Gabriele Cosmo
168 lines
4.8 KiB
C++
168 lines
4.8 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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//
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//
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/// \file SDDData.hh
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/// \brief Definition of the SDDData class
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#ifndef SDDDATA_HH
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#define SDDDATA_HH
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#include <string>
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#include <vector>
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#include <sstream>
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#include <map>
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#include "Damage.hh"
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class SDDData
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{
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public:
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/** SDD header structure
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*
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* Define the content of SSD file header
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*/
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struct SDDHeader
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{
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std::string sdd_version{""};
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std::string software{""};
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std::string author{""};
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std::string sim_details{""};
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std::string src_details{""};
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int src_type{0};
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std::vector<int> src_pdg;
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std::vector<double> src_energy;
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std::string energy_dist{""};
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std::vector<double> part_fraction;
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std::vector<double> dose;
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double dose_rate{0};
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std::string target{""};
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std::vector<double> volumes;
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std::vector<double> chromo_size;
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double dna_density{0};
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std::vector<double> cell_cycle;
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std::vector<int> dna_struct;
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int vitro_vivo{0};
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std::string proliferation{""};
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std::vector<double> microenv;
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std::vector<double> damage_def;
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double time{0};
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std::vector<int> damage_prim_count;
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std::vector<bool> entries;
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std::string info{""};
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};
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/** SDD damage structure
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*
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* Define the content of a damage as stored in SDD file
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*/
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struct SDDDamage
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{
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std::vector<int> classification;
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std::vector<double> coordinates;
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std::vector<int> chromo_ID;
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std::vector<double> chromo_position;
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std::vector<int> cause;
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std::vector<int> types;
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std::vector<int> break_spec;
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std::vector<int> dna_seq;
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std::vector<double> lesion_time;
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std::vector<int> particles;
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std::vector<double> energy;
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std::vector<double> translation;
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std::vector<double> direction;
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std::vector<double> particle_time;
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};
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/** Constructor */
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SDDData(std::string /*p_name*/);
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/** Destructor */
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~SDDData() = default;
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/** Read header
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* Reads and returns the header of a SDD file
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*/
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SDDHeader ReadHeader();
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/** Chromosome sizes
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* Returns the list of sizes of each chromosome in the cell geometry
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*/
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std::map<int,unsigned long long int> GetChromosomeBpSizesMap(double &sum);
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/** Dose
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* Returns the absorbed dose
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*/
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double GetDose();
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/** Parse data
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* Parse data of SDD files and stores the data
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* as SDDDamage in data_
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*/
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void ParseData();
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/** Get SDD damage
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* Returns all the SDD damage (i.e. data_)
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*/
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std::vector<SDDDamage>& GetSDDDamage(){return data_;};
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/** Get Damage
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* Returns all the damage that have been converted into lighter object
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* see Damage class
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*/
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std::map<unsigned int,std::map<unsigned int,std::vector<Damage> > > GetAllDamage();
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private:
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std::string filename_;
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SDDHeader header_;
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std::vector<SDDDamage> data_;
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void ParseLineData(std::string&);
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void ReadString(std::ifstream&,std::string&);
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void ReadInt(std::ifstream&,int&);
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void ReadInts(std::ifstream&,std::vector<int>&);
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void ReadDouble(std::ifstream&,double&);
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void ReadDoubles(std::ifstream&,std::vector<double>&);
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void ReadBools(std::ifstream&,std::vector<bool>&);
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void ExtractInts(std::string&,int,std::vector<int>&);
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void ExtractDoubles(std::string&,int,std::vector<double>&);
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};
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#endif // SDDDATA_HH
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