Example/ToInTag.cxx

   1 /*=========================================================================
   2
   3   Program:   gdcm
   4   Module:    $RCSfile: ToInTag.cxx,v $
   5   Language:  C++
   6   Date:      $Date: 2007/07/04 15:40:51 $
   7   Version:   $Revision: 1.16 $
   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_NAME_SPACE::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 (sorted by Trigger Time /                             ",
  65    "                               Encoding Direction (Row, Column)           ",
  66    "                                                                          ",
  67    "      Note : when (0008|1090) [Model Name ] equals 'TrioTim ' :           ",
  68    "         - (0008|103e)[Series Description ] is checked for                ",
  69    "            '90' (-> COL) or '0' (-> ROW)                                 ",
  70    "         - (0x0020, 0x000e) [Series Instance UID] is NOT dealt with,      ",
  71    "           since row an col tagging are in 2 different Series             ",
  72    "           DO NOT supply a directory holding different exams              ",
  73    "           for the same Slice level!                                      ",
  74    "      uses :                                                              ",
  75    "           0x0021, 0x1020 : 'SLICE INDEX'                                 ",
  76    "           0x0021, 0x1040 : 'FRAME INDEX'                                 ",
  77    "           0x0020, 0x0012 : 'SESSION INDEX'  (Acquisition Number)         ",
  78    "                                                                          ",
  79    " usage:                                                                   ",
  80    " -----                                                                    ",
  81    " ToInTag          dirin=rootDirectoryName                                 ",
  82    "                  dirout=outputDirectoryName                              ",
  83    "                  {  [keep= list of seriesNumber to process]              ",
  84    "                   | [drop= list of seriesNumber to ignore] }             ",
  85    "                  [taggrid] [skel]                                        ",
  86    "                  [input = {ACR|DCM}]                                     ",
  87    "                  [extent=image suffix (.IMA, .NEMA, .DCM, ...)]          ",
  88    "                  [listonly] [split] [rubout]                             ",
  89    "                  [noshadowseq][noshadow][noseq] [verbose] [debug]        ",
  90    "                                                                          ",
  91    " dirout : will be created if doesn't exist                                ",
  92    " keep : if user wants to process a limited number of series               ",
  93    "            he gives the list of 'SeriesNumber' (tag 0020|0011)           ",
  94    " drop : if user wants to ignore a limited number of series                ",
  95    "            he gives the list of 'SeriesNumber' (tag 0020|0011)           ",
  96    "        SeriesNumber are short enough to be human readable                ",
  97    "        e.g : 1030,1035,1043                                              ",
  98    " taggrid : user knows all the images are 'grid' -ie: not 'col', not 'raw'-",
  99    " extent : DO NOT forget the leading '.' !                                 ",
 100    " skel: name skeleton eg : patName_1.nema -> skel=patName_                 ",
 101    " split: creates a tree-like structure of directories as :                 ",
 102    "        - Patient                                                         ",
 103    "        -- Serie                                                          ",
 104    "        --- Position                                                      ",
 105    "        ---- Images (sorted by Trigger Time /                             ",
 106    "                               Encoding Direction (Row, Column)           ",
 107    " rubout : user asks to rubout burnt-in image number                       ",
 108    " noshadowseq: user doesn't want to load Private Sequences                 ",
 109    " noshadow : user doesn't want to load Private groups (odd number)         ",
 110    " noseq    : user doesn't want to load Sequences                           ",
 111    " verbose  : user wants to run the program in 'verbose mode'               ",
 112    " debug    : *developer*  wants to run the program in 'debug mode'         ",
 113    FINISH_USAGE
 114
 115    std::cout << "inside ToInTag" << std::endl;
 116
 117    // ----- Initialize Arguments Manager ------
 118
 119    GDCM_NAME_SPACE::ArgMgr *am = new GDCM_NAME_SPACE::ArgMgr(argc, argv);
 120
 121    if (argc == 1 || am->ArgMgrDefined("usage"))
 122    {
 123       am->ArgMgrUsage(usage); // Display 'usage'
 124       delete am;
 125       return 0;
 126    }
 127
 128    const char *dirNamein;
 129    dirNamein  = am->ArgMgrGetString("dirin",".");
 130
 131    const char *dirNameout;
 132    dirNameout  = am->ArgMgrGetString("dirout",".");
 133
 134    int loadMode = GDCM_NAME_SPACE::LD_ALL;
 135    if ( am->ArgMgrDefined("noshadowseq") )
 136       loadMode |= GDCM_NAME_SPACE::LD_NOSHADOWSEQ;
 137    else
 138    {
 139    if ( am->ArgMgrDefined("noshadow") )
 140          loadMode |= GDCM_NAME_SPACE::LD_NOSHADOW;
 141       if ( am->ArgMgrDefined("noseq") )
 142          loadMode |= GDCM_NAME_SPACE::LD_NOSEQ;
 143    }
 144
 145    if (am->ArgMgrDefined("debug"))
 146       GDCM_NAME_SPACE::Debug::DebugOn();
 147
 148    int verbose  = am->ArgMgrDefined("verbose");
 149    int split    = am->ArgMgrDefined("split");
 150    int listonly = am->ArgMgrDefined("listonly");
 151
 152    bool rubout = ( 0 != am->ArgMgrDefined("rubout") );
 153
 154    int nbSeriesToKeep;
 155    int *seriesToKeep = am->ArgMgrGetListOfInt("keep", &nbSeriesToKeep);
 156    int nbSeriesToDrop;
 157    int *seriesToDrop = am->ArgMgrGetListOfInt("drop", &nbSeriesToDrop);
 158
 159    if ( nbSeriesToKeep!=0 && nbSeriesToDrop!=0)
 160    {
 161       std::cout << "KEEP and DROP are mutually exclusive !" << std::endl;
 162       delete am;
 163       return 0;
 164    }
 165
 166    int taggrid = am->ArgMgrDefined("taggrid");
 167
 168    int hasSkel = am->ArgMgrDefined("skel");
 169    const char *skel;
 170    if (hasSkel)
 171       skel = am->ArgMgrGetString("skel");
 172
 173    const char *extent  = am->ArgMgrGetString("extent",".DCM");
 174
 175    // if unused Param we give up
 176    if ( am->ArgMgrPrintUnusedLabels() )
 177    {
 178       am->ArgMgrUsage(usage);
 179       delete am;
 180       return 0;
 181    }
 182    delete am;  // we don't need Argument Manager any longer
 183
 184    // ----- Begin Processing -----
 185
 186    if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(dirNamein) )
 187    {
 188       std::cout << "KO : [" << dirNamein << "] is not a Directory." << std::endl;
 189       return 0;
 190
 191    }
 192    else
 193    {
 194       std::cout << "OK : [" << dirNamein << "] is a Directory." << std::endl;
 195    }
 196
 197    std::string systemCommand;
 198
 199    std::cout << "Check for output directory :[" << dirNameout << "]."
 200              <<std::endl;
 201    if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(dirNameout) )    // dirout not found
 202    {
 203       std::string strDirNameout(dirNameout);          // to please gcc 4
 204       systemCommand = "mkdir " +strDirNameout;        // create it!
 205       if (verbose)
 206          std::cout << systemCommand << std::endl;
 207       system (systemCommand.c_str());
 208       if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(dirNameout) ) // be sure it worked
 209       {
 210           std::cout << "KO : not a dir : [" << dirNameout << "] (creation failure ?)" << std::endl;
 211       return 0;
 212
 213       }
 214       else
 215       {
 216         std::cout << "Directory [" << dirNameout << "] created." << std::endl;
 217       }
 218    }
 219    else
 220    {
 221        std::cout << "Output Directory [" << dirNameout << "] already exists; Used as is." << std::endl;
 222    }
 223
 224    std::string strDirNamein(dirNamein);
 225    GDCM_NAME_SPACE::DirList dirList(strDirNamein, true); // get recursively the list of files
 226
 227    if (listonly)
 228    {
 229       std::cout << "------------List of found files ------------" << std::endl;
 230       dirList.Print();
 231       std::cout << std::endl;
 232    }
 233
 234    GDCM_NAME_SPACE::DirListType fileNames;
 235    fileNames = dirList.GetFilenames();
 236    GDCM_NAME_SPACE::SerieHelper *s;              // Needed to use SerieHelper::AddSeriesDetail()
 237    s = GDCM_NAME_SPACE::SerieHelper::New();
 238
 239    std::string token = "%%%"; // Hope it's enough!
 240 /*
 241    std::cout << "---------------Print Serie--------------" << std::endl;
 242    s->SetDirectory(dirNamein, true); // true : recursive exploration
 243    s->SetUseSeriesDetails(true);
 244    s->AddSeriesDetail(0x0018, 0x1312);
 245    s->Print();
 246 */
 247
 248    GDCM_NAME_SPACE::File *f;
 249    GDCM_NAME_SPACE::FileHelper *fh;
 250    std::vector<std::string> tokens;
 251    std::vector<std::string> tokensForFileName;
 252
 253    // For Siemens pb, we need Manufacturer's Model Name
 254
 255    GDCM_NAME_SPACE::DirListType::iterator it1 = fileNames.begin();
 256    f = GDCM_NAME_SPACE::File::New();
 257    f->SetLoadMode(GDCM_NAME_SPACE::LD_ALL);
 258    f->SetFileName( *it1 );
 259    f->Load();
 260    std::string modelName = f->GetEntryString(0x0008,0x1090);
 261    f->Delete();
 262
 263 /*
 264    std::cout << "---------------Print Unique Series identifiers---------"
 265              << std::endl;
 266    std::string uniqueSeriesIdentifier;
 267
 268    for (GDCM_NAME_SPACE::DirListType::iterator it) = fileNames.begin();
 269                                     it != fileNames.end();
 270                                   ++it)
 271    {
 272       std::cout << "File Name : " << *it << std::endl;
 273       f = GDCM_NAME_SPACE::File::New();
 274       f->SetLoadMode(GDCM_NAME_SPACE::LD_ALL);
 275       f->SetFileName( *it );
 276       f->Load();
 277
 278       uniqueSeriesIdentifier=s->CreateUniqueSeriesIdentifier(f);
 279       std::cout << "                           [" <<
 280                uniqueSeriesIdentifier  << "]" << std::endl;
 281       f->Delete();
 282    }
 283 */
 284
 285    if (verbose)
 286       std::cout << "------------------Print Break levels-----------------" << std::endl;
 287
 288    std::string userFileIdentifier;
 289    SortedFiles sf;
 290
 291    s->AddSeriesDetail(0x0010, 0x0010, false); // Patient's Name
 292    // for Siemens TrioTim, don't deal with 'Series Instance UID'
 293    if ( !GDCM_NAME_SPACE::Util::DicomStringEqual(modelName,"TrioTim") )
 294       s->AddSeriesDetail(0x0020, 0x000e, false); // Series Instance UID
 295    else
 296       s->AddSeriesDetail(0x9999, 0x9999, false); // dirty trick to ignore 'Series Instance UID'
 297    s->AddSeriesDetail(0x0020, 0x0032, false); // Image Position (Patient)
 298    s->AddSeriesDetail(0x0018, 0x1060, true);  // Trigger Time (true: convert to keep numerical order)
 299    s->AddSeriesDetail(0x0018, 0x1312, false); // In-plane Phase Encoding Direction
 300    s->AddSeriesDetail(0x0008, 0x103e, false); // Series Description (special Siemens ...)
 301
 302    //uint8_t *imageData; // Useless : pixels will not be loaded
 303                          //          (images are overwritten)
 304
 305    for (GDCM_NAME_SPACE::DirListType::iterator it = fileNames.begin();
 306                                     it != fileNames.end();
 307                                   ++it)
 308    {
 309       f = GDCM_NAME_SPACE::File::New();
 310       f->SetLoadMode(loadMode);
 311       f->SetFileName( *it );
 312       f->Load();
 313
 314       std::string strSeriesNumber;
 315       int seriesNumber;
 316       int j;
 317
 318       // keep only requested Series
 319       bool keep = false;
 320       if (nbSeriesToKeep != 0)
 321       {
 322          strSeriesNumber = f->GetEntryString(0x0020, 0x0011 );
 323          seriesNumber = atoi( strSeriesNumber.c_str() );
 324          for (j=0;j<nbSeriesToKeep; j++)
 325          {
 326             if(seriesNumber == seriesToKeep[j])
 327             {
 328                keep = true;
 329                break;
 330             }
 331          }
 332          if ( !keep)
 333          {
 334             f->Delete();
 335             continue;
 336          }
 337       }
 338       // drop all unrequested Series
 339       bool drop = false;
 340       if (nbSeriesToDrop != 0)
 341       {
 342          strSeriesNumber = f->GetEntryString(0x0020, 0x0011 );
 343          seriesNumber = atoi( strSeriesNumber.c_str() );
 344          for (j=0;j<nbSeriesToDrop; j++)
 345          {
 346             if(seriesNumber == seriesToDrop[j])
 347             {
 348                drop = true;
 349                break;
 350             }
 351         }
 352         if (drop)
 353         {
 354            f->Delete();
 355            continue;
 356         }
 357       }
 358
 359       userFileIdentifier=s->CreateUserDefinedFileIdentifier(f);
 360       tokens.clear();
 361       GDCM_NAME_SPACE::Util::Tokenize (userFileIdentifier, tokens, token);
 362
 363       int imageNum; // Within FileName
 364       char newName[1024];
 365
 366       if ( tokens[3] == GDCM_NAME_SPACE::GDCM_UNFOUND)  // sometimes Trigger Time is not found. CreateUserDefinedFileIdentifier is not aware of the pb.
 367       {
 368          ///this is a trick to build up a lexicographical compliant name :
 369          ///     eg : fich001.ima vs fich100.ima as opposed to fich1.ima vs fich100.ima
 370          std::string name = GDCM_NAME_SPACE::Util::GetName( *it );
 371          if (hasSkel)
 372          {
 373             GDCM_NAME_SPACE::Util::Tokenize (name, tokensForFileName, skel);
 374             imageNum = atoi ( tokensForFileName[0].c_str() );
 375             // probabely we could write something much more complicated using C++ !
 376             sprintf (newName, "%s%06d%s", skel, imageNum, extent);
 377             tokens[3] = newName;
 378             tokensForFileName.clear();
 379          }
 380          else
 381             tokens[3] = name;
 382
 383
 384          userFileIdentifier = tokens[0] + token + tokens[1] + token + tokens[2] + token
 385                     + tokens[3] + token + tokens[4] + token + tokens[5] + token;
 386       }
 387       if (verbose)
 388          std::cout << "[" << userFileIdentifier  << "] : " << *it << std::endl;
 389
 390       // storing in a map ensures automatic sorting !
 391       sf[userFileIdentifier] = f;
 392    }
 393
 394    if (verbose)
 395       std::cout << "  " << std::endl;
 396
 397    std::string fullFilename, lastFilename;
 398    std::string previousPatientName, currentPatientName;
 399    std::string previousSerieInstanceUID, currentSerieInstanceUID;
 400    std::string previousImagePosition, currentImagePosition;
 401    std::string previousPhaseEncodingDirection, currentPhaseEncodingDirection;
 402    std::string previousTriggerTime, currentTriggerTime;
 403
 404    std::string currentStudyUID;
 405    std::string seriesDescription;
 406
 407    std::string writeDir, currentWriteDir;
 408    std::string currentPatientWriteDir, currentSerieWriteDir,
 409                currentPositionWriteDir, currentPhaseEncodingDirectionWriteDir;
 410
 411    std::string fullWriteFilename;
 412    std::string strExtent(extent);
 413
 414    writeDir = GDCM_NAME_SPACE::Util::NormalizePath(dirNameout);
 415    SortedFiles::iterator it2;
 416
 417    previousPatientName            = "";
 418    previousSerieInstanceUID       = "";
 419    previousImagePosition          = "";
 420    previousPhaseEncodingDirection = "";
 421    previousTriggerTime            = "";
 422
 423    int sliceIndex = 0; // Is incremented *at the beginning* of processing
 424    int frameIndex;
 425    if (taggrid)
 426        frameIndex = 0;
 427    else
 428        frameIndex = 1;
 429
 430    int flag       = 0;
 431
 432    GDCM_NAME_SPACE::File *currentFile;
 433
 434    std::string defaultStudyUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 435    std::string defaultSerieUID;
 436
 437    for (it2 = sf.begin() ; it2 != sf.end(); ++it2)
 438    {
 439       currentFile = it2->second;
 440
 441       fullFilename =  currentFile->GetFileName();
 442       lastFilename =  GDCM_NAME_SPACE::Util::GetName( fullFilename );
 443       if (verbose)
 444       std::cout <<" ------------------------------------------------------------------------------"
 445                 << std::endl << " Deal with [" << it2->first << "] : ["<<fullFilename << "]"
 446                 << std::endl;
 447
 448       tokens.clear();
 449       GDCM_NAME_SPACE::Util::Tokenize (it2->first, tokens, token);
 450
 451       currentPatientName            = tokens[0];
 452       currentSerieInstanceUID       = tokens[1];
 453       currentImagePosition          = tokens[2];
 454       currentTriggerTime            = tokens[3];
 455       currentPhaseEncodingDirection = tokens[4];
 456       seriesDescription             = tokens[5];  // For Siemens pb
 457
 458       if ( currentImagePosition[0] == '-')
 459           currentImagePosition[0] = 'M';
 460       if ( currentImagePosition[0] == '+')
 461           currentImagePosition[0] = 'P';
 462
 463       // Add a default ImagePositionPatient to avoid confusion at post processing time
 464       if ( currentFile->GetEntryString(0x0020,0x0032) == GDCM_NAME_SPACE::GDCM_UNFOUND &&
 465            currentFile->GetEntryString(0x0020,0x0030) == GDCM_NAME_SPACE::GDCM_UNFOUND )
 466       {
 467          currentFile->InsertEntryString("0.\\0.\\0.",0x0020, 0x0032, "DS" );
 468       }
 469
 470       // Add a default ImagePositionPatient to avoid confusion at post processing time
 471       if ( currentFile->GetEntryString(0x0020,0x0037) == GDCM_NAME_SPACE::GDCM_UNFOUND &&
 472            currentFile->GetEntryString(0x0020,0x0035) == GDCM_NAME_SPACE::GDCM_UNFOUND )
 473       {
 474          currentFile->InsertEntryString("1.\\0.\\0.\\0.\\1.\\0.",0x0020, 0x0037, "DS" );
 475       }
 476
 477       if (previousPatientName != currentPatientName)
 478       {
 479          if ( currentFile->GetEntryString(0x0020,0x000d) == GDCM_NAME_SPACE::GDCM_UNFOUND)
 480          {
 481             if (verbose)
 482                std::cout << "--- new  Study UID created" << std::endl;
 483             defaultStudyUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 484             currentFile->InsertEntryString(defaultStudyUID, 0x0020, 0x000d, "UI" );
 485          }
 486
 487          previousPatientName = currentPatientName;
 488          if (verbose)
 489             std::cout << "==== new Patient  [" << currentPatientName  << "]" << std::endl;
 490
 491          previousPatientName            = currentPatientName;
 492          previousSerieInstanceUID       = ""; //currentSerieInstanceUID;
 493          previousImagePosition          = ""; //currentImagePosition;
 494          previousTriggerTime            = "";
 495          previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection;
 496
 497          currentPatientWriteDir = writeDir + currentPatientName;
 498          //if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(currentPatientWriteDir) )
 499            {
 500               systemCommand   = "mkdir " + currentPatientWriteDir;
 501               if (verbose)
 502                  std::cout << systemCommand << std::endl;
 503               system ( systemCommand.c_str() );
 504          }
 505       }
 506
 507       if ( GDCM_NAME_SPACE::Util::DicomStringEqual(modelName,"TrioTim") ) // for Siemens TrioTim , don't deal with 'Series Instance UID'
 508
 509       if (previousSerieInstanceUID != currentSerieInstanceUID)
 510       {
 511          if (verbose)
 512             std::cout << "==== === new Serie [" << currentSerieInstanceUID << "]"
 513                       << std::endl;
 514
 515          if ( currentFile->GetEntryString(0x0020,0x000e) == GDCM_NAME_SPACE::GDCM_UNFOUND)
 516          {
 517             if (verbose)
 518                std::cout << "--- --- new  Serie UID created" << std::endl;
 519             defaultSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 520             currentFile->InsertEntryString(defaultSerieUID, 0x0020, 0x000e, "UI" );
 521          }
 522
 523          if (split)
 524          {
 525              currentSerieWriteDir  = currentPatientWriteDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR
 526                              + currentSerieInstanceUID;
 527              systemCommand   = "mkdir " + currentSerieWriteDir;
 528              system (systemCommand.c_str());
 529          }
 530          previousSerieInstanceUID       = currentSerieInstanceUID;
 531          previousImagePosition          = ""; //currentImagePosition;
 532          previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection;
 533       }
 534       // end of modelName != "TrioTim "
 535
 536       if (previousImagePosition != currentImagePosition)
 537       {
 538          frameIndex = 1;
 539          flag = 0;
 540          if (verbose)
 541             std::cout << "=== === === new Position [" << currentImagePosition  << "]"
 542                       << std::endl;
 543          if (split)
 544          {
 545              currentPositionWriteDir  = currentSerieWriteDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR
 546                              + currentImagePosition;
 547              systemCommand   = "mkdir " + currentPositionWriteDir;
 548              system (systemCommand.c_str());
 549          }
 550          previousImagePosition          = currentImagePosition;
 551          previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection;
 552          if (split)
 553             sliceIndex = 1; // only *one* slice in a given directory
 554          else
 555             sliceIndex += 1;
 556       }
 557
 558 // We don't split on Row/Column!
 559 /*
 560       if (previousPhaseEncodingDirection != currentPhaseEncodingDirection)
 561       {
 562          if (verbose)
 563             std::cout << "==== === === === new PhaseEncodingDirection ["
 564                       << currentPhaseEncodingDirection  << "]" << std::endl;
 565
 566          if (split)
 567          {
 568              currentPhaseEncodingDirectionWriteDir  = currentPositionWriteDir
 569                              + GDCM_NAME_SPACE::GDCM_FILESEPARATOR
 570                              + currentPhaseEncodingDirection;
 571              systemCommand   = "mkdir " + currentPhaseEncodingDirectionWriteDir;
 572              system (systemCommand.c_str());
 573          }
 574
 575          previousPhaseEncodingDirection = currentPhaseEncodingDirection;
 576       }
 577 */
 578
 579       if ( GDCM_NAME_SPACE::Debug::GetDebugFlag())
 580          std::cout << "--- --- --- --- --- " << it2->first << "  "
 581                    << (it2->second)->GetFileName() << " "
 582                    << GDCM_NAME_SPACE::Util::GetName( fullFilename ) << std::endl;
 583
 584       // Transform the image to be 'Brucker-Like'
 585       // ----------------------------------------
 586
 587       // Deal with 0x0019, 0x1000 : 'FOV'
 588       int nX = currentFile->GetXSize();
 589       int nY = currentFile->GetYSize();
 590       float pxSzX = currentFile->GetXSpacing();
 591       float pxSzY = currentFile->GetYSpacing();
 592       char fov[64];
 593       sprintf(fov, "%f\\%f",nX*pxSzX, nY*pxSzY);
 594       if (currentFile->IsVRCoherent(0x0019) == 1 )
 595          currentFile->InsertEntryString(fov, 0x0019, 0x1000, "  ");
 596       else
 597          currentFile->InsertEntryString(fov, 0x0019, 0x1000, "DS");
 598
 599
 600       // Deal with 0x0020, 0x0012 : 'SESSION INDEX'  (Acquisition Number)
 601       std::string chSessionIndex;
 602       // CLEANME
 603
 604       if (taggrid)
 605       {
 606          chSessionIndex = "1";
 607       }
 608       else
 609       {
 610       /* for SIEMENS MRI :
 611         D 0008|1090 [LO] [Manufacturer's Model Name ] [Triotim ]
 612         we have to deal with :
 613
 614         D 0008|103e [LO]  [Series Description ] [fl2d9_line PA 15 90deg] or anything that contains '90' !
 615         D 0008|103e [LO]  [Series Description ] [fl2d9_line PA 15 0deg ]
 616         (everything is flagged as 'ROW')
 617       */
 618
 619          if ( GDCM_NAME_SPACE::Util::DicomStringEqual(modelName,"TrioTim") )
 620          {
 621             if (seriesDescription.find("90", 0) != std::string::npos)
 622                chSessionIndex = "1";  // 90 deg -> COL
 623             else if (seriesDescription.find("0", 0)!= std::string::npos)
 624                chSessionIndex = "2";  // 0 deg -> ROW
 625             else
 626             {
 627                std::cout << "====================== seriesDescription doesn't contain"
 628                          << " neither '90' nor '0' (?!?) : ["
 629                          << seriesDescription << "]" << std::endl;
 630                chSessionIndex = "1";
 631             }
 632          }
 633          else  // for all other 'normal' cases
 634          {
 635             if (currentPhaseEncodingDirection == "COL" || currentPhaseEncodingDirection == "COL " || currentPhaseEncodingDirection == " COL")
 636                chSessionIndex = "1";
 637             else if (currentPhaseEncodingDirection == "ROW" || currentPhaseEncodingDirection == "ROW "|| currentPhaseEncodingDirection == " ROW")
 638                chSessionIndex = "2";
 639             else
 640             {
 641                std::cout << "====================== PhaseEncodingDirection "
 642                          << " neither COL nor ROW (?!?) : [ "
 643                          << currentPhaseEncodingDirection << "]" << std::endl;
 644                chSessionIndex = "1";
 645             }
 646          }
 647       }
 648
 649       if (currentFile->IsVRCoherent(0x0020) == 1 )
 650          currentFile->InsertEntryString(chSessionIndex, 0x0020, 0x0012, "  ");
 651       else
 652          currentFile->InsertEntryString(chSessionIndex, 0x0020, 0x0012, "IS");
 653
 654       // Deal with  0x0021, 0x1020 : 'SLICE INDEX'
 655       char chSliceIndex[5];
 656       sprintf(chSliceIndex, "%04d", sliceIndex);
 657       std::string strChSliceIndex(chSliceIndex);
 658
 659       // Deal with  0x0021, 0x1040 : 'FRAME INDEX'
 660       char chFrameIndex[5];
 661       sprintf(chFrameIndex, "%04d", frameIndex);
 662
 663       std::string stringVR;
 664       if (currentFile->IsVRCoherent(0x0021) == 1 )
 665          stringVR = "  ";
 666       else
 667         stringVR = "IS";
 668
 669       currentFile->InsertEntryString(strChSliceIndex, 0x0021, 0x1020, stringVR);
 670       currentFile->InsertEntryString(chFrameIndex,    0x0021, 0x1040, stringVR);
 671
 672       if (verbose) {
 673          std::cout << "0x0021, 0x1020 : strChSliceIndex " << strChSliceIndex << std::endl;
 674          std::cout << "0x0021, 0x1040 : chFrameIndex  "   << chFrameIndex    << std::endl;
 675          std::cout << "0x0020, 0x0012 : chSessionIndex "  << chSessionIndex  << std::endl;
 676       }
 677
 678       std::string strImagePositionPatient    = currentFile->GetEntryString(0x0020, 0x0032 );
 679       if (strImagePositionPatient == GDCM_NAME_SPACE::GDCM_UNFOUND)
 680       {
 681          if (verbose)
 682             std::cout << "Duplicate ImagePosition into ImagePositionPatient" << std::endl;
 683          currentFile->InsertEntryString(currentFile->GetEntryString(0x0020, 0x0030), 0x0020, 0x0032, "DS" );
 684       }
 685
 686       std::string strImageOrientationPatient = f->GetEntryString(0x0020, 0x0037 );
 687       if (strImageOrientationPatient == GDCM_NAME_SPACE::GDCM_UNFOUND)
 688       {
 689          if (verbose)
 690             std::cout << "Duplicate ImageOrientation into ImageOrientationPatient" << std::endl;
 691          currentFile->InsertEntryString(currentFile->GetEntryString(0x0020, 0x0035), 0x0020, 0x0037, "DS" );
 692       }
 693
 694       if (taggrid)
 695          frameIndex++;
 696       else
 697       {
 698          if (flag == 0)
 699          {
 700             flag = 1;
 701          }
 702          else
 703          {
 704             frameIndex++;
 705             flag = 0;
 706          }
 707       }
 708
 709       if (split)
 710
 711          //fullWriteFilename = currentPhaseEncodingDirectionWriteDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR
 712          //                                + lastFilename + strExtent;
 713          fullWriteFilename = currentPositionWriteDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR
 714                                          + lastFilename + strExtent;
 715       else
 716          fullWriteFilename = currentPatientWriteDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR
 717                                          + lastFilename + strExtent;
 718
 719       // Load the pixels in RAM.
 720
 721       fh = GDCM_NAME_SPACE::FileHelper::New(currentFile);
 722       uint8_t *imageData = fh->GetImageDataRaw(); // Don't convert (Gray Pixels + LUT) into (RGB pixels) ?!?
 723       fh->SetWriteTypeToDcmExplVR();
 724
 725       if (rubout) {
 726          // Put to Black the burnt-in number.
 727          nX = currentFile->GetXSize();
 728          nY = currentFile->GetYSize();
 729          for(int y=nY-15; y<nY; y++)
 730             for(int x=nX/3; x<nX/2+50; x++)
 731               imageData[ y*nX*2 + x ] = 0;
 732       }
 733
 734       // We didn't make any computation on the pixels -> keep unchanged the following :
 735       // 'Media Storage SOP Class UID' (0x0002,0x0002)
 736       // 'SOP Class UID'               (0x0008,0x0016)
 737       // 'Image Type'                  (0x0008,0x0008)
 738       // 'Conversion Type'             (0x0008,0x0064)
 739       fh->SetContentType(GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE);
 740
 741       if (!fh->Write(fullWriteFilename))
 742       {
 743          std::cout << "Fail to write :[" << fullWriteFilename << "]"
 744                    << std::endl;
 745       }
 746       fh->Delete();
 747    }
 748    return 0;
 749  }
 750