Gabriele Cosmo
138 lines
5.3 KiB
C++
138 lines
5.3 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 ScanDamage.hh
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/// \brief Definition of the ScanDamage class
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#ifndef ScanDamage_h
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#define ScanDamage_h
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#include <map>
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#include <vector>
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#include <string>
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#include <tuple>
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#include <set>
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#include "Damage.hh"
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#include <filesystem>
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namespace fs = std::filesystem;
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class TFile;
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using ullint = unsigned long long int;
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//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
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struct VoxelData
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{
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VoxelData(int chromo, int domain, ullint firstBpCN)
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{
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fChromosome = chromo;
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fDomain = domain;
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fFirstBpCopyNum = firstBpCN;
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}
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~VoxelData() {}
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int fChromosome{0};
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int fDomain{0};
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ullint fFirstBpCopyNum{0};
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};
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//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
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typedef std::vector<std::vector<ullint> > Table;
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//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
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class Trier {
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public:
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bool operator()(const std::vector<ullint>& a, const std::vector<ullint>& b)
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{
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bool bb = false;
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if(a[0] < b[0]) bb = true;
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return bb;
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}
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};
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//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
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class ScanDamage
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{
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public:
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ScanDamage();
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~ScanDamage() = default;
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std::map<unsigned int,std::map<unsigned int,std::vector<Damage> > > ExtractDamage();
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void SetThresholdEnergy(double e) {fThresholdEnergy = e;}
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void SetProbabilityForIndirectSBSelection(double p) {fProbabilityForIndirectSB = p;}
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double GetThresholdEnergy() {return fThresholdEnergy;}
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double GetProbabilityForIndirectSBSelection() {return fProbabilityForIndirectSB;}
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std::map<int, Table> GetMergedSBData() {return fMergedTables;}
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double GetEdepSumInNucleus() {return fEdepSumInNucleus;} //eV
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double GetTotalNbBpPlacedInGeo() {return fTotalNbBpPlacedInGeo;}
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double GetTotalNbHistonePlacedInGeo() {return fTotalNbHistonePlacedInGeo;}
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double GetNucleusVolume() {return fNucleusVolume;}
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double GetNucleusMassDensity() {return fNucleusMassDensity;}
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double GetNucleusMass() {return fNucleusMass;}
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std::map<int,ullint> GetChromosomeBpSizesMap() {return fChromosomeBpMap;}
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void SkipScanningIndirectDamage() {fSkipScanningIndirectDamage = true;}
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bool SkippedScanningIndirectDamage() {return fSkipScanningIndirectDamage;}
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private:
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void ScanDamageFromPhys();
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void ScanDamageFromChem();
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void RetrieveVoxelBp();
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void FillVoxelData();
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void AnaPhysRootFile(const std::string fileName);
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void AnaChemRootFile(fs::directory_entry entry);
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void AnaPhysRootTree1(TFile*);
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void AnaPhysRootTree2(TFile*);
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void SortPhysTableWithSelection();
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void SortChemTableWithSelection();
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void ReadCellandVoxelDefFilePaths();
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void MergeDamageFromPhysChem();
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std::tuple<unsigned int, unsigned int> GetEventNberAndVoxelNberFromChemRoot(const std::string fileNam);
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double fThresholdEnergy{17.5};//eV
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std::string fCellDefFilePath{""};
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std::set<std::string> fVoxelDefFilesList;
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std::map<std::string, int> fBpPerVoxel;
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std::vector<VoxelData> fVoxels;
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std::map<int, Table> fphysTables, fphysSlectedTables, fchemTables, fchemSlectedTables,fMergedTables;
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std::map<unsigned int,std::map<unsigned int,std::vector<Damage> > > fDamage;
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double fEdepSumInNucleus{0}; //eV
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int corruptedFiles = 0;
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double fTotalNbBpPlacedInGeo{0};
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double fTotalNbHistonePlacedInGeo{0};
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double fNucleusVolume{0};
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double fNucleusMassDensity{0};
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double fNucleusMass{0};
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double fProbabilityForIndirectSB{0.4};
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std::map<int,ullint> fChromosomeBpMap; //Store number of Bp in each Chomosomes;
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bool fSkipScanningIndirectDamage{false};
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};
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//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
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#endif
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