Example/ToInTag.cxx

   1 /*=========================================================================
   2
   3   Program:   gdcm
   4   Module:    $RCSfile: ToInTag.cxx,v $
   5   Language:  C++
   6   Date:      $Date: 2006/06/30 09:58:08 $
   7   Version:   $Revision: 1.6 $
   8
   9   Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
  10   l'Image). All rights reserved. See Doc/License.txt or
  11   http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
  12
  13      This software is distributed WITHOUT ANY WARRANTY; without even
  14      the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15      PURPOSE.  See the above copyright notices for more information.
  16
  17 =========================================================================*/
  18 #include "gdcmDocEntry.h"
  19 #include "gdcmDicomDir.h"
  20 #include "gdcmDicomDirPatient.h"
  21 #include "gdcmFile.h"
  22 #include "gdcmFileHelper.h"
  23 #include "gdcmDirList.h"
  24 #include "gdcmDebug.h"
  25 #include "gdcmArgMgr.h"
  26 #include "gdcmUtil.h"
  27 #include "gdcmSerieHelper.h"
  28
  29 #include <iostream>
  30
  31 /**
  32   * \brief
  33   *          - explores recursively the given directory
  34   *          - keeps the requested series
  35   *          - orders the gdcm-readable found Files
  36   *            according to their Patient/Study/Serie/Image characteristics
  37   *          - fills a single level Directory with *all* the files,
  38   *            converted into a Brucker-like Dicom, Intags compliant
  39   */
  40
  41 typedef std::map<std::string, gdcm::File*> SortedFiles;
  42
  43 int main(int argc, char *argv[])
  44 {
  45    START_USAGE(usage)
  46    " \n ToInTag :\n                                                           ",
  47    " - explores recursively the given directory,                              ",
  48    " - keeps the requested series/ drops the unrequested series               ",
  49    " - orders the gdcm-readable found Files according to their                ",
  50    "           (0x0010, 0x0010) Patient's Name                                ",
  51    "           (0x0020, 0x000e) Series Instance UID                           ",
  52    "           (0x0020, 0x0032) Image Position (Patient)                      ",
  53    "           (0x0018, 0x1060) Trigger Time                                  ",
  54    "           (0x0018, 0x1312) In-plane Phase Encoding Direction             ",
  55    " - fills a single level (*) Directory with *all* the files,               ",
  56    "           converted into a Brucker-like Dicom, InTags compliant          ",
  57    "   (*) actually : creates as many directories as Patients                 ",
  58    "                  -that shouldn't appear, but being carefull is better ! -",
  59    " or                                                                       ",
  60    " - fills a tree-like structure of directories as :                        ",
  61    "        - Patient                                                         ",
  62    "        -- Serie                                                          ",
  63    "        --- Position                                                      ",
  64    "            Images are (sorted by Trigger Time /                          ",
  65    "                     Encoding Direction (Row, Column)                     ",
  66    "      use :                                                               ",
  67    "           0x0021, 0x1020 : 'SLICE INDEX'                                 ",
  68    "           0x0021, 0x1040 : 'FRAME INDEX'                                 ",
  69    "           0x0020, 0x0012 : 'SESSION INDEX'  (Acquisition Number)         ",
  70    " usage:                                                                   ",
  71    " PhilipsToBrucker dirin=rootDirectoryName                                 ",
  72    "                  dirout=outputDirectoryName                              ",
  73    "                  {  [keep= list of seriesNumber to process]              ",
  74    "                   | [drop= list of seriesNumber to ignore] }             ",
  75    "                  [taggrid] [skel]                                        ",
  76    "                  [input = {ACR|DCM}]                                     ",
  77    "                  [extent=image suffix (.IMA, .NEMA, .DCM, ...)]          ",
  78    "                  [listonly] [split]                                      ",
  79    "                  [noshadowseq][noshadow][noseq] [verbose] [debug]        ",
  80    "                                                                          ",
  81    " dirout : will be created if doesn't exist                                ",
  82    " keep : if user wants to process a limited number of series               ",
  83    "            he gives the list of 'SeriesNumber' (tag 0020|0011)           ",
  84    " drop : if user wants to ignore a limited number of series                ",
  85    "            he gives the list of 'SeriesNumber' (tag 0020|0011)           ",
  86    "        SeriesNumber are short enough to be human readable                ",
  87    "        e.g : 1030,1035,1043                                              ",
  88    " taggrid : user knows all the images are 'grid' -ie : not 'col', not 'raw'",
  89    " extent : DO NOT forget the leading '.' !                                 ",
  90    " skel: name skeleton eg : patName_1.nema -> skel=patName_                 ",
  91    " split: creates a tree-like structure of directories as :                 ",
  92    "        - Patient                                                         ",
  93    "        -- Serie                                                          ",
  94    "        --- Position                                                      ",
  95    "            Images are (sorted by Trigger Time /                          ",
  96    "                     Encoding Direction (Row, Column)                     ",
  97    " noshadowseq: user doesn't want to load Private Sequences                 ",
  98    " noshadow : user doesn't want to load Private groups (odd number)         ",
  99    " noseq    : user doesn't want to load Sequences                           ",
 100    " verbose  : user wants to run the program in 'verbose mode'               ",
 101    " debug    : *developer*  wants to run the program in 'debug mode'         ",
 102    FINISH_USAGE
 103
 104    std::cout << "inside ToInTag" << std::endl;
 105
 106    // ----- Initialize Arguments Manager ------
 107
 108    gdcm::ArgMgr *am = new gdcm::ArgMgr(argc, argv);
 109
 110    if (argc == 1 || am->ArgMgrDefined("usage"))
 111    {
 112       am->ArgMgrUsage(usage); // Display 'usage'
 113       delete am;
 114       return 0;
 115    }
 116
 117    const char *dirNamein;
 118    dirNamein  = am->ArgMgrGetString("dirin",".");
 119
 120    const char *dirNameout;
 121    dirNameout  = am->ArgMgrGetString("dirout",".");
 122
 123    int loadMode = gdcm::LD_ALL;
 124    if ( am->ArgMgrDefined("noshadowseq") )
 125       loadMode |= gdcm::LD_NOSHADOWSEQ;
 126    else
 127    {
 128    if ( am->ArgMgrDefined("noshadow") )
 129          loadMode |= gdcm::LD_NOSHADOW;
 130       if ( am->ArgMgrDefined("noseq") )
 131          loadMode |= gdcm::LD_NOSEQ;
 132    }
 133
 134    if (am->ArgMgrDefined("debug"))
 135       gdcm::Debug::DebugOn();
 136
 137    int verbose  = am->ArgMgrDefined("verbose");
 138    int split    = am->ArgMgrDefined("split");
 139    int listonly = am->ArgMgrDefined("listonly");
 140
 141    int nbSeriesToKeep;
 142    int *seriesToKeep = am->ArgMgrGetListOfInt("keep", &nbSeriesToKeep);
 143    int nbSeriesToDrop;
 144    int *seriesToDrop = am->ArgMgrGetListOfInt("drop", &nbSeriesToDrop);
 145
 146    if ( nbSeriesToKeep!=0 && nbSeriesToDrop!=0)
 147    {
 148       std::cout << "KEEP and DROP are mutually exclusive !" << std::endl;
 149       delete am;
 150       return 0;
 151    }
 152
 153    int taggrid = am->ArgMgrDefined("taggrid");
 154
 155    int hasSkel = am->ArgMgrDefined("skel");
 156    const char *skel;
 157    if (hasSkel)
 158       skel = am->ArgMgrGetString("skel");
 159
 160    const char *extent  = am->ArgMgrGetString("extent",".DCM");
 161
 162    // if unused Param we give up
 163    if ( am->ArgMgrPrintUnusedLabels() )
 164    {
 165       am->ArgMgrUsage(usage);
 166       delete am;
 167       return 0;
 168    }
 169    delete am;  // we don't need Argument Manager any longer
 170
 171    // ----- Begin Processing -----
 172
 173    if ( ! gdcm::DirList::IsDirectory(dirNamein) )
 174    {
 175       std::cout << "KO : [" << dirNamein << "] is not a Directory." << std::endl;
 176       return 0;
 177
 178    }
 179    else
 180    {
 181       std::cout << "OK : [" << dirNamein << "] is a Directory." << std::endl;
 182    }
 183
 184    std::string systemCommand;
 185
 186    std::cout << "Check for output directory :[" << dirNameout << "]."
 187              <<std::endl;
 188    if ( ! gdcm::DirList::IsDirectory(dirNameout) )    // dirout not found
 189    {
 190       std::string strDirNameout(dirNameout);          // to please gcc 4
 191       systemCommand = "mkdir " +strDirNameout;        // create it!
 192       if (verbose)
 193          std::cout << systemCommand << std::endl;
 194       system (systemCommand.c_str());
 195       if ( ! gdcm::DirList::IsDirectory(dirNameout) ) // be sure it worked
 196       {
 197           std::cout << "KO : not a dir : [" << dirNameout << "] (creation failure ?)" << std::endl;
 198       return 0;
 199
 200       }
 201       else
 202       {
 203         std::cout << "Directory [" << dirNameout << "] created." << std::endl;
 204       }
 205    }
 206    else
 207    {
 208        std::cout << "Output Directory [" << dirNameout << "] already exists; Used as is." << std::endl;
 209    }
 210
 211    std::string strDirNamein(dirNamein);
 212    gdcm::DirList dirList(strDirNamein, true); // get recursively the list of files
 213
 214    if (listonly)
 215    {
 216       std::cout << "------------List of found files ------------" << std::endl;
 217       dirList.Print();
 218       std::cout << std::endl;
 219    }
 220
 221    gdcm::DirListType fileNames;
 222    fileNames = dirList.GetFilenames();
 223    gdcm::SerieHelper *s;              // Needed only to may use SerieHelper::AddSeriesDetail()
 224    s = gdcm::SerieHelper::New();
 225
 226    std::string token = "%%%"; // Hope it's enough!
 227 /*
 228    std::cout << "---------------Print Serie--------------" << std::endl;
 229    s->SetDirectory(dirNamein, true); // true : recursive exploration
 230    s->SetUseSeriesDetails(true);
 231    s->AddSeriesDetail(0x0018, 0x1312);
 232    s->Print();
 233 */
 234
 235    gdcm::File *f;
 236    gdcm::FileHelper *fh;
 237    std::vector<std::string> tokens;
 238    std::vector<std::string> tokensForFileName;
 239 /*
 240    std::cout << "---------------Print Unique Series identifiers---------"
 241              << std::endl;
 242    std::string uniqueSeriesIdentifier;
 243
 244    for (gdcm::DirListType::iterator it) = fileNames.begin();
 245                                     it != fileNames.end();
 246                                   ++it)
 247    {
 248       std::cout << "File Name : " << *it << std::endl;
 249       f = gdcm::File::New();
 250       f->SetLoadMode(gdcm::LD_ALL);
 251       f->SetFileName( *it );
 252       f->Load();
 253
 254       uniqueSeriesIdentifier=s->CreateUniqueSeriesIdentifier(f);
 255       std::cout << "                           [" <<
 256                uniqueSeriesIdentifier  << "]" << std::endl;
 257       f->Delete();
 258    }
 259 */
 260
 261    if (verbose)
 262       std::cout << "------------------Print Break levels-----------------" << std::endl;
 263
 264    std::string userFileIdentifier;
 265    SortedFiles sf;
 266
 267    s->AddSeriesDetail(0x0010, 0x0010, false); // Patient's Name
 268    s->AddSeriesDetail(0x0020, 0x000e, false); // Series Instance UID
 269    s->AddSeriesDetail(0x0020, 0x0032, false); // Image Position (Patient)
 270    s->AddSeriesDetail(0x0018, 0x1060, true);  // Trigger Time (true: convert to keep numerical order)
 271    s->AddSeriesDetail(0x0018, 0x1312, false); // In-plane Phase Encoding Direction
 272
 273    //uint8_t *imageData; // Useless : pixels will not be loaded
 274                          //          (images are overwritten)
 275
 276    for (gdcm::DirListType::iterator it = fileNames.begin();
 277                                     it != fileNames.end();
 278                                   ++it)
 279    {
 280       f = gdcm::File::New();
 281       f->SetLoadMode(loadMode);
 282       f->SetFileName( *it );
 283       f->Load();
 284
 285
 286       std::string strSeriesNumber;
 287       int seriesNumber;
 288       int j;
 289
 290       // keep only requested Series
 291       bool keep = false;
 292       if (nbSeriesToKeep != 0)
 293       {
 294          strSeriesNumber = f->GetEntryString(0x0020, 0x0011 );
 295          seriesNumber = atoi( strSeriesNumber.c_str() );
 296          for (j=0;j<nbSeriesToKeep; j++)
 297          {
 298             if(seriesNumber == seriesToKeep[j])
 299             {
 300                keep = true;
 301                break;
 302             }
 303          }
 304          if ( !keep)
 305          {
 306             f->Delete();
 307             continue;
 308          }
 309       }
 310       // drop all unrequested Series
 311       bool drop = false;
 312       if (nbSeriesToDrop != 0)
 313       {
 314          strSeriesNumber = f->GetEntryString(0x0020, 0x0011 );
 315          seriesNumber = atoi( strSeriesNumber.c_str() );
 316          for (j=0;j<nbSeriesToDrop; j++)
 317          {
 318             if(seriesNumber == seriesToDrop[j])
 319             {
 320                drop = true;
 321                break;
 322             }
 323         }
 324         if (drop)
 325         {
 326            f->Delete();
 327            continue;
 328         }
 329       }
 330
 331       userFileIdentifier=s->CreateUserDefinedFileIdentifier(f);
 332       tokens.clear();
 333       gdcm::Util::Tokenize (userFileIdentifier, tokens, token);
 334
 335       int imageNum; // Within FileName
 336       char newName[1024];
 337
 338       if ( tokens[3] == "gdcmUnfound")  // sometimes Trigger Time is not found. CreateUserDefinedFileIdentifier is not aware of the pb.
 339       {
 340          ///this is a trick to build up a lexicographical compliant name :
 341          ///     eg : fich001.ima vs fich100.ima as opposed to fich1.ima vs fich100.ima
 342          std::string name = gdcm::Util::GetName( *it );
 343          if (hasSkel)
 344          {
 345             gdcm::Util::Tokenize (name, tokensForFileName, skel);
 346             imageNum = atoi ( tokensForFileName[0].c_str() );
 347             // probabely we could write something much more complicated using C++ !
 348             sprintf (newName, "%s%06d%s", skel, imageNum, extent);
 349             tokens[3] = newName;
 350             tokensForFileName.clear();
 351          }
 352          else
 353             tokens[3] = name;
 354
 355
 356          userFileIdentifier = tokens[0] + token + tokens[1] + token + tokens[2] + token
 357                     + tokens[3] + token + tokens[4] + token;
 358       }
 359       if (verbose)
 360          std::cout << "[" << userFileIdentifier  << "]" << std::endl;
 361
 362       // storing in a map ensures automatic sorting !
 363       sf[userFileIdentifier] = f;
 364    }
 365
 366    if (verbose)
 367       std::cout << "  " << std::endl;
 368
 369    std::string fullFilename, lastFilename;
 370    std::string previousPatientName, currentPatientName;
 371    std::string previousSerieInstanceUID, currentSerieInstanceUID;
 372    std::string previousImagePosition, currentImagePosition;
 373    std::string previousPhaseEncodingDirection, currentPhaseEncodingDirection;
 374    std::string previousTriggerTime, currentTriggerTime;
 375
 376    std::string currentStudyUID;
 377
 378    std::string writeDir, currentWriteDir;
 379    std::string currentPatientWriteDir, currentSerieWriteDir,
 380                currentPositionWriteDir, currentPhaseEncodingDirectionWriteDir;
 381
 382    std::string fullWriteFilename;
 383    std::string strExtent(extent);
 384
 385    writeDir = gdcm::Util::NormalizePath(dirNameout);
 386    SortedFiles::iterator it2;
 387
 388    previousPatientName            = "";
 389    previousSerieInstanceUID       = "";
 390    previousImagePosition          = "";
 391    previousPhaseEncodingDirection = "";
 392    previousTriggerTime            = "";
 393
 394    int sliceIndex = 0; // Is incremented *at the beginning* of processing
 395    int frameIndex;
 396    if (taggrid)
 397        frameIndex = 0;
 398    else
 399        frameIndex = 1;
 400
 401    int flag       = 0;
 402
 403    gdcm::File *currentFile;
 404
 405    std::string defaultStudyUID =  gdcm::Util::CreateUniqueUID();
 406    std::string defaultSerieUID;
 407
 408    for (it2 = sf.begin() ; it2 != sf.end(); ++it2)
 409    {
 410       currentFile = it2->second;
 411
 412       fullFilename =  currentFile->GetFileName();
 413       lastFilename =  gdcm::Util::GetName( fullFilename );
 414       std::cout << " --------------------------------------------------"
 415                 << " Rewrite [" <<lastFilename << "]" << std::endl;
 416
 417       tokens.clear();
 418       gdcm::Util::Tokenize (it2->first, tokens, token);
 419
 420       currentPatientName            = tokens[0];
 421       currentSerieInstanceUID       = tokens[1];
 422       currentImagePosition          = tokens[2];
 423       currentTriggerTime            = tokens[3];
 424       currentPhaseEncodingDirection = tokens[4];
 425
 426       if ( currentImagePosition[0] == '-')
 427           currentImagePosition[0] = 'M';
 428       if ( currentImagePosition[0] == '+')
 429           currentImagePosition[0] = 'P';
 430
 431       if (previousPatientName != currentPatientName)
 432       {
 433          if ( currentFile->GetEntryString(0x0020,0x000d) == gdcm::GDCM_UNFOUND)
 434          {
 435             if (verbose)
 436                std::cout << "--- new  Study UID created" << std::endl;
 437             defaultStudyUID =  gdcm::Util::CreateUniqueUID();
 438             currentFile->InsertEntryString(defaultStudyUID, 0x0020, 0x000d, "UI" );
 439          }
 440
 441          previousPatientName = currentPatientName;
 442          if (verbose)
 443             std::cout << "==== new Patient  [" << currentPatientName  << "]" << std::endl;
 444
 445          previousPatientName            = currentPatientName;
 446          previousSerieInstanceUID       = ""; //currentSerieInstanceUID;
 447          previousImagePosition          = ""; //currentImagePosition;
 448          previousTriggerTime            = "";
 449          previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection;
 450
 451          currentPatientWriteDir = writeDir + currentPatientName;
 452          //if ( ! gdcm::DirList::IsDirectory(currentPatientWriteDir) )
 453            {
 454               systemCommand   = "mkdir " + currentPatientWriteDir;
 455               if (verbose)
 456                  std::cout << systemCommand << std::endl;
 457               system ( systemCommand.c_str() );
 458          }
 459       }
 460
 461       if (previousSerieInstanceUID != currentSerieInstanceUID)
 462       {
 463          if (verbose)
 464             std::cout << "==== === new Serie [" << currentSerieInstanceUID << "]"
 465                       << std::endl;
 466
 467          if ( currentFile->GetEntryString(0x0020,0x000e) == gdcm::GDCM_UNFOUND)
 468          {
 469             if (verbose)
 470                std::cout << "--- --- new  Serie UID created" << std::endl;
 471             defaultSerieUID =  gdcm::Util::CreateUniqueUID();
 472             currentFile->InsertEntryString(defaultSerieUID, 0x0020, 0x000e, "UI" );
 473          }
 474
 475          if (split)
 476          {
 477              currentSerieWriteDir  = currentPatientWriteDir + gdcm::GDCM_FILESEPARATOR
 478                              + currentSerieInstanceUID;
 479              systemCommand   = "mkdir " + currentSerieWriteDir;
 480              system (systemCommand.c_str());
 481          }
 482          previousSerieInstanceUID       = currentSerieInstanceUID;
 483          previousImagePosition          = ""; //currentImagePosition;
 484          previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection;
 485       }
 486
 487       if (previousImagePosition != currentImagePosition)
 488       {
 489          frameIndex = 1;
 490          flag = 0;
 491          if (verbose)
 492             std::cout << "=== === === new Position [" << currentImagePosition  << "]"
 493                       << std::endl;
 494          if (split)
 495          {
 496              currentPositionWriteDir  = currentSerieWriteDir + gdcm::GDCM_FILESEPARATOR
 497                              + currentImagePosition;
 498              systemCommand   = "mkdir " + currentPositionWriteDir;
 499              system (systemCommand.c_str());
 500          }
 501          previousImagePosition          = currentImagePosition;
 502          previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection;
 503          if (split)
 504             sliceIndex = 1; // only *one* slice in a given directory
 505          else
 506             sliceIndex += 1;
 507       }
 508       if (verbose)
 509          std::cout << "Slice Index : " << sliceIndex << std::endl;
 510
 511 // We don't split on Row/Column!
 512 /*
 513       if (previousPhaseEncodingDirection != currentPhaseEncodingDirection)
 514       {
 515          if (verbose)
 516             std::cout << "==== === === === new PhaseEncodingDirection ["
 517                       << currentPhaseEncodingDirection  << "]" << std::endl;
 518
 519          if (split)
 520          {
 521              currentPhaseEncodingDirectionWriteDir  = currentPositionWriteDir
 522                              + gdcm::GDCM_FILESEPARATOR
 523                              + currentPhaseEncodingDirection;
 524              systemCommand   = "mkdir " + currentPhaseEncodingDirectionWriteDir;
 525              system (systemCommand.c_str());
 526          }
 527
 528          previousPhaseEncodingDirection = currentPhaseEncodingDirection;
 529       }
 530 */
 531
 532       if (verbose)
 533          std::cout << "--- --- --- --- --- " << (it2->second)->GetFileName()
 534                    << std::endl;
 535
 536       if ( gdcm::Debug::GetDebugFlag())
 537          std::cout << "--- --- --- --- --- " << it2->first << "  "
 538                    << (it2->second)->GetFileName() << " "
 539                    << gdcm::Util::GetName( fullFilename ) << std::endl;
 540
 541       // Transform the image to be 'Brucker-Like'
 542       // ----------------------------------------
 543
 544       // Deal with 0x0019, 0x1000 : 'FOV'
 545       int nX = currentFile->GetXSize();
 546       int nY = currentFile->GetYSize();
 547       float pxSzX = currentFile->GetXSpacing();
 548       float pxSzY = currentFile->GetYSpacing();
 549       char fov[64];
 550       sprintf(fov, "%f\\%f",nX*pxSzX, nY*pxSzY);
 551       if (currentFile->IsVRCoherent(0x0019) == 1 )
 552          currentFile->InsertEntryString(fov, 0x0019, 0x1000, "  ");
 553       else
 554          currentFile->InsertEntryString(fov, 0x0019, 0x1000, "DS");
 555
 556
 557       // Deal with 0x0020, 0x0012 : 'SESSION INDEX'  (Acquisition Number)
 558       std::string chSessionIndex;
 559       // CLEANME
 560       if (taggrid)
 561          chSessionIndex = "1";
 562       else
 563       {
 564          if (currentPhaseEncodingDirection == "COL" || currentPhaseEncodingDirection == "COL " || currentPhaseEncodingDirection == " COL")
 565             chSessionIndex = "1";
 566          else if (currentPhaseEncodingDirection == "ROW" || currentPhaseEncodingDirection == "ROW "|| currentPhaseEncodingDirection == " ROW")
 567             chSessionIndex = "2";
 568          else
 569          {
 570             std::cout << "====================== PhaseEncodingDirection "
 571                       << " neither COL nor ROW (?!?) : [ "
 572                       << currentPhaseEncodingDirection << "]" << std::endl;
 573             chSessionIndex = "1";
 574          }
 575       }
 576       if (currentFile->IsVRCoherent(0x0020) == 1 )
 577          currentFile->InsertEntryString(chSessionIndex, 0x0020, 0x0012, "  ");
 578       else
 579          currentFile->InsertEntryString(chSessionIndex, 0x0020, 0x0012, "IS");
 580
 581       // Deal with  0x0021, 0x1020 : 'SLICE INDEX'
 582       char chSliceIndex[5];
 583       sprintf(chSliceIndex, "%04d", sliceIndex);
 584       std::string strChSliceIndex(chSliceIndex);
 585
 586       // Deal with  0x0021, 0x1040 : 'FRAME INDEX'
 587       char chFrameIndex[5];
 588       sprintf(chFrameIndex, "%04d", frameIndex);
 589
 590       std::string stringVR;
 591       if (currentFile->IsVRCoherent(0x0021) == 1 )
 592          stringVR = "  ";
 593       else
 594         stringVR = "IS";
 595
 596       currentFile->InsertEntryString(strChSliceIndex, 0x0021, 0x1020, stringVR);
 597       currentFile->InsertEntryString(chFrameIndex,    0x0021, 0x1040, stringVR);
 598
 599
 600       std::string strImagePositionPatient    = currentFile->GetEntryString(0x0020, 0x0032 );
 601       if (strImagePositionPatient == gdcm::GDCM_UNFOUND)
 602       {
 603          if (verbose)
 604             std::cout << "Duplicate ImagePosition into ImagePositionPatient" << std::endl;
 605          currentFile->InsertEntryString(currentFile->GetEntryString(0x0020, 0x0030), 0x0020, 0x0032, "DS" );
 606       }
 607
 608       std::string strImageOrientationPatient = f->GetEntryString(0x0020, 0x0037 );
 609       if (strImageOrientationPatient == gdcm::GDCM_UNFOUND)
 610       {
 611          if (verbose)
 612             std::cout << "Duplicate ImageOrientation into ImageOrientationPatient" << std::endl;
 613          currentFile->InsertEntryString(currentFile->GetEntryString(0x0020, 0x0035), 0x0020, 0x0037, "DS" );
 614       }
 615
 616       if (taggrid)
 617          frameIndex++;
 618       else
 619       {
 620          if (flag == 0)
 621          {
 622             flag = 1;
 623          }
 624          else
 625          {
 626             frameIndex++;
 627             flag = 0;
 628          }
 629       }
 630       if (verbose)
 631          std::cout << "Frame Index : " << frameIndex << std::endl;
 632
 633       if (split)
 634
 635          //fullWriteFilename = currentPhaseEncodingDirectionWriteDir + gdcm::GDCM_FILESEPARATOR
 636          //                                + lastFilename + strExtent;
 637          fullWriteFilename = currentPositionWriteDir + gdcm::GDCM_FILESEPARATOR
 638                                          + lastFilename + strExtent;
 639       else
 640          fullWriteFilename = currentPatientWriteDir + gdcm::GDCM_FILESEPARATOR
 641                                          + lastFilename + strExtent;
 642
 643       /*
 644       systemCommand  = "cp " + fullFilename + " " + fullWriteFilename;
 645       std::cout << systemCommand << std::endl;
 646       system (  systemCommand.c_str() );
 647       */
 648
 649       // Load the pixels in RAM.
 650
 651       fh = gdcm::FileHelper::New(currentFile);
 652       uint8_t *imageData = fh->GetImageDataRaw(); // Don't convert (Gray Pixels + LUT) into (RGB pixels) ?!?
 653       fh->SetWriteTypeToDcmExplVR();
 654       // We didn't modify pixels -> keep unchanged the following :
 655       // 'Media Storage SOP Class UID' (0x0002,0x0002)
 656       // 'SOP Class UID'               (0x0008,0x0016)
 657       // 'Image Type'                  (0x0008,0x0008)
 658       // 'Conversion Type'             (0x0008,0x0064)
 659
 660       // Put to Black the burnt-in number.
 661       nX = currentFile->GetXSize();
 662       nY = currentFile->GetYSize();
 663       for(int y=nY-15; y<nY; y++)
 664          for(int x=nX/3; x<nX/2+50; x++)
 665            imageData[ y*nX*2 + x ] = 0;
 666
 667       fh->SetContentType(gdcm::UNMODIFIED_PIXELS_IMAGE);
 668       if (!fh->Write(fullWriteFilename))
 669       {
 670          std::cout << "Fail to write :[" << fullWriteFilename << "]"
 671                    << std::endl;
 672       }
 673       fh->Delete();
 674    }
 675    return 0;
 676  }