( !fileH->Write(dcmImageName)) {
1461       std::cout << "Failed for [" << dcmImageName << "]\n"
1462                 << "           File is unwrittable" << std::endl;
1463       file->Delete();
1464       fileH->Delete();
1465       throw ( BrukerHopelessException ("Level 1 Unable to write Dicom file "));
1466    }
1467    //if (verbose)
1468    //   file->Print();
1469
1470    file->Delete();
1471    fileH->Delete();
1472 }
1473
1474