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 //
  39 // e.g : at level 0, in : B67d1.Bp1
  40 //
  41 //           1  2  3  4  5  6  AdjStatePerStudy  subject
  42 //
  43
  44    std::string strDirNamein(InputDirName);
  45
  46 /* */
  47    GDCM_NAME_SPACE::DirList dirList(strDirNamein, false, true); // DON'T get recursively the list of files
  48
  49    GDCM_NAME_SPACE::DirListType fileNames;
  50    fileNames = dirList.GetFilenames();
  51
  52    std::string path = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()));
  53
  54    std::string subject =  path +
  55                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
  56                           "subject";
  57
  58     std::string acqp = path +
  59                        GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
  60                        "acqp";
  61
  62     if ( boost::filesystem::is_regular(subject) )
  63        subjectFound = true;
  64     else
  65        subjectFound = false; // user passed only a 'serie', not a 'study
  66
  67     if ( boost::filesystem::is_regular(acqp) )
  68        acqpFound= true;
  69     else
  70        acqpFound = false; // user passed a 'non study' directory; Hope it's a 'set of studies' directory!
  71
  72    int type;
  73    if  (subjectFound )  type = 1; // user passed a 'study
  74    else if  (acqpFound) type = 2; // user passed a 'serie'
  75    else                 type = 3; // user passed a 'non study' directory; Hope it's a 'set of studies' directory!
  76 /* */
  77
  78
  79    // 1 : if subjectFound                       : user passed a Single Study Directory
  80    // 2 : if NOT subjectFound and acqpFound     : user passed a Serie Directory
  81    // 3 : if NOT subjectFound and NOT acqpFound : user passed a 'non Study Directory' (Hope it's a set of Single Study Directories)
  82
  83   // int type = CheckUserDirectory(InputDirName);
  84
  85    switch (type)
  86    {
  87       case 1: {
  88          bool canOpen;
  89          canOpen =br_subject.LoadFile(subject);
  90          if (!canOpen)
  91          {
  92             std::cout << "Hopeless! 'subject' found / cannot be open" << std::endl;
  93             throw ( BrukerHopelessException ("Hopeless! 'subject' found in root input directory / cannot be open"));
  94          }
  95          else
  96          {
  97             br_subject.FillMap();
  98          }
  99    //br_subject.PrintSelf();
 100
 101   // get info for 'Study Description'
 102
 103           BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string");
 104           subject_name = b_name.GetStringValue()[0];
 105           strPatientName = subject_name;
 106           cleanString(subject_name);
 107           DealWithSingleStudyDirectory (fileNames);
 108           break;
 109        }
 110
 111        case 2: {
 112            subject_name = "defaultPatName";
 113            strPatientName = subject_name;
 114            DealWithSingleStudyDirectory (fileNames);
 115            break;
 116        }
 117
 118        case 3: {
 119          std::cout << " user passed a 'non study' directory; Hope it's a 'set of studies' directory!, not yet dealt with" << std::endl;
 120        }
 121    }
 122 }
 123
 124 void Bruker2Dicom::DealWithSingleStudyDirectory (GDCM_NAME_SPACE::DirListType &fileNames)
 125 {
 126      bool res;
 127     // creation directory : 'nom du patient'
 128     std::string tempStringPatDir(OutputDirName);
 129     tempStringPatDir = tempStringPatDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + subject_name;
 130
 131     res=CreateDirectory(tempStringPatDir);
 132     if (!res) {
 133        std::cout << "[" << tempStringPatDir << "] Directory creation failure " << std::endl;
 134        throw ( BrukerHopelessException ("Patient directory creation failure "));
 135     }
 136
 137     if (subjectFound)
 138     {
 139        BrukerFieldData b_entry=br_subject.GetFieldData("SUBJECT_entry");
 140        subject_entry = b_entry.GetStringValue()[0];
 141        //cleanString(subject_entry);
 142        subject_entry = subject_entry.substr(11, subject_entry.size()-11);
 143
 144        BrukerFieldData b_position=br_subject.GetFieldData("SUBJECT_position");
 145        subject_position = b_position.GetStringValue()[0];
 146        //cleanString(subject_position);
 147        subject_position = subject_position.substr(9, subject_position.size()-9);
 148
 149        BrukerFieldData b_date=br_subject.GetFieldData("SUBJECT_date");
 150        subject_date = b_date.GetStringValue()[0];
 151        strStudyTimeDate = subject_date;
 152        cleanString(subject_date);
 153
 154        BrukerFieldData b_study_name=br_subject.GetFieldData("SUBJECT_study_name");
 155        subject_study_name = b_study_name.GetStringValue()[0];
 156        subject_study_name = subject_study_name.substr(1, subject_study_name.size()-2);
 157        cleanString(subject_study_name);
 158    }
 159    else  // Desperate trick when file 'subject' is missing
 160    {
 161       subject_entry      = "HeadFirst";            // Why not?
 162       subject_position   = "Supine";               // Why not?
 163       strStudyTimeDate   = "06_06_06_6_June_1666"; // Why not?
 164       subject_date       = "6_June_1666";          // Why not?
 165       subject_study_name = "defStudyName";         // Why not?
 166    }
 167     // subject_name is already in 'Patient Name'
 168     strStudyDescr = /*subject_name + "." + */ subject_study_name + "." + subject_entry + "." + subject_position + "." + subject_date;
 169
 170     // creation directory : 'nom de la Study'
 171
 172     std::string tempStringStudyDir(OutputDirName);
 173     tempStringStudyDir = tempStringPatDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + strStudyDescr;
 174
 175     res=CreateDirectory(tempStringStudyDir);
 176     if (!res) {
 177        std::cout << "[" << tempStringStudyDir << "] Directory creation failure " << std::endl;
 178        throw ( BrukerHopelessException ("Study directory creation failure "));
 179     }
 180
 181    char outputDirName[(unsigned int) PATH_MAX+2];
 182
 183    strStudyUID    = GDCM_NAME_SPACE::Util::CreateUniqueUID();
 184    serieNumber    = 0;
 185    instanceNumber = 0;
 186
 187    // -----------------------------------------------------
 188    // Iterate to ALL the objets(files/directories) found in the input directory
 189    // (this is level ZERO)
 190    // each Directory (name : 1, 2, 3, ...) will be a Dicom Serie
 191    // -----------------------------------------------------
 192
 193    GDCM_NAME_SPACE::DirListType::iterator it;
 194
 195    for (it = fileNames.begin();
 196          it != fileNames.end();
 197        ++it)
 198    {
 199       if ( boost::filesystem::is_directory(*it) )
 200       {
 201          if (verbose)
 202             std::cout << "[" << *it << "] is a directory" << std::endl;
 203
 204          if((*it) == "AdjStatePerStudy")  // avoid trouble with new version 'AdjStatePerStudy' directory
 205             continue;
 206
 207          //BrukerDataSet br_acqp;
 208          std::string strAcqp;
 209          strAcqp = (*it) +
 210                    GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 211                    "acqp";
 212
 213          br_acqp.LoadFile(strAcqp);
 214          br_acqp.FillMap();
 215
 216 //std::cout << "out of br_acqp.FillMap " << std::endl;
 217          std::string acqp_scan_name;
 218          std::string acqp_method;
 219          std::string acqp_protocol_location;
 220
 221          BrukerFieldData b_protocol_location=br_acqp.GetFieldData("ACQ_protocol_location");
 222          acqp_protocol_location = b_protocol_location.GetStringValue()[0];
 223          cleanString(acqp_protocol_location);
 224
 225 //std::cout << "out of br_acqp.FillMap 1" << std::endl;
 226          BrukerFieldData b_scan_name=br_acqp.GetFieldData("ACQ_scan_name");
 227 //std::cout << "out of br_acqp.FillMap 11" << std::endl;
 228          acqp_scan_name = b_scan_name.GetStringValue()[0];
 229 //std::cout << "out of br_acqp.FillMap 12 [" << acqp_scan_name << "]" << std::endl;
 230          cleanString(acqp_scan_name);
 231 //std::cout << "out of br_acqp.FillMap 2" << std::endl;
 232          BrukerFieldData b_method=br_acqp.GetFieldData("ACQ_method");
 233          b_method.PrintSelf();
 234          acqp_method = b_method.GetStringValue()[0];
 235
 236          cleanString(acqp_method);
 237 //std::cout << "out of br_acqp.FillMap 3" << std::endl;
 238          BrukerFieldData b_list_size = br_acqp.GetFieldData("ACQ_O1_list_size");
 239 //std::cout << "out of br_acqp.FillMap 4" << std::endl;
 240          //b_list_size.PrintSelf(); //JP
 241
 242          nbSlices =  b_list_size.GetIntValue()[0];
 243 //std::cout << "out of br_acqp.FillMap 5" << std::endl;
 244          strSerieDescr = GDCM_NAME_SPACE::Util::GetName(*it)
 245                        /*  + "." + acqp_protocol_location */ // always the same (in each acquisition)
 246                          + "." + acqp_scan_name
 247                          + "." + acqp_method.c_str();
 248
 249          sprintf(outputDirName, "%s%c%s", tempStringStudyDir.c_str(),                //OutputDirName.c_str(),
 250                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 251                           strSerieDescr.c_str() );
 252
 253          std::cout << " ================================================================================\n"
 254                    << " === [" << GDCM_NAME_SPACE::Util::GetName(*it) << "] -> [" << strSerieDescr << "]\n"
 255                    << " ================================================================================"
 256                    << std::endl;
 257         std::string strOutputDirName(outputDirName);
 258         if (verbose)
 259            printf ("outputDirName [%s]\n", outputDirName);
 260         try {
 261            DealWithNiveau1(*it, strOutputDirName);
 262         }
 263         catch (BrukerHopelessException &e)
 264         {
 265          std::cout << "And Exception was thrown in DealWithNiveau1 (" << e.what() << ") " << std::endl;
 266          continue;
 267         }
 268       }
 269    } // end of : for (GDCM_NAME_SPACE::DirListType::iterator it
 270 }
 271
 272 // =====================================================================
 273
 274 void Bruker2Dicom::DealWithNiveau1(std::string &level1Directory, std::string &currentOutputDirName) {
 275 //
 276 // e.g. : at level 1, in B67d1.Bp1/6
 277 //
 278 // acqp  fid  imnd  pdata  pulseprogram  spnam0  spnam1
 279
 280    bool res = CreateDirectory(currentOutputDirName);
 281
 282    if (!res) {
 283       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 284       throw ( BrukerHopelessException ("Level 1 output directory creation failure "));
 285      // exit (0);
 286    }
 287    GDCM_NAME_SPACE::DirList dirList(level1Directory, false, true); // DON'T get recursively the list of files
 288    GDCM_NAME_SPACE::DirListType fileNames;
 289    fileNames = dirList.GetFilenames();
 290    // -----------------------------------------------------
 291    // Iterate to ALL the objets(files/directories) found in the input directory
 292    // -----------------------------------------------------
 293    GDCM_NAME_SPACE::DirListType::iterator it;
 294
 295    for (it = fileNames.begin();
 296         it != fileNames.end();
 297       ++it)
 298    {
 299       if ( boost::filesystem::is_regular(*it) )
 300       //if ( ! boost::filesystem::is_directory(*it) )
 301       {
 302          if (verbose)
 303             std::cout << "--- [" << *it << "] is a file." << std::endl;
 304       }
 305    }
 306
 307    char outputDirName[(unsigned int) PATH_MAX+2];
 308    //std::string firstName;
 309    bool canOpen;
 310    for (it = fileNames.begin();
 311         it != fileNames.end();
 312       ++it)
 313    {
 314       if ( boost::filesystem::is_directory(*it) )
 315       {
 316          // will be always "pdata" ...
 317          if (verbose)
 318             std::cout << "--- [" << *it << "] is a directory" << std::endl;
 319
 320               /* a recuperer :
 321               if (FileLine.startsWith("##$ACQ_size=")) {
 322               if (FileLine.startsWith("##$NI=")) {
 323               if (FileLine.startsWith("##$NR=")) {
 324               if (FileLine.startsWith("##$ACQ_obj_order=")) {
 325               if (FileLine.startsWith("##$ACQ_word_size=")) {
 326               if (FileLine.startsWith("##$BYTORDA=")) {
 327               if (FileLine.startsWith("##$PULPROG=")) {
 328               */
 329
 330          sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 331                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 332                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str());
 333          std::string strOutputDirName(outputDirName);
 334          //br1.PrintSelf();
 335
 336           std::string strMethod;
 337           //std::string firstName = *(fileNames.begin());
 338
 339           strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin())) +
 340                       GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 341                       "method";
 342             // std::cout << "---strMethod (for method)=> [" << strMethod << "]" << std::endl;
 343           canOpen = br_method.LoadFile(strMethod);
 344           if (!canOpen)
 345           {
 346              strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
 347                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 348                          "imnd";
 349              //std::cout << "---strMethod (for imnd) => [" << strMethod << "]" << std::endl;
 350              canOpen = br_method.LoadFile(strMethod);
 351              if (!canOpen)
 352              {
 353                 std::cout << "Hopeless! neither 'method' nor 'imnd' found in ["
 354                           << level1Directory  << "]; we skip it!" << std::endl;
 355                 continue;
 356                 //throw ( BrukerHopelessException ("Hopeless! neither 'method' nor 'imnd' found "));
 357                 //exit(0);  /// \TODO throw an exception !
 358              }
 359           }
 360           if (verbose)
 361              std::cout << "open => [" << strMethod << "] successfully" << std::endl;
 362           br_method.FillMap();
 363
 364           /* a recuperer :
 365              ##$PVM_Fov (dimension)  // ou plutot RECO_fov !
 366           */
 367   /*
 368           dans method (pour perfusion  seulement?) :
 369           ##$PVM_ObjOrderList=( 8 )
 370           0 2 4 6 1 3 5 7
 371           ##$PVM_NSPacks=2
 372           ##$PVM_SPackArrNSlices=( 2 )
 373           7 1
 374   */
 375          try {
 376             DealWithNiveau2(*it, strOutputDirName);
 377          }
 378          catch (BrukerHopelessException &e)
 379          {
 380             std::cout << "And Exception was thrown in DealWithNiveau2 (" << e.what() << ") " << std::endl;
 381             continue;
 382          }
 383       }
 384    }
 385 }
 386
 387 // =====================================================================
 388
 389 void Bruker2Dicom::DealWithNiveau2(std::string &level2Directory, std::string &currentOutputDirName) {
 390
 391 // e.g. : at level 2 in B67d1.Bp1/6/pdata
 392 //
 393 // acqp  fid  imnd  pdata  pulseprogram  spnam0  spnam1
 394 //
 395
 396    bool res = CreateDirectory(currentOutputDirName);
 397
 398    if (!res) {
 399       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 400       throw ( BrukerHopelessException ("Hopeless! Level2 output directory creation failure"));
 401       //exit (0);
 402    }
 403
 404    GDCM_NAME_SPACE::DirList dirList(level2Directory, false, true); // DON'T get recursively the list of files
 405
 406    GDCM_NAME_SPACE::DirListType fileNames;
 407    fileNames = dirList.GetFilenames();
 408
 409    char outputDirName[(unsigned int) PATH_MAX+2];
 410
 411    // -----------------------------------------------------
 412    // Iterate to ALL the objets(files/directories) found in the input directory
 413    // -----------------------------------------------------
 414    GDCM_NAME_SPACE::DirListType::iterator it;
 415    bool canOpen;
 416
 417    if (verbose)
 418    for (it = fileNames.begin();
 419         it != fileNames.end();
 420       ++it)
 421    {
 422       if ( ! boost::filesystem::is_directory(*it) )
 423       {
 424          std::cout << "--- --- [" << *it << "] is a file.." << std::endl;
 425       }
 426    }
 427
 428    for (it = fileNames.begin();
 429          it != fileNames.end();
 430        ++it)
 431    {
 432       if ( boost::filesystem::is_directory(*it) )
 433       {
 434
 435          if (verbose)
 436             std::cout << "--- --- [" << *it << "] is a directory" << std::endl;
 437
 438         // sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 439         //                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 440         //                                GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
 441   // MUST be 'pdata'!
 442
 443 //
 444 // (interest of previous method :
 445 // If unaware user changed the pdata name, it goes on working
 446 //
 447           std::string str_isa;
 448           str_isa = (*it) +
 449                     GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 450                    "isa";
 451
 452           std::string str_isa_func_name;
 453           canOpen = br_isa.LoadFile(str_isa);
 454           if (!canOpen)
 455           {
 456              sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 457                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 458                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
 459           }
 460           else
 461           {
 462              br_isa.FillMap();
 463              BrukerFieldData b_isa_func_name = br_isa.GetFieldData("ISA_func_name");
 464
 465              str_isa_func_name = b_isa_func_name.GetStringValue()[0];
 466              cleanString(str_isa_func_name);
 467
 468              sprintf(outputDirName, "%s%c%s.%s", currentOutputDirName.c_str(),
 469                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 470                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str(),
 471              str_isa_func_name.c_str());
 472           }
 473           std::string strOutputDirName(outputDirName);
 474           try {
 475              DealWithNiveau3(*it, strOutputDirName);
 476           }
 477           catch (BrukerHopelessException &e)
 478           {
 479              std::cout << "And Exception was thrown in DealWithNiveau3 (" << e.what() << "); "
 480                        << " We skip [" << level2Directory << "]" << std::endl;
 481              continue;
 482           }
 483           catch (BrukerInitException &e)
 484           {
 485              std::cout << "And Init Exception was thrown in DealWithNiveau3 (" << e.what() << "); "
 486                        << " We skip [" << level2Directory << "]" << std::endl;
 487              continue;
 488           }
 489       }
 490    }
 491 }
 492
 493 //
 494 // =====================================================================
 495 //
 496
 497 void Bruker2Dicom::DealWithNiveau3(std::string &level3Directory, std::string &currentOutputDirName){
 498
 499 //
 500 // e.g. at level 3, in
 501
 502    // just to be able to go on checking // JP
 503    if ( GDCM_NAME_SPACE::Util::GetName(level3Directory) != "1")
 504       return;
 505
 506    bool res = CreateDirectory(currentOutputDirName);
 507
 508    if (!res)
 509    {
 510       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 511       throw ( BrukerHopelessException ("Hopeless! Level3 output directory creation failure"));
 512       //exit (0);
 513    }
 514
 515    GDCM_NAME_SPACE::DirList dirList(level3Directory, false, true); // DON'T get recursively the list of files
 516    GDCM_NAME_SPACE::DirListType::iterator it;
 517    GDCM_NAME_SPACE::DirListType fileNames;
 518    fileNames = dirList.GetFilenames();
 519
 520    char original2dseqName       [(unsigned int) PATH_MAX+2];
 521    char original2dseqName_XXX   [(unsigned int) PATH_MAX+2];
 522    char currentOutputMhdDirName [(unsigned int) PATH_MAX+2];
 523
 524    char outputMhdFileName       [(unsigned int) PATH_MAX+2];
 525    char output2dseqSliceFileName[(unsigned int) PATH_MAX+6]; // think about extra '.dcm'
 526    char output2dseqName         [(unsigned int) PATH_MAX+6];
 527    char output2dseqCartoName    [(unsigned int) PATH_MAX+6];
 528
 529    char copyFile[PATH_MAX + PATH_MAX + 5]; // Should be enough!
 530    bool canOpen;
 531
 532    //-------------- try d3proc;
 533    char char_d3proc[(unsigned int) PATH_MAX+2];
 534
 535    sprintf(char_d3proc,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"d3proc" );
 536
 537    if (verbose)
 538       std::cout << "d3proc: --- => [" << char_d3proc << "]" << std::endl;
 539    std::string str_d3proc(char_d3proc);
 540    canOpen = br_d3proc.LoadFile(str_d3proc);
 541
 542    if (!canOpen)
 543    {
 544       std::cout << "Hopeless! no 'd3proc' found" << std::endl;
 545       throw ( BrukerHopelessException ("Hopeless! no 'd3proc' found"));
 546       //exit(0);  /// \TODO throw an exception !
 547    }
 548
 549    canOpen = br_d3proc.FillMap();
 550    if (!canOpen)
 551    {
 552       std::cout << "Hopeless! FillMap failed on 'd3proc'" << std::endl;
 553       throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'd3proc'"));
 554       //exit(0);  /// \TODO throw an exception !
 555    }
 556
 557    //-------------- end try d3proc;
 558
 559
 560  // -------------------try reco
 561
 562    char char_reco[(unsigned int) PATH_MAX+2];
 563
 564    sprintf(char_reco,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
 565     //str_d3proc = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
 566     //             GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 567     //             "d3proc";
 568    if (verbose)
 569       std::cout << "reco: --- => [" << char_reco << "]" << std::endl;
 570
 571    std::string str_reco(char_reco);
 572    canOpen = br_reco.LoadFile(str_reco);
 573
 574    if (!canOpen) // we try in directory ../1
 575    {
 576       if (verbose)
 577          std::cout << "[" << str_reco << "] not found " << std::endl;
 578       std::string lastDirName = GDCM_NAME_SPACE::Util::GetPath(level3Directory);
 579       //lastDirName = GDCM_NAME_SPACE::Util::GetPath(lastDirName);
 580       sprintf(char_reco,"%s%c1%c%s", lastDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
 581       //str_reco=char_reco;
 582       canOpen = br_reco.LoadFile(str_reco);
 583       if (!canOpen)
 584       {
 585          std::cout << "Hopeless! cannot find 'reco' in [" << str_reco << "]"  << std::endl;
 586          throw ( BrukerHopelessException ("Hopeless! cannot find 'reco'"));
 587          //exit(0);  /// \TODO throw an exception !
 588       }
 589    } else {
 590       if (verbose)
 591          std::cout << "[" << str_reco << "] successfully Loaded " << std::endl;
 592    }
 593
 594    canOpen = br_reco.FillMap();
 595    if (!canOpen)
 596    {
 597       std::cout << "Hopeless! FillMap failed on [" << str_reco << "]" << std::endl;
 598       throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'reco'"));
 599       //exit(0);  /// \TODO throw an exception !
 600    } else {
 601       if (verbose)
 602          std::cout << "[" << str_reco << "] successfully Mapped" << std::endl;
 603    }
 604
 605    //std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
 606    // br_reco.PrintSelf();
 607    // std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
 608    // -------------------end try reco
 609
 610
 611    BrukerFieldData bX = br_d3proc.GetFieldData("IM_SIX");
 612    int NX = bX.GetIntValue()[0];
 613
 614    if (verbose)
 615       std::cout << "IM_SIX " << NX << std::endl;
 616    BrukerFieldData bY=br_d3proc.GetFieldData("IM_SIY");
 617    int NY = bY.GetIntValue()[0];
 618
 619    if (verbose)
 620          std::cout << "IM_SIY " << NY << std::endl;
 621    /// \todo : check if there are actually 3 dimensions or only 2
 622
 623    BrukerFieldData bZ= br_d3proc.GetFieldData("IM_SIZ");
 624    int nbFrames = bZ.GetIntValue()[0];
 625    if (verbose)
 626          std::cout << "IM_SIZ " << nbFrames << std::endl;
 627
 628         // WARNING DATTYPE is, either in {ip_short, ip_int, ip_char, ...}, or in {1, 2, 3, ...}
 629
 630    BrukerFieldData bDPT = br_d3proc.GetFieldData("DATTYPE");
 631
 632    std::string mhdDataPixelType;
 633    int pixelSize;
 634    getImhDataType(bDPT, mhdDataPixelType, pixelSize);
 635
 636
 637  /*
 638
 639  // See mail Denis :
 640  // En regle generale il vaut mieux que l'on passe par RECO_*
 641  // pour extraire les parametres de l'image
 642  //
 643
 644    BrukerFieldData fov = br_method.GetFieldData("PVM_Fov");
 645    double fovX = fov.GetDoubleValue()[0];
 646    double fovY = fov.GetDoubleValue()[1];
 647    if (verbose)
 648       std::cout << "FOV (ds method) " << fovX << " " << fovY << std::endl;
 649
 650    BrukerFieldData spatResol = br_method.GetFieldData("PVM_SpatResol");
 651    double spatResolX = spatResol.GetDoubleValue()[0];
 652    double spatResolY = spatResol.GetDoubleValue()[1];
 653    if (verbose)
 654       std::cout << "SpatResol (ds method) " << spatResolX << " " << spatResolY << std::endl;
 655
 656 */
 657
 658 /* ------  */
 659 // Better we use 'get' accessors from BrukerImage class, as Denis wrote them
 660
 661    BrukerFieldData fov = br_reco.GetFieldData("RECO_fov");
 662    double fovX = fov.GetDoubleValue()[0];
 663    double fovY = fov.GetDoubleValue()[1];
 664    if (verbose)
 665       std::cout << "FOV (ds reco) " << fovX << " " << fovY << std::endl;
 666
 667    BrukerFieldData size = br_reco.GetFieldData("RECO_size");
 668    double sizeX = size.GetDoubleValue()[0];
 669    double sizeY = size.GetDoubleValue()[1];
 670
 671    if (verbose)
 672       std::cout << "SIZE (ds reco) " << sizeX << " " << sizeY << std::endl;
 673
 674    double spatResolX = fovX / sizeX;
 675    double spatResolY = fovY / sizeY;
 676
 677    if (verbose)
 678       std::cout << "spatResol (ds reco : fov/size) " << spatResolX << " " << spatResolY << std::endl;
 679
 680 /* ------  */
 681
 682    /// \TODO probabely a more sophisticated accessor will be necessary :
 683    ///  (cf : non contiguous slices, overlapping, slice thickness, space between slices, etc)
 684
 685    BrukerFieldData bsliceDistance = br_method.GetFieldData("PVM_SPackArrSliceDistance");
 686    double sliceDistance = bsliceDistance.GetDoubleValue()[0];
 687
 688    if (verbose)
 689       std::cout << "SPackArrSliceDistance (ds method) " << sliceDistance << std::endl;
 690
 691 // ----------------------------------------------------------------------------------------
 692
 693    if (mhd)
 694    {
 695       sprintf(currentOutputMhdDirName, "%s%c%s", currentOutputDirName.c_str(),
 696                                GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "MhdFiles");
 697       std::string strCurrentOutputMhdDirName(currentOutputMhdDirName);
 698
 699       res = CreateDirectory( strCurrentOutputMhdDirName );
 700       if (!res) {
 701          std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 702          throw ( BrukerHopelessException ("Hopeless!FillMap failed on 'reco'"));
 703          //exit (0);
 704       }
 705
 706       if (verbose)
 707          std::cout << "Directory creation [" <<  currentOutputDirName << "]" << std::endl;
 708    }  // end if mhd
 709
 710    if (verbose)
 711          std::cout << "nbFrames " << nbFrames << std::endl;
 712    if (verbose)
 713          std::cout << "nbSlices " << nbSlices << std::endl;
 714    int k;
 715    int nbInstants = nbFrames/nbSlices;
 716    if (verbose)
 717          std::cout << "nbInstants (deduced)" << nbInstants << std::endl;
 718    int instantNb;
 719    int sliceNb;
 720    FILE *fp;  // for MHD files
 721
 722    sprintf( original2dseqName, "%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "2dseq");
 723
 724 /**/
 725   // \TODO : tenir compte du bazar precedent
 726
 727     // load 2dseq in memory
 728
 729    fp = fopen(original2dseqName, "rb");
 730    if (!fp)
 731    {
 732       // try 2dseq_Angio2D ?!?
 733
 734       sprintf( original2dseqName_XXX, "%s%s", original2dseqName, "_Angio2D");
 735       fp = fopen(original2dseqName_XXX, "rb");
 736       if (!fp)
 737       {
 738          std::cout << "Cannot open [" << original2dseqName << "] nor [" <<  original2dseqName_XXX << "] for reading" << std::endl;
 739          fclose(fp);
 740          throw ( BrukerHopelessException ("Hopeless! Cannot open '2dseq'"));
 741          //exit (0);
 742       }
 743    }
 744
 745    unsigned char *buffer_2dseq = new unsigned char[NX*NY*pixelSize*nbSlices*nbInstants];
 746    ///\ TODO : find a safer way to be sure to read everything!
 747    size_t lgr = fread(buffer_2dseq, 1, NX*NY*pixelSize*nbSlices*nbInstants, fp);
 748
 749    // This one will be important!
 750    // ---------------------------
 751    try {
 752       imageSet = CreateImageSet ( );
 753    }
 754    catch (BrukerInitException& e)
 755    {
 756       if (verbose)
 757          std::cout <<  "an Init Exception was thrown in CreateImageSet ( ); " << e.what()
 758                    <<  "catched in DealWithNiveau3" << std::endl;
 759       //return;
 760       throw (e);
 761    }
 762
 763    serieNumber++;
 764    strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 765    if (nbInstants==1) // creer un seul fichier .mhd  pour toutes les Slices! (images natives)
 766    {
 767        if (verbose)
 768           std::cout << "Single instant : do not split" << std::endl;
 769        if (mhd)
 770        {
 771              sprintf(outputMhdFileName, "%s%cMhdData_All_the_Slices.mhd", currentOutputMhdDirName,
 772                                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 773              fp=fopen(outputMhdFileName, "w");
 774              if (!fp)
 775              {
 776                 std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 777                 throw ( BrukerHopelessException ("Hopeless! Cannot open  mhd file for writting"));
 778                 //exit(0);
 779              }
 780              else
 781              {
 782                fprintf(fp, "ObjectType = Image\n");
 783                fprintf(fp, "NDims = 3\n" );
 784                fprintf(fp, "BinaryData = True \n" );
 785                fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 786                fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices );
 787                fprintf(fp, "HeaderSize = %d\n", 0);
 788                //fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
 789                fprintf(fp, "ElementSpacing = %lf %lf %lf\n", spatResolX, spatResolY, sliceDistance );
 790                fprintf(fp, "Position = 0 0 %d\n", 0 );
 791                fprintf(fp, "Offset = 0 0 0\n" );
 792                fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 793                fprintf(fp, "ElementNumberOfChannels = 1\n" );
 794                fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
 795                fprintf(fp, "ElementDataFile = %s\n", "../2dseq_All_the_Slices" );
 796                fclose(fp);
 797              }
 798              sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices",
 799                                        currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 800              fp=fopen(output2dseqSliceFileName, "wb");
 801              if (!fp)
 802              {
 803                 std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 804                 throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseq file for writting"));
 805              }
 806              else
 807              {
 808                 fwrite( buffer_2dseq, NX*NY*pixelSize, nbSlices, fp);
 809              }
 810              fclose(fp);
 811              serieNumber ++;
 812              strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 813        }  // end if mhd
 814        if (dicom)
 815        {
 816              sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices.dcm",
 817                                        currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 818
 819             /* ----------- Write Dicom Image  ---------------*/
 820              MakeDicomImage(buffer_2dseq,
 821                NX,
 822                NY,
 823                nbFrames,
 824                pixelSize,
 825                //fovX/NY, fovY/NY, sliceDistance,
 826                spatResolX, spatResolY, sliceDistance,
 827                output2dseqSliceFileName,
 828                subject_name,
 829                day,
 830                strStudyUID,
 831                strSerieUID,
 832                strStudyDescr,
 833                strSerieDescr,
 834                strStudyTimeDate,
 835                0,// index frame number
 836                GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
 837              );
 838        }  // end if dicom
 839    }  // end if nbInstants = 1
 840
 841    else  // more than ONE instant
 842    {
 843           // Interleaved !
 844           // it's (slice1,slide2, ...)t1 ; (slice1,slide2, ...)t2 ; ...
 845          unsigned char *pixelsForCurrentSlice = new unsigned char[NX*NY*pixelSize*nbInstants];
 846
 847          k = 0;
 848          for (sliceNb=0; sliceNb<nbSlices; sliceNb++)
 849          {
 850             if (mhd)
 851             {
 852                sprintf(outputMhdFileName, "%s%cMhdData_%03d.mhd", currentOutputMhdDirName,
 853                                         GDCM_NAME_SPACE::GDCM_FILESEPARATOR, k  );
 854                if (verbose)
 855                   std::cout << "--- Output MHD file [" << outputMhdFileName << "]" << std::endl;
 856                fp=fopen(outputMhdFileName, "w");
 857                if (!fp)
 858                {
 859                    std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 860                    throw ( BrukerHopelessException ("Hopeless! Cannot open  mhd file for writting"));
 861                    //exit(0);
 862                }
 863                else
 864                {
 865             /* ----------- Write MHD Image  ---------------*/
 866                 //if (verbose)
 867                 //   std::cout << "Open sucessfully[" << outputMhdFileName << "] for writting" << std::endl;
 868                    fprintf(fp, "ObjectType = Image\n");
 869                    fprintf(fp, "NDims = 3\n" );
 870                    fprintf(fp, "BinaryData = True \n" );
 871                    fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 872                    fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbInstants);
 873                    fprintf(fp, "HeaderSize = %d\n", 0);
 874                    //fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, 1.0 ); //
 875                    fprintf(fp, "ElementSpacing = %lf %lf %lf\n",spatResolX, spatResolY, 1.0 ); //slice distance : no meaning for temporal serie
 876                    fprintf(fp, "Position = 0 0 %d\n", sliceNb );
 877                    fprintf(fp, "Offset = 0 0 0\n" );
 878                    fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 879                    fprintf(fp, "ElementNumberOfChannels = 1\n" );
 880                    fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
 881                    fprintf(fp, "ElementDataFile = ..%c2dseq_Slice_%d\n", GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb );
 882                    fclose(fp);
 883                } // end write MHD
 884
 885                sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d",
 886                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,sliceNb);
 887                fp=fopen(output2dseqSliceFileName, "wb");
 888                if (!fp)
 889                {
 890                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 891                    throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseqSliceFile file for writting"));
 892                    //exit (0);
 893                }
 894                int frameSize = NX*NY*pixelSize;
 895                for (instantNb=0; instantNb<nbInstants; instantNb++)
 896                {
 897 // std::cout << "------------SN " << sliceNb << " IN " << instantNb <<  " T " << nbSlices*instantNb + sliceNb << std::endl;
 898                     fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
 899                             frameSize,
 900                             1, fp);
 901                }
 902                fclose(fp);
 903 // std::cout << "end writting[" << output2dseqSliceFileName << "]" << std::endl;
 904             }  // end if mhd
 905
 906             if (dicom)
 907             {
 908                // desperate try !
 909              /*
 910                sprintf(output2dseqSliceFileName, "%sdummy_buffer",
 911                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 912                fp=fopen(output2dseqSliceFileName, "wb");
 913                if (!fp)
 914                {
 915                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 916                    exit (0);
 917                }
 918                int frameSize = NX*NY*pixelSize;
 919                for (instantNb=0; instantNb<nbInstants; instantNb++)
 920                {
 921 // std::cout << "------------SN " << sliceNb << " IN " << instantNb <<  " T " << nbSlices*instantNb + sliceNb << std::endl;
 922                     fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
 923                             frameSize,
 924                             1, fp);
 925                }
 926                fclose(fp);
 927
 928                fp=fopen(output2dseqSliceFileName, "rb");
 929                if (!fp)
 930                {
 931                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for reading" << std::endl;
 932                    exit (0);
 933                }
 934                fread( pixelsForCurrentSlice,
 935                             frameSize*nbInstants,
 936                             1, fp);
 937                fclose(fp);
 938               // end of desperate try !
 939               */
 940
 941                /* ----------- Write Dicom Image  ---------------*/
 942
 943                int frameSize = NX*NY*pixelSize;
 944                for (instantNb=0; instantNb<nbInstants; instantNb++)
 945                {
 946                   memcpy(pixelsForCurrentSlice + frameSize*instantNb, buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize, frameSize);
 947                }
 948
 949                int indOfFirsImageWithinImageSet =  nbSlices*instantNb;
 950                sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d.dcm",
 951                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb);
 952
 953                MakeDicomImage(
 954                   pixelsForCurrentSlice,
 955                   NX,
 956                   NY,
 957                   nbInstants,
 958                   pixelSize,
 959                   spatResolX, spatResolY, sliceDistance,
 960                   //fovX/NY, fovY/NY, sliceDistance,
 961                   output2dseqSliceFileName,
 962                   subject_name,
 963                   day,
 964                   strStudyUID,
 965                   strSerieUID,
 966                   strStudyDescr,
 967                   strSerieDescr,
 968                   strStudyTimeDate,
 969                   sliceNb*nbInstants,
 970                   GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
 971                );
 972                if (verbose)
 973                   std::cout << "--- Output DCM file [" << output2dseqSliceFileName << "]" << std::endl;
 974
 975            } // en if dicom
 976
 977         k++;
 978         }
 979         delete [] pixelsForCurrentSlice;
 980      }  // end nbInstants == 1
 981    delete [] buffer_2dseq;
 982 /**/
 983
 984
 985    // -----------------------------------------------------
 986    //  deal with MatLab-generated Carto file.
 987    // -----------------------------------------------------
 988
 989    dealWithCarto(fileNames,  NX,  NY,  nbSlices, /*fovX, fovY,*/ spatResolX, spatResolY, sliceDistance,
 990                    copyFile, currentOutputDirName, outputMhdFileName, output2dseqCartoName);
 991 }
 992
 993
 994 // ===========================================================================================
 995
 996 void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX, int NY, int nbSlices,
 997                                  /*double fovX, double fovY, */
 998                                  double spatResolX, double spatResolY, double sliceDistance,
 999                                  char *copyFile, std::string &currentOutputDirName,
1000                                  char *outputMhdFileName, char *output2dseqCartoName)
1001 {
1002    // -----------------------------------------------------
1003    //  deal with MatLab-generated Carto file.
1004    // -----------------------------------------------------
1005
1006    const char *code[] = { "ADC", "adc", "TTP", "ttp", "PEAK", "peak", "" };  // add more carto file name identifiers if necessary; end with ""
1007    const char *separator[] =  { "_", ".", "-", "" }; //  add more, if necessary, to ckeck for 2dseq.ADC, 2dseq_ADC, 2dseq-ADC, etc; end with ""
1008    int icode;
1009    int iseparator;
1010    GDCM_NAME_SPACE::DirListType::iterator it;
1011    char file_name_ident[500];
1012    FILE *fp;
1013
1014    // Iterate to ALL the objets(files/directories) found in the input directory
1015    for (it = fileNames.begin();
1016         it != fileNames.end();
1017       ++it)
1018    {
1019       if ( boost::filesystem::is_regular(*it) )
1020       //if ( ! boost::filesystem::is_directory(*it) )
1021       {
1022          if (verbose)
1023             std::cout << "--- [" << *it << "] is a file..." << std::endl;
1024
1025          icode      = 0;
1026          while (code[icode][0] != 0)
1027          {
1028          iseparator = 0;
1029          while (separator[iseparator][0] != 0)
1030          {
1031             sprintf(file_name_ident, "2dseq%s%s",separator[iseparator],code[icode]); // e.g  "2dseq_ADC"
1032             //if (verbose)
1033             //   std::cout << "check name ["<<(*it) << "] for string [" << file_name_ident << "]" << std::endl;
1034             std::string::size_type loc = (*it).rfind(file_name_ident);
1035
1036             if ( loc != std::string::npos )
1037             {
1038
1039        ///\ TODO : find a safer way to be sure to read everything!
1040               unsigned char *buffer_carto = new unsigned char[NX*NY*sizeof(double)*nbSlices];
1041               fp = fopen ( (*it).c_str(), "rb");
1042               if (!fp){
1043                  std::cout << "Cannot open [" << *it << "] for reading" << std::endl;
1044                  throw ( BrukerHopelessException ("Level 1 Unable to open 'carto' file "));
1045                }
1046                fread(buffer_carto, NX*NY*sizeof(double), nbSlices, fp);
1047
1048                     // ?!?  sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() ,
1049                std::cout << "Deal with Carto file :[" <<*it << "], computed length : "
1050                          << NX*NY*sizeof(double)*nbSlices << std::endl;
1051                std::string lastFileName = GDCM_NAME_SPACE::Util::GetName((*it).c_str());
1052                if (mhd)
1053                {
1054                   // Copy the data file in the new directory
1055                   sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() ,
1056                             currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str());
1057                   system(copyFile);
1058                   sprintf(outputMhdFileName, "%s%c%s%s",
1059                                          currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".mhd" );
1060                   if (verbose)
1061                     std::cout << "--- Output Carto MHD file [" << outputMhdFileName << "]" << std::endl;
1062
1063                   FILE *fp;
1064                   fp=fopen(outputMhdFileName, "w");
1065                   if (!fp)
1066                   {
1067                      std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
1068                   }
1069                   else
1070                   {
1071                      fprintf(fp, "ObjectType = Image\n");
1072                      fprintf(fp, "NDims = 3\n" );
1073                      fprintf(fp, "BinaryData = True \n" );
1074                      fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
1075                      fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices);
1076                      fprintf(fp, "HeaderSize = %d\n", 0 );
1077                      fprintf(fp, "ElementSpacing = %lf %lf %lf\n",spatResolX, spatResolY, sliceDistance );
1078                      fprintf(fp, "Position = 0 0 0\n" );
1079                      fprintf(fp, "Offset = 0 0 0\n" );
1080                      fprintf(fp, "CenterOfRotation = 0 0 0\n" );
1081                      fprintf(fp, "ElementNumberOfChannels = 1\n" );
1082                      fprintf(fp, "ElementType = %s\n", "MET_DOUBLE" );
1083                      fprintf(fp, "ElementDataFile = %s\n", lastFileName.c_str() );
1084
1085                      fclose(fp);
1086                   }
1087                   if (verbose)
1088                      std::cout << "--- end write Carto MHD file [" << outputMhdFileName << "]" << std::endl;
1089                }  // end if mhd
1090
1091             // ----------- Write Dicom Image  ---------------
1092
1093                if (dicom)
1094                {
1095                   sprintf(output2dseqCartoName, "%s%c%s%s",
1096                                        currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".dcm" );
1097                   if (verbose)
1098                      std::cout << "--- end create name output2dseqCartoName file [" << output2dseqCartoName << "]" << std::endl;
1099
1100                   strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID(); //New SerieUID for each carto.
1101                   std::string strNewSerieDescr(strSerieDescr+ "_" +GDCM_NAME_SPACE::Util::GetName((*it).c_str()));
1102                   MakeDicomImage(buffer_carto,
1103                      NX,
1104                      NY,
1105                      nbSlices,
1106                      8, // pixelSize
1107                      //fovX/NY, fovY/NY, sliceDistance,
1108                      spatResolX, spatResolY, sliceDistance,
1109                      output2dseqCartoName,
1110                      subject_name,
1111                      day,
1112                      strStudyUID,
1113                      strSerieUID,
1114                      strStudyDescr,
1115                      strNewSerieDescr,
1116                      strStudyTimeDate,
1117                      0,
1118                      GDCM_NAME_SPACE::CREATED_IMAGE
1119                   );
1120                }  // end if dicom
1121
1122                delete [] buffer_carto;
1123                if (verbose)
1124                   std::cout << "--- End writing Carto DICOM file [" << output2dseqCartoName << "]" << std::endl;
1125                break; // don't check for more ident on same file name!
1126
1127             }  // end deal with _ADC, -adc, etc
1128           iseparator ++;
1129           }  // end iterate speparators
1130           icode++;
1131           } // end iterate code
1132       } // end boost::filesystem::is_regular(*it)
1133    } // end iterate on all objects (files, dir, etc)
1134 } // end method
1135
1136
1137 // ==========================================================================================================
1138
1139 int Bruker2Dicom::CheckUserDirectory(std::string &userDirName)
1140 {
1141    GDCM_NAME_SPACE::DirList dirList(userDirName, false, true); // DON'T get recursively the list of files
1142
1143    GDCM_NAME_SPACE::DirListType fileNames;
1144    fileNames = dirList.GetFilenames();
1145
1146    std::string path = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()));
1147
1148    std::string subject =  path +
1149                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
1150                           "subject";
1151
1152     std::string acqp = path +
1153                        GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
1154                        "acqp";
1155
1156     if ( boost::filesystem::is_regular(subject) )
1157        subjectFound = true; // user passed a 'study
1158     else
1159        subjectFound = false; // user didnt' pass a 'study
1160
1161     if ( boost::filesystem::is_regular(acqp) )
1162        acqpFound= true; // user passes a 'serie', not a 'study'
1163     else
1164        acqpFound = false; // user passed a 'non study' directory; Hope it's a 'set of studies' directory!
1165
1166    int type;
1167    if  (subjectFound )  type = 1; // user passed a 'study
1168    else if  (acqpFound) type = 2; // user passed a 'serie'
1169    else                 type = 3; // user passed a 'non study' directory; Hope it's a 'set of studies' directory!
1170
1171    return type;
1172 }
1173
1174
1175 // ==========================================================================================================
1176
1177 bool Bruker2Dicom::CreateDirectory(std::string &OutputDirName)
1178 {
1179    std::string systemCommand;
1180
1181    if (verbose)
1182       std::cout << "Check for output directory :[" << OutputDirName << "]."
1183                 <<std::endl;
1184    if ( ! boost::filesystem::is_directory(OutputDirName) )    // dirout not found
1185    {
1186       systemCommand = "mkdir " + OutputDirName;        // create it!
1187       if (verbose)
1188          std::cout << systemCommand << std::endl;
1189       system (systemCommand.c_str());
1190       if ( ! boost::filesystem::is_directory(OutputDirName) ) // be sure it worked
1191       {
1192          if (verbose)
1193             std::cout << "KO : not a dir : [" << OutputDirName << "] (creation failure ?)" << std::endl;
1194          //return 0;
1195          throw ( BrukerHopelessException ("Level 1 output directory creation failure "));
1196       }
1197       else
1198       {
1199          if (verbose)
1200            std::cout << "Directory [" << OutputDirName << "] created." << std::endl;
1201       }
1202    }
1203    else
1204    {
1205        if (verbose)
1206             std::cout << "Output Directory [" << OutputDirName << "] already exists; Used as is." << std::endl;
1207    }
1208    return 1;
1209 }
1210
1211
1212 // ===========================================================================================
1213
1214 /// \TODO move cleanString to 'crea' ?
1215
1216 void Bruker2Dicom::cleanString(std::string &s)
1217 {
1218    int l = s.size();
1219    if (s[l-1] == 0x0A || s[l-1] == 0x0D ) // CR or NL
1220    {
1221       l--;
1222       s = s.substr(0, l);
1223    }
1224    if (s[l-1] == ' ' ) // blank space
1225    {
1226       l--;
1227       s = s.substr(0, l);
1228    }
1229
1230    if (s[0] == '<')
1231       s= s.substr(1,l-2);
1232    std::string repChar("_");
1233    GDCM_NAME_SPACE::Util::ReplaceSpecChar(s, repChar);
1234 }
1235
1236
1237
1238 // ===========================================================================================
1239
1240
1241 void Bruker2Dicom::getImhDataType(BrukerFieldData &bDPT, std::string &mhdDataPixelType, int &pixelSize)
1242 {
1243    if(bDPT.GetDataType() == "string")
1244    {
1245          std::string brukerDataPixelType = bDPT.GetStringValue()[0];
1246          if (verbose)
1247             std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
1248          //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
1249
1250          if (brukerDataPixelType ==  "ip_short") {
1251             mhdDataPixelType = "MET_USHORT";
1252             pixelSize = 2;
1253          }
1254          if (brukerDataPixelType ==  "ip_int") {
1255             mhdDataPixelType = "MET_UINT";
1256             pixelSize = 4;
1257          }
1258          if (brukerDataPixelType ==  "ip_char") {
1259              mhdDataPixelType = "MET_UCHAR";
1260              pixelSize = 1;
1261          }
1262                   /// \TODO : finish the list
1263     /*
1264     case 0 : fp << "ElementType = MET_CHAR" << std::endl;
1265       break;
1266     case 1 : fp << "ElementType = MET_UCHAR" << std::endl;
1267       break;
1268     case 2 : fp << "ElementType = MET_SHORT" << std::endl;
1269       break;
1270     case 3 : fp << "ElementType = MET_USHORT" << std::endl;
1271       break;
1272     case 4 : fp << "ElementType = MET_INT" << std::endl;
1273       break;
1274     case 5 : fp << "ElementType = MET_UINT" << std::endl;
1275       break;
1276     case 6 : fp << "ElementType = MET_FLOAT" << std::endl;
1277       break;
1278     case 7 : fp << "ElementType = MET_DOUBLE" << std::endl;
1279     */
1280     }
1281     else
1282     {
1283          int brukerDataPixelType = bDPT.GetIntValue()[0];
1284          if (verbose)
1285             std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
1286          //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
1287
1288 // Cross your fingers !!!
1289
1290 // pb : found values : 2, 3, 5
1291
1292          if (brukerDataPixelType ==  2) {
1293             mhdDataPixelType = "MET_USHORT";
1294             pixelSize = 2;
1295          }
1296          if (brukerDataPixelType ==  3) {
1297             mhdDataPixelType = "MET_USHORT";
1298             pixelSize = 2;
1299          }
1300          if (brukerDataPixelType ==  1) {
1301             mhdDataPixelType = "MET_UCHAR";
1302             pixelSize = 1;
1303          }
1304     }
1305 }
1306
1307 // ===========================================================================================
1308
1309 std::vector<BrukerImage> Bruker2Dicom::CreateImageSet ( )
1310 {
1311          std::vector<BrukerImage> imageSet;
1312          br_acqp.SetLoopStructure();
1313          std::vector<int> tempVect                      = br_acqp.GetLoopStructure() ;
1314          std::map<std::string, BrukerFieldData> map     = br_acqp.GetBrukerHeaderMap();
1315
1316          bool result                                    = br_acqp.ObjectVaryingProperties.init(map,tempVect);
1317
1318          if (result == false)
1319          {
1320             throw ( BrukerInitException  ("ObjectVaryingProperties.init() failure in Bruker2Dicom::CreateImageSet()") );
1321          }
1322
1323          br_acqp.SetImageLoopStructure();
1324          br_acqp.SetBrukerImageList();
1325          std::vector<std::vector<int> > brukerImageList = br_acqp.GetBrukerImageList();
1326
1327          BrukerImage image(br_acqp,br_reco);
1328          image.Init(br_acqp,br_reco,1);
1329
1330          for(int i=0;i<brukerImageList.size();i++)
1331          {
1332             image.Init(br_acqp,br_reco,i);
1333             imageSet.push_back(image);
1334          }
1335
1336  // Just for checking
1337  /*
1338
1339          std::vector<std::vector <double> > imageOrientation;
1340          std::vector <double> imagePosition;
1341          for(int i=0;i<brukerImageList.size();i++)
1342          {
1343            // fread(buffer_2dseq, NX*NY*pixelSize*nbSlices*nbInstants, 1, fp);
1344
1345            imagePosition = imageSet[i].getTranslationVectorRPS2XYZ();
1346            std::cout << "Position " << imagePosition[0] << " "
1347                      << imagePosition[1] << " "  << imagePosition[2] ;
1348            imageOrientation =  imageSet[i].getRotationMatrixRPS2XYZ();
1349            std::cout << "\t  Orientation " ;
1350            for(int i1=0; i1<3;i1++)for(int i2=0; i2<3;i2++)
1351               std::cout << imageOrientation[i1][i2] << " ";CreateImageSet
1352
1353            //std::cout << "\t  Abs Time " << imageSet[i].getAbsoluteTimePosition();
1354            std::cout << "\t  Relat Time " << imageSet[i].getRelativeTimePosition();
1355
1356            std::cout << "\t [";
1357            for (int i3=0; i3<imageSet[i].getLoopStamp().size();i3++)
1358               std::cout << " " << imageSet[i].getLoopStamp()[i3];
1359            std::cout << "]" << std::endl;
1360          }
1361 */
1362    return imageSet;
1363 }
1364
1365 // ===========================================================================================
1366
1367 void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels,
1368               int X,
1369               int Y,
1370               int nbFrames,
1371               int pixelSize,
1372               double spacingX, double spacingY, double sliceDistance,
1373               std::string dcmImageName,
1374               const std::string &patientName,
1375               const char *day,
1376               std::string &studyUID,
1377               std::string &serieUID,
1378               std::string &studyDescr,
1379               std::string &serieDescr,
1380               std::string &strStudyTimeDate,
1381               int imgNum,
1382               GDCM_NAME_SPACE::ImageContentType contentType
1383       )
1384 {
1385    std::ostringstream str;
1386
1387    GDCM_NAME_SPACE::File *file;
1388    file = GDCM_NAME_SPACE::File::New();
1389
1390   // Set the image size
1391    str.str("");
1392    str << X;
1393    file->InsertEntryString(str.str(),0x0028,0x0011,"US"); // Columns
1394    str.str("");
1395    str << Y;
1396    file->InsertEntryString(str.str(),0x0028,0x0010,"US"); // Rows
1397
1398    if (nbFrames != 1)
1399    {
1400       str.str("");
1401       str << nbFrames;
1402       file->InsertEntryString(str.str(),0x0028,0x0008,"IS"); // Number of Frames
1403    }
1404
1405   // Set the pixel type
1406   //      //8, 16, 32, 64 (for double ?)
1407    str.str("");
1408    str << pixelSize*8;
1409    file->InsertEntryString(str.str(),0x0028,0x0100,"US"); // Bits Allocated
1410
1411    file->InsertEntryString(str.str(),0x0028,0x0101,"US"); // Bits Stored
1412
1413    str.str("");
1414    str << pixelSize*8-1;
1415    file->InsertEntryString(str.str(),0x0028,0x0102,"US"); // High Bit
1416
1417   // Set the pixel representation // 0/1 , 0=unsigned
1418    file->InsertEntryString("1",0x0028,0x0103, "US"); // Pixel Representation
1419
1420   // Set the samples per pixel // 1:Grey level, 3:RGB
1421    file->InsertEntryString("1",0x0028,0x0002, "US"); // Samples per Pixel
1422
1423 //  0028 0030 DS 2 Pixel Spacing
1424    str.str("");
1425    str << spacingX << "\\" << spacingY;
1426    file->InsertEntryString(str.str(),0x0028,0x0030, "DS"); // Pixel Spacing
1427
1428  //   0018 0050 DS 1 Slice Thickness
1429    str.str("");
1430    str << sliceDistance;
1431    file->InsertEntryString(str.str(),0x0018,0x0050, "DS");
1432
1433 //    0020 0011 IS 1 Series Number
1434    str.str("");
1435    str << serieNumber;
1436    file->InsertEntryString(str.str(),0x0020,0x0011, "IS");
1437
1438 //    0020|0013 [IS]  [Instance Number]
1439    instanceNumber++;
1440    str.str("");
1441    str << instanceNumber;
1442    file->InsertEntryString(str.str(),0x0020,0x0013, "IS");
1443
1444   // 1.2.840.10008.5.1.4.1.1.4.1 : Enhanced MR Image Storage
1445  //  file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0002, 0x0002, "UI");  // [Media Storage SOP Class UID]
1446   // file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0008, 0x0016, "UI");  // [SOP Class UID]
1447
1448 // OK : MR is NOT multiframe, but I want just a quick an dirty solution
1449
1450 // 1.2.840.10008.5.1.4.1.1.4         MR Image Storage
1451    file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0002, 0x0002, "UI");  // [Media Storage SOP Class UID]
1452    file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0008, 0x0016, "UI");  // [SOP Class UID]
1453
1454   // if (strlen(patientName) != 0)
1455    file->InsertEntryString(patientName.c_str(),0x0010,0x0010, "PN"); // Patient's Name
1456    file->InsertEntryString(patientName.c_str(),0x0010,0x0020, "LO"); // Patient's ID
1457
1458    file->InsertEntryString(studyUID, 0x0020, 0x000d, "UI");
1459    file->InsertEntryString(serieUID, 0x0020, 0x000e, "UI");
1460
1461 //  0008 0020 DA 1 Study Date
1462 //  0008 0030 TM 1 Study Time
1463
1464 /// \TODO split into 2 strings!
1465    file->InsertEntryString(strStudyTimeDate.substr(10,11).c_str(),0x0008,0x0020, "DA");
1466    file->InsertEntryString(strStudyTimeDate.substr(1,8).c_str(),  0x0008,0x0030, "TM");
1467
1468    file->InsertEntryString(studyDescr, 0x0008,0x1030, "LO");  // Study Description
1469    file->InsertEntryString(serieDescr, 0x0008,0x103e, "LO");  // Series Description
1470
1471 //0008|0060 [CS] [Modality]
1472    file->InsertEntryString("MR",0x0008,0x0060, "CS");
1473
1474 // 0020 0037 DS 6 Image Orientation (Patient)
1475    char charImageOrientation[256];
1476
1477 /*
1478 std::cout << "charImageOrientation  " <<
1479                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0] << " " <<
1480                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1] << " " <<
1481                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2] << " " <<
1482                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0] << " " <<
1483                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1] << " " <<
1484                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] << std::endl ;
1485 */
1486    sprintf(charImageOrientation,"%f\\%f\\%f \\ %f\\%f\\%f",
1487                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0],
1488                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1],
1489                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2],
1490                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0],
1491                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1],
1492                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] ) ;
1493
1494    file->InsertEntryString(charImageOrientation,0x0020,0x0037, "DS");
1495
1496 // 0020 0032 DS 3 Image Position (Patient)
1497
1498    char charImagePosition[256];
1499    sprintf(charImagePosition,"%f\\%f\\%f",
1500                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[0],
1501                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[1],
1502                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[2]);
1503
1504    file->InsertEntryString(charImagePosition,0x0020,0x0032, "DS");  //0020 0032 DS 3 Image Position (Patient)
1505
1506 // 0020 0x1041 DS 1 Slice Location
1507 //        sprintf(charImagePosition,"%f",float(imgNum));
1508 //        file->InsertEntryString(charImagePosition,0x0020,0x1041, "DS");
1509 /*
1510   // Set Rescale Intercept
1511         str.str("");
1512         str << div;
1513         file->InsertEntryString(str.str(),0x0028,0x1052,"DS");
1514
1515   // Set Rescale Slope
1516         str.str("");
1517         str << mini;
1518         file->InsertEntryString(str.str(),0x0028,0x1053,"DS");
1519 */
1520
1521    GDCM_NAME_SPACE::FileHelper *fileH;
1522    fileH = GDCM_NAME_SPACE::FileHelper::New(file);
1523    fileH->SetContentType(contentType);
1524
1525    // cast is just to avoid warnings (*no* conversion is performed)
1526    //fileH->SetImageData((uint8_t *)img,int(maxX*maxY)*sizeof(uint16_t)); // troubles when maxX, mayY are *actually* float!
1527
1528 //std::cout << "--------------------------------  X*Y*nbFrames*pixelSize " << X << " " << Y << " " << nbFrames << " " << pixelSize << std::endl;
1529
1530    fileH->SetImageData((uint8_t *)tabPixels, X*Y*nbFrames*pixelSize);
1531    fileH->SetWriteModeToRaw();
1532    fileH->SetWriteTypeToDcmExplVR();
1533    if( !fileH->Write(dcmImageName)) {
1534       std::cout << "Failed for [" << dcmImageName << "]\n"
1535                 << "           File is unwrittable" << std::endl;
1536       file->Delete();
1537       fileH->Delete();
1538       throw ( BrukerHopelessException ("Level 1 Unable to write Dicom file "));
1539    }
1540    //if (verbose)
1541    //   file->Print();
1542
1543    file->Delete();
1544    fileH->Delete();
1545 }