Example/ToInTag.cxx

   1 /*=========================================================================
   2
   3   Program:   gdcm
   4   Module:    $RCSfile: ToInTag.cxx,v $
   5   Language:  C++
   6   Date:      $Date: 2006/11/15 15:56:56 $
   7   Version:   $Revision: 1.8 $
   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    " ToInTag          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       std::string strSeriesNumber;
 286       int seriesNumber;
 287       int j;
 288
 289       // keep only requested Series
 290       bool keep = false;
 291       if (nbSeriesToKeep != 0)
 292       {
 293          strSeriesNumber = f->GetEntryString(0x0020, 0x0011 );
 294          seriesNumber = atoi( strSeriesNumber.c_str() );
 295          for (j=0;j<nbSeriesToKeep; j++)
 296          {
 297             if(seriesNumber == seriesToKeep[j])
 298             {
 299                keep = true;
 300                break;
 301             }
 302          }
 303          if ( !keep)
 304          {
 305             f->Delete();
 306             continue;
 307          }
 308       }
 309       // drop all unrequested Series
 310       bool drop = false;
 311       if (nbSeriesToDrop != 0)
 312       {
 313          strSeriesNumber = f->GetEntryString(0x0020, 0x0011 );
 314          seriesNumber = atoi( strSeriesNumber.c_str() );
 315          for (j=0;j<nbSeriesToDrop; j++)
 316          {
 317             if(seriesNumber == seriesToDrop[j])
 318             {
 319                drop = true;
 320                break;
 321             }
 322         }
 323         if (drop)
 324         {
 325            f->Delete();
 326            continue;
 327         }
 328       }
 329
 330       userFileIdentifier=s->CreateUserDefinedFileIdentifier(f);
 331       tokens.clear();
 332       gdcm::Util::Tokenize (userFileIdentifier, tokens, token);
 333
 334       int imageNum; // Within FileName
 335       char newName[1024];
 336
 337       if ( tokens[3] == "gdcmUnfound")  // sometimes Trigger Time is not found. CreateUserDefinedFileIdentifier is not aware of the pb.
 338       {
 339          ///this is a trick to build up a lexicographical compliant name :
 340          ///     eg : fich001.ima vs fich100.ima as opposed to fich1.ima vs fich100.ima
 341          std::string name = gdcm::Util::GetName( *it );
 342          if (hasSkel)
 343          {
 344             gdcm::Util::Tokenize (name, tokensForFileName, skel);
 345             imageNum = atoi ( tokensForFileName[0].c_str() );
 346             // probabely we could write something much more complicated using C++ !
 347             sprintf (newName, "%s%06d%s", skel, imageNum, extent);
 348             tokens[3] = newName;
 349             tokensForFileName.clear();
 350          }
 351          else
 352             tokens[3] = name;
 353
 354
 355          userFileIdentifier = tokens[0] + token + tokens[1] + token + tokens[2] + token
 356                     + tokens[3] + token + tokens[4] + token;
 357       }
 358       if (verbose)
 359          std::cout << "[" << userFileIdentifier  << "]" << std::endl;
 360
 361       // storing in a map ensures automatic sorting !
 362       sf[userFileIdentifier] = f;
 363    }
 364
 365    if (verbose)
 366       std::cout << "  " << std::endl;
 367
 368    std::string fullFilename, lastFilename;
 369    std::string previousPatientName, currentPatientName;
 370    std::string previousSerieInstanceUID, currentSerieInstanceUID;
 371    std::string previousImagePosition, currentImagePosition;
 372    std::string previousPhaseEncodingDirection, currentPhaseEncodingDirection;
 373    std::string previousTriggerTime, currentTriggerTime;
 374
 375    std::string currentStudyUID;
 376
 377    std::string writeDir, currentWriteDir;
 378    std::string currentPatientWriteDir, currentSerieWriteDir,
 379                currentPositionWriteDir, currentPhaseEncodingDirectionWriteDir;
 380
 381    std::string fullWriteFilename;
 382    std::string strExtent(extent);
 383
 384    writeDir = gdcm::Util::NormalizePath(dirNameout);
 385    SortedFiles::iterator it2;
 386
 387    previousPatientName            = "";
 388    previousSerieInstanceUID       = "";
 389    previousImagePosition          = "";
 390    previousPhaseEncodingDirection = "";
 391    previousTriggerTime            = "";
 392
 393    int sliceIndex = 0; // Is incremented *at the beginning* of processing
 394    int frameIndex;
 395    if (taggrid)
 396        frameIndex = 0;
 397    else
 398        frameIndex = 1;
 399
 400    int flag       = 0;
 401
 402    gdcm::File *currentFile;
 403
 404    std::string defaultStudyUID =  gdcm::Util::CreateUniqueUID();
 405    std::string defaultSerieUID;
 406
 407    for (it2 = sf.begin() ; it2 != sf.end(); ++it2)
 408    {
 409       currentFile = it2->second;
 410
 411       fullFilename =  currentFile->GetFileName();
 412       lastFilename =  gdcm::Util::GetName( fullFilename );
 413       std::cout << " --------------------------------------------------"
 414                 << " Rewrite [" <<lastFilename << "]" << std::endl;
 415
 416       tokens.clear();
 417       gdcm::Util::Tokenize (it2->first, tokens, token);
 418
 419       currentPatientName            = tokens[0];
 420       currentSerieInstanceUID       = tokens[1];
 421       currentImagePosition          = tokens[2];
 422       currentTriggerTime            = tokens[3];
 423       currentPhaseEncodingDirection = tokens[4];
 424
 425       if ( currentImagePosition[0] == '-')
 426           currentImagePosition[0] = 'M';
 427       if ( currentImagePosition[0] == '+')
 428           currentImagePosition[0] = 'P';
 429
 430       // Add a default ImagePositionPatient to avoid confusion at post processing time
 431       if ( currentFile->GetEntryString(0x0020,0x0032) == gdcm::GDCM_UNFOUND &&
 432            currentFile->GetEntryString(0x0020,0x0030) == gdcm::GDCM_UNFOUND )
 433       {
 434          currentFile->InsertEntryString("0.\\0.\\0.",0x0020, 0x0032, "DS" );
 435       }
 436
 437       // Add a default ImagePositionPatient to avoid confusion at post processing time
 438       if ( currentFile->GetEntryString(0x0020,0x0037) == gdcm::GDCM_UNFOUND &&
 439            currentFile->GetEntryString(0x0020,0x0035) == gdcm::GDCM_UNFOUND )
 440       {
 441          currentFile->InsertEntryString("1.\\0.\\0.\\0.\\1.\\0.",0x0020, 0x0037, "DS" );
 442       }
 443
 444       if (previousPatientName != currentPatientName)
 445       {
 446          if ( currentFile->GetEntryString(0x0020,0x000d) == gdcm::GDCM_UNFOUND)
 447          {
 448             if (verbose)
 449                std::cout << "--- new  Study UID created" << std::endl;
 450             defaultStudyUID =  gdcm::Util::CreateUniqueUID();
 451             currentFile->InsertEntryString(defaultStudyUID, 0x0020, 0x000d, "UI" );
 452          }
 453
 454          previousPatientName = currentPatientName;
 455          if (verbose)
 456             std::cout << "==== new Patient  [" << currentPatientName  << "]" << std::endl;
 457
 458          previousPatientName            = currentPatientName;
 459          previousSerieInstanceUID       = ""; //currentSerieInstanceUID;
 460          previousImagePosition          = ""; //currentImagePosition;
 461          previousTriggerTime            = "";
 462          previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection;
 463
 464          currentPatientWriteDir = writeDir + currentPatientName;
 465          //if ( ! gdcm::DirList::IsDirectory(currentPatientWriteDir) )
 466            {
 467               systemCommand   = "mkdir " + currentPatientWriteDir;
 468               if (verbose)
 469                  std::cout << systemCommand << std::endl;
 470               system ( systemCommand.c_str() );
 471          }
 472       }
 473
 474       if (previousSerieInstanceUID != currentSerieInstanceUID)
 475       {
 476          if (verbose)
 477             std::cout << "==== === new Serie [" << currentSerieInstanceUID << "]"
 478                       << std::endl;
 479
 480          if ( currentFile->GetEntryString(0x0020,0x000e) == gdcm::GDCM_UNFOUND)
 481          {
 482             if (verbose)
 483                std::cout << "--- --- new  Serie UID created" << std::endl;
 484             defaultSerieUID =  gdcm::Util::CreateUniqueUID();
 485             currentFile->InsertEntryString(defaultSerieUID, 0x0020, 0x000e, "UI" );
 486          }
 487
 488          if (split)
 489          {
 490              currentSerieWriteDir  = currentPatientWriteDir + gdcm::GDCM_FILESEPARATOR
 491                              + currentSerieInstanceUID;
 492              systemCommand   = "mkdir " + currentSerieWriteDir;
 493              system (systemCommand.c_str());
 494          }
 495          previousSerieInstanceUID       = currentSerieInstanceUID;
 496          previousImagePosition          = ""; //currentImagePosition;
 497          previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection;
 498       }
 499
 500       if (previousImagePosition != currentImagePosition)
 501       {
 502          frameIndex = 1;
 503          flag = 0;
 504          if (verbose)
 505             std::cout << "=== === === new Position [" << currentImagePosition  << "]"
 506                       << std::endl;
 507          if (split)
 508          {
 509              currentPositionWriteDir  = currentSerieWriteDir + gdcm::GDCM_FILESEPARATOR
 510                              + currentImagePosition;
 511              systemCommand   = "mkdir " + currentPositionWriteDir;
 512              system (systemCommand.c_str());
 513          }
 514          previousImagePosition          = currentImagePosition;
 515          previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection;
 516          if (split)
 517             sliceIndex = 1; // only *one* slice in a given directory
 518          else
 519             sliceIndex += 1;
 520       }
 521       if (verbose)
 522          std::cout << "Slice Index : " << sliceIndex << std::endl;
 523
 524 // We don't split on Row/Column!
 525 /*
 526       if (previousPhaseEncodingDirection != currentPhaseEncodingDirection)
 527       {
 528          if (verbose)
 529             std::cout << "==== === === === new PhaseEncodingDirection ["
 530                       << currentPhaseEncodingDirection  << "]" << std::endl;
 531
 532          if (split)
 533          {
 534              currentPhaseEncodingDirectionWriteDir  = currentPositionWriteDir
 535                              + gdcm::GDCM_FILESEPARATOR
 536                              + currentPhaseEncodingDirection;
 537              systemCommand   = "mkdir " + currentPhaseEncodingDirectionWriteDir;
 538              system (systemCommand.c_str());
 539          }
 540
 541          previousPhaseEncodingDirection = currentPhaseEncodingDirection;
 542       }
 543 */
 544
 545       if (verbose)
 546          std::cout << "--- --- --- --- --- " << (it2->second)->GetFileName()
 547                    << std::endl;
 548
 549       if ( gdcm::Debug::GetDebugFlag())
 550          std::cout << "--- --- --- --- --- " << it2->first << "  "
 551                    << (it2->second)->GetFileName() << " "
 552                    << gdcm::Util::GetName( fullFilename ) << std::endl;
 553
 554       // Transform the image to be 'Brucker-Like'
 555       // ----------------------------------------
 556
 557       // Deal with 0x0019, 0x1000 : 'FOV'
 558       int nX = currentFile->GetXSize();
 559       int nY = currentFile->GetYSize();
 560       float pxSzX = currentFile->GetXSpacing();
 561       float pxSzY = currentFile->GetYSpacing();
 562       char fov[64];
 563       sprintf(fov, "%f\\%f",nX*pxSzX, nY*pxSzY);
 564       if (currentFile->IsVRCoherent(0x0019) == 1 )
 565          currentFile->InsertEntryString(fov, 0x0019, 0x1000, "  ");
 566       else
 567          currentFile->InsertEntryString(fov, 0x0019, 0x1000, "DS");
 568
 569
 570       // Deal with 0x0020, 0x0012 : 'SESSION INDEX'  (Acquisition Number)
 571       std::string chSessionIndex;
 572       // CLEANME
 573       if (taggrid)
 574          chSessionIndex = "1";
 575       else
 576       {
 577          if (currentPhaseEncodingDirection == "COL" || currentPhaseEncodingDirection == "COL " || currentPhaseEncodingDirection == " COL")
 578             chSessionIndex = "1";
 579          else if (currentPhaseEncodingDirection == "ROW" || currentPhaseEncodingDirection == "ROW "|| currentPhaseEncodingDirection == " ROW")
 580             chSessionIndex = "2";
 581          else
 582          {
 583             std::cout << "====================== PhaseEncodingDirection "
 584                       << " neither COL nor ROW (?!?) : [ "
 585                       << currentPhaseEncodingDirection << "]" << std::endl;
 586             chSessionIndex = "1";
 587          }
 588       }
 589       if (currentFile->IsVRCoherent(0x0020) == 1 )
 590          currentFile->InsertEntryString(chSessionIndex, 0x0020, 0x0012, "  ");
 591       else
 592          currentFile->InsertEntryString(chSessionIndex, 0x0020, 0x0012, "IS");
 593
 594       // Deal with  0x0021, 0x1020 : 'SLICE INDEX'
 595       char chSliceIndex[5];
 596       sprintf(chSliceIndex, "%04d", sliceIndex);
 597       std::string strChSliceIndex(chSliceIndex);
 598
 599       // Deal with  0x0021, 0x1040 : 'FRAME INDEX'
 600       char chFrameIndex[5];
 601       sprintf(chFrameIndex, "%04d", frameIndex);
 602
 603       std::string stringVR;
 604       if (currentFile->IsVRCoherent(0x0021) == 1 )
 605          stringVR = "  ";
 606       else
 607         stringVR = "IS";
 608
 609       currentFile->InsertEntryString(strChSliceIndex, 0x0021, 0x1020, stringVR);
 610       currentFile->InsertEntryString(chFrameIndex,    0x0021, 0x1040, stringVR);
 611
 612
 613       std::string strImagePositionPatient    = currentFile->GetEntryString(0x0020, 0x0032 );
 614       if (strImagePositionPatient == gdcm::GDCM_UNFOUND)
 615       {
 616          if (verbose)
 617             std::cout << "Duplicate ImagePosition into ImagePositionPatient" << std::endl;
 618          currentFile->InsertEntryString(currentFile->GetEntryString(0x0020, 0x0030), 0x0020, 0x0032, "DS" );
 619       }
 620
 621       std::string strImageOrientationPatient = f->GetEntryString(0x0020, 0x0037 );
 622       if (strImageOrientationPatient == gdcm::GDCM_UNFOUND)
 623       {
 624          if (verbose)
 625             std::cout << "Duplicate ImageOrientation into ImageOrientationPatient" << std::endl;
 626          currentFile->InsertEntryString(currentFile->GetEntryString(0x0020, 0x0035), 0x0020, 0x0037, "DS" );
 627       }
 628
 629       if (taggrid)
 630          frameIndex++;
 631       else
 632       {
 633          if (flag == 0)
 634          {
 635             flag = 1;
 636          }
 637          else
 638          {
 639             frameIndex++;
 640             flag = 0;
 641          }
 642       }
 643       if (verbose)
 644          std::cout << "Frame Index : " << frameIndex << std::endl;
 645
 646       if (split)
 647
 648          //fullWriteFilename = currentPhaseEncodingDirectionWriteDir + gdcm::GDCM_FILESEPARATOR
 649          //                                + lastFilename + strExtent;
 650          fullWriteFilename = currentPositionWriteDir + gdcm::GDCM_FILESEPARATOR
 651                                          + lastFilename + strExtent;
 652       else
 653          fullWriteFilename = currentPatientWriteDir + gdcm::GDCM_FILESEPARATOR
 654                                          + lastFilename + strExtent;
 655
 656       /*
 657       systemCommand  = "cp " + fullFilename + " " + fullWriteFilename;
 658       std::cout << systemCommand << std::endl;
 659       system (  systemCommand.c_str() );
 660       */
 661
 662       // Load the pixels in RAM.
 663
 664       fh = gdcm::FileHelper::New(currentFile);
 665       uint8_t *imageData = fh->GetImageDataRaw(); // Don't convert (Gray Pixels + LUT) into (RGB pixels) ?!?
 666       fh->SetWriteTypeToDcmExplVR();
 667       // We didn't modify pixels -> keep unchanged the following :
 668       // 'Media Storage SOP Class UID' (0x0002,0x0002)
 669       // 'SOP Class UID'               (0x0008,0x0016)
 670       // 'Image Type'                  (0x0008,0x0008)
 671       // 'Conversion Type'             (0x0008,0x0064)
 672
 673       // Put to Black the burnt-in number.
 674       nX = currentFile->GetXSize();
 675       nY = currentFile->GetYSize();
 676       for(int y=nY-15; y<nY; y++)
 677          for(int x=nX/3; x<nX/2+50; x++)
 678            imageData[ y*nX*2 + x ] = 0;
 679
 680       fh->SetContentType(gdcm::UNMODIFIED_PIXELS_IMAGE);
 681       if (!fh->Write(fullWriteFilename))
 682       {
 683          std::cout << "Fail to write :[" << fullWriteFilename << "]"
 684                    << std::endl;
 685       }
 686       fh->Delete();
 687    }
 688    return 0;
 689  }