Import Geant4 9.1.0 source tree
This commit is contained in:
Gabriele Cosmo
@@ -1,109 +0,0 @@
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//
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// ********************************************************************
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// * License and Disclaimer *
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||||
// * *
|
||||
// * 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. *
|
||||
// ********************************************************************
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||||
//
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// The code was written by :
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// *Louis Archambault louis.archambault@phy.ulaval.ca,
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// *Luc Beaulieu beaulieu@phy.ulaval.ca
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// +Vincent Hubert-Tremblay at tigre.2@sympatico.ca
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//
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//
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// *Centre Hospitalier Universitaire de Quebec (CHUQ),
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// Hotel-Dieu de Quebec, departement de Radio-oncologie
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// 11 cote du palais. Quebec, QC, Canada, G1R 2J6
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// tel (418) 525-4444 #6720
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// fax (418) 691 5268
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//
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// + Université Laval, Québec (QC) Canada
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//*******************************************************
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//
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//
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// DicomConfiguration.hh :
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// - Handling of the header of *.g4 files
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// - Reading <Data.dat> file
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#ifndef DicomConfiguration_h
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#define DicomConfiguration_h 1
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#include "globals.hh"
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#include <vector>
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class DicomConfiguration
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{
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public:
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DicomConfiguration();
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~DicomConfiguration() { }
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// This function reads <Data.dat>, return true or false
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// if successfull or not
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G4bool ReadDataFile();
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G4int GetCompressionValue() {return compressionValue;}
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G4int GetTotalNumberOfFile() {return totalNumberOfFile;}
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std::vector<G4String> GetListOfFile() {return listOfFile;}
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G4int GetTotalRows() {return totalRows;}
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G4int GetTotalColumns() {return totalColumns;}
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G4int GetTotalPixels() {return totalPixels;}
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//G4int GetTotalPixels() {return densityValue.size();}
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G4double GetXPixelSpacing() {return xPixelSpacing;}
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G4double GetYPixelSpacing() {return yPixelSpacing;}
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G4double GetSliceThickness() {return sliceTickness;}
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std::vector<G4double> GetSliceLocation() {return sliceLocation;}
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G4int IsCompressionUsed() {return compressionUsed;}
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G4double GetDensityValue(G4int i);
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void ClearDensityData() {densityValue.clear(); };
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G4int ReadG4File(G4String g4File);
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private:
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static short compressionValue;
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static G4int totalNumberOfFile;
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static std::vector<G4String> listOfFile;
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static short totalRows;
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static short totalColumns;
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static G4int totalPixels;
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static G4double xPixelSpacing;
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static G4double yPixelSpacing;
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static G4double sliceTickness;
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static std::vector<G4double> sliceLocation;
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static short compressionUsed;
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static std::vector<G4double> densityValue;
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};
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#endif
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@@ -0,0 +1,108 @@
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//
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// ********************************************************************
|
||||
// * License and Disclaimer *
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||||
// * *
|
||||
// * 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. *
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||||
// ********************************************************************
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//
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// Author: P. Arce
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// History: 30.11.07 First version
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//*******************************************************
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//
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// DicomDetectorConstruction.hh :
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// - Start the building of the geometry
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// - Initialisation of materials
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// - Creation of the world
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// - Reading of the DICOM data
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//*******************************************************
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#ifndef DicomDetectorConstruction_h
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#define DicomDetectorConstruction_h 1
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#include "globals.hh"
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#include "G4VUserDetectorConstruction.hh"
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#include "DicomPatientZSliceHeader.hh"
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class G4Material;
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class G4Box;
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class G4LogicalVolume;
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class DicomDetectorConstruction : public G4VUserDetectorConstruction
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{
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public:
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DicomDetectorConstruction();
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~DicomDetectorConstruction();
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G4VPhysicalVolume* Construct();
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// trigger the construction of the geometry
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protected:
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void InitialisationOfMaterials();
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// create the original materials
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void ReadPatientData();
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// read the DICOM files describing the patient
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void ReadPatientDataFile(const G4String& fname);
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// read one of the DICOM files describing the patient (usually one per Z slice). Build a DicomPatientZSliceHeader for each file
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void MergeZSliceHeaders();
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// merge the slice headers of all the files
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G4Material* BuildMaterialWithChangingDensity( const G4Material* origMate, float density, G4String newMateName );
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// build a new material if the density of the voxel is different to the other voxels
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G4String ftoa(float flo);
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// convert a float to a string
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void ConstructPatientContainer();
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virtual void ConstructPatient() = 0;
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// construct the patient volumes. This method should be implemented for each of the derived classes
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protected:
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G4Material* air;
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// World ...
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G4Box* world_solid;
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G4LogicalVolume* world_logic;
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G4VPhysicalVolume* world_phys;
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G4Box* container_solid;
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G4LogicalVolume* container_logic;
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G4VPhysicalVolume* container_phys;
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G4int fNoFiles; // number of DICOM files
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std::vector<G4Material*> fOriginalMaterials; // list of original materials
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std::vector<G4Material*> fMaterials; // list of new materials created to distinguish different density voxels that have the same original materials
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size_t* fMateIDs; // index of material of each voxel
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std::map<G4int,G4double> fDensityDiffs; // Density difference to distinguish material for each original material (by index)
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std::vector<DicomPatientZSliceHeader*> fZSliceHeaders; // list of z slice header (one per DICOM files)
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DicomPatientZSliceHeader* fZSliceHeaderMerged; // z slice header resulted from merging all z slice headers
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G4int nVoxelX, nVoxelY, nVoxelZ;
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G4double voxelHalfDimX, voxelHalfDimY, voxelHalfDimZ;
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};
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#endif
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@@ -1,102 +0,0 @@
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//
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// ********************************************************************
|
||||
// * 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. *
|
||||
// ********************************************************************
|
||||
//
|
||||
// The code was written by :
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||||
// *Louis Archambault louis.archambault@phy.ulaval.ca,
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||||
// *Luc Beaulieu beaulieu@phy.ulaval.ca
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// +Vincent Hubert-Tremblay at tigre.2@sympatico.ca
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//
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//
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// *Centre Hospitalier Universitaire de Quebec (CHUQ),
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// Hotel-Dieu de Quebec, departement de Radio-oncologie
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||||
// 11 cote du palais. Quebec, QC, Canada, G1R 2J6
|
||||
// tel (418) 525-4444 #6720
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||||
// fax (418) 691 5268
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||||
//
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// + Université Laval, Québec (QC) Canada
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//*******************************************************//
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//*******************************************************
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//
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// DicomGeometry.hh :
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// - Start the building of the geometry
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// - Creation of the world and other "mother"(middle) volume
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// - Initialisation of patient geometry
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// - Initialisation of HeaD geometry
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// - Functions are in DicomGeometry.cc, PatientConstructor.cc
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//*******************************************************
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#ifndef DicomGeometry_h
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#define DicomGeometry_h 1
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#include "globals.hh"
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#include "G4VUserDetectorConstruction.hh"
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class DicomConfiguration;
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class DicomPatientConstructor;
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class G4Material;
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class G4LogicalVolume;
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class G4PhysicalVolume;
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class G4Box;
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class DicomGeometry : public G4VUserDetectorConstruction
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{
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public:
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DicomGeometry();
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~DicomGeometry();
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G4VPhysicalVolume* Construct();
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private:
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void InitialisationOfMaterials();
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void PatientConstruction();
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DicomPatientConstructor* patientConstructor;
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//Materials ...
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G4Material* trabecularBone;
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G4Material* denseBone;
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G4Material* liver;
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G4Material* muscle;
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G4Material* phantom;
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G4Material* breast;
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G4Material* adiposeTissue;
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G4Material* lungexhale;
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G4Material* lunginhale;
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G4Material* air;
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// World ...
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G4Box* solidWorld;
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G4LogicalVolume* logicWorld;
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G4VPhysicalVolume* physiWorld;
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G4VPhysicalVolume* parameterisedPhysVolume;
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G4VPhysicalVolume* physicalLungINhale;
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};
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#endif
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@@ -57,6 +57,8 @@
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#define DicomHandler_h 1
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#include <cstdio>
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#include <map>
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#include <fstream>
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#include "globals.hh"
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@@ -68,17 +70,17 @@ public:
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~DicomHandler();
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G4int readHeader(FILE *,char *);
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G4int readData(FILE *,char *); // note: always use readHeader
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G4int ReadFile(FILE *,char *);
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G4int ReadData(FILE *,char *); // note: always use readHeader
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// before readData
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// use ImageMagick to display the image
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//G4int displayImage(char[500]);
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void checkFileFormat();
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void CheckFileFormat();
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private:
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template <class Type> void getValue(char *, Type &);
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template <class Type> void GetValue(char *, Type &);
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private:
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@@ -86,12 +88,14 @@ private:
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const int LINEBUFFSIZE;
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const int FILENAMESIZE;
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void storeInformation(char *);
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void getInformation(G4int &, char *);
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G4double pixel2density(G4int pixel);
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void GetInformation(G4int &, char *);
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G4double Pixel2density(G4int pixel);
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void ReadMaterialIndices( std::ifstream& finData);
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size_t GetMaterialIndex( G4double density );
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void StoreData(std::ofstream& foutG4DCM);
|
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|
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short compression;
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G4int max;
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G4int nFiles;
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short rows;
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short columns;
|
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short bitAllocated;
|
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@@ -105,6 +109,9 @@ private:
|
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|
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G4bool littleEndian, implicitEndian;
|
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short pixelRepresentation;
|
||||
|
||||
G4int** tab;
|
||||
std::map<G4double,G4String> fMaterialIndices;
|
||||
};
|
||||
#endif
|
||||
|
||||
|
||||
@@ -0,0 +1,130 @@
|
||||
//
|
||||
// ********************************************************************
|
||||
// * 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. *
|
||||
// ********************************************************************
|
||||
//
|
||||
#ifndef RE02NESTEDPARAMETERISATION_HH
|
||||
#define RE02NESTEDPARAMETERISATION_HH
|
||||
|
||||
#include "G4Types.hh"
|
||||
#include "G4VNestedParameterisation.hh"
|
||||
#include "G4ThreeVector.hh"
|
||||
#include <vector>
|
||||
|
||||
class G4VPhysicalVolume;
|
||||
class G4VTouchable;
|
||||
class G4VSolid;
|
||||
class G4Material;
|
||||
|
||||
// CSG Entities which may be parameterised/replicated
|
||||
//
|
||||
class G4Box;
|
||||
class G4Tubs;
|
||||
class G4Trd;
|
||||
class G4Trap;
|
||||
class G4Cons;
|
||||
class G4Sphere;
|
||||
class G4Orb;
|
||||
class G4Torus;
|
||||
class G4Para;
|
||||
class G4Polycone;
|
||||
class G4Polyhedra;
|
||||
class G4Hype;
|
||||
|
||||
class DicomNestedPhantomParameterisation: public G4VNestedParameterisation
|
||||
{
|
||||
public: // with description
|
||||
|
||||
DicomNestedPhantomParameterisation(const G4ThreeVector& voxelSize,
|
||||
std::vector<G4Material*>& mat);
|
||||
virtual ~DicomNestedPhantomParameterisation();
|
||||
|
||||
// Methods required in derived classes
|
||||
// -----------------------------------
|
||||
virtual G4Material* ComputeMaterial(G4VPhysicalVolume *currentVol,
|
||||
const G4int repNo,
|
||||
const G4VTouchable *parentTouch=0
|
||||
);
|
||||
// Required method, as it is the reason for this class.
|
||||
// Must cope with parentTouch=0 for navigator's SetupHierarchy
|
||||
|
||||
virtual G4int GetNumberOfMaterials() const;
|
||||
virtual G4Material* GetMaterial(G4int idx) const;
|
||||
// Needed to define materials for instances of Nested Parameterisation
|
||||
// Current convention: each call should return the materials
|
||||
// of all instances with the same mother/ancestor volume.
|
||||
size_t GetMaterialIndex( size_t nx, size_t ny, size_t nz) const;
|
||||
size_t GetMaterialIndex( size_t copyNo) const;
|
||||
void SetMaterialIndices( size_t* matInd ){
|
||||
fMaterialIndices = matInd; }
|
||||
void SetNoVoxel( size_t nx, size_t ny, size_t nz );
|
||||
|
||||
virtual void ComputeTransformation(const G4int no,
|
||||
G4VPhysicalVolume *currentPV) const;
|
||||
|
||||
// Methods optional in derived classes
|
||||
// -----------------------------------
|
||||
|
||||
// Additional standard Parameterisation methods,
|
||||
// which can be optionally defined, in case solid is used.
|
||||
|
||||
virtual void ComputeDimensions(G4Box &,
|
||||
const G4int,
|
||||
const G4VPhysicalVolume *) const;
|
||||
|
||||
private: // Dummy declarations to get rid of warnings ...
|
||||
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 (G4Orb&,const G4int,const G4VPhysicalVolume*)
|
||||
const {}
|
||||
void ComputeDimensions (G4Torus&,const G4int,const G4VPhysicalVolume*)
|
||||
const {}
|
||||
void ComputeDimensions (G4Para&,const G4int,const G4VPhysicalVolume*)
|
||||
const {}
|
||||
void ComputeDimensions (G4Hype&,const G4int,const G4VPhysicalVolume*)
|
||||
const {}
|
||||
void ComputeDimensions (G4Tubs&,const G4int,const G4VPhysicalVolume*)
|
||||
const {}
|
||||
void ComputeDimensions (G4Polycone&,const G4int,const G4VPhysicalVolume*)
|
||||
const {}
|
||||
void ComputeDimensions (G4Polyhedra&,const G4int,const G4VPhysicalVolume*)
|
||||
const {}
|
||||
|
||||
private:
|
||||
G4double fdX,fdY,fdZ;
|
||||
G4int fnX,fnY,fnZ;
|
||||
|
||||
//
|
||||
std::vector<G4Material*> fMaterials;
|
||||
|
||||
size_t* fMaterialIndices;
|
||||
// Index in fMaterials that correspond to each voxel.
|
||||
};
|
||||
|
||||
#endif
|
||||
@@ -1,100 +0,0 @@
|
||||
//
|
||||
// ********************************************************************
|
||||
// * 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. *
|
||||
// ********************************************************************
|
||||
//
|
||||
// The code was written by :
|
||||
// *Louis Archambault louis.archambault@phy.ulaval.ca,
|
||||
// *Luc Beaulieu beaulieu@phy.ulaval.ca
|
||||
// +Vincent Hubert-Tremblay at tigre.2@sympatico.ca
|
||||
//
|
||||
//
|
||||
// *Centre Hospitalier Universitaire de Quebec (CHUQ),
|
||||
// Hotel-Dieu de Quebec, departement de Radio-oncologie
|
||||
// 11 cote du palais. Quebec, QC, Canada, G1R 2J6
|
||||
// tel (418) 525-4444 #6720
|
||||
// fax (418) 691 5268
|
||||
//
|
||||
// + Université Laval, Québec (QC) Canada
|
||||
//*******************************************************//
|
||||
//
|
||||
//---------------------------------------------------------------------------
|
||||
/// Octree encapsulates a volumetric compressed representation of the
|
||||
/// vector field used for the reconstruction of a 3D model from multiple
|
||||
/// range images or curves.
|
||||
///
|
||||
/// It is assumed that the space occupied by octree is a cube whose
|
||||
/// bottom-left-front corner is at origin (0,0,0) while the opposite corner
|
||||
/// (top,right,back) is at ( mSize,mSize,mSize). Resolution of an octree
|
||||
/// denotes the number of voxels along each axis such
|
||||
/// that the resolution = 2^mNoLevels.
|
||||
// -------------------------------------------------------------------------
|
||||
|
||||
#ifndef DICOMOCTREE_HH
|
||||
#define DICOMOCTREE_HH
|
||||
|
||||
#include "globals.hh"
|
||||
#include "DicomOctreeNode.hh"
|
||||
#include "DicomOctreeMiddleNode.hh"
|
||||
#include "DicomOctreeTerminalNode.hh"
|
||||
|
||||
class DicomOctreeNode;
|
||||
class DicomOctreeMiddleNode;
|
||||
class DicomTerminalNode;
|
||||
class DicomOctree;
|
||||
|
||||
class DicomOctree
|
||||
{
|
||||
public:
|
||||
|
||||
DicomOctree( G4int noLevels, G4double size );
|
||||
~DicomOctree();
|
||||
|
||||
DicomOctreeNode* CreateNode( G4double i, G4double j, G4double k, G4int level );
|
||||
DicomOctreeNode* operator()( G4double nodeX, G4double nodeY,
|
||||
G4double nodeZ, G4int level );
|
||||
void DeleteTree();
|
||||
|
||||
G4int CountMemory( G4int rMiddle, G4int rTerminal );
|
||||
|
||||
DicomOctreeNode* Root() { return mRoot; }
|
||||
G4double Size() { return mSize; }
|
||||
G4int NoLevels() { return mNoLevels; }
|
||||
//G4bool Resolution() { return ( 1 << mNoLevels ); }
|
||||
G4int GetIndexChild() { return indexChild;}
|
||||
private:
|
||||
void CountRecursive( DicomOctreeNode* pNode, G4int rMiddle, G4int rTerminal );
|
||||
// Root node of the tree
|
||||
DicomOctreeMiddleNode* mRoot;
|
||||
|
||||
// In an octree, size denotes physical size of the cube,
|
||||
// ie length of its sides (which are assumed equal).
|
||||
G4double mSize;
|
||||
|
||||
// Number of levels denotes the maximal number of
|
||||
// nodes in a single branch, starting from the root node.
|
||||
G4int mNoLevels;
|
||||
G4int indexChild;
|
||||
};
|
||||
#endif
|
||||
|
||||
@@ -1,75 +0,0 @@
|
||||
//
|
||||
// ********************************************************************
|
||||
// * 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. *
|
||||
// ********************************************************************
|
||||
//
|
||||
// The code was written by :
|
||||
// *Louis Archambault louis.archambault@phy.ulaval.ca,
|
||||
// *Luc Beaulieu beaulieu@phy.ulaval.ca
|
||||
// +Vincent Hubert-Tremblay at tigre.2@sympatico.ca
|
||||
//
|
||||
//
|
||||
// *Centre Hospitalier Universitaire de Quebec (CHUQ),
|
||||
// Hotel-Dieu de Quebec, departement de Radio-oncologie
|
||||
// 11 cote du palais. Quebec, QC, Canada, G1R 2J6
|
||||
// tel (418) 525-4444 #6720
|
||||
// fax (418) 691 5268
|
||||
//
|
||||
// + Université Laval, Québec (QC) Canada
|
||||
//*******************************************************//
|
||||
#ifndef DICOMOCTREENODE_H
|
||||
#define DICOMOCTREENODE_H
|
||||
#include "globals.hh"
|
||||
|
||||
enum OctreeNodeType { MIDDLE_NODE, TERMINAL_NODE };
|
||||
|
||||
// OctreeNode represents a single node in the Octree.
|
||||
class DicomOctreeNode
|
||||
{
|
||||
public:
|
||||
|
||||
DicomOctreeNode();
|
||||
~DicomOctreeNode();
|
||||
|
||||
DicomOctreeNode( DicomOctreeNode* pParent );
|
||||
|
||||
G4double Density(){return mDensity;}
|
||||
|
||||
virtual DicomOctreeNode*& operator []( G4int index ) = 0;
|
||||
|
||||
virtual OctreeNodeType Type() = 0;
|
||||
|
||||
const DicomOctreeNode* Parent(){ return mParent; }
|
||||
|
||||
virtual G4int FindChild( const DicomOctreeNode* pNode ) = 0;
|
||||
|
||||
static G4int InstanceCounter() { return mInstanceCounter; }
|
||||
|
||||
virtual G4int MemSize() = 0;
|
||||
|
||||
private:
|
||||
static G4int mInstanceCounter;
|
||||
DicomOctreeNode* mParent;
|
||||
G4double mDensity;
|
||||
};
|
||||
#endif
|
||||
@@ -1,189 +0,0 @@
|
||||
//
|
||||
// ********************************************************************
|
||||
// * 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. *
|
||||
// ********************************************************************
|
||||
//
|
||||
// The code was written by :
|
||||
// *Louis Archambault louis.archambault@phy.ulaval.ca,
|
||||
// *Luc Beaulieu beaulieu@phy.ulaval.ca
|
||||
// +Vincent Hubert-Tremblay at tigre.2@sympatico.ca
|
||||
//
|
||||
//
|
||||
// *Centre Hospitalier Universitaire de Quebec (CHUQ),
|
||||
// Hotel-Dieu de Quebec, departement de Radio-oncologie
|
||||
// 11 cote du palais. Quebec, QC, Canada, G1R 2J6
|
||||
// tel (418) 525-4444 #6720
|
||||
// fax (418) 691 5268
|
||||
//
|
||||
// + Université Laval, Québec (QC) Canada
|
||||
//*******************************************************//
|
||||
#ifndef DicomPatientParameterisation_h
|
||||
#define DicomPatientParameterisation_h 1
|
||||
|
||||
#include "globals.hh"
|
||||
#include "G4VPVParameterisation.hh"
|
||||
#include <vector>
|
||||
|
||||
class G4VPhysicalVolume;
|
||||
class G4LogicalVolume;
|
||||
class G4Box;
|
||||
class G4Material;
|
||||
class G4VisAttributes;
|
||||
class DicomConfiguration;
|
||||
class DicomPatientParameterisation : public G4VPVParameterisation
|
||||
{
|
||||
public:
|
||||
|
||||
DicomPatientParameterisation(G4int NoVoxels,
|
||||
G4double maxDensity,
|
||||
G4double minDensity ,
|
||||
G4Material* lunginhale,
|
||||
G4Material* lungexhale,
|
||||
G4Material* adipose,
|
||||
G4Material* breast,
|
||||
G4Material* phantom,
|
||||
G4Material* muscle,
|
||||
G4Material* liver,
|
||||
G4Material* denseBone,
|
||||
G4Material* trabecularBone);
|
||||
|
||||
virtual ~DicomPatientParameterisation();
|
||||
|
||||
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(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 {}
|
||||
|
||||
G4Material* ComputeMaterial(const G4int copyNo,
|
||||
G4VPhysicalVolume* physVol,
|
||||
const G4VTouchable*);
|
||||
|
||||
void GetDensity( G4double maxDensity, G4double minDensity );
|
||||
|
||||
private:
|
||||
|
||||
//materials ...
|
||||
G4Material* lungExhale;
|
||||
G4Material* lungInhale;
|
||||
G4Material* adiposeTissue;
|
||||
G4Material* breastTissue;
|
||||
G4Material* phantomTissue;
|
||||
G4Material* muscleTissue;
|
||||
G4Material* liverTissue;
|
||||
G4Material* denseBoneTissue;
|
||||
G4Material* trabecularBoneTissue;
|
||||
|
||||
G4VisAttributes* attributeAir;
|
||||
G4VisAttributes* attributeLungINhale;
|
||||
G4VisAttributes* attributeLungEXhale;
|
||||
G4VisAttributes* attributeAdipose;
|
||||
G4VisAttributes* attributeBreast;
|
||||
G4VisAttributes* attributePhantom;
|
||||
G4VisAttributes* attributeMuscle;
|
||||
G4VisAttributes* attributeLiver;
|
||||
G4VisAttributes* attributeTrabecularBone;
|
||||
G4VisAttributes* attributeDenseBone;
|
||||
|
||||
G4int max;
|
||||
short compression;
|
||||
|
||||
FILE* readData;
|
||||
short columns,rows;
|
||||
G4double pixelSpacingX;
|
||||
G4double pixelSpacingY;
|
||||
G4double sliceThickness;
|
||||
G4double sliceLocation;
|
||||
|
||||
std::vector<G4double> density;
|
||||
std::vector<G4double> patientPlacementX;
|
||||
std::vector<G4double> patientPlacementY;
|
||||
std::vector<G4double> patientPlacementZ;
|
||||
|
||||
|
||||
//G4LogicalVolume* LogicalVolumeParam;
|
||||
|
||||
G4double middleLocationValue;
|
||||
|
||||
private:
|
||||
|
||||
void readColorChart();
|
||||
class ColorChart {
|
||||
public:
|
||||
G4double density;
|
||||
G4double color[3];
|
||||
G4double alpha;
|
||||
enum {CRED, CGREEN, CBLUE};
|
||||
};
|
||||
std::vector<ColorChart> colorChart;
|
||||
G4int numColorChart;
|
||||
G4double getChartColor(G4int, G4double density);
|
||||
};
|
||||
#endif
|
||||
|
||||
|
||||
|
||||
@@ -0,0 +1,106 @@
|
||||
//
|
||||
// ********************************************************************
|
||||
// * 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. *
|
||||
// ********************************************************************
|
||||
//
|
||||
// Author: P. Arce
|
||||
// History: 30.11.07 First version
|
||||
//*******************************************************
|
||||
//
|
||||
// DicomPatientZSliceHeader.hh :
|
||||
// - Contains the meta data information corresponding to one or several Z slices (number of voxels, dimension)
|
||||
//*******************************************************
|
||||
|
||||
#ifndef DicomPatientZSliceHeader_h
|
||||
#define DicomPatientZSliceHeader_h 1
|
||||
|
||||
#include "globals.hh"
|
||||
class G4material;
|
||||
#include <fstream>
|
||||
#include <vector>
|
||||
|
||||
|
||||
class DicomPatientZSliceHeader
|
||||
{
|
||||
public:
|
||||
|
||||
DicomPatientZSliceHeader( const DicomPatientZSliceHeader& rhs );
|
||||
// build object copying an existing one (except Z dimensions)
|
||||
|
||||
DicomPatientZSliceHeader( std::ifstream& fin );
|
||||
// build object reading data from a file
|
||||
|
||||
~DicomPatientZSliceHeader(){};
|
||||
|
||||
// Get and set methods
|
||||
G4int GetNoVoxelX() const { return fNoVoxelX; };
|
||||
G4int GetNoVoxelY() const { return fNoVoxelY; };
|
||||
G4int GetNoVoxelZ() const { return fNoVoxelZ; };
|
||||
G4int GetNoVoxels() const { return fNoVoxelX*fNoVoxelY*fNoVoxelZ; };
|
||||
|
||||
G4double GetMinX() const { return fMinX; };
|
||||
G4double GetMinY() const { return fMinY; };
|
||||
G4double GetMinZ() const { return fMinZ; };
|
||||
G4double GetMaxX() const { return fMaxX; };
|
||||
G4double GetMaxY() const { return fMaxY; };
|
||||
G4double GetMaxZ() const { return fMaxZ; };
|
||||
|
||||
G4double GetVoxelHalfX() const { return (fMaxX-fMinX)/fNoVoxelX/2.; };
|
||||
G4double GetVoxelHalfY() const { return (fMaxY-fMinY)/fNoVoxelY/2.; };
|
||||
G4double GetVoxelHalfZ() const { return (fMaxZ-fMinZ)/fNoVoxelZ/2.; };
|
||||
|
||||
std::vector<G4String> GetMaterialNames() const { return fMaterialNames; };
|
||||
|
||||
|
||||
void SetNoVoxelX(const G4int val) { fNoVoxelX = val; }
|
||||
void SetNoVoxelY(const G4int val) { fNoVoxelY = val; }
|
||||
void SetNoVoxelZ(const G4int val) { fNoVoxelZ = val; }
|
||||
|
||||
void SetMinX(const G4double val) { fMinX = val; };
|
||||
void SetMaxX(const G4double val) { fMaxX = val; };
|
||||
void SetMinY(const G4double val) { fMinY = val; };
|
||||
void SetMaxY(const G4double val) { fMaxY = val; };
|
||||
void SetMinZ(const G4double val) { fMinZ = val; };
|
||||
void SetMaxZ(const G4double val) { fMaxZ = val; };
|
||||
|
||||
void SetMaterialNames(std::vector<G4String>& mn ){ fMaterialNames = mn; }
|
||||
|
||||
|
||||
void operator+=( const DicomPatientZSliceHeader& rhs );
|
||||
DicomPatientZSliceHeader operator+( const DicomPatientZSliceHeader& rhs );
|
||||
// add two slices that have the same dimensions, merging them in Z
|
||||
|
||||
private:
|
||||
G4bool CheckMaterialExists( const G4String& mateName );
|
||||
// check that material read exists as a G4Material
|
||||
|
||||
private:
|
||||
G4int fNoVoxelX, fNoVoxelY, fNoVoxelZ; // number of voxels in each dimensions
|
||||
G4double fMinX,fMinY,fMinZ; // minimum extension of voxels (position of wall)
|
||||
G4double fMaxX,fMaxY,fMaxZ; // maximum extension of voxels (position of wall)
|
||||
|
||||
std::vector<G4String> fMaterialNames; // list of material names
|
||||
|
||||
};
|
||||
|
||||
#endif
|
||||
Regular → Executable
+30
-35
@@ -23,45 +23,40 @@
|
||||
// * acceptance of all terms of the Geant4 Software license. *
|
||||
// ********************************************************************
|
||||
//
|
||||
// The code was written by :
|
||||
// *Louis Archambault louis.archambault@phy.ulaval.ca,
|
||||
// *Luc Beaulieu beaulieu@phy.ulaval.ca
|
||||
// +Vincent Hubert-Tremblay at tigre.2@sympatico.ca
|
||||
// class DicomPhantomParameterisationColour
|
||||
//
|
||||
//
|
||||
// *Centre Hospitalier Universitaire de Quebec (CHUQ),
|
||||
// Hotel-Dieu de Quebec, departement de Radio-oncologie
|
||||
// 11 cote du palais. Quebec, QC, Canada, G1R 2J6
|
||||
// tel (418) 525-4444 #6720
|
||||
// fax (418) 691 5268
|
||||
//
|
||||
// + Université Laval, Québec (QC) Canada
|
||||
//*******************************************************//
|
||||
#ifndef DicomPatientConstructor_h
|
||||
#define DicomPatientConstructor_h 1
|
||||
// Class description:
|
||||
//
|
||||
// Class inherited from G4PhantomParameterisation to provide different colour for each material
|
||||
// History:
|
||||
// - Created. P. Arce, 5 December 2007
|
||||
// *********************************************************************
|
||||
|
||||
#include "globals.hh"
|
||||
#ifndef DicomPhantomParameterisationColour_HH
|
||||
#define DicomPhantomParameterisationColour_HH
|
||||
|
||||
class DicomPatientConstructor
|
||||
#include <map>
|
||||
|
||||
#include "G4PhantomParameterisation.hh"
|
||||
class G4VisAttributes;
|
||||
|
||||
class DicomPhantomParameterisationColour : public G4PhantomParameterisation
|
||||
{
|
||||
public:
|
||||
public: // with description
|
||||
|
||||
DicomPhantomParameterisationColour();
|
||||
~DicomPhantomParameterisationColour();
|
||||
|
||||
virtual G4Material* ComputeMaterial(const G4int repNo,
|
||||
G4VPhysicalVolume *currentVol,
|
||||
const G4VTouchable *parentTouch=0);
|
||||
|
||||
private:
|
||||
void ReadColourData();
|
||||
|
||||
DicomPatientConstructor() {;}
|
||||
~DicomPatientConstructor() {;}
|
||||
|
||||
G4int FindingNbOfVoxels(G4double maxDensity, G4double minDensity);
|
||||
|
||||
// Functions to use ROI (region of interest), contour usually drawn by the
|
||||
// physician to identify tumor volume and organ at risk
|
||||
// under development ...
|
||||
// void readContour();
|
||||
//G4bool isWithin(G4double,G4double,G4double);
|
||||
|
||||
private:
|
||||
G4double pixelSpacingX;
|
||||
G4double pixelSpacingY;
|
||||
G4double sliceThickness;
|
||||
G4double sliceLocation;
|
||||
G4int lenc,lenr;
|
||||
private:
|
||||
std::map<G4String,G4VisAttributes*> fColours;
|
||||
};
|
||||
|
||||
|
||||
#endif
|
||||
@@ -36,6 +36,9 @@
|
||||
// fax (418) 691 5268
|
||||
//
|
||||
// + Université Laval, Québec (QC) Canada
|
||||
//
|
||||
// History: 30.11.07 P.Arce modified so that some particles reach patient voxels
|
||||
//
|
||||
//*******************************************************
|
||||
|
||||
#ifndef DicomPrimaryGeneratorAction_h
|
||||
|
||||
+20
-26
@@ -23,38 +23,32 @@
|
||||
// * acceptance of all terms of the Geant4 Software license. *
|
||||
// ********************************************************************
|
||||
//
|
||||
// The code was written by :
|
||||
// *Louis Archambault louis.archambault@phy.ulaval.ca,
|
||||
// *Luc Beaulieu beaulieu@phy.ulaval.ca
|
||||
// +Vincent Hubert-Tremblay at tigre.2@sympatico.ca
|
||||
// Author: P. Arce
|
||||
// History: 30.11.07 First version
|
||||
//*******************************************************
|
||||
//
|
||||
//
|
||||
// *Centre Hospitalier Universitaire de Quebec (CHUQ),
|
||||
// Hotel-Dieu de Quebec, departement de Radio-oncologie
|
||||
// 11 cote du palais. Quebec, QC, Canada, G1R 2J6
|
||||
// tel (418) 525-4444 #6720
|
||||
// fax (418) 691 5268
|
||||
//
|
||||
// + Université Laval, Québec (QC) Canada
|
||||
//*******************************************************//
|
||||
#ifndef DicomOctreeTerminalNode_h
|
||||
#define DicomOctreeTerminalNode_h
|
||||
// NestedParamDicomDetectorConstruction.hh :
|
||||
// - Construct the patient using DicomPhantomParameterisationColour
|
||||
//*******************************************************
|
||||
|
||||
class DicomOctreeTerminalNode : public DicomOctreeNode
|
||||
#ifndef NestedParamDicomDetectorConstruction_h
|
||||
#define NestedParamDicomDetectorConstruction_h 1
|
||||
|
||||
#include "globals.hh"
|
||||
#include "DicomDetectorConstruction.hh"
|
||||
|
||||
class NestedParamDicomDetectorConstruction : public DicomDetectorConstruction
|
||||
{
|
||||
public:
|
||||
DicomOctreeTerminalNode(DicomOctreeNode* pParent );
|
||||
~ DicomOctreeTerminalNode();
|
||||
|
||||
public:
|
||||
// ---- MGP ---- Replace *& with proper design of the operator
|
||||
DicomOctreeNode*& operator []( G4int index );
|
||||
G4int MemSize();
|
||||
|
||||
OctreeNodeType Type() {return TERMINAL_NODE;}
|
||||
G4int FindChild( const DicomOctreeNode* ) {return -1;}
|
||||
NestedParamDicomDetectorConstruction();
|
||||
~NestedParamDicomDetectorConstruction();
|
||||
|
||||
private:
|
||||
static DicomOctreeNode* mNull;
|
||||
|
||||
virtual void ConstructPatient();
|
||||
|
||||
};
|
||||
|
||||
#endif
|
||||
|
||||
+20
-29
@@ -23,41 +23,32 @@
|
||||
// * acceptance of all terms of the Geant4 Software license. *
|
||||
// ********************************************************************
|
||||
//
|
||||
// The code was written by :
|
||||
// *Louis Archambault louis.archambault@phy.ulaval.ca,
|
||||
// *Luc Beaulieu beaulieu@phy.ulaval.ca
|
||||
// +Vincent Hubert-Tremblay at tigre.2@sympatico.ca
|
||||
// Author: P. Arce
|
||||
// History: 30.11.07 First version
|
||||
//*******************************************************
|
||||
//
|
||||
//
|
||||
// *Centre Hospitalier Universitaire de Quebec (CHUQ),
|
||||
// Hotel-Dieu de Quebec, departement de Radio-oncologie
|
||||
// 11 cote du palais. Quebec, QC, Canada, G1R 2J6
|
||||
// tel (418) 525-4444 #6720
|
||||
// fax (418) 691 5268
|
||||
//
|
||||
// + Université Laval, Québec (QC) Canada
|
||||
//*******************************************************//
|
||||
#ifndef DicomOctreeMiddleNode_h
|
||||
#define DicomOctreeMiddleNode_h
|
||||
#include "globals.hh"
|
||||
class DicomOctree;
|
||||
// RegularDicomDetectorConstruction.hh :
|
||||
// - Construct the patient using DicomPhantomParameterisationColour
|
||||
//*******************************************************
|
||||
|
||||
class DicomOctreeMiddleNode : public DicomOctreeNode
|
||||
#ifndef RegularDicomDetectorConstruction_h
|
||||
#define RegularDicomDetectorConstruction_h 1
|
||||
|
||||
#include "globals.hh"
|
||||
#include "DicomDetectorConstruction.hh"
|
||||
|
||||
class RegularDicomDetectorConstruction : public DicomDetectorConstruction
|
||||
{
|
||||
public:
|
||||
DicomOctreeMiddleNode();
|
||||
~DicomOctreeMiddleNode();
|
||||
|
||||
public:
|
||||
void ResetFamily();
|
||||
DicomOctreeMiddleNode( DicomOctreeNode* pParent );
|
||||
G4int FindChild( const DicomOctreeNode* pNode );
|
||||
G4int MemSize();
|
||||
DicomOctreeNode*& operator []( G4int index ) {return mChildren[index];}
|
||||
OctreeNodeType Type() {return MIDDLE_NODE;}
|
||||
RegularDicomDetectorConstruction();
|
||||
~RegularDicomDetectorConstruction();
|
||||
|
||||
private:
|
||||
DicomOctreeNode* mChildren[8];
|
||||
DicomOctree* octree;
|
||||
|
||||
virtual void ConstructPatient();
|
||||
|
||||
};
|
||||
|
||||
#endif
|
||||
|
||||
Reference in New Issue
Block a user