DicomPartialDetectorConstruction.cc

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// $Id: DicomPartialDetectorConstruction.cc 73076 2013-08-16 07:45:30Z gcosmo $
//
/// \file medical/DICOM/src/DicomPartialDetectorConstruction.cc
/// \brief Implementation of the DicomPartialDetectorConstruction class
//

#include "globals.hh"

#include "DicomPartialDetectorConstruction.hh"

#include "G4Box.hh"
#include "G4LogicalVolume.hh"
#include "G4VPhysicalVolume.hh"
#include "G4PVPlacement.hh"
#include "G4PVParameterised.hh"
#include "G4Material.hh"
#include "G4Element.hh"
#include "G4VisAttributes.hh"
#include "G4Colour.hh"
#include "G4ios.hh"
#include "G4PartialPhantomParameterisation.hh"
#include "G4NistManager.hh"
#include "G4UIcommand.hh"
#include "G4Tubs.hh"

#include "G4tgbVolumeMgr.hh"
#include "G4tgbMaterialMgr.hh"
#include "G4tgrMessenger.hh"
#include "G4tgrMessenger.hh"

#include "G4SystemOfUnits.hh"

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
DicomPartialDetectorConstruction::DicomPartialDetectorConstruction()
 : DicomDetectorConstruction(),
   fPartialPhantomParam(0),
   fNVoxels(0),
   fDimX(0),
   fDimY(0),
   fDimZ(0),
   fOffsetX(0),
   fOffsetY(0),
   fOffsetZ(0),
   fMateIDs(0)
{
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
DicomPartialDetectorConstruction::~DicomPartialDetectorConstruction()
{
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
G4VPhysicalVolume* DicomPartialDetectorConstruction::Construct()
{
  InitialisationOfMaterials();

  //----- Build world
  G4double worldXDimension = 1.*m;
  G4double worldYDimension = 1.*m;
  G4double worldZDimension = 1.*m;

  G4Box* world_box = new G4Box( "WorldSolid",
                          worldXDimension,
                          worldYDimension,
                          worldZDimension );

  fWorld_logic = new G4LogicalVolume( world_box,
                                    fAir,
                                    "WorldLogical",
                                    0, 0, 0 );

  G4VPhysicalVolume* world_phys = new G4PVPlacement( 0,
                                  G4ThreeVector(0,0,0),
                                  "World",
                                  fWorld_logic,
                                  0,
                                  false,
                                  0 );

  ReadPhantomData();

  ConstructPhantomContainer();
  ConstructPhantom();

  return world_phys;
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
void DicomPartialDetectorConstruction::ReadPhantomData()
{
    G4String dataFile = "Data.dat";
    std::ifstream finDF(dataFile.c_str());
    G4String fname;
    if(finDF.good() != 1 ) {
        G4Exception(" DicomPartialDetectorConstruction::ReadPhantomData",
                    "",
                    FatalErrorInArgument,
                    " Problem reading data file: Data.dat");
    }

    G4int compression;
    finDF >> compression; // not used here

    G4int numFiles;
    finDF >> numFiles;  // only 1 file supported for the moment
    if( numFiles != 1 ) {
        G4Exception("DicomPartialDetectorConstruction::ReadPhantomData",
                    "",
                    FatalErrorInArgument,
                    "More than 1 DICOM file is not supported");
    }
    for(G4int i = 0; i < numFiles; i++ ) {
        finDF >> fname;
        //--- Read one data file
        fname += ".g4pdcm";
        ReadPhantomDataFile(fname);
    }

    finDF.close();

}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
void DicomPartialDetectorConstruction::ReadPhantomDataFile(const G4String& fname)
{
  //  G4String filename = "phantom.g4pdcm";
#ifdef G4VERBOSE
  G4cout << " DicomDetectorConstruction::ReadPhantomDataFile opening file " << fname << G4endl;
#endif
  std::ifstream fin(fname.c_str(), std::ios_base::in);
  if( !fin.is_open() ) {
    G4Exception("DicomPartialDetectorConstruction::ReadPhantomDataFile",
                "",
                FatalException,
                G4String("File not found " + fname).c_str());
  }
 G4int nMaterials;
  fin >> nMaterials;
  G4String stemp;
  G4int nmate;
  for( G4int ii = 0; ii < nMaterials; ii++ ){
    fin >> nmate >> stemp;
    G4cout << "DicomPartialDetectorConstruction::ReadPhantomData reading nmate "
    << ii << " = " << nmate << " mate " << stemp << G4endl;
    if( ii != nmate ) G4Exception("DicomPartialDetectorConstruction::ReadPhantomData",
                                  "",
                                  FatalErrorInArgument,
                                  "Material number should be in increasing order: \
                                  wrong material number ");

  }

  fin >> fNVoxelX >> fNVoxelY >> fNVoxelZ;
  G4cout << "DicomPartialDetectorConstruction::ReadPhantomData nVoxel X/Y/Z "
  << fNVoxelX << " " << fNVoxelY << " " << fNVoxelZ << G4endl;
  fin >> fOffsetX >> fDimX;
  fDimX = (fDimX - fOffsetX)/fNVoxelX;
  fin >> fOffsetY >> fDimY;
  fDimY = (fDimY - fOffsetY)/fNVoxelY;
  fin >> fOffsetZ >> fDimZ;
  fDimZ = (fDimZ - fOffsetZ)/fNVoxelZ;
  G4cout << "DicomPartialDetectorConstruction::ReadPhantomData voxelDimX "
  << fDimX << " fOffsetX " << fOffsetX << G4endl;
  G4cout << "DicomPartialDetectorConstruction::ReadPhantomData voxelDimY "
  << fDimY << " fOffsetY " << fOffsetY << G4endl;
  G4cout << "DicomPartialDetectorConstruction::ReadPhantomData voxelDimZ "
  << fDimZ << " fOffsetZ " << fOffsetZ << G4endl;

  //--- Read voxels that are filled
  fNVoxels = 0;
  //  G4bool* isFilled = new G4bool[fNVoxelX*fNVoxelY*fNVoxelZ];
  //  fFilledIDs = new size_t[fNVoxelZ*fNVoxelY+1];
  //?  fFilledIDs.insert(0);
  int ifxmin1, ifxmax1;
  for( G4int iz = 0; iz < fNVoxelZ; iz++ ) {
    std::map< G4int, G4int > ifmin, ifmax;
    for( G4int iy = 0; iy < fNVoxelY; iy++ ) {
      fin >> ifxmin1 >> ifxmax1;
      // check coherence ...

      ifmin[iy] = ifxmin1;
      ifmax[iy] = ifxmax1;
      G4int ifxdiff = ifxmax1-ifxmin1+1;
      if( ifxmax1 == -1 && ifxmin1 == -1 ) ifxdiff = 0;
      //      fFilledIDs.insert(std::multimap<G4int,size_t>::value_type(ifxdiff+fNVoxels, ifxmin1));
      fFilledIDs.insert(std::pair<size_t,size_t>(ifxdiff+fNVoxels-1, ifxmin1));
      G4cout << "DicomPartialDetectorConstruction::ReadPhantomData insert FilledIDs "
      << ifxdiff+fNVoxels-1 << " min " << ifxmin1 << " N= " << fFilledIDs.size() << G4endl;
      //filledIDs[iz*fNVoxelY+iy+1] = ifxmax1-ifxmin1+1;
      for( G4int ix = 0; ix < fNVoxelX; ix++ ) {
        //        G4cout << "REGNAV DicomPartialDetectorConstruction::ReadPhantomData checking
        //  to add voxel iz " << iz << " iy " << iy << " ix " << ix << "  min= "
        //  << ifxmin1 << " max= " << ifxmax1 << G4endl;
        //        G4int copyNo = ix + (iy)*fNVoxelX + (iz)*fNVoxelX*fNVoxelY;
        if( ix >= G4int(ifxmin1) && ix <= G4int(ifxmax1) ) {
          //          isFilled[copyNo] = true;
          fNVoxels++;
        } else {
          //          isFilled[copyNo] = false;
        }
      }
    }
    fFilledMins[iz] = ifmin;
    fFilledMaxs[iz] = ifmax;
  }

  //--- Read material IDs
  G4int mateID1;
  fMateIDs = new size_t[fNVoxelX*fNVoxelY*fNVoxelZ];
  G4int copyNo = 0;
  for( G4int iz = 0; iz < fNVoxelZ; iz++ ) {
    std::map< G4int, G4int > ifmin = fFilledMins[iz];
    std::map< G4int, G4int > ifmax = fFilledMaxs[iz];
    for( G4int iy = 0; iy < fNVoxelY; iy++ ) {
      ifxmin1 = ifmin[iy];
      ifxmax1 = ifmax[iy];
      for( G4int ix = 0; ix < fNVoxelX; ix++ ) {
        if( ix >= G4int(ifxmin1) && ix <= G4int(ifxmax1) ) {
          fin >> mateID1;
          if( mateID1 < 0 || mateID1 >= nMaterials ) {
            G4Exception("DicomPartialDetectorConstruction::ReadPhantomData",
                        "",
                        FatalException,
                        G4String("Wrong index in phantom file: It should be between 0 and "
                                 + G4UIcommand::ConvertToString(nMaterials-1)
                                 + ", while it is "
                                 + G4UIcommand::ConvertToString(mateID1)).c_str());
          }
          fMateIDs[copyNo] = mateID1;
          copyNo++;
        }
      }
    }
  }

  ReadVoxelDensitiesPartial( fin );

  fin.close();
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
void DicomPartialDetectorConstruction::ReadVoxelDensitiesPartial( std::ifstream& fin )
{
    std::map<G4int, std::pair<G4double,G4double> > densiMinMax;
    std::map<G4int, std::pair<G4double,G4double> >::iterator mpite;
    for( size_t ii = 0; ii < fOriginalMaterials.size(); ii++ ){
        densiMinMax[ii] = std::pair<G4double,G4double>(DBL_MAX,-DBL_MAX);
    }

    //----- Define density differences (maximum density difference to create a new material)
    char* part = getenv( "DICOM_CHANGE_MATERIAL_DENSITY" );
    G4double densityDiff = -1.;
    if( part ) densityDiff = G4UIcommand::ConvertToDouble(part);
    std::map<G4int,G4double> densityDiffs;
    if( densityDiff != -1. ) {
        for( size_t ii = 0; ii < fOriginalMaterials.size(); ii++ ){
            densityDiffs[ii] = densityDiff; //currently all materials with same step
        }
    }else {
        if( fMaterials.size() == 0 ) { // do it only for first slice
            for( unsigned int ii = 0; ii < fOriginalMaterials.size(); ii++ ){
                fMaterials.push_back( fOriginalMaterials[ii] );
            }
        }
    }

  //  densityDiffs[0] = 0.0001; //fAir

  //--- Calculate the average material density for each material/density bin
  std::map< std::pair<G4Material*,G4int>, matInfo* > newMateDens;

  G4double dens1;
  size_t ifxmin1, ifxmax1;

  //---- Read the material densities
  G4int copyNo = 0;
  for( G4int iz = 0; iz < fNVoxelZ; iz++ ) {
    std::map< G4int, G4int > ifmin = fFilledMins[iz];
    std::map< G4int, G4int > ifmax = fFilledMaxs[iz];
    for( G4int iy = 0; iy < fNVoxelY; iy++ ) {
      ifxmin1 = ifmin[iy];
      ifxmax1 = ifmax[iy];
      for( G4int ix = 0; ix < fNVoxelX; ix++ ) {
        if( ix >= G4int(ifxmin1) && ix <= G4int(ifxmax1) ) {
          fin >> dens1;
          //        G4cout << ix << " " << iy << " " << iz << " filling fMateIDs "
          //    << copyNo << " = " <<  atoi(stemp.c_str())-1 << " " << stemp << G4endl;

        //--- store the minimum and maximum density for each material (just for printing)
          mpite = densiMinMax.find( fMateIDs[copyNo] );
          if( dens1 < (*mpite).second.first ) (*mpite).second.first = dens1;
          if( dens1 > (*mpite).second.second ) (*mpite).second.second = dens1;

          //--- Get material from original list of material in file
          int mateID = fMateIDs[copyNo];
          G4Material* mate = fOriginalMaterials[mateID];
          //        G4cout << copyNo << " mateID " << mateID << G4endl;
          //--- Check if density is equal to the original material density
          if( std::fabs(dens1 - mate->GetDensity()/g*cm3 ) < 1.e-9 ) continue;

          //--- Build material name with fOriginalMaterials name + density
          //        float densityBin = densityDiffs[mateID] *
          //        (G4int(dens1/densityDiffs[mateID])+0.5);
          G4String newMateName = mate->GetName();

          G4int densityBin = 0;
          //        G4cout << " densityBin " << densityBin << " "
          //        << dens1 << " " <<densityDiffs[mateID] << G4endl;

          if( densityDiff != -1.) {
            densityBin = (G4int(dens1/densityDiffs[mateID]));
            newMateName = mate->GetName()+G4UIcommand::ConvertToString(densityBin);
          }

          //--- Look if it is the first voxel with this material/densityBin
          std::pair<G4Material*,G4int> matdens(mate, densityBin );

          std::map< std::pair<G4Material*,G4int>, matInfo* >::iterator mppite
          = newMateDens.find( matdens );
          if( mppite != newMateDens.end() ){
            matInfo* mi = (*mppite).second;
            mi->sumdens += dens1;
            mi->nvoxels++;
            fMateIDs[copyNo] = fOriginalMaterials.size()-1 + mi->id;
            //          G4cout << copyNo << " mat new again "
            //      << fOriginalMaterials.size()-1 + mi->id << " " << mi->id << G4endl;
          } else {
            matInfo* mi = new matInfo;
            mi->sumdens = dens1;
            mi->nvoxels = 1;
            mi->id = newMateDens.size()+1;
            newMateDens[matdens] = mi;
            fMateIDs[copyNo] = fOriginalMaterials.size()-1 + mi->id;
            //          G4cout << copyNo << " mat new first "
            //          << fOriginalMaterials.size()-1 + mi->id << G4endl;
          }
          copyNo++;
        //        G4cout << ix << " " << iy << " " << iz
        //  << " filling fMateIDs " << copyNo << " = " << atoi(cid)-1 << G4endl;
                                      //        fMateIDs[copyNo] = atoi(cid)-1;
        }
      }
    }
  }

  //----- Build the list of phantom materials that go to Parameterisation
  //--- Add original materials
  std::vector<G4Material*>::const_iterator mimite;
  for( mimite = fOriginalMaterials.begin(); mimite != fOriginalMaterials.end(); mimite++ ){
    fPhantomMaterials.push_back( (*mimite) );
  }
  //
  //---- Build and add new materials
  std::map< std::pair<G4Material*,G4int>, matInfo* >::iterator mppite;
  for( mppite= newMateDens.begin(); mppite != newMateDens.end(); mppite++ ){
    G4double averdens = (*mppite).second->sumdens/(*mppite).second->nvoxels;
    G4double saverdens = G4int(1000.001*averdens)/1000.;
    G4cout << "GmReadPhantomGeometry::ReadVoxelDensities AVER DENS " << averdens << " -> "
    << saverdens << " -> " << G4int(1000*averdens) << " " << G4int(1000*averdens)/1000 << " "
    <<  G4int(1000*averdens)/1000. << G4endl;

    G4cout << "GmReadPhantomGeometry::ReadVoxelDensities AVER DENS " << averdens << " -> "
    << saverdens << " -> " << G4UIcommand::ConvertToString(saverdens) << " Nvoxels "
    <<(*mppite).second->nvoxels << G4endl;
    G4String mateName = ((*mppite).first).first->GetName() + "_" +
    G4UIcommand::ConvertToString(saverdens);
    fPhantomMaterials.push_back( BuildMaterialWithChangingDensity( (*mppite).first.first,
    averdens, mateName ) );
  }

}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
void DicomPartialDetectorConstruction::ConstructPhantomContainer()
{
  //build a clinder that encompass the partial phantom built in the example
  // /dicom/intersectWithUserVolume 0. 0. 0. 0.*deg 0. 0. TUBE 0. 200. 100.
  //---- Extract number of voxels and voxel dimensions

  G4String contname= "PhantomContainer";

  //----- Define the volume that contains all the voxels
  G4Tubs* container_tube = new G4Tubs(contname,0., 200., 100., 0., 360*deg);

  fContainer_logic =
    new G4LogicalVolume( container_tube,
                         fAir,
                         contname,
                         0, 0, 0 );

  G4ThreeVector posCentreVoxels(0.,0.,0.);
  //G4cout << " PhantomContainer posCentreVoxels " << posCentreVoxels << G4endl;
  G4RotationMatrix* rotm = new G4RotationMatrix;

  fContainer_phys =
    new G4PVPlacement(rotm,  // rotation
                      posCentreVoxels,
                      fContainer_logic,     // The logic volume
                      contname,  // Name
                      fWorld_logic,  // Mother
                      false,           // No op. bool.
                      1);              // Copy number

}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
void DicomPartialDetectorConstruction::ConstructPhantom()
{
  G4String OptimAxis = "kXAxis";
  G4bool bSkipEqualMaterials = 0;
  G4int regStructureID = 2;

  G4ThreeVector posCentreVoxels(0.,0.,0.);

  //----- Build phantom
  G4String voxelName = "phantom";
  G4Box* phantom_solid = new G4Box(voxelName, fDimX/2., fDimY/2., fDimZ/2. );
  G4LogicalVolume* phantom_logic =
    new G4LogicalVolume( phantom_solid,
                         fAir,
                         voxelName,
                         0, 0, 0 );
  G4bool pVis = 0;
  if( !pVis ) {
    G4VisAttributes* visAtt = new G4VisAttributes( FALSE );
    phantom_logic->SetVisAttributes( visAtt );
  }

  G4double theSmartless = 0.5;
  //  fContainer_logic->SetSmartless( theSmartless );
  phantom_logic->SetSmartless( theSmartless );

  fPartialPhantomParam = new G4PartialPhantomParameterisation();

  fPartialPhantomParam->SetMaterials( fPhantomMaterials );
  fPartialPhantomParam->SetVoxelDimensions( fDimX/2., fDimY/2., fDimZ/2. );
  fPartialPhantomParam->SetNoVoxel( fNVoxelX, fNVoxelY, fNVoxelZ );
  fPartialPhantomParam->SetMaterialIndices( fMateIDs );

  fPartialPhantomParam->SetFilledIDs(fFilledIDs);

  fPartialPhantomParam->SetFilledMins(fFilledMins);

  fPartialPhantomParam->BuildContainerWalls();

  //  G4cout << " Number of Materials " << fPhantomMaterials.size() << G4endl;
  //  G4cout << " SetMaterialIndices(0) " << fMateIDs[0] << G4endl;

  G4PVParameterised * phantom_phys = 0;
  if( OptimAxis == "kUndefined" ) {
    phantom_phys = new G4PVParameterised(voxelName,phantom_logic,fContainer_logic,
                                         kUndefined, fNVoxels, fPartialPhantomParam);
  } else   if( OptimAxis == "kXAxis" ) {
    //    G4cout << " optim kX " << G4endl;
    phantom_phys = new G4PVParameterised(voxelName,phantom_logic,fContainer_logic,
                                // kXAxis, fNVoxelX*fNVoxelY*fNVoxelZ, fPartialPhantomParam);
                                          kXAxis, fNVoxels, fPartialPhantomParam);
    fPartialPhantomParam->SetSkipEqualMaterials(bSkipEqualMaterials);
  } else {
    G4Exception("GmReadPhantomGeometry::ConstructPhantom",
                "",
                FatalErrorInArgument,
                (G4String("Wrong argument to parameter GmReadPhantomGeometry:Phantom:OptimAxis:\
                Only allowed 'kUndefined' or 'kXAxis', it is: "+OptimAxis).c_str()));
  }

  phantom_phys->SetRegularStructureId(regStructureID);

    //    G4cout << " GmReadPhantomGeometry  phantom_phys " << phantom_phys << " trans "
    //      << phantom_phys->GetTranslation() << G4endl;
  //-  fPartialPhantomParam->BuildContainerSolid(cont_phys);

  //  G4cout << " GmReadPhantomGeometry::constructPhantom ended " << G4endl;

}