Example/ToMRIregister.cxx

   1 /*=========================================================================
   2
   3   Program:   gdcm
   4   Module:    $RCSfile: ToMRIregister.cxx,v $
   5   Language:  C++
   6   Date:      $Date: 2011/03/29 07:35:58 $
   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
  19 #include "gdcmSerieHelper.h"
  20 #include "gdcmFile.h"
  21 #include "gdcmFileHelper.h"
  22 #include "gdcmDebug.h"
  23 #include "gdcmDirList.h"
  24 #include "gdcmUtil.h"
  25 #include "gdcmDataEntry.h"
  26 #include "gdcmArgMgr.h"
  27 #include <iostream>
  28 #include <sstream>
  29
  30 bool AquisitionTime_0008_0032_Compare(GDCM_NAME_SPACE::File *file1, GDCM_NAME_SPACE::File *file2);
  31
  32 bool AquisitionTime_0008_0032_Compare(GDCM_NAME_SPACE::File *file1, GDCM_NAME_SPACE::File *file2)
  33 {
  34    return file1->GetEntryString(0x0008,0x0032) < file2->GetEntryString(0x0008,0x0032);
  35 }
  36
  37 int main(int argc, char *argv[])
  38 {
  39
  40    START_USAGE(usage)
  41    "\n ToMriregister :\n                                                      ",
  42    " - Converts the Siemens Sonata MRI '*tfl2d1'                              ",
  43    " to be processable by MriRegister software                                ",
  44    " - May be used as a template for GDCM_NAME_SPACE::SerieHelper use.        ",
  45    "                                                                          ",
  46    "usage: ToMriRegister dirin=inputDirectoryName                             ",
  47    "                     dirout=outputDirectoryName                           ",
  48    "                     [ { [noshadowseq] | [noshadow][noseq] } ] [debug]    ",
  49    "                                                                          ",
  50    "       inputDirectoryName : user wants to analyze *all* the files         ",
  51    "                            within the directory                          ",
  52    "       noshadowseq: user doesn't want to load Private Sequences           ",
  53    "       noshadow   : user doesn't want to load Private groups (odd number) ",
  54    "       noseq      : user doesn't want to load Sequences                   ",
  55    "       verbose    : user wants to run the program in 'verbose mode'       ",
  56    "       debug      : developer wants to run the program in 'debug mode'    ",
  57    FINISH_USAGE
  58
  59    // ----- Initialize Arguments Manager ------
  60
  61    GDCM_NAME_SPACE::ArgMgr *am = new GDCM_NAME_SPACE::ArgMgr(argc, argv);
  62
  63    if (am->ArgMgrDefined("usage") || argc == 1)
  64    {
  65       am->ArgMgrUsage(usage); // Display 'usage'
  66       delete am;
  67       return 0;
  68    }
  69
  70    if (am->ArgMgrDefined("debug"))
  71       GDCM_NAME_SPACE::Debug::DebugOn();
  72
  73    int verbose  = am->ArgMgrDefined("verbose");
  74
  75    int loadMode = GDCM_NAME_SPACE::LD_ALL;
  76    if ( am->ArgMgrDefined("noshadowseq") )
  77       loadMode |= GDCM_NAME_SPACE::LD_NOSHADOWSEQ;
  78    else
  79    {
  80       if ( am->ArgMgrDefined("noshadow") )
  81          loadMode |= GDCM_NAME_SPACE::LD_NOSHADOW;
  82       if ( am->ArgMgrDefined("noseq") )
  83          loadMode |= GDCM_NAME_SPACE::LD_NOSEQ;
  84    }
  85
  86    const char *dirIn  = am->ArgMgrGetString("dirin");
  87    if (dirIn == 0)
  88    {
  89        std::cout <<std::endl
  90                  << "'dirin=' must be present;"
  91                  <<  std::endl;
  92        am->ArgMgrUsage(usage); // Display 'usage'
  93        delete am;
  94        return 0;
  95    }
  96
  97    const char *dirOut  = am->ArgMgrGetString("dirout");
  98    if (dirOut == 0)
  99    {
 100        std::cout <<std::endl
 101                  << "'dirout=' must be present;"
 102                  <<  std::endl;
 103        am->ArgMgrUsage(usage); // Display 'usage'
 104        delete am;
 105        return 0;
 106    }
 107
 108    /* if unused Param we give up */
 109    if ( am->ArgMgrPrintUnusedLabels() )
 110    {
 111       am->ArgMgrUsage(usage);
 112       delete am;
 113       return 0;
 114    }
 115
 116    delete am;  // ------ we don't need Arguments Manager any longer ------
 117
 118    // ======================== more checking on the params ==============
 119
 120    if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(dirIn) )
 121    {
 122       std::cout << "KO : [" << dirIn << "] is not a Directory." << std::endl;
 123       return 0;
 124
 125    }
 126    else
 127    {
 128       if (verbose)
 129          std::cout << "OK : [" << dirIn << "] is a Directory." << std::endl;
 130    }
 131
 132    std::string systemCommand;
 133    std::string strDirNameout(dirOut);          // to please gcc 4
 134    if (verbose)
 135       std::cout << "Check for output directory :[" << dirOut << "]."
 136              <<std::endl;
 137    if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(dirOut) )    // dirout not found
 138    {
 139       systemCommand = "mkdir " + strDirNameout;   // create it!
 140       if (verbose)
 141          std::cout << systemCommand << std::endl;
 142       system (systemCommand.c_str());
 143       if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(dirOut) ) // be sure it worked
 144       {
 145           std::cout << "KO : not a dir : [" << dirOut
 146                     << "] (creation failure ?)" << std::endl;
 147       return 0;
 148
 149       }
 150       else
 151       {
 152         if (verbose)
 153            std::cout << "Directory [" << dirOut << "] created." << std::endl;
 154       }
 155    }
 156    else
 157    {
 158       if (verbose)
 159          std::cout << "Output Directory [" << dirOut
 160                    << "] already exists; Used as is." << std::endl;
 161    }
 162
 163    // ========================== Now, we can do the job! ================
 164
 165    // Just to see *all* the file names:
 166
 167    GDCM_NAME_SPACE::DirList dirList(dirIn,true); // gets (recursively) the file list
 168    GDCM_NAME_SPACE::DirListType fileList = dirList.GetFilenames();
 169    for( GDCM_NAME_SPACE::DirListType::iterator it  = fileList.begin();
 170                                  it != fileList.end();
 171                                  ++it )
 172    {
 173       std::cout << "file [" << it->c_str() << "]" << std::endl;
 174    }
 175
 176    GDCM_NAME_SPACE::SerieHelper *s;
 177
 178    s = GDCM_NAME_SPACE::SerieHelper::New();
 179    s->SetLoadMode(GDCM_NAME_SPACE::LD_NOSEQ);     // Don't load Sequences
 180
 181    // we could choose to ignore some Files
 182    //GDCM_NAME_SPACE::TagKey t(0x0010,0x0024);  // [Sequence Name]
 183    // Keep only files where restriction is true
 184    //s->AddRestriction(t, "*tfl2d1 ", GDCM_NAME_SPACE::GDCM_EQUAL);
 185
 186    s->SetDirectory(dirIn, true); // true : recursive exploration
 187
 188 /*
 189    std::cout << " ---------------------------------------- "
 190              << "'Single UID' Filesets found in :["
 191              << dirName << "]" << std::endl;
 192
 193    s->Print();
 194    std::cout << " ------------------------------------- Result after splitting"
 195              << std::endl;
 196 */
 197    int nbFiles;
 198    std::string fullFilename, lastFilename;
 199    char fullWriteFilename[1024]; // should be enough.
 200
 201    std::ostringstream str;
 202
 203    GDCM_NAME_SPACE::XCoherentFileSetmap xcm;
 204    GDCM_NAME_SPACE::FileHelper *fh;
 205
 206    // will be used for ordering.
 207    s->SetUserLessThanFunction(AquisitionTime_0008_0032_Compare);
 208    int serieNumber = 0;
 209    int sliceNumber = 0;
 210    int imageNumber = 0;
 211
 212    // For all the Single SerieUID Files Sets of the GDCM_NAME_SPACE::Serie
 213    GDCM_NAME_SPACE::FileList *l = s->GetFirstSingleSerieUIDFileSet();
 214
 215    char numero[5];
 216    while (l)
 217    {
 218       nbFiles = l->size() ;
 219       if ( l->size() < 8 ) // Hope we skip Scout views !
 220       {
 221          std::cout << "Ignore the 'Single SerieUID' FileSet :["
 222                    << s->GetCurrentSerieUIDFileSetUID()
 223                    << "]  " << nbFiles << " long" << std::endl;
 224          std::cout << "-----------------------------------" << std::endl;
 225       }
 226       else
 227       {
 228          std::cout << "Split the 'Single SerieUID' FileSet :["
 229                    << s->GetCurrentSerieUIDFileSetUID()
 230                    << "]  " << nbFiles << " long" << std::endl;
 231          std::cout << "-----------------------------------" << std::endl;
 232
 233          xcm = s->SplitOnPosition(l);
 234
 235          //int sliceNumber = 0;
 236
 237          double position =0.0;
 238          char charPosition[10];
 239
 240          for (GDCM_NAME_SPACE::XCoherentFileSetmap::iterator i = xcm.begin();
 241                                                   i != xcm.end();
 242                                                 ++i)
 243          {
 244              std::cout << "Position : ";
 245              std::cout << "[" << (*i).first << "]" << std::endl;
 246
 247             s->OrderFileList((*i).second);  // sort the current XCoherent Fileset
 248
 249             position = position + 1.0;
 250             sprintf(charPosition, "%f", position);
 251
 252             //int imageNumber = 0;
 253             for ( GDCM_NAME_SPACE::FileList::iterator it =  ((*i).second)->begin();
 254                                            it != ((*i).second)->end();
 255                                          ++it)
 256             {
 257
 258             // Set the DataElements MriRegister needs to be happy
 259             // Probabely one of the following (check it !):
 260             /*
 261                0020 0011 IS 1 Series Number
 262                0020 0012 IS 1 Acquisition Number
 263                0020 0013 IS 1 Instance Number
 264            */
 265
 266            /*
 267             Sure it needs ACR-NEMA elements : Study ID                20, 10 ?
 268                                               Image Number            20, 12 ?
 269                                               Location ('atof-able') -> 20, 50 ?
 270            */
 271             (*it)->InsertEntryString(charPosition,0x0020,0x0050, "DS");
 272
 273
 274             (*it)->InsertEntryString("0",0x0008,0x0000, "UL"); // Needs to be present (actual length doesn't matter !)
 275
 276             str.str("");
 277             str << serieNumber;
 278             (*it)->InsertEntryString(str.str(),0x0020,0x0011, "IS"); // Series Number
 279
 280            /*
 281             str.str("");
 282             str << imageNumber;
 283             (*it)->InsertEntryString(str.str(),0x0020,0x0012, "IS"); // Acquisition Number
 284             (*it)->InsertEntryString(str.str(),0x0020,0x0013, "IS"); // Instance Number
 285            */
 286
 287    sprintf(numero, "%04d", imageNumber);
 288    (*it)->InsertEntryString(numero,0x0020,0x0012, "IS"); // Acquisition Number
 289    (*it)->InsertEntryString(numero,0x0020,0x0013, "IS"); // Instance Number
 290
 291             // Load the pixels in RAM.
 292
 293                fh = GDCM_NAME_SPACE::FileHelper::New(*it);
 294                uint8_t *imageData = fh->GetImageDataRaw(); // Don't convert (Gray Pixels + LUT) into (RGB pixels) ?!?
 295                if (!imageData)
 296                   std::cout << "fail to read [" << (*it)->GetFileName() << std::endl;
 297                fh->SetWriteTypeToAcr();
 298                fh->SetContentType(GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE);
 299
 300                // forge the file name
 301
 302                fullFilename = (*it)->GetFileName();
 303                lastFilename =  GDCM_NAME_SPACE::Util::GetName( fullFilename );
 304                //fullWriteFilename = strDirNameout + GDCM_NAME_SPACE::GDCM_FILESEPARATOR
 305                //                                  + lastFilename;
 306                sprintf(fullWriteFilename, "%s%c%04d-%04d-%04d.dcm",
 307                                       dirOut, GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 308                                       serieNumber, sliceNumber, imageNumber);
 309
 310                if (verbose)
 311                {
 312                  // show [sliceLocation 0x0020,1041 (if any)] old name, -> newname
 313                  std::string strSliceLocation;
 314                  /*
 315                  GDCM_NAME_SPACE::DataEntry e = (*it)->GetDataEntry(0x0020,0x1041);
 316                  if (e)
 317                     strSliceLocation = e->GetString();
 318                  else
 319                     strSliceLocation = "";
 320                  */
 321                   strSliceLocation = (*it)->GetDataEntry(0x0020,0x1041)->GetString();
 322                   std::cout <<strSliceLocation << ": " << fullFilename << " -> " << fullWriteFilename << std::endl;
 323                }
 324                // Write it, now
 325
 326                fh->SetWriteTypeToAcrLibido();
 327
 328                if (!fh->Write(fullWriteFilename))
 329                {
 330                   std::cout << "Fail to write :[" << fullWriteFilename << "]"
 331                             << std::endl;
 332                }
 333
 334                ///\todo FIXME segfaults if uncommented ?!?
 335                // delete(imageData);
 336                (*it)->Delete();
 337                fh->Delete();
 338
 339                imageNumber++;
 340
 341             }
 342             std::cout << std::endl;
 343             sliceNumber++;
 344          }
 345       }
 346       serieNumber++;
 347       l = s->GetNextSingleSerieUIDFileSet();
 348    }
 349    s->Delete();
 350    return 0;
 351 }