lib/src1/bruker2dicom.cxx

   1 #include "bruker2dicom.h"
   2 #include <boost/filesystem/path.hpp>
   3 #include <boost/filesystem/operations.hpp>
   4 #include "brukerexception.h"
   5
   6 #ifndef PATH_MAX // If not defined yet : do it
   7    #define PATH_MAX 2048
   8 #endif
   9
  10
  11
  12 bool Bruker2Dicom::Execute()
  13 {
  14    // ----- Check input values -----
  15
  16    bool bigEndian = GDCM_NAME_SPACE::Util::IsCurrentProcessorBigEndian();
  17
  18    //if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(InputDirName) )
  19    if ( ! boost::filesystem::is_directory(InputDirName) )
  20    {
  21       std::cout << "KO : [" << InputDirName << "] is not a Directory." << std::endl;
  22       return 0;
  23    }
  24    else
  25    {
  26       if (verbose)
  27          std::cout << "OK : [" << InputDirName << "] is a Directory." << std::endl;
  28    }
  29
  30    std::string strDirNameOut(OutputDirName);
  31    bool res=CreateDirectory(strDirNameOut);
  32    if (!res) {
  33       std::cout << "[" << OutputDirName << "] Directory creation failure " << std::endl;
  34       //exit (0);
  35       throw ( BrukerHopelessException ("Output directory creation failure "));
  36    }
  37
  38    std::string strDirNamein(InputDirName);
  39    GDCM_NAME_SPACE::DirList dirList(strDirNamein, false, true); // DON'T get recursively the list of files
  40    std::string strDirNameout(OutputDirName);
  41
  42 /*
  43    if (listonly)
  44    {
  45       std::cout << "------------List of found files ------------" << std::endl;
  46       dirList.Print();
  47       std::cout << std::endl;
  48       return 1;
  49    }
  50 */
  51
  52 //
  53 // e.g : at level 0, in : B67d1.Bp1
  54 //
  55 //           1  2  3  4  5  6  AdjStatePerStudy  subject
  56 //
  57
  58    GDCM_NAME_SPACE::DirListType fileNames;
  59    fileNames = dirList.GetFilenames();
  60    bool canOpen;
  61    std::string outputFileName;
  62
  63
  64   // BrukerDataSet br_subject;
  65    std::string subject;
  66    subject = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
  67              GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
  68              "subject";
  69    if (verbose)
  70         std::cout << " Subject : [" <<  subject << "]" << std::endl;
  71    canOpen =br_subject.LoadFile(subject);
  72
  73    if (!canOpen)
  74    {
  75       std::cout << "Hopeless! no 'subject' found" << std::endl;
  76       throw ( BrukerHopelessException ("Hopeless! no 'subject' found in root input directory "));
  77       //exit(0);  /// \TODO throw an exception !
  78    }
  79    else
  80    {
  81       br_subject.FillMap();
  82    }
  83    //br_subject.PrintSelf();
  84
  85   // get info for 'Study Description'
  86
  87          BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string");
  88          std::string subject_name = b_name.GetStringValue()[0];
  89          strPatientName = subject_name;
  90          cleanString(subject_name);
  91
  92          BrukerFieldData b_entry=br_subject.GetFieldData("SUBJECT_entry");
  93          std::string subject_entry = b_entry.GetStringValue()[0];
  94          //cleanString(subject_entry);
  95          subject_entry = subject_entry.substr(11, subject_entry.size()-11);
  96
  97          BrukerFieldData b_position=br_subject.GetFieldData("SUBJECT_position");
  98          std::string subject_position = b_position.GetStringValue()[0];
  99          //cleanString(subject_position);
 100          subject_position = subject_position.substr(9, subject_position.size()-9);
 101
 102          BrukerFieldData b_date=br_subject.GetFieldData("SUBJECT_date");
 103          std::string subject_date = b_date.GetStringValue()[0];
 104          strStudyTimeDate = subject_date;
 105          cleanString(subject_date);
 106
 107          BrukerFieldData b_study_name=br_subject.GetFieldData("SUBJECT_study_name");
 108          std::string subject_study_name = b_study_name.GetStringValue()[0];
 109          subject_study_name = subject_study_name.substr(1, subject_study_name.size()-2);
 110          cleanString(subject_date);
 111
 112    // subject_name is already in 'Patient Name'
 113    strStudyDescr = /*subject_name + "." + */ subject_study_name + "." + subject_entry + "." + subject_position + "." + subject_date;
 114
 115    char outputDirName[(unsigned int) PATH_MAX+2];
 116
 117    strStudyUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 118    serieNumber = 0;
 119    instanceNumber = 0;
 120    // -----------------------------------------------------
 121    // Iterate to ALL the objets(files/directories) found in the input directory
 122    // (this is level ZERO)
 123    // each Directory (name : 1, 2, 3, ...) will be a Dicom Serie
 124    // -----------------------------------------------------
 125
 126    GDCM_NAME_SPACE::DirListType::iterator it;
 127
 128    for (it = fileNames.begin();
 129          it != fileNames.end();
 130        ++it)
 131    {
 132       if ( boost::filesystem::is_directory(*it) )
 133       {
 134          if (verbose)
 135             std::cout << "[" << *it << "] is a directory" << std::endl;
 136
 137          //BrukerDataSet br_acqp;
 138          std::string strAcqp;
 139          strAcqp = (*it) +
 140                    GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 141                    "acqp";
 142
 143          br_acqp.LoadFile(strAcqp);
 144          br_acqp.FillMap();
 145
 146          std::string acqp_scan_name;
 147          std::string acqp_method;
 148          std::string acqp_protocol_location;
 149
 150          BrukerFieldData b_protocol_location=br_acqp.GetFieldData("ACQ_protocol_location");
 151          acqp_protocol_location = b_protocol_location.GetStringValue()[0];
 152          cleanString(acqp_protocol_location);
 153
 154          BrukerFieldData b_scan_name=br_acqp.GetFieldData("ACQ_scan_name");
 155          acqp_scan_name = b_scan_name.GetStringValue()[0];
 156          cleanString(acqp_scan_name);
 157
 158          BrukerFieldData b_method=br_acqp.GetFieldData("ACQ_method");
 159          acqp_method = b_method.GetStringValue()[0];
 160          cleanString(acqp_method);
 161
 162          BrukerFieldData b_list_size = br_acqp.GetFieldData("ACQ_O1_list_size");
 163          //b_list_size.PrintSelf(); //JP
 164
 165          nbSlices =  b_list_size.GetIntValue()[0];
 166
 167          strSerieDescr = GDCM_NAME_SPACE::Util::GetName(*it)
 168                        /*  + "." + acqp_protocol_location */ // always the same (in each acquisition)
 169                          + "." + acqp_scan_name
 170                          + "." + acqp_method.c_str();
 171
 172          sprintf(outputDirName, "%s%c%s", OutputDirName.c_str(),
 173                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 174                           strSerieDescr.c_str() );
 175
 176          std::cout << " ================================================================================\n"
 177                    << " === [" << GDCM_NAME_SPACE::Util::GetName(*it) << "] -> [" << strSerieDescr << "]\n"
 178                    << " ================================================================================"
 179                    << std::endl;
 180
 181
 182         if (verbose)
 183            printf ("outputDirName [%s]\n", outputDirName);
 184
 185         DealWithNiveau1(*it, outputDirName);
 186       }
 187    } // end of : for (GDCM_NAME_SPACE::DirListType::iterator it
 188 }
 189
 190
 191 // =====================================================================
 192
 193 void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string currentOutputDirName) {
 194 //
 195 // e.g. : at level 1, in B67d1.Bp1/6
 196 //
 197 // acqp  fid  imnd  pdata  pulseprogram  spnam0  spnam1
 198
 199    bool res = CreateDirectory(currentOutputDirName);
 200
 201    if (!res) {
 202       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 203       throw ( BrukerHopelessException ("Level 1 output directory creation failure "));
 204      // exit (0);
 205    }
 206    GDCM_NAME_SPACE::DirList dirList(level1Directory, false, true); // DON'T get recursively the list of files
 207    GDCM_NAME_SPACE::DirListType fileNames;
 208    fileNames = dirList.GetFilenames();
 209    // -----------------------------------------------------
 210    // Iterate to ALL the objets(files/directories) found in the input directory
 211    // -----------------------------------------------------
 212    GDCM_NAME_SPACE::DirListType::iterator it;
 213
 214    for (it = fileNames.begin();
 215         it != fileNames.end();
 216       ++it)
 217    {
 218       if ( boost::filesystem::is_regular(*it) )
 219       //if ( ! boost::filesystem::is_directory(*it) )
 220       {
 221          if (verbose)
 222             std::cout << "--- [" << *it << "] is a file." << std::endl;
 223       }
 224    }
 225
 226    char outputDirName[(unsigned int) PATH_MAX+2];
 227    //std::string firstName;
 228    bool canOpen;
 229    for (it = fileNames.begin();
 230         it != fileNames.end();
 231       ++it)
 232    {
 233       if ( boost::filesystem::is_directory(*it) )
 234       {
 235          // will be always "pdata" ...
 236          if (verbose)
 237             std::cout << "--- [" << *it << "] is a directory" << std::endl;
 238
 239               /* a recuperer :
 240               if (FileLine.startsWith("##$ACQ_size=")) {
 241               if (FileLine.startsWith("##$NI=")) {
 242               if (FileLine.startsWith("##$NR=")) {
 243               if (FileLine.startsWith("##$ACQ_obj_order=")) {
 244               if (FileLine.startsWith("##$ACQ_word_size=")) {
 245               if (FileLine.startsWith("##$BYTORDA=")) {
 246               if (FileLine.startsWith("##$PULPROG=")) {
 247               */
 248
 249          sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 250                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 251                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str());
 252          //br1.PrintSelf();
 253
 254           std::string strMethod;
 255           //std::string firstName = *(fileNames.begin());
 256
 257           strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin())) +
 258                       GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 259                       "method";
 260             // std::cout << "---strMethod (for method)=> [" << strMethod << "]" << std::endl;
 261           canOpen = br_method.LoadFile(strMethod);
 262           if (!canOpen)
 263           {
 264              strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
 265                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 266                          "imnd";
 267              //std::cout << "---strMethod (for imnd) => [" << strMethod << "]" << std::endl;
 268              canOpen = br_method.LoadFile(strMethod);
 269              if (!canOpen)
 270              {
 271                 std::cout << "Hopeless! neither 'method' nor 'imnd' found" << std::endl;
 272                 throw ( BrukerHopelessException ("Hopeless! neither 'method' nor 'imnd' found "));
 273                 //exit(0);  /// \TODO throw an exception !
 274              }
 275           }
 276           if (verbose)
 277              std::cout << "open => [" << strMethod << "] successfully" << std::endl;
 278           br_method.FillMap();
 279
 280           /* a recuperer :
 281              ##$PVM_Fov (dimension)
 282           */
 283   /*
 284           dans method (pour perfusion  seulement?) :
 285           ##$PVM_ObjOrderList=( 8 )
 286           0 2 4 6 1 3 5 7
 287           ##$PVM_NSPacks=2
 288           ##$PVM_SPackArrNSlices=( 2 )
 289           7 1
 290   */
 291          DealWithNiveau2(*it,outputDirName );
 292       }
 293    }
 294 }
 295
 296 // =====================================================================
 297
 298 void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string currentOutputDirName) {
 299
 300 // e.g. : at level 2 in B67d1.Bp1/6/pdata
 301 //
 302 // acqp  fid  imnd  pdata  pulseprogram  spnam0  spnam1
 303 //
 304
 305    bool res = CreateDirectory(currentOutputDirName);
 306
 307    if (!res) {
 308       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 309       throw ( BrukerHopelessException ("Hopeless! Level2 output directory creation failure"));
 310       //exit (0);
 311    }
 312
 313    GDCM_NAME_SPACE::DirList dirList(level2Directory, false, true); // DON'T get recursively the list of files
 314
 315    GDCM_NAME_SPACE::DirListType fileNames;
 316    fileNames = dirList.GetFilenames();
 317
 318    char outputDirName[(unsigned int) PATH_MAX+2];
 319
 320    // -----------------------------------------------------
 321    // Iterate to ALL the objets(files/directories) found in the input directory
 322    // -----------------------------------------------------
 323    GDCM_NAME_SPACE::DirListType::iterator it;
 324    bool canOpen;
 325
 326    if (verbose)
 327    for (it = fileNames.begin();
 328         it != fileNames.end();
 329       ++it)
 330    {
 331       if ( ! boost::filesystem::is_directory(*it) )
 332       {
 333          std::cout << "--- --- [" << *it << "] is a file.." << std::endl;
 334       }
 335
 336    }
 337
 338    for (it = fileNames.begin();
 339          it != fileNames.end();
 340        ++it)
 341    {
 342       if ( boost::filesystem::is_directory(*it) )
 343       {
 344
 345          if (verbose)
 346             std::cout << "--- --- [" << *it << "] is a directory" << std::endl;
 347
 348         // sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 349         //                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 350         //                                GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
 351   // MUST be 'pdata'!
 352
 353 //
 354 // (interest of previous method :
 355 // If unaware user changed the pdata name, it goes on working
 356 //
 357           std::string str_isa;
 358           str_isa = (*it) +
 359                     GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 360                    "isa";
 361
 362           std::string str_isa_func_name;
 363           canOpen = br_isa.LoadFile(str_isa);
 364           if (!canOpen)
 365           {
 366              sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 367                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 368                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
 369           }
 370           else
 371           {
 372              br_isa.FillMap();
 373              BrukerFieldData b_isa_func_name = br_isa.GetFieldData("ISA_func_name");
 374
 375              str_isa_func_name = b_isa_func_name.GetStringValue()[0];
 376              cleanString(str_isa_func_name);
 377
 378              sprintf(outputDirName, "%s%c%s.%s", currentOutputDirName.c_str(),
 379                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 380                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str(),
 381              str_isa_func_name.c_str());
 382           }
 383           DealWithNiveau3(*it, outputDirName);
 384       }
 385    }
 386 }
 387
 388
 389 //
 390 // =====================================================================
 391 //
 392
 393 void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string currentOutputDirName){
 394
 395 //
 396 // e.g. at level 3, in
 397
 398    // just to be able to go on checking // JP
 399    if ( GDCM_NAME_SPACE::Util::GetName(level3Directory) != "1")
 400       return;
 401
 402    bool res = CreateDirectory(currentOutputDirName);
 403
 404    if (!res)
 405    {
 406       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 407       throw ( BrukerHopelessException ("Hopeless! Level3 output directory creation failure"));
 408       //exit (0);
 409    }
 410
 411    GDCM_NAME_SPACE::DirList dirList(level3Directory, false, true); // DON'T get recursively the list of files
 412    GDCM_NAME_SPACE::DirListType::iterator it;
 413    GDCM_NAME_SPACE::DirListType fileNames;
 414    fileNames = dirList.GetFilenames();
 415
 416    char original2dseqName       [(unsigned int) PATH_MAX+2];
 417    char currentOutputMhdDirName [(unsigned int) PATH_MAX+2];
 418
 419    char outputMhdFileName       [(unsigned int) PATH_MAX+2];
 420    char output2dseqSliceFileName[(unsigned int) PATH_MAX+6]; // think about extra '.dcm'
 421    char output2dseqName         [(unsigned int) PATH_MAX+6];
 422    char output2dseqCartoName    [(unsigned int) PATH_MAX+6];
 423
 424    char copyFile[PATH_MAX + PATH_MAX + 5]; // Should be enough!
 425    bool canOpen;
 426
 427    //-------------- try d3proc;
 428    char char_d3proc[(unsigned int) PATH_MAX+2];
 429
 430    sprintf(char_d3proc,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"d3proc" );
 431
 432    if (verbose)
 433       std::cout << "d3proc: --- => [" << char_d3proc << "]" << std::endl;
 434    std::string str_d3proc(char_d3proc);
 435    canOpen = br_d3proc.LoadFile(str_d3proc);
 436
 437    if (!canOpen)
 438    {
 439       std::cout << "Hopeless! no 'd3proc' found" << std::endl;
 440       throw ( BrukerHopelessException ("Hopeless! no 'd3proc' found"));
 441       //exit(0);  /// \TODO throw an exception !
 442    }
 443
 444    canOpen = br_d3proc.FillMap();
 445    if (!canOpen)
 446    {
 447       std::cout << "Hopeless! FillMap failed on 'd3proc'" << std::endl;
 448       throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'd3proc'"));
 449       //exit(0);  /// \TODO throw an exception !
 450    }
 451
 452    //-------------- end try d3proc;
 453
 454
 455  // -------------------try reco
 456
 457    char char_reco[(unsigned int) PATH_MAX+2];
 458
 459    sprintf(char_reco,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
 460     //str_d3proc = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
 461     //             GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 462     //             "d3proc";
 463    if (verbose)
 464       std::cout << "reco --- => [" << char_reco << "]" << std::endl;
 465    std::string str_reco(char_reco);
 466    canOpen = br_reco.LoadFile(str_reco);
 467
 468    if (!canOpen) // we try in directory ../1
 469    {
 470       if (verbose)
 471          std::cout << "[" << str_reco << "] not found " << std::endl;
 472       std::string lastDirName = GDCM_NAME_SPACE::Util::GetPath(level3Directory);
 473       //lastDirName = GDCM_NAME_SPACE::Util::GetPath(lastDirName);
 474       sprintf(char_reco,"%s%c1%c%s", lastDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
 475       str_reco=char_reco;
 476       canOpen = br_reco.LoadFile(str_reco);
 477       if (!canOpen)
 478       {
 479          std::cout << "Hopeless! cannot find 'reco' in [" << str_reco << "]"  << std::endl;
 480          throw ( BrukerHopelessException ("Hopeless! cannot find 'reco'"));
 481          //exit(0);  /// \TODO throw an exception !
 482       }
 483    }
 484
 485    canOpen = br_reco.FillMap();
 486    if (!canOpen)
 487    {
 488       std::cout << "Hopeless! FillMap failed on [" << str_reco << "]" << std::endl;
 489       throw ( BrukerHopelessException ("Hopeless!FillMap failed on 'reco'"));
 490       //exit(0);  /// \TODO throw an exception !
 491    }
 492    //std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
 493    // br_reco.PrintSelf();
 494    // std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
 495
 496    // -------------------end try reco
 497
 498
 499    BrukerFieldData bX = br_d3proc.GetFieldData("IM_SIX");
 500    int NX = bX.GetIntValue()[0];
 501
 502    if (verbose)
 503       std::cout << "IM_SIX " << NX << std::endl;
 504    BrukerFieldData bY=br_d3proc.GetFieldData("IM_SIY");
 505    int NY = bY.GetIntValue()[0];
 506
 507    if (verbose)
 508          std::cout << "IM_SIY " << NY << std::endl;
 509    /// \todo : check if there are actually 3 dimensions or only 2
 510
 511    BrukerFieldData bZ= br_d3proc.GetFieldData("IM_SIZ");
 512    int nbFrames = bZ.GetIntValue()[0];
 513    if (verbose)
 514          std::cout << "IM_SIZ " << nbFrames << std::endl;
 515
 516         // WARNING DATTYPE is, either in {ip_short, ip_int, ip_char, ...}, or in {1, 2, 3, ...}
 517
 518    BrukerFieldData bDPT = br_d3proc.GetFieldData("DATTYPE");
 519
 520    std::string mhdDataPixelType;
 521    int pixelSize;
 522    getImhDataType(bDPT, mhdDataPixelType, pixelSize);
 523
 524    BrukerFieldData fov = br_method.GetFieldData("PVM_Fov");
 525    double fovX = fov.GetDoubleValue()[0];
 526    double fovY = fov.GetDoubleValue()[1];
 527    if (verbose)
 528       std::cout << "FOV (ds method) " << fovX << " " << fovY << std::endl;
 529
 530    /// \TODO probabely a more sophisticated accessor will be necessary :
 531    ///  (cf : non contiguous slices, overlapping, slice thickness, space between slices, etc)
 532    BrukerFieldData bsliceDistance = br_method.GetFieldData("PVM_SPackArrSliceDistance");
 533    double sliceDistance = bsliceDistance.GetDoubleValue()[0];
 534
 535    if (mhd)
 536    {
 537       sprintf(currentOutputMhdDirName, "%s%c%s", currentOutputDirName.c_str(),
 538                                GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "MhdFiles");
 539       res = CreateDirectory( currentOutputMhdDirName );
 540       if (!res) {
 541          std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 542          throw ( BrukerHopelessException ("Hopeless!FillMap failed on 'reco'"));
 543          //exit (0);
 544       }
 545
 546       if (verbose)
 547          std::cout << "Directory creation [" <<  currentOutputDirName << "]" << std::endl;
 548    }  // end if mhd
 549
 550    if (verbose)
 551          std::cout << "nbFrames " << nbFrames << std::endl;
 552    if (verbose)
 553          std::cout << "nbSlices " << nbSlices << std::endl;
 554    int k;
 555    int nbInstants = nbFrames/nbSlices;
 556    if (verbose)
 557          std::cout << "nbInstants (deduced )" << nbInstants << std::endl;
 558    int instantNb;
 559    int sliceNb;
 560    FILE *fp;  // for MHD files
 561
 562    sprintf( original2dseqName, "%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "2dseq");
 563
 564 /**/
 565   // \TODO : tenir compte du bazar precedent
 566
 567     // load 2dseq in memory
 568
 569    fp = fopen(original2dseqName, "rb");
 570    if (!fp)
 571    {
 572       std::cout << "Cannot open [" << original2dseqName << "] for reading" << std::endl;
 573       throw ( BrukerHopelessException ("Hopeless! Cannot open '2dseq'"));
 574       //exit (0);
 575    }
 576
 577    unsigned char *buffer_2dseq = new unsigned char[NX*NY*pixelSize*nbSlices*nbInstants];
 578    ///\ TODO : find a safer way to be sure to read everything!
 579    size_t lgr = fread(buffer_2dseq, 1, NX*NY*pixelSize*nbSlices*nbInstants, fp);
 580
 581    // This one will be important!
 582    // ---------------------------
 583    try {
 584       imageSet = CreateImageSet ( );
 585    }
 586    catch (BrukerInitException& e)
 587    {
 588       std::cout <<  "Exception " << e.what() << std::endl;
 589       return;
 590    }
 591
 592    serieNumber++;
 593    strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 594    if (nbInstants==1) // creer un seul fichier .mhd  pour toutes les Slices! (images natives)
 595    {
 596        if (verbose)
 597           std::cout << "Single instant : do not split" << std::endl;
 598        if (mhd)
 599        {
 600              sprintf(outputMhdFileName, "%s%cMhdData_All_the_Slices.mhd", currentOutputMhdDirName,
 601                                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 602              fp=fopen(outputMhdFileName, "w");
 603              if (!fp)
 604              {
 605                 std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 606                 throw ( BrukerHopelessException ("Hopeless! Cannot open  mhd file for writting"));
 607                 //exit(0);
 608              }
 609              else
 610              {
 611                fprintf(fp, "ObjectType = Image\n");
 612                fprintf(fp, "NDims = 3\n" );
 613                fprintf(fp, "BinaryData = True \n" );
 614                fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 615                fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices );
 616                fprintf(fp, "HeaderSize = %d\n", 0);
 617                fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
 618                fprintf(fp, "Position = 0 0 %d\n", 0 );
 619                fprintf(fp, "Offset = 0 0 0\n" );
 620                fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 621                fprintf(fp, "ElementNumberOfChannels = 1\n" );
 622                fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
 623                fprintf(fp, "ElementDataFile = %s\n", "../2dseq_All_the_Slices" );
 624                fclose(fp);
 625              }
 626              sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices",
 627                                        currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 628              fp=fopen(output2dseqSliceFileName, "wb");
 629              if (!fp)
 630              {
 631                 std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 632                 throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseq file for writting"));
 633              }
 634              else
 635              {
 636                 fwrite( buffer_2dseq, NX*NY*pixelSize, nbSlices, fp);
 637              }
 638              fclose(fp);
 639              serieNumber ++;
 640              strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 641        }  // end if mhd
 642        if (dicom)
 643        {
 644              sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices.dcm",
 645                                        currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 646
 647             /* ----------- Write Dicom Image  ---------------*/
 648              MakeDicomImage(buffer_2dseq,
 649                NX,
 650                NY,
 651                nbFrames,
 652                pixelSize,
 653                fovX/NY, fovY/NY, sliceDistance,
 654                output2dseqSliceFileName,
 655                strPatientName,
 656                day,
 657                strStudyUID,
 658                strSerieUID,
 659                strStudyDescr,
 660                strSerieDescr,
 661                strStudyTimeDate,
 662                0,// index frame number
 663                GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
 664              );
 665        }  // end if dicom
 666    }  // end if nbInstants = 1
 667
 668    else  // more than ONE instant
 669    {
 670           // Interleaved !
 671           // it's (slice1,slide2, ...)t1 ; (slice1,slide2, ...)t2 ; ...
 672
 673          unsigned char *pixelsForCurrentSlice = new unsigned char[NX*NY*pixelSize*nbInstants];
 674
 675          k = 0;
 676          for (sliceNb=0; sliceNb<nbSlices; sliceNb++)
 677          {
 678             if (mhd)
 679             {
 680                sprintf(outputMhdFileName, "%s%cMhdData_%03d.mhd", currentOutputMhdDirName,
 681                                         GDCM_NAME_SPACE::GDCM_FILESEPARATOR, k  );
 682                if (verbose)
 683                   std::cout << "--- Output MHD file [" << outputMhdFileName << "]" << std::endl;
 684                fp=fopen(outputMhdFileName, "w");
 685                if (!fp)
 686                {
 687                    std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 688                    throw ( BrukerHopelessException ("Hopeless! Cannot open  mhd file for writting"));
 689                    //exit(0);
 690                }
 691                else
 692                {
 693             /* ----------- Write MHD Image  ---------------*/
 694                 //if (verbose)
 695                 //   std::cout << "Open sucessfully[" << outputMhdFileName << "] for writting" << std::endl;
 696                    fprintf(fp, "ObjectType = Image\n");
 697                    fprintf(fp, "NDims = 3\n" );
 698                    fprintf(fp, "BinaryData = True \n" );
 699                    fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 700                    fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbInstants);
 701                    fprintf(fp, "HeaderSize = %d\n", 0);
 702                    fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, 1.0 ); // slice distance : no meaning for temporal serie
 703                    fprintf(fp, "Position = 0 0 %d\n", sliceNb );
 704                    fprintf(fp, "Offset = 0 0 0\n" );
 705                    fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 706                    fprintf(fp, "ElementNumberOfChannels = 1\n" );
 707                    fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
 708                    fprintf(fp, "ElementDataFile = ..%c2dseq_Slice_%d\n", GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb );
 709                    fclose(fp);
 710                } // end write MHD
 711
 712                sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d",
 713                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,sliceNb);
 714                fp=fopen(output2dseqSliceFileName, "wb");
 715                if (!fp)
 716                {
 717                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 718                    throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseqSliceFile file for writting"));
 719                    //exit (0);
 720                }
 721                int frameSize = NX*NY*pixelSize;
 722                for (instantNb=0; instantNb<nbInstants; instantNb++)
 723                {
 724 // std::cout << "------------SN " << sliceNb << " IN " << instantNb <<  " T " << nbSlices*instantNb + sliceNb << std::endl;
 725                     fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
 726                             frameSize,
 727                             1, fp);
 728                }
 729                fclose(fp);
 730 // std::cout << "end writting[" << output2dseqSliceFileName << "]" << std::endl;
 731             }  // end if mhd
 732
 733             if (dicom)
 734             {
 735                // desperate try !
 736              /*
 737                sprintf(output2dseqSliceFileName, "%sdummy_buffer",
 738                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 739                fp=fopen(output2dseqSliceFileName, "wb");
 740                if (!fp)
 741                {
 742                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 743                    exit (0);
 744                }
 745                int frameSize = NX*NY*pixelSize;
 746                for (instantNb=0; instantNb<nbInstants; instantNb++)
 747                {
 748 // std::cout << "------------SN " << sliceNb << " IN " << instantNb <<  " T " << nbSlices*instantNb + sliceNb << std::endl;
 749                     fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
 750                             frameSize,
 751                             1, fp);
 752                }
 753                fclose(fp);
 754
 755                fp=fopen(output2dseqSliceFileName, "rb");
 756                if (!fp)
 757                {
 758                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for reading" << std::endl;
 759                    exit (0);
 760                }
 761                fread( pixelsForCurrentSlice,
 762                             frameSize*nbInstants,
 763                             1, fp);
 764                fclose(fp);
 765               // end of desperate try !
 766               */
 767
 768                /* ----------- Write Dicom Image  ---------------*/
 769
 770                int frameSize = NX*NY*pixelSize;
 771                for (instantNb=0; instantNb<nbInstants; instantNb++)
 772                {
 773                   memcpy(pixelsForCurrentSlice + frameSize*instantNb, buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize, frameSize);
 774                }
 775
 776                int indOfFirsImageWithinImageSet =  nbSlices*instantNb;
 777                sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d.dcm",
 778                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb);
 779
 780                MakeDicomImage(
 781                   pixelsForCurrentSlice,
 782                   NX,
 783                   NY,
 784                   nbInstants,
 785                   pixelSize,
 786                   fovX/NY, fovY/NY, sliceDistance,
 787                   output2dseqSliceFileName,
 788                   strPatientName,
 789                   day,
 790                   strStudyUID,
 791                   strSerieUID,
 792                   strStudyDescr,
 793                   strSerieDescr,
 794                   strStudyTimeDate,
 795                   sliceNb*nbInstants,
 796                   GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
 797                );
 798                if (verbose)
 799                   std::cout << "--- Output DCM file [" << output2dseqSliceFileName << "]" << std::endl;
 800
 801            } // en if dicom
 802
 803         k++;
 804         }
 805         delete [] pixelsForCurrentSlice;
 806      }  // end nbInstants == 1
 807    delete [] buffer_2dseq;
 808 /**/
 809
 810
 811    // -----------------------------------------------------
 812    //  deal with MatLab-generated Carto file.
 813    // -----------------------------------------------------
 814
 815    dealWithCarto(fileNames,  NX,  NY,  nbSlices, fovX, fovY, sliceDistance,
 816                    copyFile, currentOutputDirName, outputMhdFileName, output2dseqCartoName);
 817 }
 818
 819
 820 // ===========================================================================================
 821
 822 void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX, int NY, int nbSlices,
 823                                  double fovX, double fovY, double sliceDistance,
 824                                  char *copyFile, std::string &currentOutputDirName,
 825                                  char *outputMhdFileName, char *output2dseqCartoName)
 826 {
 827    // -----------------------------------------------------
 828    //  deal with MatLab-generated Carto file.
 829    // -----------------------------------------------------
 830
 831    char *code[] ={ "ADC", "adc", "TTP", "ttp", "PEAK", "peak", "" };  // add more carto file name identifiers if necessary; end with ""
 832    int icode;
 833    GDCM_NAME_SPACE::DirListType::iterator it;
 834    char file_name_ident[500];
 835    FILE *fp;
 836
 837    // Iterate to ALL the objets(files/directories) found in the input directory
 838    for (it = fileNames.begin();
 839         it != fileNames.end();
 840       ++it)
 841    {
 842       if ( boost::filesystem::is_regular(*it) )
 843       //if ( ! boost::filesystem::is_directory(*it) )
 844       {
 845          if (verbose)
 846             std::cout << "--- [" << *it << "] is a file..." << std::endl;
 847
 848          icode = 0;
 849
 850          while (code[icode][0] != 0)
 851          {
 852             sprintf(file_name_ident, "2dseq.%s",code[icode]); // e.g  "2dseq_ADC"
 853             std::string::size_type loc = (*it).rfind(file_name_ident);
 854
 855             if ( loc != std::string::npos )
 856             {
 857
 858        ///\ TODO : find a safer way to be sure to read everything!
 859               unsigned char *buffer_carto = new unsigned char[NX*NY*sizeof(double)*nbSlices];
 860               fp = fopen ( (*it).c_str(), "rb");
 861               if (!fp){
 862                  std::cout << "Cannot open [" << *it << "] for reading" << std::endl;
 863
 864                }
 865                fread(buffer_carto, NX*NY*sizeof(double), nbSlices, fp);
 866
 867                std::cout << "Deal with Carto file :[" <<*it << "], computed length : "
 868                          << NX*NY*sizeof(double)*nbSlices << std::endl;
 869                   std::string lastFileName = GDCM_NAME_SPACE::Util::GetName((*it).c_str());
 870                if (mhd)
 871                {
 872                   // Copy the data file in the new directory
 873                   sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() ,
 874                             currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str());
 875                   system(copyFile);
 876                   sprintf(outputMhdFileName, "%s%c%s%s",
 877                                        currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".mhd" );
 878                   if (verbose)
 879                     std::cout << "--- Output Carto MHD file [" << outputMhdFileName << "]" << std::endl;
 880
 881                   FILE *fp;
 882                   fp=fopen(outputMhdFileName, "w");
 883                   if (!fp)
 884                   {
 885                      std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 886                   }
 887                   else
 888                   {
 889                      fprintf(fp, "ObjectType = Image\n");
 890                      fprintf(fp, "NDims = 3\n" );
 891                      fprintf(fp, "BinaryData = True \n" );
 892                      fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 893                      fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices);
 894                      fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
 895                      fprintf(fp, "HeaderSize = %d\n", 0 );
 896                      fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
 897                      fprintf(fp, "Position = 0 0 0\n" );
 898                      fprintf(fp, "Offset = 0 0 0\n" );
 899                      fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 900                      fprintf(fp, "ElementNumberOfChannels = 1\n" );
 901                      fprintf(fp, "ElementType = %s\n", "MET_DOUBLE" );
 902                      fprintf(fp, "ElementDataFile = %s\n", lastFileName.c_str() );
 903
 904                      fclose(fp);
 905                   }
 906                   if (verbose)
 907                      std::cout << "--- end write Carto MHD file [" << outputMhdFileName << "]" << std::endl;
 908                }  // end if mhd
 909
 910             // ----------- Write Dicom Image  ---------------
 911
 912                if (dicom)
 913                {
 914                   sprintf(output2dseqCartoName, "%s%c%s%s",
 915                                        currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".dcm" );
 916                   if (verbose)
 917                      std::cout << "--- end create name output2dseqCartoName file [" << output2dseqCartoName << "]" << std::endl;
 918
 919                   strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID(); //New SerieUID for each carto.
 920                   std::string strNewSerieDescr(strSerieDescr+ "_" +GDCM_NAME_SPACE::Util::GetName((*it).c_str()));
 921                   MakeDicomImage(buffer_carto,
 922                      NX,
 923                      NY,
 924                      nbSlices,
 925                      8, // pixelSize
 926                      fovX/NY, fovY/NY, sliceDistance,
 927                      output2dseqCartoName,
 928                      strPatientName,
 929                      day,
 930                      strStudyUID,
 931                      strSerieUID,
 932                      strStudyDescr,
 933                      strNewSerieDescr,
 934                      strStudyTimeDate,
 935                      0,
 936                      GDCM_NAME_SPACE::CREATED_IMAGE
 937                   );
 938                }  // end if dicom
 939
 940                delete [] buffer_carto;
 941                if (verbose)
 942                   std::cout << "--- End writing Carto DICOM file [" << output2dseqCartoName << "]" << std::endl;
 943                break; // don't check for more ident on same file name!
 944
 945             }
 946             icode++;
 947          }
 948       }
 949    } // end iterate on files
 950 }
 951
 952
 953 // ==========================================================================================================
 954
 955 bool Bruker2Dicom::CreateDirectory(std::string OutputDirName)
 956 {
 957    std::string systemCommand;
 958
 959    if (verbose)
 960       std::cout << "Check for output directory :[" << OutputDirName << "]."
 961                 <<std::endl;
 962    if ( ! boost::filesystem::is_directory(OutputDirName) )    // dirout not found
 963    {
 964       std::string strDirNameout(OutputDirName);        // to please gcc 4
 965       systemCommand = "mkdir " + strDirNameout;        // create it!
 966       if (verbose)
 967          std::cout << systemCommand << std::endl;
 968       system (systemCommand.c_str());
 969       if ( ! boost::filesystem::is_directory(OutputDirName) ) // be sure it worked
 970       {
 971          if (verbose)
 972             std::cout << "KO : not a dir : [" << OutputDirName << "] (creation failure ?)" << std::endl;
 973          return 0;
 974          /// \todo : THROW AN EXCEPTION
 975       }
 976       else
 977       {
 978          if (verbose)
 979            std::cout << "Directory [" << OutputDirName << "] created." << std::endl;
 980       }
 981    }
 982    else
 983    {
 984        if (verbose)
 985           std::cout << "Output Directory [" << OutputDirName << "] already exists; Used as is." << std::endl;
 986    }
 987
 988    return 1;
 989
 990 }
 991
 992
 993 // ===========================================================================================
 994
 995 /// \TODO move cleanString to 'crea' ?
 996
 997 void Bruker2Dicom::cleanString(std::string &s)
 998 {
 999    int l = s.size();
1000    if (s[l-1] == 0x0A || s[l-1] == 0x0D ) // CR or NL
1001    {
1002       l--;
1003       s = s.substr(0, l);
1004    }
1005    if (s[l-1] == ' ' ) // blank space
1006    {
1007       l--;
1008       s = s.substr(0, l);
1009    }
1010
1011    if (s[0] == '<')
1012       s= s.substr(1,l-2);
1013    std::string repChar("_");
1014    GDCM_NAME_SPACE::Util::ReplaceSpecChar(s, repChar);
1015 }
1016
1017
1018
1019 // ===========================================================================================
1020
1021
1022 void Bruker2Dicom::getImhDataType(BrukerFieldData &bDPT, std::string &mhdDataPixelType, int &pixelSize)
1023 {
1024    if(bDPT.GetDataType() == "string")
1025    {
1026          std::string brukerDataPixelType = bDPT.GetStringValue()[0];
1027          if (verbose)
1028             std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
1029          //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
1030
1031          if (brukerDataPixelType ==  "ip_short") {
1032             mhdDataPixelType = "MET_USHORT";
1033             pixelSize = 2;
1034          }
1035          if (brukerDataPixelType ==  "ip_int") {
1036             mhdDataPixelType = "MET_UINT";
1037             pixelSize = 4;
1038          }
1039          if (brukerDataPixelType ==  "ip_char") {
1040              mhdDataPixelType = "MET_UCHAR";
1041              pixelSize = 1;
1042          }
1043                   /// \TODO : finish the list
1044     /*
1045     case 0 : fp << "ElementType = MET_CHAR" << std::endl;
1046       break;
1047     case 1 : fp << "ElementType = MET_UCHAR" << std::endl;
1048       break;
1049     case 2 : fp << "ElementType = MET_SHORT" << std::endl;
1050       break;
1051     case 3 : fp << "ElementType = MET_USHORT" << std::endl;
1052       break;
1053     case 4 : fp << "ElementType = MET_INT" << std::endl;
1054       break;
1055     case 5 : fp << "ElementType = MET_UINT" << std::endl;
1056       break;
1057     case 6 : fp << "ElementType = MET_FLOAT" << std::endl;
1058       break;
1059     case 7 : fp << "ElementType = MET_DOUBLE" << std::endl;
1060     */
1061     }
1062     else
1063     {
1064          int brukerDataPixelType = bDPT.GetIntValue()[0];
1065          if (verbose)
1066             std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
1067          //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
1068
1069 // Cross your fingers !!!
1070
1071 // pb : found values : 2, 3, 5
1072
1073          if (brukerDataPixelType ==  2) {
1074             mhdDataPixelType = "MET_USHORT";
1075             pixelSize = 2;
1076          }
1077          if (brukerDataPixelType ==  3) {
1078             mhdDataPixelType = "MET_USHORT";
1079             pixelSize = 2;
1080          }
1081          if (brukerDataPixelType ==  1) {
1082             mhdDataPixelType = "MET_UCHAR";
1083             pixelSize = 1;
1084          }
1085     }
1086 }
1087
1088 // ===========================================================================================
1089
1090 std::vector<BrukerImage> Bruker2Dicom::CreateImageSet ( )
1091 {
1092          std::vector<BrukerImage> imageSet;
1093          br_acqp.SetLoopStructure();
1094          std::vector<int> tempVect                      = br_acqp.GetLoopStructure() ;
1095          std::map<std::string, BrukerFieldData> map     = br_acqp.GetBrukerHeaderMap();
1096          bool result                                    = br_acqp.ObjectVaryingProperties.init(map,tempVect);
1097
1098          if (result == false)
1099          {
1100             throw ( BrukerInitException  ("Bruker2Dicom::CreateImageSet failure ") );
1101          }
1102
1103          br_acqp.SetImageLoopStructure();
1104          br_acqp.SetBrukerImageList();
1105          std::vector<std::vector<int> > brukerImageList = br_acqp.GetBrukerImageList();
1106
1107          BrukerImage image(br_acqp,br_reco);
1108          image.Init(br_acqp,br_reco,1);
1109
1110          for(int i=0;i<brukerImageList.size();i++)
1111          {
1112             image.Init(br_acqp,br_reco,i);
1113             imageSet.push_back(image);
1114          }
1115
1116  // Just for checking
1117  /*
1118
1119          std::vector<std::vector <double> > imageOrientation;
1120          std::vector <double> imagePosition;
1121          for(int i=0;i<brukerImageList.size();i++)
1122          {
1123            // fread(buffer_2dseq, NX*NY*pixelSize*nbSlices*nbInstants, 1, fp);
1124
1125            imagePosition = imageSet[i].getTranslationVectorRPS2XYZ();
1126            std::cout << "Position " << imagePosition[0] << " "
1127                      << imagePosition[1] << " "  << imagePosition[2] ;
1128            imageOrientation =  imageSet[i].getRotationMatrixRPS2XYZ();
1129            std::cout << "\t  Orientation " ;
1130            for(int i1=0; i1<3;i1++)for(int i2=0; i2<3;i2++)
1131               std::cout << imageOrientation[i1][i2] << " ";
1132
1133            //std::cout << "\t  Abs Time " << imageSet[i].getAbsoluteTimePosition();
1134            std::cout << "\t  Relat Time " << imageSet[i].getRelativeTimePosition();
1135
1136            std::cout << "\t [";
1137            for (int i3=0; i3<imageSet[i].getLoopStamp().size();i3++)
1138               std::cout << " " << imageSet[i].getLoopStamp()[i3];
1139            std::cout << "]" << std::endl;
1140          }
1141 */
1142    return imageSet;
1143 }
1144
1145 // ===========================================================================================
1146
1147 void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels,
1148               int X,
1149               int Y,
1150               int nbFrames,
1151               int pixelSize,
1152               double spacingX, double spacingY, double sliceDistance,
1153               std::string dcmImageName,
1154               const std::string &patientName,
1155               const char *day,
1156               std::string &studyUID,
1157               std::string &serieUID,
1158               std::string &studyDescr,
1159               std::string &serieDescr,
1160               std::string &strStudyTimeDate,
1161               int imgNum,
1162               GDCM_NAME_SPACE::ImageContentType contentType
1163       )
1164 {
1165    std::ostringstream str;
1166
1167    GDCM_NAME_SPACE::File *file;
1168    file = GDCM_NAME_SPACE::File::New();
1169
1170   // Set the image size
1171    str.str("");
1172    str << X;
1173    file->InsertEntryString(str.str(),0x0028,0x0011,"US"); // Columns
1174    str.str("");
1175    str << Y;
1176    file->InsertEntryString(str.str(),0x0028,0x0010,"US"); // Rows
1177
1178    if (nbFrames != 1)
1179    {
1180       str.str("");
1181       str << nbFrames;
1182       file->InsertEntryString(str.str(),0x0028,0x0008,"IS"); // Number of Frames
1183    }
1184
1185   // Set the pixel type
1186   //      //8, 16, 32, 64 (for double ?)
1187    str.str("");
1188    str << pixelSize*8;
1189    file->InsertEntryString(str.str(),0x0028,0x0100,"US"); // Bits Allocated
1190
1191    file->InsertEntryString(str.str(),0x0028,0x0101,"US"); // Bits Stored
1192
1193    str.str("");
1194    str << pixelSize*8-1;
1195    file->InsertEntryString(str.str(),0x0028,0x0102,"US"); // High Bit
1196
1197   // Set the pixel representation // 0/1 , 0=unsigned
1198    file->InsertEntryString("1",0x0028,0x0103, "US"); // Pixel Representation
1199
1200   // Set the samples per pixel // 1:Grey level, 3:RGB
1201    file->InsertEntryString("1",0x0028,0x0002, "US"); // Samples per Pixel
1202
1203 //  0028 0030 DS 2 Pixel Spacing
1204    str.str("");
1205    str << spacingX << "\\" << spacingY;
1206    file->InsertEntryString(str.str(),0x0028,0x0030, "DS"); // Pixel Spacing
1207
1208  //   0018 0050 DS 1 Slice Thickness
1209    str.str("");
1210    str << sliceDistance;
1211    file->InsertEntryString(str.str(),0x0018,0x0050, "DS");
1212
1213 //    0020 0011 IS 1 Series Number
1214    str.str("");
1215    str << serieNumber;
1216    file->InsertEntryString(str.str(),0x0020,0x0011, "IS");
1217
1218 //    0020|0013 [IS]  [Instance Number]
1219    instanceNumber++;
1220    str.str("");
1221    str << instanceNumber;
1222    file->InsertEntryString(str.str(),0x0020,0x0013, "IS");
1223
1224
1225   // 1.2.840.10008.5.1.4.1.1.4.1 : Enhanced MR Image Storage
1226  //  file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0002, 0x0002, "UI");  // [Media Storage SOP Class UID]
1227   // file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0008, 0x0016, "UI");  // [SOP Class UID]
1228
1229
1230 // OK : MR is NOT multiframe, but I want just a quick an dirty solution
1231
1232 // 1.2.840.10008.5.1.4.1.1.4         MR Image Storage
1233    file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0002, 0x0002, "UI");  // [Media Storage SOP Class UID]
1234    file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0008, 0x0016, "UI");  // [SOP Class UID]
1235
1236   // if (strlen(patientName) != 0)
1237    file->InsertEntryString(patientName.c_str(),0x0010,0x0010, "PN"); // Patient's Name
1238
1239    file->InsertEntryString(studyUID, 0x0020, 0x000d, "UI");
1240    file->InsertEntryString(serieUID, 0x0020, 0x000e, "UI");
1241
1242 //  0008 0020 DA 1 Study Date
1243 //  0008 0030 TM 1 Study Time
1244
1245 /// \TODO split into 2 strings!
1246    file->InsertEntryString(strStudyTimeDate.substr(10,11).c_str(),0x0008,0x0020, "DA");
1247    file->InsertEntryString(strStudyTimeDate.substr(1,8).c_str(),  0x0008,0x0030, "TM");
1248
1249    file->InsertEntryString(studyDescr, 0x0008,0x1030, "LO");  // Study Description
1250    file->InsertEntryString(serieDescr, 0x0008,0x103e, "LO");  // Series Description
1251
1252 //0008|0060 [CS] [Modality]
1253    file->InsertEntryString("MR",0x0008,0x0060, "CS");
1254
1255 // 0020 0037 DS 6 Image Orientation (Patient)
1256    char charImageOrientation[256];
1257
1258 /*
1259 std::cout << "charImageOrientation  " <<
1260                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0] << " " <<
1261                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1] << " " <<
1262                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2] << " " <<
1263                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0] << " " <<
1264                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1] << " " <<
1265                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] << std::endl ;
1266 */
1267    sprintf(charImageOrientation,"%f\\%f\\%f \\ %f\\%f\\%f",
1268                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0],
1269                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1],
1270                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2],
1271                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0],
1272                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1],
1273                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] ) ;
1274
1275    file->InsertEntryString(charImageOrientation,0x0020,0x0037, "DS");
1276
1277
1278 // 0020 0032 DS 3 Image Position (Patient)
1279
1280    char charImagePosition[256];
1281    sprintf(charImagePosition,"%f\\%f\\%f",
1282                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[0],
1283                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[1],
1284                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[2]);
1285
1286    file->InsertEntryString(charImagePosition,0x0020,0x0032, "DS");  //0020 0032 DS 3 Image Position (Patient)
1287
1288
1289
1290 // 0020 0x1041 DS 1 Slice Location
1291 //        sprintf(charImagePosition,"%f",float(imgNum));
1292 //        file->InsertEntryString(charImagePosition,0x0020,0x1041, "DS");
1293 /*
1294   // Set Rescale Intercept
1295         str.str("");
1296         str << div;
1297         file->InsertEntryString(str.str(),0x0028,0x1052,"DS");
1298
1299   // Set Rescale Slope
1300         str.str("");
1301         str << mini;
1302         file->InsertEntryString(str.str(),0x0028,0x1053,"DS");
1303 */
1304
1305    GDCM_NAME_SPACE::FileHelper *fileH;
1306    fileH = GDCM_NAME_SPACE::FileHelper::New(file);
1307    fileH->SetContentType(contentType);
1308
1309    // cast is just to avoid warnings (*no* conversion is performed)
1310    //fileH->SetImageData((uint8_t *)img,int(maxX*maxY)*sizeof(uint16_t)); // troubles when maxX, mayY are *actually* float!
1311
1312 //std::cout << "--------------------------------  X*Y*nbFrames*pixelSize " << X << " " << Y << " " << nbFrames << " " << pixelSize << std::endl;
1313
1314    fileH->SetImageData((uint8_t *)tabPixels, X*Y*nbFrames*pixelSize);
1315    fileH->SetWriteModeToRaw();
1316    fileH->SetWriteTypeToDcmExplVR();
1317    if( !fileH->Write(dcmImageName))
1318       std::cout << "Failed for [" << dcmImageName << "]\n"
1319                 << "           File is unwrittable" << std::endl;
1320
1321    if (verbose)
1322       file->Print();
1323
1324    file->Delete();
1325    fileH->Delete();
1326 }
1327
1328