lib/src1/bruker2dicom.cxx

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