Example/MagnetomVisionToBrucker.cxx

   1 /*=========================================================================
   2
   3   Program:   gdcm
   4   Module:    $RCSfile: MagnetomVisionToBrucker.cxx,v $
   5   Language:  C++
   6   Date:      $Date: 2006/01/31 11:42:08 $
   7   Version:   $Revision: 1.4 $
   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 MagnetomVisionToBrucker :\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 (RET)                          ",
  54    "           (0x0018, 0x1060) Trigger Time                                  ",
  55    " - fills a single level (*) Directory with *all* the files,               ",
  56    "           converted into a Brucker-like Dicom, InTags compliant          ",
  57    "   (*) actually : creates as many directories as Patients                 ",
  58    "                  -that shouldn't appear, but being carefull is better ! -",
  59    " or                                                                       ",
  60    " - fills a tree-like structure of directories as :                        ",
  61    "        - Patient                                                         ",
  62    "        -- Serie                                                          ",
  63    "        --- Position                                                      ",
  64    "            Images are (sorted by Trigger Time /                          ",
  65    "                     Encoding Direction (Row, Column)                     ",
  66    "      use :                                                               ",
  67    "           0x0021, 0x1020 : 'SLICE INDEX'                                 ",
  68    "           0x0021, 0x1040 : 'FRAME INDEX'                                 ",
  69    "           0x0020, 0x0012 : 'SESSION INDEX'  (Acquisition Number)         ",
  70    " usage:                                                                   ",
  71    " PhilipsToBrucker dirin=rootDirectoryName                                 ",
  72    "                  dirout=outputDirectoryName                              ",
  73    "                  {  [keep= list of seriesNumber to process]              ",
  74    "                   | [drop= list of seriesNumber to ignore] }             ",
  75    "                  [input = {ACR|DCM}]                                     ",
  76    "                  [extent=image suffix (.IMA, .NEMA, .DCM, ...)]          ",
  77    "                  [listonly] [split]                                      ",
  78    "                  [noshadowseq][noshadow][noseq] [verbose] [debug]        ",
  79    "                                                                          ",
  80    " dirout : will be created if doesn't exist                                ",
  81    " keep : if user wants to process a limited number of series               ",
  82    "            he gives the list of 'SeriesNumber' (tag 0020|0011)           ",
  83    " drop : if user wants to ignore a limited number of series                ",
  84    "            he gives the list of 'SeriesNumber' (tag 0020|0011)           ",
  85    "        SeriesNumber are short enough to be human readable                ",
  86    "        e.g : 1030,1035,1043                                              ",
  87    " extent : DO NOT forget the leading '.' !                                 ",
  88    " split: creates a tree-like structure of directories as :                 ",
  89    "        - Patient                                                         ",
  90    "        -- Serie                                                          ",
  91    "        --- Position                                                      ",
  92    "            Images are (sorted by Trigger Time /                          ",
  93    " noshadowseq: user doesn't want to load Private Sequences                 ",
  94    " noshadow : user doesn't want to load Private groups (odd number)         ",
  95    " noseq    : user doesn't want to load Sequences                           ",
  96    " verbose  : user wants to run the program in 'verbose mode'               ",
  97    " debug    : *developer*  wants to run the program in 'debug mode'         ",
  98    FINISH_USAGE
  99
 100    // ----- Initialize Arguments Manager ------
 101
 102    gdcm::ArgMgr *am = new gdcm::ArgMgr(argc, argv);
 103
 104    if (argc == 1 || am->ArgMgrDefined("usage"))
 105    {
 106       am->ArgMgrUsage(usage); // Display 'usage'
 107       delete am;
 108       return 0;
 109    }
 110
 111    const char *dirNamein;
 112    dirNamein  = am->ArgMgrGetString("dirin",".");
 113
 114    const char *dirNameout;
 115    dirNameout  = am->ArgMgrGetString("dirout",".");
 116
 117    int loadMode = gdcm::LD_ALL;
 118    if ( am->ArgMgrDefined("noshadowseq") )
 119       loadMode |= gdcm::LD_NOSHADOWSEQ;
 120    else
 121    {
 122    if ( am->ArgMgrDefined("noshadow") )
 123          loadMode |= gdcm::LD_NOSHADOW;
 124       if ( am->ArgMgrDefined("noseq") )
 125          loadMode |= gdcm::LD_NOSEQ;
 126    }
 127
 128    if (am->ArgMgrDefined("debug"))
 129       gdcm::Debug::DebugOn();
 130
 131    int verbose  = am->ArgMgrDefined("verbose");
 132    int split    = am->ArgMgrDefined("split");
 133    int listonly = am->ArgMgrDefined("listonly");
 134
 135    int nbSeriesToKeep;
 136    int *seriesToKeep = am->ArgMgrGetListOfInt("keep", &nbSeriesToKeep);
 137    int nbSeriesToDrop;
 138    int *seriesToDrop = am->ArgMgrGetListOfInt("drop", &nbSeriesToDrop);
 139
 140    if ( nbSeriesToKeep!=0 && nbSeriesToDrop!=0)
 141    {
 142       std::cout << "KEEP and DROP are mutually exclusive !" << std::endl;
 143       delete am;
 144       return 0;
 145    }
 146
 147    const char *extent  = am->ArgMgrGetString("extent",".DCM");
 148
 149    // if unused Param we give up
 150    if ( am->ArgMgrPrintUnusedLabels() )
 151    {
 152       am->ArgMgrUsage(usage);
 153       delete am;
 154       return 0;
 155    }
 156    delete am;  // we don't need Argument Manager any longer
 157
 158    // ----- Begin Processing -----
 159
 160    if ( ! gdcm::DirList::IsDirectory(dirNamein) )
 161    {
 162       std::cout << "KO : [" << dirNamein << "] is not a Directory." << std::endl;
 163       exit(0);
 164    }
 165    else
 166    {
 167       std::cout << "OK : [" << dirNamein << "] is a Directory." << std::endl;
 168    }
 169
 170    std::string systemCommand;
 171
 172    std::cout << "Check for output directory :[" << dirNameout << "]."
 173              <<std::endl;
 174    if ( ! gdcm::DirList::IsDirectory(dirNameout) )    // dirout not found
 175    {
 176       std::string strDirNameout(dirNameout);          // to please gcc 4
 177       systemCommand = "mkdir " +strDirNameout;        // create it!
 178       if (verbose)
 179          std::cout << systemCommand << std::endl;
 180       system (systemCommand.c_str());
 181       if ( ! gdcm::DirList::IsDirectory(dirNameout) ) // be sure it worked
 182       {
 183           std::cout << "KO : not a dir : [" << dirNameout << "] (creation failure ?)" << std::endl;
 184           exit(0);
 185       }
 186       else
 187       {
 188         std::cout << "Directory [" << dirNameout << "] created." << std::endl;
 189       }
 190    }
 191    else
 192    {
 193        std::cout << "Output Directory [" << dirNameout << "] already exists; Used as is." << std::endl;
 194    }
 195
 196    std::string strDirNamein(dirNamein);
 197    gdcm::DirList dirList(strDirNamein, true); // get recursively the list of files
 198
 199    if (listonly)
 200    {
 201       std::cout << "------------List of found files ------------" << std::endl;
 202       dirList.Print();
 203    }
 204
 205    gdcm::DirListType fileNames;
 206    fileNames = dirList.GetFilenames();
 207    gdcm::SerieHelper *s;              // Needed only to may use SerieHelper::AddSeriesDetail()
 208    s = gdcm::SerieHelper::New();
 209
 210 /*
 211    std::cout << "---------------Print Serie--------------" << std::endl;
 212    s->SetDirectory(dirNamein, true); // true : recursive exploration
 213    s->SetUseSeriesDetails(true);
 214    s->AddSeriesDetail(0x0018, 0x1312);
 215    s->Print();
 216 */
 217
 218    gdcm::File *f;
 219    gdcm::FileHelper *fh;
 220 /*
 221    std::cout << "---------------Print Unique Series identifiers---------"
 222              << std::endl;
 223    std::string uniqueSeriesIdentifier;
 224
 225    for (gdcm::DirListType::iterator it = fileNames.begin();
 226                                     it != fileNames.end();
 227                                   ++it)
 228    {
 229       std::cout << "File Name : " << *it << std::endl;
 230       f = gdcm::File::New();
 231       f->SetLoadMode(gdcm::LD_ALL);
 232       f->SetFileName( *it );
 233       f->Load();
 234
 235       uniqueSeriesIdentifier=s->CreateUniqueSeriesIdentifier(f);
 236       std::cout << "                           [" <<
 237                uniqueSeriesIdentifier  << "]" << std::endl;
 238       f->Delete();
 239    }
 240 */
 241
 242    if (verbose)
 243       std::cout << "------------------Print Break levels-----------------" << std::endl;
 244
 245    std::string userFileIdentifier;
 246    SortedFiles sf;
 247
 248    s->AddSeriesDetail(0x0010, 0x0010, false); // Patient's Name
 249    s->AddSeriesDetail(0x0020, 0x0010, false); // Study ID - Siemens, in that time!
 250    s->AddSeriesDetail(0x0020, 0x0030, false); // Image Position (RET)
 251    s->AddSeriesDetail(0x0020, 0x0013, false);  // Instance Number
 252             //(called 'Trigger Time' in order not to change too much the code)
 253
 254    for (gdcm::DirListType::iterator it = fileNames.begin();
 255                                     it != fileNames.end();
 256                                   ++it)
 257    {
 258       f = gdcm::File::New();
 259       f->SetLoadMode(loadMode);
 260       f->SetFileName( *it );
 261       f->Load();
 262
 263       // keep only requested Series
 264       std::string strSeriesNumber;
 265       int seriesNumber;
 266       int j;
 267
 268       bool keep = false;
 269       if (nbSeriesToKeep != 0)
 270       {
 271          strSeriesNumber = f->GetEntryString(0x0020, 0x0011 );
 272          seriesNumber = atoi( strSeriesNumber.c_str() );
 273          for (j=0;j<nbSeriesToKeep; j++)
 274          {
 275             if(seriesNumber == seriesToKeep[j])
 276             {
 277                keep = true;
 278                break;
 279             }
 280          }
 281          if ( !keep)
 282          {
 283             f->Delete();
 284             continue;
 285          }
 286       }
 287       // drop all unrequested Series
 288       bool drop = false;
 289       if (nbSeriesToDrop != 0)
 290       {
 291          strSeriesNumber = f->GetEntryString(0x0020, 0x0011 );
 292          seriesNumber = atoi( strSeriesNumber.c_str() );
 293          for (j=0;j<nbSeriesToDrop; j++)
 294          {
 295             if(seriesNumber == seriesToDrop[j])
 296             {
 297                drop = true;
 298                break;
 299             }
 300         }
 301         if (drop)
 302         {
 303            f->Delete();
 304            continue;
 305         }
 306       }
 307
 308       userFileIdentifier=s->CreateUserDefinedFileIdentifier(f);
 309      // userFileIdentifier += "_";
 310       //userFileIdentifier += *it;
 311       std::cout << "                           [" <<
 312               userFileIdentifier  << "]" << std::endl;
 313
 314       // storing in a map ensures automatic sorting !
 315       sf[userFileIdentifier] = f;
 316    }
 317
 318    std::vector<std::string> tokens;
 319    std::string fullFilename, lastFilename;
 320    std::string previousPatientName, currentPatientName;
 321    std::string previousSerieInstanceUID, currentSerieInstanceUID;
 322    std::string previousImagePosition, currentImagePosition;
 323    //std::string previousPhaseEncodingDirection, currentPhaseEncodingDirection;
 324    std::string previousTriggerTime, currentTriggerTime;
 325
 326    std::string writeDir, currentWriteDir;
 327    std::string currentPatientWriteDir, currentSerieWriteDir,
 328                currentPositionWriteDir; // currentPhaseEncodingDirectionWriteDir;
 329
 330    std::string fullWriteFilename;
 331    std::string strExtent(extent);
 332
 333    writeDir = gdcm::Util::NormalizePath(dirNameout);
 334    SortedFiles::iterator it2;
 335
 336    previousPatientName            = "";
 337    previousSerieInstanceUID       = "";
 338    previousImagePosition          = "";
 339    //previousPhaseEncodingDirection = "";
 340    previousTriggerTime            = "";
 341
 342    int sliceIndex = 1;
 343    int frameIndex = 1;
 344    int flag       = 0;
 345
 346    gdcm::File *currentFile;
 347
 348    for (it2 = sf.begin() ; it2 != sf.end(); ++it2)
 349    {
 350       currentFile = it2->second;
 351
 352       fullFilename =  currentFile->GetFileName();
 353       lastFilename =  gdcm::Util::GetName( fullFilename );
 354       std::cout << "Try to write" <<lastFilename << std::endl;
 355
 356       tokens.clear();
 357       gdcm::Util::Tokenize (it2->first, tokens, "_");
 358
 359       currentPatientName            = tokens[0];
 360       currentSerieInstanceUID       = tokens[1];
 361       currentImagePosition          = tokens[2];
 362       currentTriggerTime            = tokens[3];
 363       //currentPhaseEncodingDirection = tokens[4];
 364
 365       if ( currentImagePosition[0] == '-')
 366           currentImagePosition[0] = 'M';
 367       if ( currentImagePosition[0] == '+')
 368           currentImagePosition[0] = 'P';
 369
 370       if (previousPatientName != currentPatientName)
 371       {
 372          previousPatientName = currentPatientName;
 373          if (verbose)
 374             std::cout << "==== new Patient  [" << currentPatientName  << "]" << std::endl;
 375
 376          previousPatientName            = currentPatientName;
 377          previousSerieInstanceUID       = ""; //currentSerieInstanceUID;
 378          previousImagePosition          = ""; //currentImagePosition;
 379          previousTriggerTime            = "";
 380         // previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection;
 381
 382          currentPatientWriteDir = writeDir + currentPatientName;
 383          //if ( ! gdcm::DirList::IsDirectory(currentPatientWriteDir) )
 384            {
 385               systemCommand   = "mkdir " + currentPatientWriteDir;
 386               if (verbose)
 387                  std::cout << systemCommand << std::endl;
 388               system ( systemCommand.c_str() );
 389          }
 390       }
 391
 392       if (previousSerieInstanceUID != currentSerieInstanceUID)
 393       {
 394          if (verbose)
 395             std::cout << "==== === new Serie [" << currentSerieInstanceUID << "]"
 396                       << std::endl;
 397          if (split)
 398          {
 399              currentSerieWriteDir  = currentPatientWriteDir + gdcm::GDCM_FILESEPARATOR
 400                              + currentSerieInstanceUID;
 401              systemCommand   = "mkdir " + currentSerieWriteDir;
 402              system (systemCommand.c_str());
 403          }
 404          previousSerieInstanceUID       = currentSerieInstanceUID;
 405          previousImagePosition          = ""; //currentImagePosition;
 406          //previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection;
 407       }
 408
 409       if (previousImagePosition != currentImagePosition)
 410       {
 411          frameIndex = 1;
 412          flag = 0;
 413          if (verbose)
 414             std::cout << "=== === === new Position [" << currentImagePosition  << "]"
 415                       << std::endl;
 416          if (split)
 417          {
 418              currentPositionWriteDir  = currentSerieWriteDir + gdcm::GDCM_FILESEPARATOR
 419                              + currentImagePosition;
 420              systemCommand   = "mkdir " + currentPositionWriteDir;
 421              system (systemCommand.c_str());
 422          }
 423          previousImagePosition          = currentImagePosition;
 424          //previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection;
 425          sliceIndex += 1;
 426       }
 427
 428 // We don't split on Row/Column!
 429 /*
 430       if (previousPhaseEncodingDirection != currentPhaseEncodingDirection)
 431       {
 432          if (verbose)
 433             std::cout << "==== === === === new PhaseEncodingDirection ["
 434                       << currentPhaseEncodingDirection  << "]" << std::endl;
 435
 436          if (split)
 437          {
 438              currentPhaseEncodingDirectionWriteDir  = currentPositionWriteDir
 439                              + gdcm::GDCM_FILESEPARATOR
 440                              + currentPhaseEncodingDirection;
 441              systemCommand   = "mkdir " + currentPhaseEncodingDirectionWriteDir;
 442              system (systemCommand.c_str());
 443          }
 444
 445          previousPhaseEncodingDirection = currentPhaseEncodingDirection;
 446       }
 447 */
 448
 449       if (verbose)
 450          std::cout << "--- --- --- --- --- " << (it2->second)->GetFileName()
 451                    << std::endl;
 452
 453       if ( gdcm::Debug::GetDebugFlag())
 454          std::cout << "--- --- --- --- --- " << it2->first << "  "
 455                    << (it2->second)->GetFileName() << " "
 456                    << gdcm::Util::GetName( fullFilename ) << std::endl;
 457
 458       // Transform the image to be 'Brucker-Like'
 459       // ----------------------------------------
 460
 461       // Deal with 0x0019, 0x1000 : 'FOV'
 462       int nX = currentFile->GetXSize();
 463       int nY = currentFile->GetYSize();
 464       float pxSzX = currentFile->GetXSpacing();
 465       float pxSzY = currentFile->GetYSpacing();
 466       char fov[64];
 467       sprintf(fov, "%f\\%f",nX*pxSzX, nY*pxSzY);
 468       currentFile->InsertEntryString(fov, 0x0019, 0x1000, "DS");
 469
 470       // Deal with 0x0020, 0x0012 : 'SESSION INDEX'  (Acquisition Number)
 471       std::string chSessionIndex = "1";
 472       /*
 473       if (currentPhaseEncodingDirection == "ROW")
 474          chSessionIndex = "1";
 475       else
 476          chSessionIndex = "2"; // suppose it's "COLUMN" !
 477       currentFile->InsertEntryString(chSessionIndex, 0x0020, 0x0012, "IS");
 478      */
 479       // Deal with  0x0021, 0x1020 : 'SLICE INDEX'
 480       char chSliceIndex[5];
 481       sprintf(chSliceIndex, "%04d", sliceIndex);
 482       std::string strChSliceIndex(chSliceIndex);
 483       currentFile->InsertEntryString(strChSliceIndex, 0x0021, 0x1020, "IS");
 484
 485       // Deal with  0x0021, 0x1040 : 'FRAME INDEX'
 486       char chFrameIndex[5];
 487       sprintf(chFrameIndex, "%04d", frameIndex);
 488       currentFile->InsertEntryString(chFrameIndex, 0x0021, 0x1040, "IS");
 489
 490       if (flag == 0)
 491       {
 492          flag = 1;
 493       }
 494       else
 495       {
 496          frameIndex++;
 497          flag = 0;
 498       }
 499
 500       if (split)
 501
 502          //fullWriteFilename = currentPhaseEncodingDirectionWriteDir + gdcm::GDCM_FILESEPARATOR
 503          //                                + lastFilename + strExtent;
 504          fullWriteFilename = currentPositionWriteDir + gdcm::GDCM_FILESEPARATOR
 505                                          + lastFilename + strExtent;
 506       else
 507          fullWriteFilename = currentPatientWriteDir + gdcm::GDCM_FILESEPARATOR
 508                                          + lastFilename + strExtent;
 509
 510       /*
 511       systemCommand  = "cp " + fullFilename + " " + fullWriteFilename;
 512       std::cout << systemCommand << std::endl;
 513       system (  systemCommand.c_str() );
 514       */
 515
 516       // Load the pixels in RAM.
 517
 518       fh = gdcm::FileHelper::New(currentFile);
 519       fh->GetImageDataRaw(); // Don't convert (Gray Pixels + LUT) into (RGB pixels) ?!?
 520       fh->SetWriteTypeToDcmExplVR();
 521       if (!fh->Write(fullWriteFilename))
 522       {
 523          std::cout << "Fail to write :[" << fullWriteFilename << "]"
 524                    << std::endl;
 525       }
 526       fh->Delete();
 527    }
 528  }