Example/PhilipsToBrucker2.cxx

   1 /*=========================================================================
   2
   3   Program:   gdcm
   4   Module:    $RCSfile: PhilipsToBrucker2.cxx,v $
   5   Language:  C++
   6   Date:      $Date: 2006/01/25 11:08:18 $
   7   Version:   $Revision: 1.6 $
   8
   9   Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
  10   l'Image). All rights reserved. See Doc/License.txt or
  11   http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
  12
  13      This software is distributed WITHOUT ANY WARRANTY; without even
  14      the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15      PURPOSE.  See the above copyright notices for more information.
  16
  17 =========================================================================*/
  18 #include "gdcmDocEntry.h"
  19 #include "gdcmDicomDir.h"
  20 #include "gdcmDicomDirPatient.h"
  21 #include "gdcmFile.h"
  22 #include "gdcmFileHelper.h"
  23 #include "gdcmDirList.h"
  24 #include "gdcmDebug.h"
  25 #include "gdcmArgMgr.h"
  26 #include "gdcmUtil.h"
  27 #include "gdcmSerieHelper.h"
  28
  29 #include <iostream>
  30
  31 /**
  32   * \brief
  33   *          - explores recursively the given directory
  34   *          - keeps the requested series
  35   *          - orders the gdcm-readable found Files
  36   *            according to their Patient/Study/Serie/Image characteristics
  37   *          - fills a single level Directory with *all* the files,
  38   *            converted into a Brucker-like Dicom, Intags compliant
  39   *
  40   */
  41
  42 typedef std::map<std::string, gdcm::File*> SortedFiles;
  43
  44 int main(int argc, char *argv[])
  45 {
  46    START_USAGE(usage)
  47    " \n PhilipsToBrucker :\n                                                  ",
  48    " - explores recursively the given directory,                              ",
  49    " - keeps the requested series/ drops the unrequested series               ",
  50    " - orders the gdcm-readable found Files according to their                ",
  51    "           (0x0010, 0x0010) Patient's Name                                ",
  52    "           (0x0020, 0x000e) Series Instance UID                           ",
  53    "           (0x0020, 0x0032) Image Position (Patient)                      ",
  54    "           (0x0018, 0x1060) Trigger Time                                  ",
  55    "           (0x0018, 0x1312) In-plane Phase Encoding Direction             ",
  56    " - fills a single level (*) Directory with *all* the files,               ",
  57    "           converted into a Brucker-like Dicom, InTags compliant          ",
  58    "   (*) actually : creates as many directories as Patients                 ",
  59    "                  -that shouldn't appear, but being carefull is better ! -",
  60    " or                                                                       ",
  61    " - fills a tree-like structure of directories as :                        ",
  62    "        - Patient                                                         ",
  63    "        -- Serie                                                          ",
  64    "        --- Position                                                      ",
  65    "            Images are (sorted by Trigger Time /                          ",
  66    "                     Encoding Direction (Row, Column)                     ",
  67    "      use :                                                               ",
  68    "           0x0021, 0x1020 : 'SLICE INDEX'                                 ",
  69    "           0x0021, 0x1040 : 'FRAME INDEX'                                 ",
  70    "           0x0020, 0x0012 : 'SESSION INDEX'  (Acquisition Number)         ",
  71    " usage:                                                                   ",
  72    " PhilipsToBrucker dirin=rootDirectoryName                                 ",
  73    "                  dirout=outputDirectoryName                              ",
  74    "                  {  [keep= list of seriesNumber to process]              ",
  75    "                   | [drop= list of seriesNumber to ignore] }             ",
  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    " extent : DO NOT forget the leading '.' !                                 ",
  89    " split: creates a tree-like structure of directories as :                 ",
  90    "        - Patient                                                         ",
  91    "        -- Serie                                                          ",
  92    "        --- Position                                                      ",
  93    "            Images are (sorted by Trigger Time /                          ",
  94    "                     Encoding Direction (Row, Column)                     ",
  95    " noshadowseq: user doesn't want to load Private Sequences                 ",
  96    " noshadow : user doesn't want to load Private groups (odd number)         ",
  97    " noseq    : user doesn't want to load Sequences                           ",
  98    " verbose  : user wants to run the program in 'verbose mode'               ",
  99    " debug    : *developer*  wants to run the program in 'debug mode'         ",
 100    FINISH_USAGE
 101
 102    // ----- Initialize Arguments Manager ------
 103
 104    gdcm::ArgMgr *am = new gdcm::ArgMgr(argc, argv);
 105
 106    if (argc == 1 || am->ArgMgrDefined("usage"))
 107    {
 108       am->ArgMgrUsage(usage); // Display 'usage'
 109       delete am;
 110       return 0;
 111    }
 112
 113    char *dirNamein;
 114    dirNamein  = am->ArgMgrGetString("dirin",(char *)".");
 115
 116    char *dirNameout;
 117    dirNameout  = am->ArgMgrGetString("dirout",(char *)".");
 118
 119    int loadMode = gdcm::LD_ALL;
 120    if ( am->ArgMgrDefined("noshadowseq") )
 121       loadMode |= gdcm::LD_NOSHADOWSEQ;
 122    else
 123    {
 124    if ( am->ArgMgrDefined("noshadow") )
 125          loadMode |= gdcm::LD_NOSHADOW;
 126       if ( am->ArgMgrDefined("noseq") )
 127          loadMode |= gdcm::LD_NOSEQ;
 128    }
 129
 130    if (am->ArgMgrDefined("debug"))
 131       gdcm::Debug::DebugOn();
 132
 133    bool verbose  = am->ArgMgrDefined("verbose");
 134    bool split    = am->ArgMgrDefined("split");
 135    bool listonly = am->ArgMgrDefined("listonly");
 136
 137    int nbSeriesToKeep;
 138    int *seriesToKeep = am->ArgMgrGetListOfInt("keep", &nbSeriesToKeep);
 139    int nbSeriesToDrop;
 140    int *seriesToDrop = am->ArgMgrGetListOfInt("drop", &nbSeriesToDrop);
 141
 142    if ( nbSeriesToKeep!=0 && nbSeriesToDrop!=0)
 143    {
 144       std::cout << "KEEP and DROP are mutually exclusive !" << std::endl;
 145       delete am;
 146       return 0;
 147    }
 148
 149    char *extent  = am->ArgMgrGetString("extent",".DCM");
 150
 151    // if unused Param we give up
 152    if ( am->ArgMgrPrintUnusedLabels() )
 153    {
 154       am->ArgMgrUsage(usage);
 155       delete am;
 156       return 0;
 157    }
 158    delete am;  // we don't need Argument Manager any longer
 159
 160    // ----- Begin Processing -----
 161
 162    if ( ! gdcm::DirList::IsDirectory(dirNamein) )
 163    {
 164       std::cout << "KO : [" << dirNamein << "] is not a Directory." << std::endl;
 165       exit(0);
 166    }
 167    else
 168    {
 169       std::cout << "OK : [" << dirNamein << "] is a Directory." << std::endl;
 170    }
 171
 172    std::string systemCommand;
 173
 174    std::cout << "Check for output directory :[" << dirNameout << "]."
 175              <<std::endl;
 176    if ( ! gdcm::DirList::IsDirectory(dirNameout) )    // dirout not found
 177    {
 178       std::string strDirNameout(dirNameout);          // to please gcc 4
 179       systemCommand = "mkdir " +strDirNameout;        // create it!
 180       if (verbose)
 181          std::cout << systemCommand << std::endl;
 182       system (systemCommand.c_str());
 183       if ( ! gdcm::DirList::IsDirectory(dirNameout) ) // be sure it worked
 184       {
 185           std::cout << "KO : not a dir : [" << dirNameout << "] (creation failure ?)" << std::endl;
 186           exit(0);
 187       }
 188       else
 189       {
 190         std::cout << "Directory [" << dirNameout << "] created." << std::endl;
 191       }
 192    }
 193    else
 194    {
 195        std::cout << "Output Directory [" << dirNameout << "] already exists; Used as is." << std::endl;
 196    }
 197
 198    std::string strDirNamein(dirNamein);
 199    gdcm::DirList dirList(strDirNamein, true); // get recursively the list of files
 200
 201    if (listonly)
 202    {
 203       std::cout << "------------List of found files ------------" << std::endl;
 204       dirList.Print();
 205    }
 206
 207    gdcm::DirListType fileNames;
 208    fileNames = dirList.GetFilenames();
 209    gdcm::SerieHelper *s;              // Needed only to may use SerieHelper::AddSeriesDetail()
 210    s = gdcm::SerieHelper::New();
 211
 212 /*
 213    std::cout << "---------------Print Serie--------------" << std::endl;
 214    s->SetDirectory(dirNamein, true); // true : recursive exploration
 215    s->SetUseSeriesDetails(true);
 216    s->AddSeriesDetail(0x0018, 0x1312);
 217    s->Print();
 218 */
 219
 220    gdcm::File *f;
 221    gdcm::FileHelper *fh;
 222 /*
 223    std::cout << "---------------Print Unique Series identifiers---------"
 224              << std::endl;
 225    std::string uniqueSeriesIdentifier;
 226
 227    for (gdcm::DirListType::iterator it = fileNames.begin();
 228                                     it != fileNames.end();
 229                                   ++it)
 230    {
 231       std::cout << "File Name : " << *it << std::endl;
 232       f = gdcm::File::New();
 233       f->SetLoadMode(gdcm::LD_ALL);
 234       f->SetFileName( *it );
 235       f->Load();
 236
 237       uniqueSeriesIdentifier=s->CreateUniqueSeriesIdentifier(f);
 238       std::cout << "                           [" <<
 239                uniqueSeriesIdentifier  << "]" << std::endl;
 240       f->Delete();
 241    }
 242 */
 243
 244    if (verbose)
 245       std::cout << "------------------Print Break levels-----------------" << std::endl;
 246
 247    std::string userFileIdentifier;
 248    SortedFiles sf;
 249
 250    s->AddSeriesDetail(0x0010, 0x0010, false); // Patient's Name
 251    s->AddSeriesDetail(0x0020, 0x000e, false); // Series Instance UID
 252    s->AddSeriesDetail(0x0020, 0x0032, false); // Image Position (Patient)
 253    s->AddSeriesDetail(0x0018, 0x1060, true);  // Trigger Time (true: convert to keep numerical order)
 254    s->AddSeriesDetail(0x0018, 0x1312, false); // In-plane Phase Encoding Direction
 255
 256    for (gdcm::DirListType::iterator it = fileNames.begin();
 257                                     it != fileNames.end();
 258                                   ++it)
 259    {
 260       f = gdcm::File::New();
 261       f->SetLoadMode(loadMode);
 262       f->SetFileName( *it );
 263       f->Load();
 264
 265       // keep only requested Series
 266       std::string strSeriesNumber;
 267       int seriesNumber;
 268       int j;
 269
 270       bool keep = false;
 271       if (nbSeriesToKeep != 0)
 272       {
 273          strSeriesNumber = f->GetEntryString(0x0020, 0x0011 );
 274          seriesNumber = atoi( strSeriesNumber.c_str() );
 275          for (j=0;j<nbSeriesToKeep; j++)
 276          {
 277             if(seriesNumber == seriesToKeep[j])
 278             {
 279                keep = true;
 280                break;
 281             }
 282          }
 283          if ( !keep)
 284          {
 285             f->Delete();
 286             continue;
 287          }
 288       }
 289       // drop all unrequested Series
 290       bool drop = false;
 291       if (nbSeriesToDrop != 0)
 292       {
 293          strSeriesNumber = f->GetEntryString(0x0020, 0x0011 );
 294          seriesNumber = atoi( strSeriesNumber.c_str() );
 295          for (j=0;j<nbSeriesToDrop; j++)
 296          {
 297             if(seriesNumber == seriesToDrop[j])
 298             {
 299                drop = true;
 300                break;
 301             }
 302         }
 303         if (drop)
 304         {
 305            f->Delete();
 306            continue;
 307         }
 308       }
 309
 310       userFileIdentifier=s->CreateUserDefinedFileIdentifier(f);
 311      // userFileIdentifier += "_";
 312       //userFileIdentifier += *it;
 313       std::cout << "                           [" <<
 314               userFileIdentifier  << "]" << std::endl;
 315
 316       // storing in a map ensures automatic sorting !
 317       sf[userFileIdentifier] = f;
 318    }
 319
 320    std::vector<std::string> tokens;
 321    std::string fullFilename, lastFilename;
 322    std::string previousPatientName, currentPatientName;
 323    std::string previousSerieInstanceUID, currentSerieInstanceUID;
 324    std::string previousImagePosition, currentImagePosition;
 325    std::string previousPhaseEncodingDirection, currentPhaseEncodingDirection;
 326    std::string previousTriggerTime, currentTriggerTime;
 327
 328    std::string writeDir, currentWriteDir;
 329    std::string currentPatientWriteDir, currentSerieWriteDir,
 330                currentPositionWriteDir, currentPhaseEncodingDirectionWriteDir;
 331
 332    std::string fullWriteFilename;
 333    std::string strExtent(extent);
 334
 335    writeDir = gdcm::Util::NormalizePath(dirNameout);
 336    SortedFiles::iterator it2;
 337
 338    previousPatientName            = "";
 339    previousSerieInstanceUID       = "";
 340    previousImagePosition          = "";
 341    previousPhaseEncodingDirection = "";
 342    previousTriggerTime            = "";
 343
 344    int sliceIndex = 0; // Is incremented *at the beginning* of processing
 345    int frameIndex = 1;
 346    int flag       = 0;
 347
 348    gdcm::File *currentFile;
 349
 350    for (it2 = sf.begin() ; it2 != sf.end(); ++it2)
 351    {
 352       currentFile = it2->second;
 353
 354       fullFilename =  currentFile->GetFileName();
 355       lastFilename =  gdcm::Util::GetName( fullFilename );
 356       std::cout << "Try to write" <<lastFilename << std::endl;
 357
 358       tokens.clear();
 359       gdcm::Util::Tokenize (it2->first, tokens, "_");
 360
 361       currentPatientName            = tokens[0];
 362       currentSerieInstanceUID       = tokens[1];
 363       currentImagePosition          = tokens[2];
 364       currentTriggerTime            = tokens[3];
 365       currentPhaseEncodingDirection = tokens[4];
 366
 367       if ( currentImagePosition[0] == '-')
 368           currentImagePosition[0] = 'M';
 369       if ( currentImagePosition[0] == '+')
 370           currentImagePosition[0] = 'P';
 371
 372       if (previousPatientName != currentPatientName)
 373       {
 374          previousPatientName = currentPatientName;
 375          if (verbose)
 376             std::cout << "==== new Patient  [" << currentPatientName  << "]" << std::endl;
 377
 378          previousPatientName            = currentPatientName;
 379          previousSerieInstanceUID       = ""; //currentSerieInstanceUID;
 380          previousImagePosition          = ""; //currentImagePosition;
 381          previousTriggerTime            = "";
 382          previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection;
 383
 384          currentPatientWriteDir = writeDir + currentPatientName;
 385          //if ( ! gdcm::DirList::IsDirectory(currentPatientWriteDir) )
 386            {
 387               systemCommand   = "mkdir " + currentPatientWriteDir;
 388               if (verbose)
 389                  std::cout << systemCommand << std::endl;
 390               system ( systemCommand.c_str() );
 391          }
 392       }
 393
 394       if (previousSerieInstanceUID != currentSerieInstanceUID)
 395       {
 396          if (verbose)
 397             std::cout << "==== === new Serie [" << currentSerieInstanceUID << "]"
 398                       << std::endl;
 399          if (split)
 400          {
 401              currentSerieWriteDir  = currentPatientWriteDir + gdcm::GDCM_FILESEPARATOR
 402                              + currentSerieInstanceUID;
 403              systemCommand   = "mkdir " + currentSerieWriteDir;
 404              system (systemCommand.c_str());
 405          }
 406          previousSerieInstanceUID       = currentSerieInstanceUID;
 407          previousImagePosition          = ""; //currentImagePosition;
 408          previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection;
 409       }
 410
 411       if (previousImagePosition != currentImagePosition)
 412       {
 413          frameIndex = 1;
 414          flag = 0;
 415          if (verbose)
 416             std::cout << "=== === === new Position [" << currentImagePosition  << "]"
 417                       << std::endl;
 418          if (split)
 419          {
 420              currentPositionWriteDir  = currentSerieWriteDir + gdcm::GDCM_FILESEPARATOR
 421                              + currentImagePosition;
 422              systemCommand   = "mkdir " + currentPositionWriteDir;
 423              system (systemCommand.c_str());
 424          }
 425          previousImagePosition          = currentImagePosition;
 426          previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection;
 427          sliceIndex += 1;
 428       }
 429
 430 // We don't split on Row/Column!
 431 /*
 432       if (previousPhaseEncodingDirection != currentPhaseEncodingDirection)
 433       {
 434          if (verbose)
 435             std::cout << "==== === === === new PhaseEncodingDirection ["
 436                       << currentPhaseEncodingDirection  << "]" << std::endl;
 437
 438          if (split)
 439          {
 440              currentPhaseEncodingDirectionWriteDir  = currentPositionWriteDir
 441                              + gdcm::GDCM_FILESEPARATOR
 442                              + currentPhaseEncodingDirection;
 443              systemCommand   = "mkdir " + currentPhaseEncodingDirectionWriteDir;
 444              system (systemCommand.c_str());
 445          }
 446
 447          previousPhaseEncodingDirection = currentPhaseEncodingDirection;
 448       }
 449 */
 450
 451       if (verbose)
 452          std::cout << "--- --- --- --- --- " << (it2->second)->GetFileName()
 453                    << std::endl;
 454
 455       if ( gdcm::Debug::GetDebugFlag())
 456          std::cout << "--- --- --- --- --- " << it2->first << "  "
 457                    << (it2->second)->GetFileName() << " "
 458                    << gdcm::Util::GetName( fullFilename ) << std::endl;
 459
 460       // Transform the image to be 'Brucker-Like'
 461       // ----------------------------------------
 462
 463       // Deal with 0x0019, 0x1000 : 'FOV'
 464       int nX = currentFile->GetXSize();
 465       int nY = currentFile->GetYSize();
 466       float pxSzX = currentFile->GetXSpacing();
 467       float pxSzY = currentFile->GetYSpacing();
 468       char fov[64];
 469       sprintf(fov, "%f\\%f",nX*pxSzX, nY*pxSzY);
 470       currentFile->InsertEntryString(fov, 0x0019, 0x1000, "DS");
 471
 472       // Deal with 0x0020, 0x0012 : 'SESSION INDEX'  (Acquisition Number)
 473       std::string chSessionIndex;
 474       if (currentPhaseEncodingDirection == "ROW")
 475          chSessionIndex = "1";
 476       else
 477          chSessionIndex = "2"; // suppose it's "COLUMN" !
 478       currentFile->InsertEntryString(chSessionIndex, 0x0020, 0x0012, "IS");
 479
 480       // Deal with  0x0021, 0x1020 : 'SLICE INDEX'
 481       char chSliceIndex[5];
 482       sprintf(chSliceIndex, "%04d", sliceIndex);
 483       std::string strChSliceIndex(chSliceIndex);
 484       currentFile->InsertEntryString(strChSliceIndex, 0x0021, 0x1020, "IS");
 485
 486       // Deal with  0x0021, 0x1040 : 'FRAME INDEX'
 487       char chFrameIndex[5];
 488       sprintf(chFrameIndex, "%04d", frameIndex);
 489       currentFile->InsertEntryString(chFrameIndex, 0x0021, 0x1040, "IS");
 490
 491       if (flag == 0)
 492       {
 493          flag = 1;
 494       }
 495       else
 496       {
 497          frameIndex++;
 498          flag = 0;
 499       }
 500
 501       if (split)
 502
 503          //fullWriteFilename = currentPhaseEncodingDirectionWriteDir + gdcm::GDCM_FILESEPARATOR
 504          //                                + lastFilename + strExtent;
 505          fullWriteFilename = currentPositionWriteDir + gdcm::GDCM_FILESEPARATOR
 506                                          + lastFilename + strExtent;
 507       else
 508          fullWriteFilename = currentPatientWriteDir + gdcm::GDCM_FILESEPARATOR
 509                                          + lastFilename + strExtent;
 510
 511       /*
 512       systemCommand  = "cp " + fullFilename + " " + fullWriteFilename;
 513       std::cout << systemCommand << std::endl;
 514       system (  systemCommand.c_str() );
 515       */
 516
 517       // Load the pixels in RAM.
 518
 519       fh = gdcm::FileHelper::New(currentFile);
 520       fh->GetImageDataRaw(); // Don't convert (Gray Pixels + LUT) into (RGB pixels) ?!?
 521       fh->SetWriteTypeToDcmExplVR();
 522       if (!fh->Write(fullWriteFilename))
 523       {
 524          std::cout << "Fail to write :[" << fullWriteFilename << "]"
 525                    << std::endl;
 526       }
 527       fh->Delete();
 528    }
 529  }