DicomPhantomZSliceHeader.cc

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// $Id: DicomPhantomZSliceHeader.cc 101109 2016-11-07 08:14:53Z gcosmo $
//
//

#include "globals.hh"
#include "G4LogicalVolume.hh"
#include "G4MaterialTable.hh"
#include "G4Material.hh"
#include "G4GeometryTolerance.hh"
#include "G4NistManager.hh"

#include "DicomPhantomZSliceHeader.hh"

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
DicomPhantomZSliceHeader::DicomPhantomZSliceHeader(const G4String& fname)
:   fNoVoxelX(0),fNoVoxelY(0),fNoVoxelZ(0),
    fMinX(0),fMinY(0),fMinZ(0),
    fMaxX(0),fMaxY(0),fMaxZ(0),
    fFilename(fname),fSliceLocation(0)
{

}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
DicomPhantomZSliceHeader::~DicomPhantomZSliceHeader()
{

}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
DicomPhantomZSliceHeader::DicomPhantomZSliceHeader( 
                              const DicomPhantomZSliceHeader& rhs )
{
    fNoVoxelX = rhs.GetNoVoxelX();
    fNoVoxelY = rhs.GetNoVoxelY();
    fNoVoxelZ = rhs.GetNoVoxelZ();
    fMinX = rhs.GetMinX();
    fMaxX = rhs.GetMaxX();
    fMinY = rhs.GetMinY();
    fMaxY = rhs.GetMaxY();
    fMinZ = rhs.GetMinZ();
    fMaxZ = rhs.GetMaxZ();
    fMaterialNames = rhs.GetMaterialNames();
    fFilename = rhs.fFilename;
    fValues = rhs.fValues;
    fMateIDs = rhs.fMateIDs;
    fSliceLocation = rhs.fSliceLocation;
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
DicomPhantomZSliceHeader::DicomPhantomZSliceHeader( std::ifstream& fin )
{
    //----- Read material indices and names
    G4int nmate;
    G4String mateindex;
    G4String matename;
    fin >> nmate;
#ifdef G4VERBOSE
    G4cout << " DicomPhantomZSliceHeader reading number of materials " 
           << nmate << G4endl;
#endif

    for( G4int im = 0; im < nmate; im++ ){
        fin >> mateindex >> matename;
#ifdef G4VERBOSE
        //G4cout << " DicomPhantomZSliceHeader reading material " << im << " : "
        //        << mateindex << "  " << matename << G4endl;
#endif

        if( ! CheckMaterialExists( matename ) ) {
            G4Exception("DicomPhantomZSliceHeader::DicomPhantomZSliceHeader",
            "A material is found in file that is not built in the C++ code",
            FatalErrorInArgument, matename.c_str());
        }

        fMaterialNames.push_back(matename);
    }

    //----- Read number of voxels
    fin >> fNoVoxelX >> fNoVoxelY >> fNoVoxelZ;
#ifdef G4VERBOSE
    G4cout << " Number of voxels " << fNoVoxelX << " " << fNoVoxelY 
           << " " << fNoVoxelZ << G4endl;
#endif

    //----- Read minimal and maximal extensions (= walls of phantom)
    fin >> fMinX >> fMaxX;
    fin >> fMinY >> fMaxY;
    fin >> fMinZ >> fMaxZ;
#ifdef G4VERBOSE
    G4cout << " Extension in X " << fMinX << " " << fMaxX << G4endl
    << " Extension in Y " << fMinY << " " << fMaxY << G4endl
    << " Extension in Z " << fMinZ << " " << fMaxZ << G4endl;
#endif

    fSliceLocation = 0.5*(fMinZ + fMaxZ);
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
G4bool DicomPhantomZSliceHeader::CheckMaterialExists( const G4String& mateName )
{
    const G4MaterialTable* matTab = G4Material::GetMaterialTable();
    std::vector<G4Material*>::const_iterator matite;
    for( matite = matTab->begin(); matite != matTab->end(); ++matite ) {
        if( (*matite)->GetName() == mateName ) { return true; }
    }

    G4Material* g4mate = G4NistManager::Instance()->FindOrBuildMaterial(mateName);
    if( g4mate ) {
      return false;
    } else {
      return true;
    }

}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
void DicomPhantomZSliceHeader::operator+=( const DicomPhantomZSliceHeader& rhs )
{
    *this = *this + rhs;
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
DicomPhantomZSliceHeader DicomPhantomZSliceHeader::operator+( 
                       const DicomPhantomZSliceHeader& rhs )
{
    //----- Check that both slices has the same dimensions
    if( fNoVoxelX != rhs.GetNoVoxelX()
       || fNoVoxelY != rhs.GetNoVoxelY() ) {
        G4cerr << "DicomPhantomZSliceHeader error adding two slice headers:\
        !!! Different number of voxels: "
        << "  X= " << fNoVoxelX << " =? " << rhs.GetNoVoxelX()
        << "  Y=  " << fNoVoxelY << " =? " << rhs.GetNoVoxelY()
        << "  Z=  " << fNoVoxelZ << " =? " << rhs.GetNoVoxelZ()
        << G4endl;
        G4Exception("DicomPhantomZSliceHeader::DicomPhantomZSliceHeader",
        "",FatalErrorInArgument,"");
    }
    //----- Check that both slices has the same extensions
    if( fMinX != rhs.GetMinX() || fMaxX != rhs.GetMaxX()
       || fMinY != rhs.GetMinY() || fMaxY != rhs.GetMaxY() ) {
        G4cerr << "DicomPhantomZSliceHeader error adding two slice headers:\
        !!! Different extensions: "
        << "  Xmin= " << fMinX << " =? " << rhs.GetMinX()
        << "  Xmax= " << fMaxX << " =? " << rhs.GetMaxX()
        << "  Ymin= " << fMinY << " =? " << rhs.GetMinY()
        << "  Ymax= " << fMaxY << " =? " << rhs.GetMaxY()
        << G4endl;
        G4Exception("DicomPhantomZSliceHeader::operator+","",
                    FatalErrorInArgument,"");
    }

    //----- Check that both slices have the same materials
    std::vector<G4String> fMaterialNames2 = rhs.GetMaterialNames();
    if( fMaterialNames.size() != fMaterialNames2.size() ) {
        G4cerr << "DicomPhantomZSliceHeader error adding two slice headers:\
        !!! Different number of materials: " << fMaterialNames.size() << " =? "
        << fMaterialNames2.size() << G4endl;
        G4Exception("DicomPhantomZSliceHeader::operator+","",
                    FatalErrorInArgument,"");
    }
    for( unsigned int ii = 0; ii < fMaterialNames.size(); ii++ ) {
        if( fMaterialNames[ii] != fMaterialNames2[ii] ) {
            G4cerr << "DicomPhantomZSliceHeader error adding two slice headers:\
            !!! Different material number " << ii << " : " 
                   << fMaterialNames[ii] << " =? "
            << fMaterialNames2[ii] << G4endl;
            G4Exception("DicomPhantomZSliceHeader::operator+","",
                        FatalErrorInArgument,"");
        }
    }

    //----- Check that the slices are contiguous in Z
    if( std::fabs( fMinZ - rhs.GetMaxZ() ) >
    G4GeometryTolerance::GetInstance()->GetRadialTolerance() &&
       std::fabs( fMaxZ - rhs.GetMinZ() ) >
       G4GeometryTolerance::GetInstance()->GetRadialTolerance() ){
        G4cerr << "DicomPhantomZSliceHeader error adding two slice headers: !!!\
        Slices are not contiguous in Z "
        << "  Zmin= " << fMinZ << " & " << rhs.GetMinZ()
        << "  Zmax= " << fMaxZ << " & " << rhs.GetMaxZ()
        << G4endl;
        G4Exception("DicomPhantomZSliceHeader::operator+","",
                    FatalErrorInArgument,"");
    }

    //----- Build slice header copying first one
    DicomPhantomZSliceHeader temp( *this );

    //----- Add data from second slice header
    temp.SetMinZ( std::min( fMinZ, rhs.GetMinZ() ) );
    temp.SetMaxZ( std::max( fMaxZ, rhs.GetMaxZ() ) );
    temp.SetNoVoxelZ( fNoVoxelZ + rhs.GetNoVoxelZ() );

    return temp;
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
void DicomPhantomZSliceHeader::DumpToFile()
{
  
  G4cout << "DicomPhantomZSliceHeader::Dumping Z Slice data to " 
         << fFilename << "..." << G4endl;
  //sleep(5);
  
  //  May seen counter-intuitive (dumping to file you are reading from), but
  //  the reason for this is modification slice spacing
  if(fMateIDs.size() == 0 || fValues.size() == 0) { ReadDataFromFile(); }
  
  
  std::ofstream out;
  out.open(fFilename.c_str());
  
  if(!out) {
    G4String descript = "DicomPhantomZSliceHeader::DumpToFile: could not open "
      +fFilename;
    G4Exception(descript.c_str(),"", FatalException, "");
  }
  
  out << fMaterialNames.size() << std::endl;
  for(unsigned int i = 0; i < fMaterialNames.size(); ++i) {
    out << i << " " << fMaterialNames.at(i) << std::endl;
  }
  
  out << fNoVoxelX << " " << fNoVoxelY << " " << fNoVoxelZ << std::endl;
  out << fMinX << " " << fMaxX << std::endl;
  out << fMinY << " " << fMaxY << std::endl;
  out << fMinZ << " " << fMaxZ << std::endl;
  
  for(unsigned int i = 0; i < fMateIDs.size(); ++i) { Print(out,fMateIDs.at(i)," "); }
  for(unsigned int i = 0; i < fValues.size(); ++i) { Print(out,fValues.at(i)," ",6); }
  
  out.close();
  
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
void DicomPhantomZSliceHeader::ReadDataFromFile()
{
  std::ifstream in;
  in.open(fFilename.c_str());
  
  if(!in) {
    G4String descript = "DicomPhantomZSliceHeader::DumpToFile: could not open "
      +fFilename;
    G4Exception(descript.c_str(),"", FatalException, "");
  }
  
  G4int nMaterials;
  in >> nMaterials;
  
  fMaterialNames.resize(nMaterials,"");
  for(G4int i = 0; i < nMaterials; ++i) {
    G4String str1, str2;
    in >> str1 >> str2;
    if(!IsInteger(str1)) {
      G4String descript = "String : " + str1 + " supposed to be integer";
      G4Exception("DicomPhantomZSliceHeader::ReadDataFromFile - error in \
       formatting: missing material index","", FatalException,descript.c_str());
    }
    G4int index = G4s2n<G4int>(str1);
    if(index > nMaterials || index < 0) {
      G4String descript = "Index : " + str1;
      G4Exception("DicomPhantomZSliceHeader::ReadDataFromFile - error:\
            bad material index","", FatalException,descript.c_str());
    }
    fMaterialNames[index] = str2;
  }
  
  in >> fNoVoxelX >> fNoVoxelY >> fNoVoxelZ;
  
  G4double tmpMinX, tmpMinY, tmpMinZ;
  G4double tmpMaxX, tmpMaxY, tmpMaxZ;
  
  in >> tmpMinX >> tmpMaxX;
  in >> tmpMinY >> tmpMaxY;
  in >> tmpMinZ >> tmpMaxZ;
  
  fMinX = (CheckConsistency(tmpMinX,fMinX,"Min X value")) ?
    fMinX : ((fMinX == 0) ? tmpMinX : fMinX);
  fMaxX = (CheckConsistency(tmpMaxX,fMaxX,"Max X value")) ?
    fMaxX : ((fMaxX == 0) ? tmpMaxX : fMaxX);
  
  fMinY = (CheckConsistency(tmpMinY,fMinY,"Min Y value")) ?
    fMinY : ((fMinY == 0) ? tmpMinY : fMinY);
  fMaxY = (CheckConsistency(tmpMaxY,fMaxY,"Max Y value")) ?
    fMaxY : ((fMaxY == 0) ? tmpMaxY : fMaxY);
  
  fMinZ = (CheckConsistency(tmpMinZ,fMinZ,"Min Z value")) ?
    fMinZ : ((fMinZ == 0) ? tmpMinZ : fMinZ);
  fMaxZ = (CheckConsistency(tmpMaxZ,fMaxZ,"Max Z value")) ?
    fMaxZ : ((fMaxZ == 0) ? tmpMaxZ : fMaxZ);
  
  fMateIDs.clear();
  fValues.clear();
  fMateIDs.resize(fNoVoxelY*fNoVoxelZ,std::vector<G4int>(fNoVoxelX,0));
  fValues.resize(fNoVoxelY*fNoVoxelZ,std::vector<G4double>(fNoVoxelX,0.));
  for(G4int k = 0; k < fNoVoxelZ; ++k) {
    for(G4int j = 0; j < fNoVoxelY; ++j) {
      for(G4int i = 0; i < fNoVoxelX; ++i) {
        G4int tmpMateID;
        in >> tmpMateID;
        G4int row = j*(k+1);
        fMateIDs[row][i] = tmpMateID;
      }
    }
  }
  
  for(G4int k = 0; k < fNoVoxelZ; ++k) {
    for(G4int j = 0; j < fNoVoxelY; ++j) {
      for(G4int i = 0; i < fNoVoxelX; ++i) {
        G4double tmpValue;
        in >> tmpValue;
        G4int row = j*(k+1);
        fValues[row][i] = tmpValue;
      }
    }
  }
  
  in.close();
}
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......