CellParameterisation Class Reference

#include <CellParameterisation.hh>

Inheritance diagram for CellParameterisation:

Collaboration diagram for CellParameterisation:

Public Member Functions
	CellParameterisation (G4Material *nucleus1, G4Material *cytoplasm1, G4Material *nucleus2, G4Material *cytoplasm2, G4Material *nucleus3, G4Material *cytoplasm3)
virtual	~CellParameterisation ()
void	ComputeTransformation (const G4int copyNo, G4VPhysicalVolume *physVol) const
void	ComputeDimensions (G4Box &, const G4int, const G4VPhysicalVolume *) const
void	ComputeDimensions (G4Tubs &, const G4int, const G4VPhysicalVolume *) const
void	ComputeDimensions (G4Trd &, const G4int, const G4VPhysicalVolume *) const
void	ComputeDimensions (G4Trap &, const G4int, const G4VPhysicalVolume *) const
void	ComputeDimensions (G4Cons &, const G4int, const G4VPhysicalVolume *) const
void	ComputeDimensions (G4Sphere &, const G4int, const G4VPhysicalVolume *) const
void	ComputeDimensions (G4Ellipsoid &, const G4int, const G4VPhysicalVolume *) const
void	ComputeDimensions (G4Orb &, const G4int, const G4VPhysicalVolume *) const
void	ComputeDimensions (G4Torus &, const G4int, const G4VPhysicalVolume *) const
void	ComputeDimensions (G4Para &, const G4int, const G4VPhysicalVolume *) const
void	ComputeDimensions (G4Polycone &, const G4int, const G4VPhysicalVolume *) const
void	ComputeDimensions (G4Polyhedra &, const G4int, const G4VPhysicalVolume *) const
void	ComputeDimensions (G4Hype &, const G4int, const G4VPhysicalVolume *) const
G4int	GetNoBoxes ()
G4Material *	ComputeMaterial (const G4int copyNo, G4VPhysicalVolume *physVol, const G4VTouchable *)
G4int	GetPhantomTotalPixels ()
G4int	GetNucleusTotalPixels ()
G4int	GetCytoplasmTotalPixels ()
G4double	GetPixelSizeX ()
G4double	GetPixelSizeY ()
G4double	GetPixelSizeZ ()
G4double	GetCytoplasmMass ()
G4double	GetNucleusMass ()
G4ThreeVector	GetVoxelThreeVector (G4int i)
G4double	GetMaterialVector (G4int i)
G4double	GetMassVector (G4int i)
G4int	GetTissueType (G4int i)
Public Member Functions inherited from G4VPVParameterisation
	G4VPVParameterisation ()
virtual	~G4VPVParameterisation ()
virtual G4VSolid *	ComputeSolid (const G4int, G4VPhysicalVolume *)
virtual G4bool	IsNested () const
virtual G4VVolumeMaterialScanner *	GetMaterialScanner ()

Static Public Member Functions
static CellParameterisation *	Instance ()

Private Attributes
G4Material *	fNucleusMaterial1
G4Material *	fCytoplasmMaterial1
G4Material *	fNucleusMaterial2
G4Material *	fCytoplasmMaterial2
G4Material *	fNucleusMaterial3
G4Material *	fCytoplasmMaterial3
G4VisAttributes *	fNucleusAttributes1
G4VisAttributes *	fCytoplasmAttributes1
G4VisAttributes *	fNucleusAttributes2
G4VisAttributes *	fCytoplasmAttributes2
G4VisAttributes *	fNucleusAttributes3
G4VisAttributes *	fCytoplasmAttributes3
G4ThreeVector *	fMapCell
G4double *	fMaterial
G4double *	fMass
G4int *	fTissueType
G4int	fPhantomTotalPixels
G4int	fNucleusTotalPixels
G4int	fCytoplasmTotalPixels
G4double	fDimCellBoxX
G4double	fDimCellBoxY
G4double	fDimCellBoxZ
G4double	fNucleusMass
G4double	fCytoplasmMass

Static Private Attributes
static CellParameterisation *	gInstance = 0

Detailed Description

Definition at line 43 of file CellParameterisation.hh.

Constructor & Destructor Documentation

CellParameterisation()

CellParameterisation::CellParameterisation	(	G4Material *	nucleus1,
		G4Material *	cytoplasm1,
		G4Material *	nucleus2,
		G4Material *	cytoplasm2,
		G4Material *	nucleus3,
		G4Material *	cytoplasm3
	)

Definition at line 46 of file CellParameterisation.cc.

{
   fNucleusMaterial1   = nucleus1;
   fCytoplasmMaterial1 = cytoplasm1;
   fNucleusMaterial2   = nucleus2;
   fCytoplasmMaterial2 = cytoplasm2;
   fNucleusMaterial3   = nucleus3;
   fCytoplasmMaterial3 = cytoplasm3;

   G4int ncols,nlines;
   G4int shiftX, shiftY, shiftZ;
   G4double x,y,z,mat,den,tmp,density;  
   G4double denCyto1, denCyto2, denCyto3, denNucl1, denNucl2, denNucl3;
   
   density=0;
   denCyto1=0;
   denCyto2=0;
   denCyto3=0;
   denNucl1=0;
   denNucl2=0;
   denNucl3=0;
   
   ncols=0; nlines=0;
    
   // READ PHANTOM 
   
   fNucleusMass = 0;
   fCytoplasmMass = 0;
    
   FILE *fMap;
   fMap = fopen("phantom.dat","r");
    
   while (1) 
   {  
      if (nlines == 0) 
      {
        ncols = fscanf(fMap,"%i %i %i",&fPhantomTotalPixels,&fNucleusTotalPixels,&fCytoplasmTotalPixels);
    fMapCell  = new G4ThreeVector[fPhantomTotalPixels];
        fMaterial = new G4double[fPhantomTotalPixels];
        fMass     = new G4double[fPhantomTotalPixels];
        fTissueType = new G4int[fPhantomTotalPixels];
      }
      
      if (nlines == 1)
      { 
        ncols = fscanf(fMap,"%lf %lf %lf",&fDimCellBoxX,&fDimCellBoxY,&fDimCellBoxZ);
        
    fDimCellBoxX=fDimCellBoxX*micrometer;
        fDimCellBoxY=fDimCellBoxY*micrometer;
        fDimCellBoxZ=fDimCellBoxZ*micrometer;
      }

      if (nlines == 2) ncols = fscanf(fMap,"%i %i %i",&shiftX,&shiftY,&shiftZ); // VOXEL SHIFT IN Z ASSUMED TO BE NEGATIVE
      
      if (nlines == 3) ncols = fscanf(fMap,"%lf %lf %lf",&denCyto1, &denCyto2, &denCyto3);
      
      if (nlines == 4) ncols = fscanf(fMap,"%lf %lf %lf",&denNucl1, &denNucl2, &denNucl3);
      
      if (nlines >  4) ncols = fscanf(fMap,"%lf %lf %lf %lf %lf %lf",&x,&y,&z,&mat,&den,&tmp);
      
      if (ncols  <  0) break;

      G4ThreeVector v(x+shiftX,y+shiftY,z-1500/(fDimCellBoxZ/micrometer)-shiftZ); // VOXEL SHIFT IN ORDER TO CENTER PHANTOM
      
      if (nlines>4) 
      {

      fMapCell[nlines-5]=v; 
      fMaterial[nlines-5]=mat;
      fMass[nlines-5]=den;
      
      // fTissueType: 1 is Cytoplasm - 2 is Nucleus
      
          if( fMaterial[nlines-5] == 2 ) // fMaterial 2 is nucleus
          {
        if( fMass[nlines-5] == 1 ) 
        {
          fTissueType[nlines-5]=2;
        }
        if( fMass[nlines-5] == 2 ) 
        {
          fTissueType[nlines-5]=2;
        }
        if( fMass[nlines-5] == 3 ) 
        {
          fTissueType[nlines-5]=2;
        }
      } 
    
          else if( fMaterial[nlines-5] == 1 ) // fMaterial 1 is cytoplasm
      {
        if( fMass[nlines-5] == 1 ) 
        {
          fTissueType[nlines-5]=1;
        }
        if( fMass[nlines-5] == 2 ) 
        {
          fTissueType[nlines-5]=2;
        }
        if( fMass[nlines-5] == 3 ) 
        {
          fTissueType[nlines-5]=1;
        }
      } 
              
      //
      
          
      if (std::abs(mat-2)<1.e-30) // NUCLEUS
          {
        if (std::abs(den-1)<1.e-30) density = denNucl1*(g/cm3);
        if (std::abs(den-2)<1.e-30) density = denNucl2*(g/cm3);
        if (std::abs(den-3)<1.e-30) density = denNucl3*(g/cm3);
        fNucleusMass   = fNucleusMass   + density * fDimCellBoxX * fDimCellBoxY * fDimCellBoxZ ;
          }

          if (std::abs(mat-1)<1.e-30) // CYTOPLASM
          { 
        if (std::abs(den-1)<1e-30) density = denCyto1*(g/cm3);
        if (std::abs(den-2)<1e-30) density = denCyto2*(g/cm3);
        if (std::abs(den-3)<1e-30) density = denCyto3*(g/cm3);
        fCytoplasmMass = fCytoplasmMass + density * fDimCellBoxX * fDimCellBoxY * fDimCellBoxZ ;
      }
      
      }   

      nlines++;    
   }
   fclose(fMap);

  // NUCLEUS IN GREEN 
  
  fNucleusAttributes1 = new G4VisAttributes;
  fNucleusAttributes1->SetColour(G4Colour(0,.8,0));
  fNucleusAttributes1->SetForceSolid(false);

  fNucleusAttributes2 = new G4VisAttributes;
  fNucleusAttributes2->SetColour(G4Colour(0,.9,0));
  fNucleusAttributes2->SetForceSolid(false);

  fNucleusAttributes3 = new G4VisAttributes;
  fNucleusAttributes3->SetColour(G4Colour(0,1,0));
  fNucleusAttributes3->SetForceSolid(false);

  // CYTOPLASM IN RED
  
  fCytoplasmAttributes1 = new G4VisAttributes;
  fCytoplasmAttributes1->SetColour(G4Colour(1,0,0));
  fCytoplasmAttributes1->SetForceSolid(false);

  fCytoplasmAttributes2 = new G4VisAttributes; // nucleoli in yellow
  fCytoplasmAttributes2->SetColour(G4Colour(1.,1.,0));
  fCytoplasmAttributes2->SetForceSolid(false);

  fCytoplasmAttributes3 = new G4VisAttributes;
  fCytoplasmAttributes3->SetColour(G4Colour(1,0,0));
  fCytoplasmAttributes3->SetForceSolid(false);

  //

  gInstance = this;
 
 }

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~CellParameterisation()

CellParameterisation::~CellParameterisation ( )

virtual

Definition at line 215 of file CellParameterisation.cc.

{
  delete[] fMapCell;
  delete[] fMaterial;
  delete[] fMass;
  delete[] fTissueType;
}

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Member Function Documentation

ComputeDimensions() [1/13]

void CellParameterisation::ComputeDimensions ( G4Box &  , const G4int  , const G4VPhysicalVolume *    ) const

virtual

Reimplemented from G4VPVParameterisation.

Definition at line 240 of file CellParameterisation.cc.

{}

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ComputeDimensions() [2/13]

void CellParameterisation::ComputeDimensions ( G4Tubs &  , const G4int  , const G4VPhysicalVolume *    ) const

inlinevirtual

Reimplemented from G4VPVParameterisation.

Definition at line 61 of file CellParameterisation.hh.

                                                                    {}

ComputeDimensions() [3/13]

void CellParameterisation::ComputeDimensions ( G4Trd &  , const G4int  , const G4VPhysicalVolume *    ) const

inlinevirtual

Reimplemented from G4VPVParameterisation.

Definition at line 65 of file CellParameterisation.hh.

                                                                    {}

ComputeDimensions() [4/13]

void CellParameterisation::ComputeDimensions ( G4Trap &  , const G4int  , const G4VPhysicalVolume *    ) const

inlinevirtual

Reimplemented from G4VPVParameterisation.

Definition at line 69 of file CellParameterisation.hh.

                                                                    {}

ComputeDimensions() [5/13]

void CellParameterisation::ComputeDimensions ( G4Cons &  , const G4int  , const G4VPhysicalVolume *    ) const

inlinevirtual

Reimplemented from G4VPVParameterisation.

Definition at line 73 of file CellParameterisation.hh.

                                                                    {}

ComputeDimensions() [6/13]

void CellParameterisation::ComputeDimensions ( G4Sphere &  , const G4int  , const G4VPhysicalVolume *    ) const

inlinevirtual

Reimplemented from G4VPVParameterisation.

Definition at line 77 of file CellParameterisation.hh.

                                                                    {}

ComputeDimensions() [7/13]

void CellParameterisation::ComputeDimensions ( G4Ellipsoid &  , const G4int  , const G4VPhysicalVolume *    ) const

inlinevirtual

Reimplemented from G4VPVParameterisation.

Definition at line 81 of file CellParameterisation.hh.

                                                                    {}

ComputeDimensions() [8/13]

void CellParameterisation::ComputeDimensions ( G4Orb &  , const G4int  , const G4VPhysicalVolume *    ) const

inlinevirtual

Reimplemented from G4VPVParameterisation.

Definition at line 85 of file CellParameterisation.hh.

                                                                    {}

ComputeDimensions() [9/13]

void CellParameterisation::ComputeDimensions ( G4Torus &  , const G4int  , const G4VPhysicalVolume *    ) const

inlinevirtual

Reimplemented from G4VPVParameterisation.

Definition at line 89 of file CellParameterisation.hh.

                                                                    {}

ComputeDimensions() [10/13]

void CellParameterisation::ComputeDimensions ( G4Para &  , const G4int  , const G4VPhysicalVolume *    ) const

inlinevirtual

Reimplemented from G4VPVParameterisation.

Definition at line 93 of file CellParameterisation.hh.

                                                                    {}

ComputeDimensions() [11/13]

void CellParameterisation::ComputeDimensions ( G4Polycone &  , const G4int  , const G4VPhysicalVolume *    ) const

inlinevirtual

Reimplemented from G4VPVParameterisation.

Definition at line 97 of file CellParameterisation.hh.

                                                                    {}

ComputeDimensions() [12/13]

void CellParameterisation::ComputeDimensions ( G4Polyhedra &  , const G4int  , const G4VPhysicalVolume *    ) const

inlinevirtual

Reimplemented from G4VPVParameterisation.

Definition at line 101 of file CellParameterisation.hh.

                                                                    {}

ComputeDimensions() [13/13]

void CellParameterisation::ComputeDimensions ( G4Hype &  , const G4int  , const G4VPhysicalVolume *    ) const

inlinevirtual

Reimplemented from G4VPVParameterisation.

Definition at line 105 of file CellParameterisation.hh.

                                                                    {}

ComputeMaterial()

G4Material * CellParameterisation::ComputeMaterial ( const G4int  copyNo, G4VPhysicalVolume *  physVol, const G4VTouchable *    )

virtual

Reimplemented from G4VPVParameterisation.

Definition at line 246 of file CellParameterisation.cc.

{
    if( fMaterial[copyNo] == 2 ) // fMaterial 2 is nucleus
        {
     if( fMass[copyNo] == 1 ) 
        {
          physVol->GetLogicalVolume()->SetVisAttributes( fNucleusAttributes1 );
          return fNucleusMaterial1;
        }
     if( fMass[copyNo] == 2 ) 
        {
          physVol->GetLogicalVolume()->SetVisAttributes( fNucleusAttributes2 );
          return fNucleusMaterial2;
        }
     if( fMass[copyNo] == 3 ) 
        {
          physVol->GetLogicalVolume()->SetVisAttributes( fNucleusAttributes3 );
          return fNucleusMaterial3;
        }
    } 
    
    else if( fMaterial[copyNo] == 1 ) // fMaterial 1 is cytoplasm
    {
     if( fMass[copyNo] == 1 ) 
        {
          physVol->GetLogicalVolume()->SetVisAttributes( fCytoplasmAttributes1 );
          return fCytoplasmMaterial1;
        }
     if( fMass[copyNo] == 2 ) 
        {
          // nucleoli so taken as nucleus !
          physVol->GetLogicalVolume()->SetVisAttributes( fCytoplasmAttributes2 );
          return fCytoplasmMaterial2;
        }
     if( fMass[copyNo] == 3 ) 
        {
          physVol->GetLogicalVolume()->SetVisAttributes( fCytoplasmAttributes3 );
          return fCytoplasmMaterial3;
        }
    } 

    return physVol->GetLogicalVolume()->GetMaterial();
}

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ComputeTransformation()

void CellParameterisation::ComputeTransformation ( const G4int  copyNo, G4VPhysicalVolume *  physVol  ) const

virtual

Implements G4VPVParameterisation.

Definition at line 226 of file CellParameterisation.cc.

{
  G4ThreeVector
    origin(
      fMapCell[copyNo].x()*fDimCellBoxX,
      fMapCell[copyNo].y()*fDimCellBoxY,
      fMapCell[copyNo].z()*fDimCellBoxZ);

    physVol->SetTranslation(origin);   
}

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GetCytoplasmMass()

G4double CellParameterisation::GetCytoplasmMass ( )

inline

Definition at line 123 of file CellParameterisation.hh.

{return fCytoplasmMass;}  

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GetCytoplasmTotalPixels()

G4int CellParameterisation::GetCytoplasmTotalPixels ( )

inline

Definition at line 119 of file CellParameterisation.hh.

{return fCytoplasmTotalPixels;}  

GetMassVector()

G4double CellParameterisation::GetMassVector ( G4int  i )

inline

Definition at line 128 of file CellParameterisation.hh.

{return fMass[i];}

GetMaterialVector()

G4double CellParameterisation::GetMaterialVector ( G4int  i )

inline

Definition at line 127 of file CellParameterisation.hh.

{return fMaterial[i];}

GetNoBoxes()

G4int CellParameterisation::GetNoBoxes ( )

inline

Definition at line 109 of file CellParameterisation.hh.

{return fPhantomTotalPixels;}

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GetNucleusMass()

G4double CellParameterisation::GetNucleusMass ( )

inline

Definition at line 124 of file CellParameterisation.hh.

{return fNucleusMass;}  

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GetNucleusTotalPixels()

G4int CellParameterisation::GetNucleusTotalPixels ( )

inline

Definition at line 118 of file CellParameterisation.hh.

{return fNucleusTotalPixels;}  

GetPhantomTotalPixels()

G4int CellParameterisation::GetPhantomTotalPixels ( )

inline

Definition at line 117 of file CellParameterisation.hh.

{return fPhantomTotalPixels;}  

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GetPixelSizeX()

G4double CellParameterisation::GetPixelSizeX ( )

inline

Definition at line 120 of file CellParameterisation.hh.

{return fDimCellBoxX;}  

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GetPixelSizeY()

G4double CellParameterisation::GetPixelSizeY ( )

inline

Definition at line 121 of file CellParameterisation.hh.

{return fDimCellBoxY;}  

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GetPixelSizeZ()

G4double CellParameterisation::GetPixelSizeZ ( )

inline

Definition at line 122 of file CellParameterisation.hh.

{return fDimCellBoxZ;}  

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GetTissueType()

G4int CellParameterisation::GetTissueType ( G4int  i )

inline

Definition at line 129 of file CellParameterisation.hh.

{return fTissueType[i];}

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GetVoxelThreeVector()

G4ThreeVector CellParameterisation::GetVoxelThreeVector ( G4int  i )

inline

Definition at line 126 of file CellParameterisation.hh.

{return fMapCell[i];}

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Instance()

static CellParameterisation* CellParameterisation::Instance ( void  )

inlinestatic

Definition at line 133 of file CellParameterisation.hh.

   {
     return gInstance; 
   }

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Member Data Documentation

fCytoplasmAttributes1

G4VisAttributes* CellParameterisation::fCytoplasmAttributes1

private

Definition at line 149 of file CellParameterisation.hh.

fCytoplasmAttributes2

G4VisAttributes* CellParameterisation::fCytoplasmAttributes2

private

Definition at line 151 of file CellParameterisation.hh.

fCytoplasmAttributes3

G4VisAttributes* CellParameterisation::fCytoplasmAttributes3

private

Definition at line 153 of file CellParameterisation.hh.

fCytoplasmMass

G4double CellParameterisation::fCytoplasmMass

private

Definition at line 168 of file CellParameterisation.hh.

fCytoplasmMaterial1

G4Material* CellParameterisation::fCytoplasmMaterial1

private

Definition at line 142 of file CellParameterisation.hh.

fCytoplasmMaterial2

G4Material* CellParameterisation::fCytoplasmMaterial2

private

Definition at line 144 of file CellParameterisation.hh.

fCytoplasmMaterial3

G4Material* CellParameterisation::fCytoplasmMaterial3

private

Definition at line 146 of file CellParameterisation.hh.

fCytoplasmTotalPixels

G4int CellParameterisation::fCytoplasmTotalPixels

private

Definition at line 162 of file CellParameterisation.hh.

fDimCellBoxX

G4double CellParameterisation::fDimCellBoxX

private

Definition at line 164 of file CellParameterisation.hh.

fDimCellBoxY

G4double CellParameterisation::fDimCellBoxY

private

Definition at line 165 of file CellParameterisation.hh.

fDimCellBoxZ

G4double CellParameterisation::fDimCellBoxZ

private

Definition at line 166 of file CellParameterisation.hh.

fMapCell

G4ThreeVector* CellParameterisation::fMapCell

private

Definition at line 155 of file CellParameterisation.hh.

fMass

G4double* CellParameterisation::fMass

private

Definition at line 157 of file CellParameterisation.hh.

fMaterial

G4double* CellParameterisation::fMaterial

private

Definition at line 156 of file CellParameterisation.hh.

fNucleusAttributes1

G4VisAttributes* CellParameterisation::fNucleusAttributes1

private

Definition at line 148 of file CellParameterisation.hh.

fNucleusAttributes2

G4VisAttributes* CellParameterisation::fNucleusAttributes2

private

Definition at line 150 of file CellParameterisation.hh.

fNucleusAttributes3

G4VisAttributes* CellParameterisation::fNucleusAttributes3

private

Definition at line 152 of file CellParameterisation.hh.

fNucleusMass

G4double CellParameterisation::fNucleusMass

private

Definition at line 167 of file CellParameterisation.hh.

fNucleusMaterial1

G4Material* CellParameterisation::fNucleusMaterial1

private

Definition at line 141 of file CellParameterisation.hh.

fNucleusMaterial2

G4Material* CellParameterisation::fNucleusMaterial2

private

Definition at line 143 of file CellParameterisation.hh.

fNucleusMaterial3

G4Material* CellParameterisation::fNucleusMaterial3

private

Definition at line 145 of file CellParameterisation.hh.

fNucleusTotalPixels

G4int CellParameterisation::fNucleusTotalPixels

private

Definition at line 161 of file CellParameterisation.hh.

fPhantomTotalPixels

G4int CellParameterisation::fPhantomTotalPixels

private

Definition at line 160 of file CellParameterisation.hh.

fTissueType

G4int* CellParameterisation::fTissueType

private

Definition at line 158 of file CellParameterisation.hh.

gInstance

CellParameterisation * CellParameterisation::gInstance = 0

staticprivate

Definition at line 170 of file CellParameterisation.hh.

---

The documentation for this class was generated from the following files:

• CellParameterisation.hh
• CellParameterisation.cc