Example/ToInTag.cxx

   1 /*=========================================================================
   2
   3   Program:   gdcm
   4   Module:    $RCSfile: ToInTag.cxx,v $
   5   Language:  C++
   6   Date:      $Date: 2007/07/04 17:39:28 $
   7   Version:   $Revision: 1.17 $
   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|IDO}]                                 ",
  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    " input : IDO when *realy* old libIDO images                               ",
 101    " skel: name skeleton eg : patName_1.nema -> skel=patName_                 ",
 102    " split: creates a tree-like structure of directories as :                 ",
 103    "        - Patient                                                         ",
 104    "        -- Serie                                                          ",
 105    "        --- Position                                                      ",
 106    "        ---- Images (sorted by Trigger Time /                             ",
 107    "                               Encoding Direction (Row, Column)           ",
 108    " rubout : user asks to rubout burnt-in image number                       ",
 109    " noshadowseq: user doesn't want to load Private Sequences                 ",
 110    " noshadow : user doesn't want to load Private groups (odd number)         ",
 111    " noseq    : user doesn't want to load Sequences                           ",
 112    " verbose  : user wants to run the program in 'verbose mode'               ",
 113    " debug    : *developer*  wants to run the program in 'debug mode'         ",
 114    FINISH_USAGE
 115
 116    std::cout << "inside ToInTag" << std::endl;
 117
 118    // ----- Initialize Arguments Manager ------
 119
 120    GDCM_NAME_SPACE::ArgMgr *am = new GDCM_NAME_SPACE::ArgMgr(argc, argv);
 121
 122    if (argc == 1 || am->ArgMgrDefined("usage"))
 123    {
 124       am->ArgMgrUsage(usage); // Display 'usage'
 125       delete am;
 126       return 0;
 127    }
 128
 129    const char *dirNamein;
 130    dirNamein  = am->ArgMgrGetString("dirin",".");
 131
 132    const char *dirNameout;
 133    dirNameout  = am->ArgMgrGetString("dirout",".");
 134
 135    int loadMode = GDCM_NAME_SPACE::LD_ALL;
 136    if ( am->ArgMgrDefined("noshadowseq") )
 137       loadMode |= GDCM_NAME_SPACE::LD_NOSHADOWSEQ;
 138    else
 139    {
 140    if ( am->ArgMgrDefined("noshadow") )
 141          loadMode |= GDCM_NAME_SPACE::LD_NOSHADOW;
 142       if ( am->ArgMgrDefined("noseq") )
 143          loadMode |= GDCM_NAME_SPACE::LD_NOSEQ;
 144    }
 145
 146    if (am->ArgMgrDefined("debug"))
 147       GDCM_NAME_SPACE::Debug::DebugOn();
 148
 149    int verbose  = am->ArgMgrDefined("verbose");
 150    int split    = am->ArgMgrDefined("split");
 151    int listonly = am->ArgMgrDefined("listonly");
 152
 153    bool rubout = ( 0 != am->ArgMgrDefined("rubout") );
 154
 155    int nbSeriesToKeep;
 156    int *seriesToKeep = am->ArgMgrGetListOfInt("keep", &nbSeriesToKeep);
 157    int nbSeriesToDrop;
 158    int *seriesToDrop = am->ArgMgrGetListOfInt("drop", &nbSeriesToDrop);
 159
 160    if ( nbSeriesToKeep!=0 && nbSeriesToDrop!=0)
 161    {
 162       std::cout << "KEEP and DROP are mutually exclusive !" << std::endl;
 163       delete am;
 164       return 0;
 165    }
 166
 167    int taggrid = am->ArgMgrDefined("taggrid");
 168
 169    int hasSkel = am->ArgMgrDefined("skel");
 170    const char *skel;
 171    if (hasSkel)
 172       skel = am->ArgMgrGetString("skel");
 173
 174    const char *extent  = am->ArgMgrGetString("extent",".DCM");
 175    const char *input  = am->ArgMgrGetString("input","DCM");
 176
 177    // if unused Param we give up
 178    if ( am->ArgMgrPrintUnusedLabels() )
 179    {
 180       am->ArgMgrUsage(usage);
 181       delete am;
 182       return 0;
 183    }
 184    delete am;  // we don't need Argument Manager any longer
 185
 186    // ----- Begin Processing -----
 187
 188    if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(dirNamein) )
 189    {
 190       std::cout << "KO : [" << dirNamein << "] is not a Directory." << std::endl;
 191       return 0;
 192
 193    }
 194    else
 195    {
 196       std::cout << "OK : [" << dirNamein << "] is a Directory." << std::endl;
 197    }
 198
 199    std::string systemCommand;
 200
 201    std::cout << "Check for output directory :[" << dirNameout << "]."
 202              <<std::endl;
 203    if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(dirNameout) )    // dirout not found
 204    {
 205       std::string strDirNameout(dirNameout);          // to please gcc 4
 206       systemCommand = "mkdir " +strDirNameout;        // create it!
 207       if (verbose)
 208          std::cout << systemCommand << std::endl;
 209       system (systemCommand.c_str());
 210       if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(dirNameout) ) // be sure it worked
 211       {
 212           std::cout << "KO : not a dir : [" << dirNameout << "] (creation failure ?)" << std::endl;
 213       return 0;
 214
 215       }
 216       else
 217       {
 218         std::cout << "Directory [" << dirNameout << "] created." << std::endl;
 219       }
 220    }
 221    else
 222    {
 223        std::cout << "Output Directory [" << dirNameout << "] already exists; Used as is." << std::endl;
 224    }
 225
 226    std::string strDirNamein(dirNamein);
 227    GDCM_NAME_SPACE::DirList dirList(strDirNamein, true); // get recursively the list of files
 228
 229    if (listonly)
 230    {
 231       std::cout << "------------List of found files ------------" << std::endl;
 232       dirList.Print();
 233       std::cout << std::endl;
 234    }
 235
 236    GDCM_NAME_SPACE::DirListType fileNames;
 237    fileNames = dirList.GetFilenames();
 238    GDCM_NAME_SPACE::SerieHelper *s;              // Needed to use SerieHelper::AddSeriesDetail()
 239    s = GDCM_NAME_SPACE::SerieHelper::New();
 240
 241    std::string token = "%%%"; // Hope it's enough!
 242 /*
 243    std::cout << "---------------Print Serie--------------" << std::endl;
 244    s->SetDirectory(dirNamein, true); // true : recursive exploration
 245    s->SetUseSeriesDetails(true);
 246    s->AddSeriesDetail(0x0018, 0x1312);
 247    s->Print();
 248 */
 249
 250    GDCM_NAME_SPACE::File *f;
 251    GDCM_NAME_SPACE::FileHelper *fh;
 252    std::vector<std::string> tokens;
 253    std::vector<std::string> tokensForFileName;
 254
 255    // For Siemens pb, we need Manufacturer's Model Name
 256
 257    GDCM_NAME_SPACE::DirListType::iterator it1 = fileNames.begin();
 258    f = GDCM_NAME_SPACE::File::New();
 259    f->SetLoadMode(GDCM_NAME_SPACE::LD_ALL);
 260    f->SetFileName( *it1 );
 261    f->Load();
 262    std::string modelName = f->GetEntryString(0x0008,0x1090);
 263    f->Delete();
 264
 265 /*
 266    std::cout << "---------------Print Unique Series identifiers---------"
 267              << std::endl;
 268    std::string uniqueSeriesIdentifier;
 269
 270    for (GDCM_NAME_SPACE::DirListType::iterator it) = fileNames.begin();
 271                                     it != fileNames.end();
 272                                   ++it)
 273    {
 274       std::cout << "File Name : " << *it << std::endl;
 275       f = GDCM_NAME_SPACE::File::New();
 276       f->SetLoadMode(GDCM_NAME_SPACE::LD_ALL);
 277       f->SetFileName( *it );
 278       f->Load();
 279
 280       uniqueSeriesIdentifier=s->CreateUniqueSeriesIdentifier(f);
 281       std::cout << "                           [" <<
 282                uniqueSeriesIdentifier  << "]" << std::endl;
 283       f->Delete();
 284    }
 285 */
 286
 287    if (verbose)
 288       std::cout << "------------------Print Break levels-----------------" << std::endl;
 289
 290    std::string userFileIdentifier;
 291    SortedFiles sf;
 292
 293    s->AddSeriesDetail(0x0010, 0x0010, false); // Patient's Name
 294    // for Siemens TrioTim, don't deal with 'Series Instance UID'
 295    if ( !GDCM_NAME_SPACE::Util::DicomStringEqual(modelName,"TrioTim") )
 296       s->AddSeriesDetail(0x0020, 0x000e, false); // Series Instance UID
 297    else
 298       s->AddSeriesDetail(0x9999, 0x9999, false); // dirty trick to ignore 'Series Instance UID'
 299    s->AddSeriesDetail(0x0020, 0x0032, false); // Image Position (Patient)
 300    s->AddSeriesDetail(0x0018, 0x1060, true);  // Trigger Time (true: convert to keep numerical order)
 301    s->AddSeriesDetail(0x0018, 0x1312, false); // In-plane Phase Encoding Direction
 302    s->AddSeriesDetail(0x0008, 0x103e, false); // Series Description (special Siemens ...)
 303
 304    //uint8_t *imageData; // Useless : pixels will not be loaded
 305                          //          (images are overwritten)
 306
 307    for (GDCM_NAME_SPACE::DirListType::iterator it = fileNames.begin();
 308                                     it != fileNames.end();
 309                                   ++it)
 310    {
 311       f = GDCM_NAME_SPACE::File::New();
 312       f->SetLoadMode(loadMode);
 313       f->SetFileName( *it );
 314       f->Load();
 315
 316       std::string strSeriesNumber;
 317       int seriesNumber;
 318       int j;
 319
 320       // keep only requested Series
 321       bool keep = false;
 322       if (nbSeriesToKeep != 0)
 323       {
 324          strSeriesNumber = f->GetEntryString(0x0020, 0x0011 );
 325          seriesNumber = atoi( strSeriesNumber.c_str() );
 326          for (j=0;j<nbSeriesToKeep; j++)
 327          {
 328             if(seriesNumber == seriesToKeep[j])
 329             {
 330                keep = true;
 331                break;
 332             }
 333          }
 334          if ( !keep)
 335          {
 336             f->Delete();
 337             continue;
 338          }
 339       }
 340       // drop all unrequested Series
 341       bool drop = false;
 342       if (nbSeriesToDrop != 0)
 343       {
 344          strSeriesNumber = f->GetEntryString(0x0020, 0x0011 );
 345          seriesNumber = atoi( strSeriesNumber.c_str() );
 346          for (j=0;j<nbSeriesToDrop; j++)
 347          {
 348             if(seriesNumber == seriesToDrop[j])
 349             {
 350                drop = true;
 351                break;
 352             }
 353         }
 354         if (drop)
 355         {
 356            f->Delete();
 357            continue;
 358         }
 359       }
 360
 361       userFileIdentifier=s->CreateUserDefinedFileIdentifier(f);
 362       tokens.clear();
 363       GDCM_NAME_SPACE::Util::Tokenize (userFileIdentifier, tokens, token);
 364
 365       int imageNum; // Within FileName
 366       char newName[1024];
 367
 368       if ( tokens[3] == GDCM_NAME_SPACE::GDCM_UNFOUND)  // sometimes Trigger Time is not found. CreateUserDefinedFileIdentifier is not aware of the pb.
 369       {
 370          ///this is a trick to build up a lexicographical compliant name :
 371          ///     eg : fich001.ima vs fich100.ima as opposed to fich1.ima vs fich100.ima
 372          std::string name = GDCM_NAME_SPACE::Util::GetName( *it );
 373          if (hasSkel)
 374          {
 375             GDCM_NAME_SPACE::Util::Tokenize (name, tokensForFileName, skel);
 376             imageNum = atoi ( tokensForFileName[0].c_str() );
 377             // probabely we could write something much more complicated using C++ !
 378             sprintf (newName, "%s%06d%s", skel, imageNum, extent);
 379             tokens[3] = newName;
 380             tokensForFileName.clear();
 381          }
 382          else
 383             tokens[3] = name;
 384
 385          // Patient's Name
 386          // Series Instance UID
 387          // Image Position (Patient)
 388          // Trigger Time
 389          // In-plane Phase Encoding Direction
 390          // Series Description
 391          // FileName
 392
 393          userFileIdentifier = tokens[0] + token + tokens[1] + token + tokens[2] + token
 394                     + tokens[3] + token + tokens[4] + token + tokens[5] + token +  tokens[6] + token;
 395       }
 396
 397       if (verbose)
 398          std::cout << "[" << userFileIdentifier  << "] : " << *it << std::endl;
 399
 400       // storing in a map ensures automatic sorting !
 401       sf[userFileIdentifier] = f;
 402    }
 403
 404    if (verbose)
 405       std::cout << "  " << std::endl;
 406
 407    std::string fullFilename, lastFilename;
 408    std::string previousPatientName, currentPatientName;
 409    std::string previousSerieInstanceUID, currentSerieInstanceUID;
 410    std::string previousImagePosition, currentImagePosition;
 411    std::string previousPhaseEncodingDirection, currentPhaseEncodingDirection;
 412    std::string previousTriggerTime, currentTriggerTime;
 413
 414    std::string currentStudyUID;
 415    std::string seriesDescription;
 416
 417    std::string writeDir, currentWriteDir;
 418    std::string currentPatientWriteDir, currentSerieWriteDir,
 419                currentPositionWriteDir, currentPhaseEncodingDirectionWriteDir;
 420
 421    std::string fullWriteFilename;
 422    std::string strExtent(extent);
 423
 424    writeDir = GDCM_NAME_SPACE::Util::NormalizePath(dirNameout);
 425    SortedFiles::iterator it2;
 426
 427    previousPatientName            = "";
 428    previousSerieInstanceUID       = "";
 429    previousImagePosition          = "";
 430    previousPhaseEncodingDirection = "";
 431    previousTriggerTime            = "";
 432
 433    int sliceIndex = 0; // Is incremented *at the beginning* of processing
 434    int frameIndex;
 435    if (taggrid)
 436        frameIndex = 0;
 437    else
 438        frameIndex = 1;
 439
 440    int flag       = 0;
 441
 442    GDCM_NAME_SPACE::File *currentFile;
 443
 444    std::string defaultStudyUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 445    std::string defaultSerieUID;
 446
 447    for (it2 = sf.begin() ; it2 != sf.end(); ++it2)
 448    {
 449       currentFile = it2->second;
 450
 451       fullFilename =  currentFile->GetFileName();
 452       lastFilename =  GDCM_NAME_SPACE::Util::GetName( fullFilename );
 453       if (verbose)
 454       std::cout <<" ------------------------------------------------------------------------------"
 455                 << std::endl << " Deal with [" << it2->first << "] : ["<<fullFilename << "]"
 456                 << std::endl;
 457
 458       tokens.clear();
 459       GDCM_NAME_SPACE::Util::Tokenize (it2->first, tokens, token);
 460
 461       currentPatientName            = tokens[0];
 462       currentSerieInstanceUID       = tokens[1];
 463       currentImagePosition          = tokens[2];
 464       currentTriggerTime            = tokens[3];
 465       currentPhaseEncodingDirection = tokens[4];
 466       seriesDescription             = tokens[5];  // For Siemens pb
 467
 468       if ( currentImagePosition[0] == '-')
 469           currentImagePosition[0] = 'M';
 470       if ( currentImagePosition[0] == '+')
 471           currentImagePosition[0] = 'P';
 472
 473       // Add a default ImagePositionPatient to avoid confusion at post processing time
 474       if ( currentFile->GetEntryString(0x0020,0x0032) == GDCM_NAME_SPACE::GDCM_UNFOUND &&
 475            currentFile->GetEntryString(0x0020,0x0030) == GDCM_NAME_SPACE::GDCM_UNFOUND )
 476       {
 477          currentFile->InsertEntryString("0.\\0.\\0.",0x0020, 0x0032, "DS" );
 478       }
 479
 480       // Add a default ImagePositionPatient to avoid confusion at post processing time
 481       if ( currentFile->GetEntryString(0x0020,0x0037) == GDCM_NAME_SPACE::GDCM_UNFOUND &&
 482            currentFile->GetEntryString(0x0020,0x0035) == GDCM_NAME_SPACE::GDCM_UNFOUND )
 483       {
 484          currentFile->InsertEntryString("1.\\0.\\0.\\0.\\1.\\0.",0x0020, 0x0037, "DS" );
 485       }
 486
 487       if (previousPatientName != currentPatientName)
 488       {
 489          if ( currentFile->GetEntryString(0x0020,0x000d) == GDCM_NAME_SPACE::GDCM_UNFOUND) // Study UID
 490          {
 491             if (verbose)
 492                std::cout << "--- new  Study UID created" << std::endl;
 493             defaultStudyUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 494          }
 495
 496          previousPatientName = currentPatientName;
 497          if (verbose)
 498             std::cout << "==== new Patient  [" << currentPatientName  << "]" << std::endl;
 499
 500          previousPatientName            = currentPatientName;
 501          previousSerieInstanceUID       = ""; //currentSerieInstanceUID;
 502          previousImagePosition          = ""; //currentImagePosition;
 503          previousTriggerTime            = "";
 504          previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection;
 505
 506          currentPatientWriteDir = writeDir + currentPatientName;
 507          //if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(currentPatientWriteDir) )
 508            {
 509               systemCommand   = "mkdir " + currentPatientWriteDir;
 510               if (verbose)
 511                  std::cout << systemCommand << std::endl;
 512               system ( systemCommand.c_str() );
 513          }
 514       }
 515       currentFile->InsertEntryString(defaultStudyUID, 0x0020, 0x000d, "UI" );
 516
 517
 518       if ( GDCM_NAME_SPACE::Util::DicomStringEqual(modelName,"TrioTim") ) // for Siemens TrioTim , don't deal with 'Series Instance UID'
 519
 520       if (previousSerieInstanceUID != currentSerieInstanceUID)
 521       {
 522          if (verbose)
 523             std::cout << "==== === new Serie [" << currentSerieInstanceUID << "]"
 524                       << std::endl;
 525
 526          if ( currentFile->GetEntryString(0x0020,0x000e) == GDCM_NAME_SPACE::GDCM_UNFOUND)
 527          {
 528             if (verbose)
 529                std::cout << "--- --- new  Serie UID created" << std::endl;
 530             defaultSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 531            // currentFile->InsertEntryString(defaultSerieUID, 0x0020, 0x000e, "UI" );
 532          }
 533
 534          if (split)
 535          {
 536              currentSerieWriteDir  = currentPatientWriteDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR
 537                              + currentSerieInstanceUID;
 538              systemCommand   = "mkdir " + currentSerieWriteDir;
 539              system (systemCommand.c_str());
 540          }
 541          previousSerieInstanceUID       = currentSerieInstanceUID;
 542          previousImagePosition          = ""; //currentImagePosition;
 543          previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection;
 544       }
 545       currentFile->InsertEntryString(defaultSerieUID, 0x0020, 0x000e, "UI" );
 546
 547       // end of modelName != "TrioTim "
 548
 549       if (previousImagePosition != currentImagePosition)
 550       {
 551          frameIndex = 1;
 552          flag = 0;
 553          if (verbose)
 554             std::cout << "=== === === new Position [" << currentImagePosition  << "]"
 555                       << std::endl;
 556          if (split)
 557          {
 558              currentPositionWriteDir  = currentSerieWriteDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR
 559                              + currentImagePosition;
 560              systemCommand   = "mkdir " + currentPositionWriteDir;
 561              system (systemCommand.c_str());
 562          }
 563          previousImagePosition          = currentImagePosition;
 564          previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection;
 565          if (split)
 566             sliceIndex = 1; // only *one* slice in a given directory
 567          else
 568             sliceIndex += 1;
 569       }
 570
 571 // We don't split on Row/Column!
 572 /*
 573       if (previousPhaseEncodingDirection != currentPhaseEncodingDirection)
 574       {
 575          if (verbose)
 576             std::cout << "==== === === === new PhaseEncodingDirection ["
 577                       << currentPhaseEncodingDirection  << "]" << std::endl;
 578
 579          if (split)
 580          {
 581              currentPhaseEncodingDirectionWriteDir  = currentPositionWriteDir
 582                              + GDCM_NAME_SPACE::GDCM_FILESEPARATOR
 583                              + currentPhaseEncodingDirection;
 584              systemCommand   = "mkdir " + currentPhaseEncodingDirectionWriteDir;
 585              system (systemCommand.c_str());
 586          }
 587
 588          previousPhaseEncodingDirection = currentPhaseEncodingDirection;
 589       }
 590 */
 591
 592       if ( GDCM_NAME_SPACE::Debug::GetDebugFlag())
 593          std::cout << "--- --- --- --- --- " << it2->first << "  "
 594                    << (it2->second)->GetFileName() << " "
 595                    << GDCM_NAME_SPACE::Util::GetName( fullFilename ) << std::endl;
 596
 597       // Transform the image to be 'Brucker-Like'
 598       // ----------------------------------------
 599
 600       // Deal with 0x0019, 0x1000 : 'FOV'
 601       int nX = currentFile->GetXSize();
 602       int nY = currentFile->GetYSize();
 603       float pxSzX = currentFile->GetXSpacing();
 604       float pxSzY = currentFile->GetYSpacing();
 605       char fov[64];
 606       sprintf(fov, "%f\\%f",nX*pxSzX, nY*pxSzY);
 607       if (currentFile->IsVRCoherent(0x0019) == 1 )
 608          currentFile->InsertEntryString(fov, 0x0019, 0x1000, "  ");
 609       else
 610          currentFile->InsertEntryString(fov, 0x0019, 0x1000, "DS");
 611
 612
 613       // Deal with 0x0020, 0x0012 : 'SESSION INDEX'  (Acquisition Number)
 614       std::string chSessionIndex;
 615       // CLEANME
 616
 617       if (taggrid)
 618       {
 619          chSessionIndex = "1";
 620       }
 621       else
 622       {
 623       /* for SIEMENS MRI :
 624         D 0008|1090 [LO] [Manufacturer's Model Name ] [Triotim ]
 625         we have to deal with :
 626
 627         D 0008|103e [LO]  [Series Description ] [fl2d9_line PA 15 90deg] or anything that contains '90' !
 628         D 0008|103e [LO]  [Series Description ] [fl2d9_line PA 15 0deg ]
 629         (everything is flagged as 'ROW')
 630       */
 631
 632          if ( GDCM_NAME_SPACE::Util::DicomStringEqual(modelName,"TrioTim") )
 633          {
 634             if (seriesDescription.find("90", 0) != std::string::npos)
 635                chSessionIndex = "1";  // 90 deg -> COL
 636             else if (seriesDescription.find("0", 0)!= std::string::npos)
 637                chSessionIndex = "2";  // 0 deg -> ROW
 638             else
 639             {
 640                std::cout << "====================== seriesDescription doesn't contain"
 641                          << " neither '90' nor '0' (?!?) : ["
 642                          << seriesDescription << "]" << std::endl;
 643                chSessionIndex = "1";
 644             }
 645          }
 646          else  // for all other 'normal' cases
 647          {
 648             if (currentPhaseEncodingDirection == "COL" || currentPhaseEncodingDirection == "COL " || currentPhaseEncodingDirection == " COL")
 649                chSessionIndex = "1";
 650             else if (currentPhaseEncodingDirection == "ROW" || currentPhaseEncodingDirection == "ROW "|| currentPhaseEncodingDirection == " ROW")
 651                chSessionIndex = "2";
 652             else
 653             {
 654                std::cout << "====================== PhaseEncodingDirection "
 655                          << " neither COL nor ROW (?!?) : [ "
 656                          << currentPhaseEncodingDirection << "]" << std::endl;
 657                chSessionIndex = "1";
 658             }
 659          }
 660       }
 661
 662       if (currentFile->IsVRCoherent(0x0020) == 1 )
 663          currentFile->InsertEntryString(chSessionIndex, 0x0020, 0x0012, "  ");
 664       else
 665          currentFile->InsertEntryString(chSessionIndex, 0x0020, 0x0012, "IS");
 666
 667       // Deal with  0x0021, 0x1020 : 'SLICE INDEX'
 668       char chSliceIndex[5];
 669       sprintf(chSliceIndex, "%04d", sliceIndex);
 670       std::string strChSliceIndex(chSliceIndex);
 671
 672       // Deal with  0x0021, 0x1040 : 'FRAME INDEX'
 673       char chFrameIndex[5];
 674       sprintf(chFrameIndex, "%04d", frameIndex);
 675
 676       std::string stringVR;
 677       if (currentFile->IsVRCoherent(0x0021) == 1 )
 678          stringVR = "  ";
 679       else
 680         stringVR = "IS";
 681
 682       currentFile->InsertEntryString(strChSliceIndex, 0x0021, 0x1020, stringVR);
 683       currentFile->InsertEntryString(chFrameIndex,    0x0021, 0x1040, stringVR);
 684
 685       if (verbose) {
 686          std::cout << "0x0021, 0x1020 : strChSliceIndex " << strChSliceIndex << std::endl;
 687          std::cout << "0x0021, 0x1040 : chFrameIndex  "   << chFrameIndex    << std::endl;
 688          std::cout << "0x0020, 0x0012 : chSessionIndex "  << chSessionIndex  << std::endl;
 689       }
 690
 691       std::string strImagePositionPatient    = currentFile->GetEntryString(0x0020, 0x0032 );
 692       if (strImagePositionPatient == GDCM_NAME_SPACE::GDCM_UNFOUND)
 693       {
 694          if (verbose)
 695             std::cout << "Duplicate ImagePosition into ImagePositionPatient" << std::endl;
 696          currentFile->InsertEntryString(currentFile->GetEntryString(0x0020, 0x0030), 0x0020, 0x0032, "DS" );
 697       }
 698
 699       std::string strImageOrientationPatient = f->GetEntryString(0x0020, 0x0037 );
 700       if (strImageOrientationPatient == GDCM_NAME_SPACE::GDCM_UNFOUND)
 701       {
 702          if (verbose)
 703             std::cout << "Duplicate ImageOrientation into ImageOrientationPatient" << std::endl;
 704          currentFile->InsertEntryString(currentFile->GetEntryString(0x0020, 0x0035), 0x0020, 0x0037, "DS" );
 705       }
 706
 707       if (taggrid  || strcmp(input, "IDO")==0 || strcmp(input, "ido")==0 )
 708          frameIndex++;
 709       else
 710       {
 711          if (flag == 0)
 712          {
 713             flag = 1;
 714          }
 715          else
 716          {
 717             frameIndex++;
 718             flag = 0;
 719          }
 720       }
 721
 722       if (split)
 723
 724          //fullWriteFilename = currentPhaseEncodingDirectionWriteDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR
 725          //                                + lastFilename + strExtent;
 726          fullWriteFilename = currentPositionWriteDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR
 727                                          + lastFilename + strExtent;
 728       else
 729          fullWriteFilename = currentPatientWriteDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR
 730                                          + lastFilename + strExtent;
 731
 732       // Load the pixels in RAM.
 733
 734       fh = GDCM_NAME_SPACE::FileHelper::New(currentFile);
 735       uint8_t *imageData = fh->GetImageDataRaw(); // Don't convert (Gray Pixels + LUT) into (RGB pixels) ?!?
 736       fh->SetWriteTypeToDcmExplVR();
 737
 738       if (rubout) {
 739          // Put to Black the burnt-in number.
 740          nX = currentFile->GetXSize();
 741          nY = currentFile->GetYSize();
 742          for(int y=nY-15; y<nY; y++)
 743             for(int x=nX/3; x<nX/2+50; x++)
 744               imageData[ y*nX*2 + x ] = 0;
 745       }
 746
 747       // We didn't make any computation on the pixels -> keep unchanged the following :
 748       // 'Media Storage SOP Class UID' (0x0002,0x0002)
 749       // 'SOP Class UID'               (0x0008,0x0016)
 750       // 'Image Type'                  (0x0008,0x0008)
 751       // 'Conversion Type'             (0x0008,0x0064)
 752       fh->SetContentType(GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE);
 753
 754       if (!fh->Write(fullWriteFilename))
 755       {
 756          std::cout << "Fail to write :[" << fullWriteFilename << "]"
 757                    << std::endl;
 758       }
 759       fh->Delete();
 760    }
 761    return 0;
 762  }
 763