Gabriele Cosmo
273 lines
8.6 KiB
C++
273 lines
8.6 KiB
C++
//
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// ********************************************************************
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// * License and Disclaimer *
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// * *
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// * The Geant4 software is copyright of the Copyright Holders of *
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// * the Geant4 Collaboration. It is provided under the terms and *
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// * conditions of the Geant4 Software License, included in the file *
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// * LICENSE and available at http://cern.ch/geant4/license . These *
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// * include a list of copyright holders. *
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// * *
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// * Neither the authors of this software system, nor their employing *
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// * institutes,nor the agencies providing financial support for this *
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// * work make any representation or warranty, express or implied, *
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// * regarding this software system or assume any liability for its *
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// * use. Please see the license in the file LICENSE and URL above *
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// * for the full disclaimer and the limitation of liability. *
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// * *
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// * This code implementation is the result of the scientific and *
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// * technical work of the GEANT4 collaboration. *
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// * By using, copying, modifying or distributing the software (or *
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// * any work based on the software) you agree to acknowledge its *
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// * use in resulting scientific publications, and indicate your *
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// * acceptance of all terms of the Geant4 Software license. *
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// ********************************************************************
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//
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// This example is provided by the Geant4-DNA collaboration
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// Any report or published results obtained using the Geant4-DNA software
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// shall cite the following Geant4-DNA collaboration publication:
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// Med. Phys. 37 (2010) 4692-4708
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// The Geant4-DNA web site is available at http://geant4-dna.org
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//
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// If you use this example, please cite the following publication:
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// Rad. Prot. Dos. 133 (2009) 2-11
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#include "CellParameterisation.hh"
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#include "G4LogicalVolume.hh"
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#include "G4SystemOfUnits.hh"
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// SINGLETON
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CellParameterisation * CellParameterisation::gInstance = 0;
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CellParameterisation::CellParameterisation
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(G4Material * nucleus1, G4Material * cytoplasm1,
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G4Material * nucleus2, G4Material * cytoplasm2,
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G4Material * nucleus3, G4Material * cytoplasm3
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)
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{
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fNucleusMaterial1 = nucleus1;
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fCytoplasmMaterial1 = cytoplasm1;
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fNucleusMaterial2 = nucleus2;
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fCytoplasmMaterial2 = cytoplasm2;
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fNucleusMaterial3 = nucleus3;
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fCytoplasmMaterial3 = cytoplasm3;
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G4int ncols,nlines;
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G4int shiftX, shiftY, shiftZ;
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G4double x,y,z,mat,den,tmp,density;
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G4double denCyto1, denCyto2, denCyto3, denNucl1, denNucl2, denNucl3;
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ncols = nlines = shiftX = shiftY = shiftZ = 0;
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x = y = z = mat = den = tmp = density =
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denCyto1 = denCyto2 = denCyto3 = denNucl1 = denNucl2 = denNucl3 = 0.0;
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// READ PHANTOM
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fNucleusMass = 0;
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fCytoplasmMass = 0;
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fDimCellBoxX = fDimCellBoxY = fDimCellBoxZ = micrometer;
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FILE *fMap;
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fMap = fopen("phantom.dat","r");
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while (1)
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{
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if (nlines == 0)
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{
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ncols = fscanf(fMap,"%i %i %i",&fPhantomTotalPixels,&fNucleusTotalPixels,&fCytoplasmTotalPixels);
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fMapCell = new G4ThreeVector[fPhantomTotalPixels];
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fMaterial = new G4double[fPhantomTotalPixels];
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fMass = new G4double[fPhantomTotalPixels];
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fTissueType = new G4int[fPhantomTotalPixels];
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}
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if (nlines == 1)
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{
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ncols = fscanf(fMap,"%lf %lf %lf",&fDimCellBoxX,&fDimCellBoxY,&fDimCellBoxZ);
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fDimCellBoxX=fDimCellBoxX*micrometer;
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fDimCellBoxY=fDimCellBoxY*micrometer;
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fDimCellBoxZ=fDimCellBoxZ*micrometer;
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}
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// VOXEL SHIFT IN Z ASSUMED TO BE NEGATIVE
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if (nlines == 2) ncols = fscanf(fMap,"%i %i %i",&shiftX,&shiftY,&shiftZ);
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if (nlines == 3) ncols = fscanf(fMap,"%lf %lf %lf",&denCyto1, &denCyto2, &denCyto3);
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if (nlines == 4) ncols = fscanf(fMap,"%lf %lf %lf",&denNucl1, &denNucl2, &denNucl3);
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if (nlines > 4) ncols = fscanf(fMap,"%lf %lf %lf %lf %lf %lf",&x,&y,&z,&mat,&den,&tmp);
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if (ncols < 0) break;
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// VOXEL SHIFT IN ORDER TO CENTER PHANTOM
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G4ThreeVector v(x+shiftX,y+shiftY,z-1500/(fDimCellBoxZ/micrometer)-shiftZ);
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if (nlines>4)
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{
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fMapCell[nlines-5]=v;
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fMaterial[nlines-5]=mat;
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fMass[nlines-5]=den;
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// fTissueType: 1 is Cytoplasm - 2 is Nucleus
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if( fMaterial[nlines-5] == 2 ) // fMaterial 2 is nucleus
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{
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if( fMass[nlines-5] == 1 )
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{
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fTissueType[nlines-5]=2;
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}
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if( fMass[nlines-5] == 2 )
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{
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fTissueType[nlines-5]=2;
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}
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if( fMass[nlines-5] == 3 )
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{
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fTissueType[nlines-5]=2;
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}
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}
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else if( fMaterial[nlines-5] == 1 ) // fMaterial 1 is cytoplasm
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{
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if( fMass[nlines-5] == 1 )
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{
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fTissueType[nlines-5]=1;
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}
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if( fMass[nlines-5] == 2 )
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{
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fTissueType[nlines-5]=2;
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}
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if( fMass[nlines-5] == 3 )
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{
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fTissueType[nlines-5]=1;
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}
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}
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//
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if (std::abs(mat-2)<1.e-30) // NUCLEUS
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{
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if (std::abs(den-1)<1.e-30) density = denNucl1*(g/cm3);
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if (std::abs(den-2)<1.e-30) density = denNucl2*(g/cm3);
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if (std::abs(den-3)<1.e-30) density = denNucl3*(g/cm3);
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fNucleusMass = fNucleusMass + density * fDimCellBoxX * fDimCellBoxY * fDimCellBoxZ ;
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}
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if (std::abs(mat-1)<1.e-30) // CYTOPLASM
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{
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if (std::abs(den-1)<1e-30) density = denCyto1*(g/cm3);
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if (std::abs(den-2)<1e-30) density = denCyto2*(g/cm3);
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if (std::abs(den-3)<1e-30) density = denCyto3*(g/cm3);
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fCytoplasmMass = fCytoplasmMass + density * fDimCellBoxX * fDimCellBoxY * fDimCellBoxZ ;
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}
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}
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nlines++;
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}
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fclose(fMap);
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// NUCLEUS IN GREEN
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fNucleusAttributes1 = new G4VisAttributes;
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fNucleusAttributes1->SetColour(G4Colour(0,.8,0));
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fNucleusAttributes1->SetForceSolid(false);
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fNucleusAttributes2 = new G4VisAttributes;
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fNucleusAttributes2->SetColour(G4Colour(0,.9,0));
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fNucleusAttributes2->SetForceSolid(false);
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fNucleusAttributes3 = new G4VisAttributes;
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fNucleusAttributes3->SetColour(G4Colour(0,1,0));
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fNucleusAttributes3->SetForceSolid(false);
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// CYTOPLASM IN RED
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fCytoplasmAttributes1 = new G4VisAttributes;
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fCytoplasmAttributes1->SetColour(G4Colour(1,0,0));
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fCytoplasmAttributes1->SetForceSolid(false);
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fCytoplasmAttributes2 = new G4VisAttributes; // nucleoli in yellow
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fCytoplasmAttributes2->SetColour(G4Colour(1.,1.,0));
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fCytoplasmAttributes2->SetForceSolid(false);
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fCytoplasmAttributes3 = new G4VisAttributes;
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fCytoplasmAttributes3->SetColour(G4Colour(1,0,0));
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fCytoplasmAttributes3->SetForceSolid(false);
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//
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gInstance = this;
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}
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CellParameterisation::~CellParameterisation()
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{
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delete[] fMapCell;
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delete[] fMaterial;
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delete[] fMass;
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delete[] fTissueType;
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}
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void CellParameterisation::ComputeTransformation
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(const G4int copyNo, G4VPhysicalVolume* physVol) const
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{
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G4ThreeVector origin
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(
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fMapCell[copyNo].x()*fDimCellBoxX,
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fMapCell[copyNo].y()*fDimCellBoxY,
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fMapCell[copyNo].z()*fDimCellBoxZ
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);
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physVol->SetTranslation(origin);
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}
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void CellParameterisation::ComputeDimensions
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(G4Box&, const G4int, const G4VPhysicalVolume*) const
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{}
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G4Material*
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CellParameterisation::ComputeMaterial(const G4int copyNo,
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G4VPhysicalVolume* physVol,
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const G4VTouchable*)
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{
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if( fMaterial[copyNo] == 2 ) // fMaterial 2 is nucleus
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{
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if( fMass[copyNo] == 1 )
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{
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physVol->GetLogicalVolume()->SetVisAttributes( fNucleusAttributes1 );
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return fNucleusMaterial1;
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}
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if( fMass[copyNo] == 2 )
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{
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physVol->GetLogicalVolume()->SetVisAttributes( fNucleusAttributes2 );
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return fNucleusMaterial2;
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}
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if( fMass[copyNo] == 3 )
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{
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physVol->GetLogicalVolume()->SetVisAttributes( fNucleusAttributes3 );
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return fNucleusMaterial3;
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}
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}
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else if( fMaterial[copyNo] == 1 ) // fMaterial 1 is cytoplasm
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{
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if( fMass[copyNo] == 1 )
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{
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physVol->GetLogicalVolume()->SetVisAttributes( fCytoplasmAttributes1 );
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return fCytoplasmMaterial1;
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}
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if( fMass[copyNo] == 2 )
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{
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// nucleoli so taken as nucleus !
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physVol->GetLogicalVolume()->SetVisAttributes( fCytoplasmAttributes2 );
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return fCytoplasmMaterial2;
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}
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if( fMass[copyNo] == 3 )
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{
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physVol->GetLogicalVolume()->SetVisAttributes( fCytoplasmAttributes3 );
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return fCytoplasmMaterial3;
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}
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}
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return physVol->GetLogicalVolume()->GetMaterial();
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}
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