DicomFileMgr.cc

Go to the documentation of this file.

//
// ********************************************************************
// * License and Disclaimer                                           *
// *                                                                  *
// * The  Geant4 software  is  copyright of the Copyright Holders  of *
// * the Geant4 Collaboration.  It is provided  under  the terms  and *
// * conditions of the Geant4 Software License,  included in the file *
// * LICENSE and available at  http://cern.ch/geant4/license .  These *
// * include a list of copyright holders.                             *
// *                                                                  *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work  make  any representation or  warranty, express or implied, *
// * regarding  this  software system or assume any liability for its *
// * use.  Please see the license in the file  LICENSE  and URL above *
// * for the full disclaimer and the limitation of liability.         *
// *                                                                  *
// * This  code  implementation is the result of  the  scientific and *
// * technical work of the GEANT4 collaboration.                      *
// * By using,  copying,  modifying or  distributing the software (or *
// * any work based  on the software)  you  agree  to acknowledge its *
// * use  in  resulting  scientific  publications,  and indicate your *
// * acceptance of all terms of the Geant4 Software license.          *
// ********************************************************************
//
#include "DicomFileMgr.hh"

#include "DicomFileCT.hh"
#include "DicomFilePET.hh"
#include "DicomFileStructure.hh"
#include "DicomFilePlan.hh"

#include "dcmtk/dcmdata/dcdeftag.h"
#include "G4tgrFileIn.hh"
#include "G4UIcommand.hh"

DicomFileMgr* DicomFileMgr::theInstance = 0;
int DicomFileMgr::verbose = 1;
 
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
DicomFileMgr* DicomFileMgr::GetInstance()
{
  if( !theInstance ) {
    theInstance = new DicomFileMgr;
  }
  return theInstance;
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
DicomFileMgr::DicomFileMgr()
{
  fCompression = 1.;
  theCTFileAll = 0;
  theStructureNCheck = 4;
  theStructureNMaxROI = 100;
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
void DicomFileMgr::Convert( G4String fileName )
{
  G4tgrFileIn fin = G4tgrFileIn::GetInstance(fileName);
  std::vector<G4String> wl; 
  // Read each file in file list
  theFileOutName = "test.g4dcm";
  int ii;
  for( ii = 0;; ii++) {
    if( ! fin.GetWordsInLine(wl) ) break;
    if( wl[0] == ":COMPRESSION" ) {
      CheckNColumns(wl,2);
      SetCompression(wl[1]);
    } else if( wl[0] == ":FILE" ) {
      CheckNColumns(wl,2);
      G4cout << "@@@@@@@ Reading FILE: " << wl[1]  << G4endl;
      AddFile(wl[1]);
    } else if( wl[0] == ":FILE_OUT" ) {
      CheckNColumns(wl,2);
      theFileOutName = wl[1];
    } else if( wl[0] == ":MATE_DENS" ) {
      CheckNColumns(wl,3);
      AddMaterialDensity(wl);
    } else if( wl[0] == ":MATE" ) {
      CheckNColumns(wl,3);
      AddMaterial(wl);
    } else if( wl[0] == ":CT2D" ) {
      CheckNColumns(wl,3);
      AddCT2Density(wl);
    } else {      
      G4Exception("DICOM2G4",
                  "Wrong argument",
                  FatalErrorInArgument,
                  G4String("UNKNOWN TAG IN FILE  "+wl[0]).c_str());
    }
    
  }
  
  
  //@@@@@@ Process files
  ProcessFiles();
  
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
void DicomFileMgr::CheckNColumns(std::vector<G4String> wl, size_t vsizeTh )
{
  if( wl.size() != vsizeTh ) {
    G4cerr << " Reading line " << G4endl;
    for( size_t ii = 0; ii < wl.size(); ii++){
      G4cerr << wl[ii] << " ";
    }
    G4cerr << G4endl;
    G4Exception("DICOM2G4",
                "D2G0010",
                FatalErrorInArgument,
                ("Wrong number of columns in line " + std::to_string(wl.size()) + " <> " 
                  + std::to_string(vsizeTh)).c_str());
  }

}


//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
void DicomFileMgr::SetCompression( G4String fComp )
{
  fCompression = G4UIcommand::ConvertToDouble(fComp);
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
void DicomFileMgr::AddFile( G4String fileName )
{
  DcmFileFormat dfile;
  if( ! (dfile.loadFile(fileName.c_str())).good() ) {
    G4Exception("DicomHandler::ReadFile",
                "dfile.loadFile",
                FatalErrorInArgument,
                ("Error reading file " + fileName).c_str());
  }
  DcmDataset* dset = dfile.getDataset();

  OFString dModality;
  if( !dset->findAndGetOFString(DCM_Modality,dModality).good() ) {
    G4Exception("DicomHandler::ReadData ",
                "",
                FatalException,
                " Have not read Modality");
  }
  
  if( dModality == "CT" ) {
    DicomFileCT* df = new DicomFileCT(dset);
    df->ReadData();
    df->SetFileName( fileName );
    // reorder by location
    theCTFiles[df->GetMaxZ()] = df;
  } else if( dModality == "RTSTRUCT" ) {     
    DicomFileStructure* df = new DicomFileStructure(dset);
    df->ReadData();
    df->SetFileName( fileName );
    //    theFiles.insert(msd::value_type(dModality,df));
    theStructFiles.push_back(df);
  } else if( dModality == "RTPLAN" ) {     
    DicomFilePlan* df = new DicomFilePlan(dset);
    df->ReadData();
    df->SetFileName( fileName );
    //    theFiles.insert(msd::value_type(dModality,df));
    thePlanFiles.push_back(df);
  } else if( dModality == "PT" ) {     
    DicomFilePET* df = new DicomFilePET(dset);
    df->ReadData();
    df->SetFileName( fileName );
    //    theFiles.insert(msd::value_type(dModality,df));
    thePETFiles[df->GetMaxZ()] = df;
    //    thePETFiles.push_back(df);
  } else {
    G4Exception("DicomFileMgr::AddFIle()",
                "DFM001",
                FatalErrorInArgument,
                (G4String("File is not of type CT or RTSTRUCT or RTPLAN, but: ") 
                 + dModality).c_str());
  }

}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
void DicomFileMgr::AddMaterial( std::vector<G4String> wl )
{
  if( theMaterials.size() > 0 && bMaterialsDensity ) {
    G4Exception("DicomFileMgr::AddMaterial",
                "DFM005",
                FatalException,
        "Trying to add a Material with :MATE and another with :MATE_DENS, check your input file");
  }
  bMaterialsDensity = false;
  theMaterials[G4UIcommand::ConvertToDouble(wl[2])] = wl[1];
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
void DicomFileMgr::AddMaterialDensity( std::vector<G4String> wl )
{
  if( theMaterialsDensity.size() > 0 && !bMaterialsDensity ) {
    G4Exception("DicomFileMgr::AddMaterial",
                "DFM005",
                FatalException,
        "Trying to add a Material with :MATE and another with :MATE_DENS, check your input file");
  }
  bMaterialsDensity = true;
  theMaterialsDensity[G4UIcommand::ConvertToDouble(wl[2])] = wl[1];
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
void DicomFileMgr::AddCT2Density( std::vector<G4String> wl)
{
  theCT2Density[G4UIcommand::ConvertToInt(wl[1])] = G4UIcommand::ConvertToDouble(wl[2]);
  G4cout << this << " AddCT2density " << theCT2Density.size() << G4endl;//GDEB

}
 
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
G4double DicomFileMgr::Hounsfield2density(Uint32 Hval)
{
  if( theCT2Density.size() == 0 ) {
    G4Exception("Hounsfield2density",
                "DCM004",
                FatalException,
                "No :CT2D line in input file");
  }
  std::map<G4int,G4double>::const_iterator ite = theCT2Density.begin();
  G4int minHval = (*ite).first;
  if( G4int(Hval) < minHval ) {
    G4Exception("DicomHandler::Hounsfield2density",
                "",
                FatalException,
                ("Hval value too small, change input file "+std::to_string(Hval) + " < " 
                 + std::to_string(minHval)).c_str());
  }

  ite = theCT2Density.end(); ite--;
  G4int maxHval = (*ite).first;
  if( G4int(Hval) > maxHval ) {
    G4Exception("DicomHandler::Hval2density",
                "",
                FatalException,
                ("Hval value too big, change CT2Density.dat file "+std::to_string(Hval) + " > " 
                 + std::to_string(maxHval)).c_str());
  }
  
  G4float density = -1.;
  G4double deltaCT = 0;
  G4double deltaDensity = 0;
  
  ite = theCT2Density.upper_bound(Hval);
  std::map<G4int,G4double>::const_iterator itePrev = ite; itePrev--;
  
  deltaCT = (*ite).first - (*itePrev).first;
  deltaDensity = (*ite).second - (*itePrev).second;
  
  // interpolating linearly
  density = (*ite).second - (((*ite).first-Hval)*deltaDensity/deltaCT );
  
  if(density < 0.) {
    G4Exception("DicomFileMgr::Hounsfiled2Density",
                "DFM002",
                FatalException,
                G4String("@@@ Error negative density = " + std::to_string(density) + " from HV = " 
                 + std::to_string(Hval)).c_str());
  }
  
  //  G4cout << " Hval2density " << Hval << " -> " << density << G4endl;//GDEB
  return density;
  
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
size_t DicomFileMgr::GetMaterialIndex( G4double Hval)
{
  std::map<G4double,G4String>::iterator ite = theMaterials.upper_bound(Hval);
  if( ite == theMaterials.end() ) {
    ite--;
    G4Exception("DicomFileMgr::GetMaterialIndex",
                "DFM004",
                FatalException,
                ("Hounsfiled value too big, change input file "+std::to_string(Hval) + " > " 
                 + std::to_string((*ite).first)).c_str());
  }

  size_t dist = std::distance( theMaterials.begin(), ite );
  
  return  dist;
  
}


//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
size_t DicomFileMgr::GetMaterialIndexByDensity( G4double density )
{
  std::map<G4double,G4String>::iterator ite = theMaterialsDensity.upper_bound(density);
  if( ite == theMaterialsDensity.end() ) {
    ite--;
    G4Exception("DicomFileMgr::GetMaterialIndexByDensity",
                "DFM003",
                FatalException,
                ("Density too big, change input file "+std::to_string(density) + " > " 
                 + std::to_string((*ite).first)).c_str());
  }

  size_t dist = std::distance( theMaterialsDensity.begin(), ite );
  
  return  dist;
  
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
void DicomFileMgr::ProcessFiles()
{
  if( theCTFiles.size() == 0 ) {
    G4Exception("CheckCTSlices",
                "DCM004",
                JustWarning,
                "No :FILE of type CT in input file");
  } else {
 
    CheckCTSlices();
    
    BuildCTMaterials();
    
    MergeCTFiles();
    
  }

  G4cout << " PROCESSING PET FILES " << thePETFiles.size() << G4endl; //GDEB
  if( thePETFiles.size() != 0 ) {

    CheckPETSlices();
    
    BuildPETActivities();
    
    MergePETFiles();

  }

  DumpToTextFile();

}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
void DicomFileMgr::CheckCTSlices()
{
  size_t nSlices = theCTFiles.size();
  G4cout << " DicomFileMgr::Checking CT slices: " << nSlices << G4endl;

  G4bool uniformSliceThickness = true;
  
  if(nSlices > 1) {
    if(nSlices == 2) {
      mdct::const_iterator ite = theCTFiles.begin();
      DicomFileCT* one = (*ite).second;
      ite++;
      DicomFileCT* two = (*ite).second;
      
      G4double real_distance = (two->GetLocation()-one->GetLocation())/2.;
      
      if(one->GetMaxZ() != two->GetMinZ()) {
        one->SetMaxZ(one->GetLocation()+real_distance);
        two->SetMinZ(two->GetLocation()-real_distance);
        //one->SetMinZ(one->GetLocation()-real_distance);
        //two->SetMaxZ(two->GetLocation()+real_distance);
        if(uniformSliceThickness) {
          one->SetMinZ(one->GetLocation()-real_distance);
          two->SetMaxZ(two->GetLocation()+real_distance);
        }
      }
    } else {
      mdct::iterator ite0 = theCTFiles.begin();
      mdct::iterator ite1 = ite0; ite1++;
      mdct::iterator ite2 = ite1; ite2++;
      for(; ite2 != theCTFiles.end(); ++ite0, ++ite1, ++ite2) {        
        DicomFileCT* prev = (DicomFileCT*)((*ite0).second);
        DicomFileCT* slice = (DicomFileCT*)((*ite1).second);
        DicomFileCT* next = (DicomFileCT*)((*ite2).second);
        G4double real_up_distance = (next->GetLocation() -
                                      slice->GetLocation())/2.;
        G4double real_down_distance = (slice->GetLocation() -
                                      prev->GetLocation())/2.;
        G4double real_distance = real_up_distance + real_down_distance;
        G4double stated_distance = slice->GetMaxZ()-slice->GetMinZ();

        if(std::fabs(real_distance - stated_distance) > 1.E-9) {
          unsigned int sliceNum = std::distance(theCTFiles.begin(),ite1);
          G4cerr << "\tDicomFileMgr::CheckCTSlices - Slice Distance Error in slice [" << sliceNum 
                 << "]: Distance between this slice and slices up and down = "
                 << real_distance
                 << " <> Slice width = " << stated_distance 
                 << " Slice locations " <<prev->GetLocation() << " : " << slice->GetLocation() 
                 << " : " << next->GetLocation()
                 << " DIFFERENCE= " << real_distance - stated_distance
                 << G4endl;
          G4cerr << "!! WARNING: Geant4 will reset slice width so that it extends between " 
                 << "lower and upper slice " << G4endl;

          slice->SetMinZ(slice->GetLocation()-real_down_distance);
          slice->SetMaxZ(slice->GetLocation()+real_up_distance);
          
          if(ite0 == theCTFiles.begin()) {
            prev->SetMaxZ(slice->GetMinZ());
            // Using below would make all slice same thickness
            //prev->SetMinZ(prev->GetLocation()-real_min_distance);
            if(uniformSliceThickness) {
              prev->SetMinZ(prev->GetLocation()-real_down_distance);
            }            
          }
          if(static_cast<unsigned int>(std::distance(theCTFiles.begin(),ite2)+1)==
             nSlices) {
            next->SetMinZ(slice->GetMaxZ());
            // Using below would make all slice same thickness
            //next->SetMaxZ(next->GetLocation()+real_max_distance);
            if(uniformSliceThickness) {
              next->SetMaxZ(next->GetLocation()+real_up_distance); }
          }
        }
      }
    }
  }
  
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
void DicomFileMgr::CheckPETSlices()
{
  size_t nSlices = thePETFiles.size();
  G4cout << " DicomFileMgr::Checking PET slices: " << nSlices << G4endl;

  G4bool uniformSliceThickness = true;
  
  if(nSlices > 1) {
    if(nSlices == 2) {
      mdpet::const_iterator ite = thePETFiles.begin();
      DicomFilePET* one = (*ite).second;
      ite++;
      DicomFilePET* two = (*ite).second;
      
      G4double real_distance = (two->GetLocation()-one->GetLocation())/2.;
      
      if(one->GetMaxZ() != two->GetMinZ()) {
        one->SetMaxZ(one->GetLocation()+real_distance);
        two->SetMinZ(two->GetLocation()-real_distance);
        //one->SetMinZ(one->GetLocation()-real_distance);
        //two->SetMaxZ(two->GetLocation()+real_distance);
        if(uniformSliceThickness) {
          one->SetMinZ(one->GetLocation()-real_distance);
          two->SetMaxZ(two->GetLocation()+real_distance);
        }
      }
    } else {
      mdpet::iterator ite0 = thePETFiles.begin();
      mdpet::iterator ite1 = ite0; ite1++;
      mdpet::iterator ite2 = ite1; ite2++;
      for(; ite2 != thePETFiles.end(); ++ite0, ++ite1, ++ite2) {        
        DicomFilePET* prev = (DicomFilePET*)((*ite0).second);
        DicomFilePET* slice = (DicomFilePET*)((*ite1).second);
        DicomFilePET* next = (DicomFilePET*)((*ite2).second);
        G4double real_up_distance = (next->GetLocation() -
                                      slice->GetLocation())/2.;
        G4double real_down_distance = (slice->GetLocation() -
                                      prev->GetLocation())/2.;
        G4double real_distance = real_up_distance + real_down_distance;
        G4double stated_distance = slice->GetMaxZ()-slice->GetMinZ();

        if(std::fabs(real_distance - stated_distance) > 1.E-9) {
          unsigned int sliceNum = std::distance(thePETFiles.begin(),ite1);
          G4cerr << "\tDicomFileMgr::CheckPETSlices - Slice Distance Error in slice [" << sliceNum 
                 << "]: Distance between this slice and slices up and down = "
                 << real_distance
                 << " <> Slice width = " << stated_distance 
                 << " Slice locations " <<prev->GetLocation() << " : " << slice->GetLocation() 
                 << " : " << next->GetLocation()
                 << " DIFFERENCE= " << real_distance - stated_distance
                 << G4endl;
          G4cerr << "!! WARNING: Geant4 will reset slice width so that it extends between " 
                 << "lower and upper slice " << G4endl;

          slice->SetMinZ(slice->GetLocation()-real_down_distance);
          slice->SetMaxZ(slice->GetLocation()+real_up_distance);
          
          if(ite0 == thePETFiles.begin()) {
            prev->SetMaxZ(slice->GetMinZ());
            // Using below would make all slice same thickness
            //prev->SetMinZ(prev->GetLocation()-real_min_distance);
            if(uniformSliceThickness) {
              prev->SetMinZ(prev->GetLocation()-real_down_distance);
            }            
          }
          if(static_cast<unsigned int>(std::distance(thePETFiles.begin(),ite2)+1)==
             nSlices) {
            next->SetMinZ(slice->GetMaxZ());
            // Using below would make all slice same thickness
            //next->SetMaxZ(next->GetLocation()+real_max_distance);
            if(uniformSliceThickness) {
              next->SetMaxZ(next->GetLocation()+real_up_distance); }
          }
        }
      }
    }
  }
  
}


//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
void DicomFileMgr::BuildCTMaterials()
{
  G4cout << " DicomFileMgr::Building Materials " << theCTFiles.size() << G4endl;//GDEB
  mdct::const_iterator ite = theCTFiles.begin();
  for( ; ite != theCTFiles.end(); ite++ ) {
    (*ite).second->BuildMaterials();
  }
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
void DicomFileMgr::BuildPETActivities()
{
  G4cout << " DicomFileMgr::Building PETData " << thePETFiles.size() << G4endl;//GDEB
  mdpet::const_iterator ite = thePETFiles.begin();
  for( ; ite != thePETFiles.end(); ite++ ) {
    (*ite).second->BuildActivities();
  }
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
void DicomFileMgr::MergeCTFiles()
{
  G4cout << " DicomFileMgr::Merging CT Files " << theCTFiles.size() << G4endl;//GDEB
  mdct::const_iterator ite = theCTFiles.begin();
  theCTFileAll = new DicomFileCT( *((*ite).second) );
  ite++;
  for( ; ite != theCTFiles.end(); ite++ ) {
    (*theCTFileAll) +=  *((*ite).second);
  }
}


//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
void DicomFileMgr::MergePETFiles()
{
  G4cout << " DicomFileMgr::Merging PET Files " << thePETFiles.size() << G4endl;//GDEB
  mdpet::const_iterator ite = thePETFiles.begin();
  thePETFileAll = new DicomFilePET( *((*ite).second) );
  ite++;
  for( ; ite != thePETFiles.end(); ite++ ) {
    (*thePETFileAll) +=  *((*ite).second);
  }
}


//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
void DicomFileMgr::DumpToTextFile()
{
  G4cout << " DicomFileMgr::Dumping To Text File " << G4endl; //GDEB
  if( theCTFiles.size() != 0 ) {
    std::ofstream fout(theFileOutName);

    if( !bMaterialsDensity ) {
      fout << theMaterials.size() << std::endl;
      std::map<G4double,G4String>::const_iterator ite;
      G4int ii = 0;
      for(ite = theMaterials.begin(); ite != theMaterials.end(); ite++, ii++){
        fout << ii << " \"" << (*ite).second << "\"" << std::endl;
      }
    } else {
      fout << theMaterialsDensity.size() << std::endl;
      std::map<G4double,G4String>::const_iterator ite;
      G4int ii = 0;
      for(ite = theMaterialsDensity.begin(); ite != theMaterialsDensity.end(); ite++, ii++){
        fout << ii << " \"" << (*ite).second << "\"" << std::endl;
      }
    }
    
    theCTFileAll->DumpHeaderToTextFile(fout);
    for( mdct::const_iterator itect = theCTFiles.begin(); itect != theCTFiles.end(); itect++ ) {
      (*itect).second->DumpMateIDsToTextFile(fout);
    }
    for( mdct::const_iterator itect = theCTFiles.begin(); itect != theCTFiles.end(); itect++ ) {
      (*itect).second->DumpDensitiesToTextFile(fout);
    }
    for( mdct::const_iterator itect = theCTFiles.begin(); itect != theCTFiles.end(); itect++ ) {
      (*itect).second->BuildStructureIDs();
      (*itect).second->DumpStructureIDsToTextFile(fout);
    }
    
    std::vector<DicomFileStructure*> dfs = GetStructFiles();
    for( size_t i1 = 0; i1 < dfs.size(); i1++ ){
      std::vector<DicomROI*> rois = dfs[i1]->GetROIs();
      for( size_t i2 = 0; i2 < rois.size(); i2++ ){
        fout << rois[i2]->GetNumber()+1 << " \"" << rois[i2]->GetName() << "\"" <<G4endl;
      }
    }
  }

  if( thePETFiles.size() != 0 ) {
    std::ofstream fout(theFileOutName);

    thePETFileAll->DumpHeaderToTextFile(fout);
    for( mdpet::const_iterator itect = thePETFiles.begin(); itect != thePETFiles.end(); itect++ ) {
      (*itect).second->DumpActivitiesToTextFile(fout);
    }
  }

  for( size_t i1 = 0; i1 < thePlanFiles.size(); i1++ ){
    thePlanFiles[i1]->DumpToFile();
  }

}