.gitignore

-*~
+# Ignore compiled files
+*.o
+*.out
+*.d
+*.so
+
+#Ignore files automatically build by ROOT
+*.pcm
+*Dict.cpp
+
+
+# Ignore log files
+*.log
+
+# Ignore build directories
+build/
+
+# Ignore data and calibration files
 *.root
 *.cal
+
+#Ignore VS code stuff
+.vscode/
+
+# config.ini
\ No newline at end of file

AculCalib/AculCalPars.cpp

+/*
+ * AculCalParameters.cpp
+ *
+ *  Created on: Oct 20, 2016
+ *      Author: vratik
+ */
+
+#include "AculCalPars.h"
+
+AculCalPars::AculCalPars() {
+	// TODO Auto-generated constructor stub
+	Reset();
+
+}
+
+AculCalPars::AculCalPars(const char* parFile) {
+	// TODO Auto-generated constructor stub
+
+	SetParFile(parFile);
+	Init();
+
+}
+AculCalPars::~AculCalPars() {
+	// TODO Auto-generated destructor stub
+}
+
+void AculCalPars::Init() {
+	SetPars();
+}
+
+void AculCalPars::SetParFile(const char* parfile) {
+
+	fParFileName = parfile;
+	return;
+}
+
+void AculCalPars::Reset() {
+	fParFileName = "";
+	fEtab.clear();
+}

AculCalib/AculCalPars.h

+/*
+ * AculCalParameters.h
+ *
+ *  Created on: Oct 20, 2016
+ *      Author: vratik
+ */
+
+#ifndef ACULCALIB_ACULCALPARS_H_
+#define ACULCALIB_ACULCALPARS_H_
+
+#include <iostream>
+#include <fstream>
+#include <vector>
+
+#include "TString.h"
+#include "TArrayD.h"
+#include "TArrayI.h"
+#include "TCutG.h"
+
+using std::cout;
+using std::cerr;
+using std::endl;
+using std::vector;
+
+class AculCalPars {
+
+protected:
+//general
+	TString fParFileName;
+
+	vector<Double_t> fEtab;		//energy which will be used for calibration
+
+	//todo energies used for calibration should be in this class
+
+
+
+public:
+	AculCalPars();
+	AculCalPars(const char* parFile);
+	virtual ~AculCalPars();
+	ClassDef(AculCalPars,1);
+
+	virtual void Init();
+
+	//getters
+	const char* GetParFileName() {return fParFileName.Data();}
+//	Int_t GetNoCrystals() {return fNoCrystals;}
+	virtual const char* GetDetName() {return 0;}
+	virtual const char* GetParticleName() {return 0;}
+	virtual Int_t GetNoRawFiles() {return 0;};
+	virtual const char* GetFileName(Int_t i) {return 0;};
+	virtual Int_t GetNoEPoints() {return 0;}
+	virtual Double_t GetCalEnergy(Int_t i) {return 0.;};
+
+	//todo check functions with cuts
+//	virtual const char* GetCutsFileName() {return 0;}
+//	virtual Int_t GetNoCuts() {return 0;}
+//	virtual TCutG* GetCut(Int_t i) {return 0;};
+	virtual TCutG* GetCut(const char* cutName, Int_t treeID = 0) {return 0;};
+	virtual Int_t GetMinChannel(Int_t energy, Int_t crystal) {return 0;};
+	virtual Int_t GetMaxChannel(Int_t energy, Int_t crystal) {return 0;};
+
+	void SetParFileName(const char* parFile) {fParFileName = parFile;}
+
+	void SetParFile(const char* parfile);
+	virtual void PrintParameters(const char* option = "") {};
+
+	virtual void Reset();
+
+protected:
+	virtual void SetPars() {};
+};
+
+#endif /* ACULCALIB_ACULCALPARS_H_ */

AculCalib/AculCalParsScint.cpp

+/*
+ * AculCalParsScint.cpp
+ *
+ *  Created on: Oct 21, 2016
+ *      Author: vratik
+ */
+
+#include "AculCalParsScint.h"
+#include "TFile.h"
+
+AculCalParsScint::AculCalParsScint() {
+	// TODO Auto-generated constructor stub
+	Reset();
+
+}
+
+AculCalParsScint::AculCalParsScint(const char* parFile) {
+	// TODO Auto-generated constructor stub
+	SetParFile(parFile);
+	Init();
+
+}
+
+AculCalParsScint::~AculCalParsScint() {
+	// TODO Auto-generated destructor stub
+}
+
+void AculCalParsScint::Init() {
+	SetPars();
+//	LoadCuts();
+}
+
+void AculCalParsScint::SetPars() {
+
+	std::ifstream infile(fParFileName.Data());
+	if ( !infile.is_open() ) {
+		printf("AculCalParsScint::ReadParFile: File %s was not open and parameters were not set.\n", fParFileName.Data());
+		Reset();
+		return;
+	}
+
+	fEnergyPoints = 0;
+
+	TString line;
+	TString word;
+
+	Int_t i, min, max;
+	Int_t lineLength = 400;
+	Char_t	det[lineLength];
+	Char_t	part[lineLength];
+	Char_t	fname[lineLength];
+	Char_t	cname[lineLength];
+
+	double en;	//energy
+
+	while (!infile.eof()) {
+		line.ReadLine(infile);
+
+		if ( line.BeginsWith("#") || line.BeginsWith("//") ) continue;
+
+		if ( line.BeginsWith("energies") ) {
+			sscanf(line.Data(), "%*s %d", &i);
+			continue;
+		}
+
+		if ( line.BeginsWith("crystals") ) {
+			sscanf(line.Data(), "%*s %d", &i);
+			fNoCrystals = i;
+			continue;
+		}
+
+		if ( line.BeginsWith("files") ) {
+			sscanf(line.Data(), "%*s %d", &i);
+			fNoFiles = i;
+			fFilePars.resize(fNoFiles);
+			for (Int_t j = 0; j < fNoFiles; j++) {
+				line.ReadLine(infile);
+				if ( line.BeginsWith("#") || line.BeginsWith("//") ) {
+					j--;
+					continue;
+				}
+				sscanf(line, "%s", fname);
+				word = fname;
+				fFilePars[j].SetRawFileName(fname);
+				fFilePars[j].SetNoCrystals(fNoCrystals);
+				fFilePars[j].Init();
+			}
+			continue;
+		}
+
+		/*if ( line.BeginsWith("cutFile") ) {
+			sscanf(line.Data(), "%*s %s %d", fname, &fNoCuts);
+			fCutsFileName = fname;
+			for (Int_t j = 0; j < fNoCuts; j++) {
+				line.ReadLine(infile);
+				if ( line.BeginsWith("#") || line.BeginsWith("//") ) {
+					j--;
+					continue;
+				}
+				sscanf(line, "%s", cname);
+				fCutName.push_back(cname);
+			}
+			continue;
+		}*/
+
+		if ( line.BeginsWith("detector") ) {
+			sscanf(line.Data(), "%*s %s %s", det, part);
+			fDetName = det;
+			fPartName = part;
+			continue;
+		}
+
+		if ( line.BeginsWith("energy") ) {
+			sscanf(line.Data(), "%*s %lf", &en);
+			fFilePars[fEnergyPoints].SetEnergy(en);
+
+			do {line.ReadLine(infile);}
+			while (line.BeginsWith("#") || line.BeginsWith("//"));
+
+			if ( line.BeginsWith("cutFile") ) {
+				Int_t noCuts;
+//				sscanf(line.Data(), "%*s %s %d", fname, &fNoCuts);
+				sscanf(line.Data(), "%*s %s %d", fname, &noCuts);
+				fFilePars[fEnergyPoints].SetNoCuts(noCuts);
+				fFilePars[fEnergyPoints].SetCutFileName(fname);
+//				cout << line << endl;
+//				cout << noCuts << endl;
+//				fCutsFileName = fname;
+				for (Int_t j = 0; j < noCuts; j++) {
+					line.ReadLine(infile);
+//					cout << line << endl;
+					if ( line.BeginsWith("#") || line.BeginsWith("//") ) {
+						j--;
+						continue;
+					}
+					sscanf(line, "%s", cname);
+					fFilePars[fEnergyPoints].SetCutName(j, cname);
+//					fCutName.push_back(cname);
+				}
+				fFilePars[fEnergyPoints].LoadCuts();
+				line.ReadLine(infile);
+//				cout << line << endl;
+//				continue;
+			}
+
+//			cout << fNoCrystals << endl;
+			for (Int_t j = 0; j < fNoCrystals; j++) {
+//				line.ReadLine(infile);
+//				cout << j << endl;
+				if ( line.BeginsWith("#") || line.BeginsWith("//") ) {
+					j--;
+					line.ReadLine(infile);
+					continue;
+				}
+				sscanf(line.Data(), "%d %d %d", &j, &min, &max);
+//				cout << j << endl;
+				fFilePars.at(fEnergyPoints).SetPeakMin(j, min);
+				fFilePars.at(fEnergyPoints).SetPeakMax(j, max);
+				line.ReadLine(infile);
+			}
+
+			fEnergyPoints++;
+			continue;
+		}
+
+//		cout << "aklsjdlaksjd" << endl;
+
+//		sscanf(line.Data(), "%d %d %d", &i, &min, &max);
+//		fFilePars.at(fEnergyPoints-1).SetPeakMin(i, min);
+//		fFilePars.at(fEnergyPoints-1).SetPeakMax(i, max);
+
+	}//while
+
+	infile.close();
+	return;
+}
+
+void AculCalParsScint::PrintParameters(const char* option) {
+
+	TString opt = option;
+
+	cout << "Parameters read from file \"" << fParFileName.Data() << "\"." << endl;
+	cout << "\tCalibration of detector \"" << fDetName << "\" with " << fNoCrystals << " crystals." << endl;
+	cout << "\tParticle: " << fPartName << endl;
+	cout << "\tInput files with raw data (" << fNoFiles << "):" << endl;
+	for (Int_t i = 0; i < (Int_t)fFilePars.size(); i++) {
+		cout << "\t " << GetFileName(i) << endl;
+	}
+
+	cout << "\tInput energies (" << fNoFiles << "):" << endl;
+	for (Int_t i = 0; i < (Int_t)fFilePars.size(); i++) {
+		cout << "\t " << fFilePars[i].GetEnergy() << " MeV" << endl;
+	}
+
+//	cout << "\tInput file with " << fNoCuts << " cuts: \"" << fCutsFileName << "\"" << endl;
+//	if (opt.Contains("all")) {
+//		for (Int_t i = 0; i < (Int_t)fCutName.size(); i++) {
+//			cout << "\t cut: \"" << fCutName[i] << "\"" << endl;
+//		}
+//	}
+
+
+
+
+	for (Int_t k = 0; k < (Int_t)fFilePars.size(); k++) {
+		cout << "\t" << fFilePars[k].GetNoCuts() << " cuts from file \"" << fFilePars[k].GetCutFileName() << "\":" << endl;
+		for (Int_t i = 0; i < fFilePars[k].GetNoCuts(); i++) {
+			cout << "\t  " << fFilePars[k].GetCut(i)->GetName() << endl;
+		}
+		if (!opt.Contains("all")) continue;
+		cout << "\tPeak limits for particular channels and energies:" << endl;
+		cout << "\t  Set number: " << k << "; energy: " << fFilePars[k].GetEnergy() << " MeV" << endl;
+		for (Int_t i = 0; i < (Int_t)fFilePars[k].GetNoCrystals(); i++) {
+			cout << "\t\t " << fFilePars[k].GetPeakMin(i) << "\t" << fFilePars[k].GetPeakMax(i) << endl;
+		}
+	}
+
+	return;
+}
+
+void AculCalParsScint::Reset() {
+
+	fNoCrystals = 0;
+
+	fParFileName = "";
+
+	fDetName = "";
+	fPartName = "";
+
+	fNoFiles = 0;
+	fFilePars.clear();
+	fEnergyPoints = 0;
+
+//	fCutsFileName = "";
+//	fNoCuts = 0;				//number of cuts
+
+//	fCutName.clear();
+
+	return;
+}
+
+const char* AculCalParsScint::GetFileName(Int_t i) {
+
+	if ( i >= (Int_t)fFilePars.size() ) {
+		cerr << "\"AculCalParsScint::GetFileName\"  index i cannot be higher than " << fFilePars.size() - 1 << endl;
+		return 0;
+	}
+	return fFilePars[i].GetRawFileName();
+}
+
+/*const char* AculCalParsScint::GetCutName(Int_t i) {
+
+	if ( i > (Int_t)fCutName.size()-1 ) {
+		cerr << "\"AculCalParsScint::GetCutName\"  index i cannot be higher than " << fCutName.size() - 1 << endl;
+		return 0;
+	}
+	return fCutName[i].Data();
+}*/
+
+/*TCutG* AculCalParsScint::GetCut(Int_t i) {
+	if ( i >= (Int_t)fCuts.size() ) {
+		cerr << "\"AculCalParsScint::GetCut\"  index i cannot be higher than " << fCuts.size() - 1 << endl;
+		return 0;
+	}
+	return &fCuts[i];
+}*/
+
+TCutG* AculCalParsScint::GetCut(const char* cutName, Int_t treeID) {
+
+	const TString cName = cutName;
+
+	if (treeID >= (Int_t)fFilePars.size()) {
+		cerr << "\"AculCalParsScint::GetCut\" treeID does not exist. It cannot be higher than "
+				<< fFilePars.size() << "." << endl;
+		return 0;
+	}
+
+//	TCutG *curCut = 0;
+	for (Int_t i = 0; i < fFilePars[treeID].GetNoCuts(); i++) {
+//		if (cName.EqualTo(fFilePars[treeID])) { return &fCuts[i]; }
+		if ( cName.EqualTo( fFilePars[treeID].GetCutName(i) ) ) {
+			return fFilePars[treeID].GetCut(i);
+//			return curCut;
+		}
+	}
+
+
+	cerr << "\"AculCalParsScint::GetCut\"  cut \"" << cutName << "\" was not found." << endl;
+	return 0;
+}
+
+Double_t AculCalParsScint::GetCalEnergy(Int_t i) {
+
+	if ( i >= (Int_t)fFilePars.size() ) {
+		cerr << "\"AculCalParsScint::GetCalEnergy\"  index i cannot be higher than " << fFilePars.size() - 1 << endl;
+		return 0;
+	}
+	return fFilePars[i].GetEnergy();
+}
+
+Int_t AculCalParsScint::GetMinChannel(Int_t energy, Int_t crystal) {
+
+	if ( energy >= (Int_t)fFilePars.size() ) {
+		cerr << "\"AculCalParsScint::GetMinChannel\"  index \"energy\" cannot be higher than "
+				<< fFilePars.size() - 1 << endl;
+		return 0;
+	}
+
+	if ( crystal >= fFilePars[energy].GetNoCrystals() ) {
+		cerr << "\"AculCalParsScint::GetMinChannel\"  index \"crystal\" cannot be higher than "
+				<< fFilePars[energy].GetNoCrystals() - 1 << endl;
+		return 0;
+	}
+
+	return fFilePars[energy].GetPeakMin(crystal);
+}
+
+Int_t AculCalParsScint::GetMaxChannel(Int_t energy, Int_t crystal) {
+
+	if ( energy >= (Int_t)fFilePars.size() ) {
+		cerr << "\"AculCalParsScint::GetMinChannel\"  index \"energy\" cannot be higher than "
+				<< fFilePars.size() - 1 << endl;
+		return 0;
+	}
+
+	if ( crystal >= fFilePars[energy].GetNoCrystals() ) {
+		cerr << "\"AculCalParsScint::GetMinChannel\"  index \"crystal\" cannot be higher than "
+				<< fFilePars[energy].GetNoCrystals() - 1 << endl;
+		return 0;
+	}
+
+	return fFilePars[energy].GetPeakMax(crystal);
+}
+
+/*void AculCalParsScint::LoadCuts() {
+
+	if (fCutsFileName.Length() == 0) {
+		printf("AculCalParsScint::LoadCuts: Name of file (*.root) with cuts was not provided.\n");
+		printf("AculCalParsScint::LoadCuts: No cuts has been loaded.\n");
+		return;
+	}
+
+	TFile cutFile(fCutsFileName.Data(), "READ");
+	if(!cutFile.IsOpen()) {
+		cerr << "\"AculCalParsScint::LoadCuts\" File " << fCutsFileName.Data()
+				<< " was not open and no cuts were loaded." << endl;
+		return;
+	}
+
+	for (Int_t i = 0; i < (Int_t)fCutName.size(); i++) {
+		TCutG *currentCut = (TCutG*)cutFile.Get(fCutName[i]);
+		if (!currentCut) {
+			cout << "\"AculCalParsScint::LoadCuts\" Cut \"" << fCutName[i]
+				<< "\" was not found in file " << fCutsFileName << "." << endl;
+			continue;
+		}
+		fCuts.push_back(*currentCut);
+	}
+
+}*/

AculCalib/AculCalParsScint.h

+/*
+ * AculCalParsScint.h
+ *
+ *  Created on: Oct 21, 2016
+ *      Author: vratik
+ */
+
+#ifndef ACULCALIB_ACULCALPARSSCINT_H_
+#define ACULCALIB_ACULCALPARSSCINT_H_
+
+#include "AculCalPars.h"
+#include "AculCalParsScintFile.h"
+//#include "TCutG.h"
+
+using std::cerr;
+
+class AculCalParsScint: public AculCalPars {
+
+private:
+	Int_t fNoCrystals;
+
+	TString fDetName;
+	TString fPartName;
+
+	Int_t fNoFiles;
+	vector<AculCalParsScintFile> fFilePars;
+	//todo following parameters should be probably moved to AculCalParsScintFile
+	//as far as they are related to each file separately
+//	vector<TString> fCutName;
+//	vector<TCutG> fCuts;
+
+	Int_t fEnergyPoints;
+
+//	TString fCutsFileName;
+//	Int_t fNoCuts;				//number of cuts
+
+public:
+	AculCalParsScint();
+	AculCalParsScint(const char* parFile);
+	virtual ~AculCalParsScint();
+	ClassDef(AculCalParsScint, 1);
+
+	virtual void Init();
+
+	void PrintParameters(const char* option = "");
+	// If option contains "all", all parameters will be printed out.
+	// By default important parameters only will be printed out.
+
+	void Reset();
+
+	//getters
+	Int_t GetNoCrystals() {return fNoCrystals;}
+	const char* GetDetName() {return fDetName.Data();}
+	const char* GetParticleName() {return fPartName.Data();}
+	Int_t GetNoRawFiles() {return fNoFiles;}
+	const char* GetFileName(Int_t i);
+	const char* GetCutName(Int_t i);
+	Int_t GetNoEPoints() {return fEnergyPoints;}
+	Double_t GetCalEnergy(Int_t i);
+//	const char* GetCutsFileName() {return fCutsFileName.Data();}
+//	Int_t GetNoCuts() {return fNoCuts;}
+//	TCutG* GetCut(Int_t i);
+	TCutG* GetCut(const char* cutName, Int_t treeID = 0);
+	Int_t GetMinChannel(Int_t energy, Int_t crystal);
+	Int_t GetMaxChannel(Int_t energy, Int_t crystal);
+
+//private:
+//	void LoadCuts();
+
+protected:
+	void SetPars();
+};
+
+#endif /* ACULCALIB_ACULCALPARSSCINT_H_ */

AculCalib/AculCalParsScintFile.cpp

+/*
+ * AculCalParsScintFile.cpp
+ *
+ *  Created on: Oct 25, 2016
+ *      Author: vratik
+ */
+
+#include "AculCalParsScintFile.h"
+
+AculCalParsScintFile::AculCalParsScintFile() {
+	// TODO Auto-generated constructor stub
+//	fFileID = 0;
+	fNoCrystals = 0;
+	fE = 0;
+	Init();
+}
+
+AculCalParsScintFile::~AculCalParsScintFile() {
+	// TODO Auto-generated destructor stub
+}
+
+void AculCalParsScintFile::Init() {
+//	fNoCrystals = 0;
+//	fE = 0;
+
+	fPeakMin.resize(fNoCrystals);
+	fPeakMax.resize(fNoCrystals);
+
+	fCutName.resize(0);
+}
+
+
+const char* AculCalParsScintFile::GetCutName(Int_t i) {
+
+	if ( i >= (Int_t)fCutName.size() ) {
+		cout << "\"AculCalParsScintFile::GetCutName\" Cut number " << i
+				<< " is not available. Maximal i can be set as "
+				<< fCutName.size() - 1 << "." << endl;
+	}
+	return fCutName[i].Data();
+}
+
+TCutG* AculCalParsScintFile::GetCut(Int_t i) {
+	if ( i >= (Int_t)fCut.size() ) {
+		cerr << "\"AculCalParsScintFile::GetCut\"  index i cannot be higher than " << fCut.size() - 1 << endl;
+		return 0;
+	}
+	return &fCut[i];
+}
+
+TCutG* AculCalParsScintFile::GetCut(const char* cutName) {
+
+	const TString cName = cutName;
+
+	for (Int_t i = 0; i <= (Int_t)fCut.size(); i++) {
+		if (cName.EqualTo(fCutName[i])) { return &fCut[i]; }
+	}
+
+
+	cerr << "\"AculCalParsScint::GetCut\"  cut \"" << cutName << "\" was not found." << endl;
+	return 0;
+}
+
+Int_t AculCalParsScintFile::GetPeakMin(Int_t crystalID) {
+	if ( crystalID >= (Int_t)fPeakMin.size() ) {
+		cerr << "\"AculCalParsScintFile::GetPeakMin\"  index \"crystal\" cannot be higher than "
+				<< fPeakMin.size() - 1 << endl;
+		return 0;
+	}
+
+	return fPeakMin[crystalID];
+}
+
+Int_t AculCalParsScintFile::GetPeakMax(Int_t crystalID) {
+	if ( crystalID >= (Int_t)fPeakMax.size() ) {
+		cerr << "\"AculCalParsScintFile::GetPeakMax\"  index \"crystal\" cannot be higher than "
+				<< fPeakMax.size() - 1 << endl;
+		return 0;
+	}
+
+	return fPeakMax[crystalID];
+}
+
+void AculCalParsScintFile::SetRawFileName(const char* filename) {
+	fFileName = filename;
+//	fFileID++;
+}
+
+void AculCalParsScintFile::SetCutFileName(const char* filename) {
+	fCutsFileName = filename;
+}
+
+void AculCalParsScintFile::SetNoCuts(Int_t noCuts) {
+	fCutName.resize(noCuts);
+}
+
+void AculCalParsScintFile::SetCutName(Int_t i, const char* cutname) {
+	if ( i >= (Int_t)fCutName.size() ) {
+		cout << "\"AculCalParsScintFile::SetCutName\" vector for cut names is not enough large. Maximal i can be set as "
+				<< fCutName.size() - 1 << "." << endl;
+	}
+	fCutName[i] = cutname;
+}
+
+void AculCalParsScintFile::SetPeakMin(Int_t crystalID, Double_t limit) {
+	if ( crystalID>=(Int_t)fPeakMin.size() ) {
+		cerr << "\"AculCalParsScintFile::SetPeakMin\" maximal allowed crystal ID is " << fPeakMin.size() << "."<< endl;
+		return;
+	}
+	fPeakMin[crystalID] = limit;
+}
+
+void AculCalParsScintFile::SetPeakMax(Int_t crystalID, Double_t limit) {
+	if ( crystalID>=(Int_t)fPeakMax.size() ) {
+		cerr << "\"AculCalParsScintFile::SetPeakMax\" maximal allowed crystal ID is " << fPeakMax.size() << "."<< endl;
+		return;
+	}
+	fPeakMax[crystalID] = limit;
+}
+
+void AculCalParsScintFile::LoadCuts() {
+
+	if (fCutsFileName.Length() == 0) {
+		printf("AculCalParsScintFile::LoadCuts: Name of file (*.root) with cuts was not provided.\n");
+		printf("AculCalParsScintFile::LoadCuts: No cuts has been loaded.\n");
+		return;
+	}
+
+	TFile cutFile(fCutsFileName.Data(), "READ");
+	if(!cutFile.IsOpen()) {
+		cerr << "\"AculCalParsScintFile::LoadCuts\" File " << fCutsFileName.Data()
+				<< " was not open and no cuts were loaded." << endl;
+		return;
+	}
+
+	for (Int_t i = 0; i < (Int_t)fCutName.size(); i++) {
+		TCutG *currentCut = (TCutG*)cutFile.Get(fCutName[i]);
+		if (!currentCut) {
+			cout << "\"AculCalParsScintFile::LoadCuts\" Cut \"" << fCutName[i]
+				<< "\" was not found in file " << fCutsFileName << "." << endl;
+			continue;
+		}
+		fCut.push_back(*currentCut);
+	}
+
+}
+
+/*void AculCalParsScintFile::Reset() {
+
+}*/

AculCalib/AculCalParsScintFile.h

+/*
+ * AculCalParsScintFile.h
+ *
+ *  Created on: Oct 25, 2016
+ *      Author: vratik
+ */
+
+#ifndef ACULCALIB_ACULCALPARSSCINTFILE_H_
+#define ACULCALIB_ACULCALPARSSCINTFILE_H_
+
+#include <vector>
+#include <iostream>
+
+#include "TFile.h"
+#include "TCutG.h"
+#include "TString.h"
+
+using std::vector;
+using std::cout;
+using std::endl;
+using std::cerr;
+
+class AculCalParsScintFile {
+private:
+
+//	UInt_t fFileID;
+	Int_t fNoCrystals;
+	Double_t fE;
+//	TCutG fCuts;
+	TString fFileName;
+
+	TString fCutsFileName;
+	vector<TString> fCutName;
+	vector<TCutG> fCut;
+
+
+	vector<Int_t> fPeakMin;
+	vector<Int_t> fPeakMax;
+
+public:
+	AculCalParsScintFile();
+	virtual ~AculCalParsScintFile();
+	ClassDef(AculCalParsScintFile, 1);
+
+	void Init();
+
+	Int_t GetNoCrystals() {return fNoCrystals;}
+	const char* GetRawFileName() {return fFileName.Data();}
+	const char* GetCutFileName() {return fCutsFileName.Data();}
+	Double_t GetEnergy() {return fE;}
+	Int_t GetNoCuts() {return (Int_t)fCut.size();}
+	const char* GetCutName(Int_t i);
+	TCutG* GetCut(Int_t i);
+	TCutG* GetCut(const char* cutName);
+	Int_t GetPeakMin(Int_t crystalID);
+	Int_t GetPeakMax(Int_t crystalID);
+
+	void SetNoCrystals(Int_t nocrystals) {fNoCrystals = nocrystals;};
+	void SetEnergy(Double_t energy) {fE = energy;};
+	void SetRawFileName(const char* filename);
+	void SetCutFileName(const char* filename);
+	void SetNoCuts(Int_t noCuts);
+	void SetCutName(Int_t i, const char* cutname);
+	void SetPeakMin(Int_t crystalID, Double_t limit);
+	void SetPeakMax(Int_t crystalID, Double_t limit);
+
+	void LoadCuts();
+//	void Reset();
+
+private:
+//	void LoadCuts();
+};
+
+#endif /* ACULCALIB_ACULCALPARSSCINTFILE_H_ */

AculCalib/AculCalParsSi.cpp

+/*
+ * AculCalParsSi.cpp
+ *
+ *  Created on: Oct 26, 2016
+ *      Author: vratik
+ */
+
+#include "AculCalParsSi.h"
+
+AculCalParsSi::AculCalParsSi() {
+	// TODO Auto-generated constructor stub
+	Reset();
+}
+
+AculCalParsSi::AculCalParsSi(const char* parFile) {
+
+	SetParFile(parFile);
+	Init();
+}
+
+AculCalParsSi::~AculCalParsSi() {
+	// TODO Auto-generated destructor stub
+}
+
+void AculCalParsSi::Init() {
+	SetELosses();
+	SetPars();
+	SetCalEnergies();
+}
+
+void AculCalParsSi::Reset() {
+	fParFileName = "";
+
+	kRaNOPEAKS = 0;
+
+	fEnergyInput.clear();
+	fLowerChannel = 0.;
+	fUpperChannel = 0.;
+	fLowerPeakRelativeHight = 0.;
+	fUpperPeakRelativeHight = 0.;
+	fPeakPositionTolerance = 0.;
+	fFitFuncLineWidth = 1;
+	fFitMinSigma = 0.;
+	fFitPeakThreshold = 0.;
+	fDeadLayer = 0.;
+
+	return;
+}
+
+void AculCalParsSi::SetPars() {
+	if (fParFileName.Length()==0) {
+		cerr << "\'AculCalibration::SetInputsParameters\" File with input parameters was not set." << endl;
+		return;
+	}
+
+	const Int_t lineLength = 400;
+	Char_t	line[lineLength];
+	Char_t	parameter[100];
+	Char_t	identificator[100];
+
+
+	std::ifstream fipr;
+	fipr.open(fParFileName.Data());
+	if (!fipr.is_open()) {
+		cerr << "\"AculCalibration::SetInputsParameters\" File with input parameters \""
+				<< fParFileName << "\" was not opened." << endl;
+		return;
+	}
+
+	cout << "\"AculCalibration::SetInputsParameters\" File with input parameters \""
+			<< fParFileName << "\" will be processed." << endl;
+
+	while (!fipr.eof()) {
+
+		fipr.getline(line, lineLength);
+		if (strlen(line) < 2) {
+			continue;
+		}
+
+		sscanf(line, "%s %s", parameter, identificator);
+
+		if ( strcmp(identificator, "noPeaks") == 0 ) {
+			kRaNOPEAKS = static_cast<Int_t>(atoi(parameter));
+			fEnergyInput.resize(kRaNOPEAKS);
+			fEtab.resize(kRaNOPEAKS);
+			for (Int_t i = 0; i < kRaNOPEAKS; i++) {
+				fipr.getline(line, lineLength);
+				sscanf(line, "%s", parameter);
+				fEnergyInput[i] = static_cast<Double_t>(atof(parameter));
+			}
+			continue;
+		}//if
+
+		if ( strcmp(identificator, "lowerChannel") == 0 ) {
+			sscanf(line, "%s", parameter);
+			fLowerChannel = static_cast<Double_t>(atof(parameter));
+		}
+
+		if ( strcmp(identificator, "upperChannel") == 0 ) {
+			sscanf(line, "%s", parameter);
+			fUpperChannel = static_cast<Double_t>(atof(parameter));
+		}
+
+		if ( strcmp(identificator, "lowerPeakHight") == 0 ) {
+			sscanf(line, "%s", parameter);
+			fLowerPeakRelativeHight = static_cast<Double_t>(atof(parameter));
+		}
+
+		if ( strcmp(identificator, "upperPeakHight") == 0 ) {
+			sscanf(line, "%s", parameter);
+			fUpperPeakRelativeHight = static_cast<Double_t>(atof(parameter));
+		}
+
+		if ( strcmp(identificator, "peakPositionTolerance") == 0 ) {
+			sscanf(line, "%s", parameter);
+			fPeakPositionTolerance = static_cast<Double_t>(atof(parameter));
+		}
+
+		if ( strcmp(identificator, "fitFunctionLineWidth") == 0 ) {
+			sscanf(line, "%s", parameter);
+			fFitFuncLineWidth = static_cast<Width_t>(atoi(parameter));
+		}
+
+		if ( strcmp(identificator, "minFitSigma") == 0 ) {
+			sscanf(line, "%s", parameter);
+			fFitMinSigma = static_cast<Double_t>(atof(parameter));
+		}
+
+		if ( strcmp(identificator, "fitHightThreshold") == 0 ) {
+			sscanf(line, "%s", parameter);
+			fFitPeakThreshold = static_cast<Double_t>(atof(parameter));
+		}
+
+		if ( strcmp(identificator, "deadLayer") == 0 ) {
+			sscanf(line, "%s", parameter);
+			fDeadLayer = static_cast<Double_t>(atof(parameter));
+		}
+
+	}
+
+
+	fipr.close();
+
+	return;
+}
+
+void AculCalParsSi::PrintParameters(const char* option)
+{
+	//print alpha source parameters
+
+	cout << "AculCalibration::PrintInputParameters:" << endl;
+	cout << "\tNumber of peaks: " << kRaNOPEAKS << endl;
+	for (Int_t i = 0; i < kRaNOPEAKS; i++) {
+		cout << "\t\tfEnergyInput[" << i << "] = " << fEnergyInput[i] << " MeV" << endl;
+	}
+	cout << "\tEnergies used for calibration:" << endl;
+	cout << "\t(deadLayer: " << fDeadLayer << " mcm)" << endl;
+	for (Int_t i = 0; i < kRaNOPEAKS; i++) {
+		cout << "\t\tfE[" << i << "] = " << fEtab[i] << " MeV" << endl;
+	}
+
+	cout << "\tlowerChannel: " << fLowerChannel << "; upperChannel: " << fUpperChannel << ";" << endl;
+	cout << "\tlowerPeakHight: " << fLowerPeakRelativeHight << "; upperPeakHight: " << fUpperPeakRelativeHight << ";" << endl;
+	cout << "\tfitHightThreshold: " << fFitPeakThreshold << "; minFitSigma: " << fFitMinSigma << ";" << endl;
+	cout << "\tpeakPositionTolerance: " << fPeakPositionTolerance << ";" << endl;
+	cout << "\tfitFunctionLineWidth: " << fFitFuncLineWidth << ";" << endl;
+
+	return;
+
+}
+
+void AculCalParsSi::SetELosses() {
+
+	Info("AculCalibration::SetELosses", "Combination of aplha particle with silicon material only.");
+	fAlphaSi.SetEL(1, 2.321); // density in g/cm3
+	fAlphaSi.AddEL(14., 28.086, 1);  //Z, mass
+//	mSi.SetZP(1., 1.);		//protons
+	fAlphaSi.SetZP(2., 4.);		//alphas, Z, A
+	fAlphaSi.SetEtab(100000, 200.);	// ?, MeV calculate ranges
+	fAlphaSi.SetDeltaEtab(300);
+}
+
+void AculCalParsSi::SetCalEnergies() {
+
+	if (fDeadLayer<=0.) {
+		Warning("AculCalibration::SetCalEnergies", "Dead layer was set equal or less than 0.");
+		for(Int_t i = 0; i < kRaNOPEAKS; i++) {
+			fEtab[i] = fEnergyInput[i];
+		}
+		Info("AculCalibration::SetCalEnergies", "Energies used for calibration are the same as input file.");
+		return;
+	}
+
+	for(Int_t i = 0; i < kRaNOPEAKS; i++) {
+		fEtab[i] = fAlphaSi.GetE(fEnergyInput[i], fDeadLayer);
+	}
+	Info("AculCalibration::SetCalEnergies", "Energies used for calibration considering %f mcm dead layer were set.", fDeadLayer);
+
+	return;
+}

AculCalib/AculCalParsSi.h

+/*
+ * AculCalParsSi.h
+ *
+ *  Created on: Oct 26, 2016
+ *      Author: vratik
+ */
+
+#ifndef ACULCALIB_ACULCALPARSSI_H_
+#define ACULCALIB_ACULCALPARSSI_H_
+
+#include "AculCalPars.h"
+#include "../TELoss/TELoss.h"
+
+class AculCalParsSi: public AculCalPars {
+private:
+	Int_t kRaNOPEAKS;
+//	TArrayD		fEnergy;		//energy after passing through deadlayer
+	vector<Double_t> fEnergyInput;		//incidental energy, set from .par
+	Double_t fLowerChannel;
+	Double_t fUpperChannel;
+	Double_t fLowerPeakRelativeHight;	//pouziva se, private
+	Double_t fUpperPeakRelativeHight;	//pouziva se, private, nastavit nenulovou prednastavenou hodnotu
+	Double_t fPeakPositionTolerance;		//pouziva se, private
+	Width_t	fFitFuncLineWidth;			//private
+	Double_t fFitMinSigma;				//pouziva se, private
+	Double_t fFitPeakThreshold;			//pouziva se, private, prozkoumat, k cemu vlastne slouzi ve fci ShowPeaks, popremyslet o vhodnem prednastaveni v konstruktoru
+	Double_t fDeadLayer;					//in mcm; it will be used for recalculation of energies outcomming from the alpha source
+
+	TELoss fAlphaSi;
+
+public:
+	AculCalParsSi();
+	AculCalParsSi(const char* parFile);
+	virtual ~AculCalParsSi();
+	ClassDef(AculCalParsSi, 1);
+
+	void Init();
+	// Function which loads text file containing parameters for calibration
+	//
+	//	-inputparfile: file containing information on calibration source
+	//	-In file with the data must be preserved systematic
+	//	-There cannot be whitelines (probably)
+	//
+	//Example of "parforcal.par" file
+	//................................................................
+	//223Ra
+	//
+	//4		nopeaks		//number of peaks
+	//4.415		E1		//in MeV
+	//5.153		E2		//in MeV
+	//5.683		E3		//in MeV
+	//7.419		E4		//in MeV
+	//100		lowerchannel	//in channels
+	//4096		upperchannel	//in channels
+	//0.1		lowerpeakhight		//in relative units
+	//0.1		upperpeakhight		//in relative units
+	//0.1		peakpositiontolerance	//in relative units
+	//2		fitfunctionlinewidth	//integer 1 - 10
+	//5		minfitsigma		//minimal sigma of the peaks to be fitted
+	//0.4		fithightthreshold	//
+	//................................................................
+	void Reset();
+
+	void PrintParameters(const char* option = "");
+	//I hope this is selfunderstanding function
+
+
+private:
+	void SetPars();
+	void SetELosses();
+	void SetCalEnergies();
+};
+
+#endif /* ACULCALIB_ACULCALPARSSI_H_ */

AculCalib/AculCalib.cpp

+#include "AculCalib.h"
+
+//----------------------------------------------------------------------------
+AculCalib::AculCalib() {
+//documentation example
+	printf("AculCalib::Default constructor called.\n");
+
+	Init();
+
+}
+
+//----------------------------------------------------------------------------
+/*AculCalib::AculCalib(const char* parfile) {
+	printf("AculCalib::Constructor called.\n");
+
+	SetParFile(parfile);
+	Init();
+
+}*/
+
+//----------------------------------------------------------------------------
+AculCalib::~AculCalib() {
+
+	printf("AculCalib::Destructor called.\n");
+
+	delete fPars;
+
+}
+
+//----------------------------------------------------------------------------
+void AculCalib::Init() {
+
+	fPars = 0;
+}
+
+//----------------------------------------------------------------------------
+void AculCalib::SetParFile(const char* parfile) {
+
+	fParFileName = parfile;
+	return;
+}
+
+//----------------------------------------------------------------------------
+void AculCalib::PrintParameters(const char* option) {
+	if (!fPars) {
+		cerr << "\"AculCalib::PrintParameters\" parameters were not initialized." << endl;
+		return;
+	}
+
+	fPars->PrintParameters(option);
+}
+
+//----------------------------------------------------------------------------
+void AculCalib::PrintCalibParameters() {
+	cout << "i\ta\t\b" << endl;
+	for (Int_t i = 0; i<=(Int_t)fA.size(); i++) {
+		cout << i << "\t" << fA[i] << "\t" << fB[i] << endl;
+	}
+}
+
+//----------------------------------------------------------------------------
+Double_t AculCalib::GetA(Int_t i) {
+	if (i >= (Int_t)fA.size()) //if i >= number of array element
+	{
+		return 0.;
+	}
+	return fA[i];
+}
+
+//----------------------------------------------------------------------------
+Double_t AculCalib::GetB(Int_t i) {
+	if (i >= (Int_t)fB.size()) //if i >= number of array element
+	{
+		return 0.;
+	}
+	return fB[i];
+}
+
+//----------------------------------------------------------------------------
+void AculCalib::CanDivider(TCanvas *c, Int_t noPads, Int_t columns, Int_t rows) {
+
+	c->Clear();
+
+	if (noPads == 16) {
+		c->Divide(4, 4);
+		return;
+	}
+
+	if (rows != 0 && columns != 0) {
+		c->Divide(columns, rows);
+		return;
+	}
+}
+
+//----------------------------------------------------------------------------
+ClassImp(AculCalib);

AculCalib/AculCalib.h

+////////////////////////////////////////////////////////////////
+//                                                            //
+// TMyClass                                                   //
+//                                                            //
+// This is the description block.                             //
+//                                                            //
+////////////////////////////////////////////////////////////////
+
+#ifndef ACULCALIB_ACULCALIB_H_
+#define ACULCALIB_ACULCALIB_H_
+
+//#include "TObject.h"
+//#include "TROOT.h"
+#include <iostream>
+#include <fstream>
+
+#include "TArrayD.h"
+#include "TString.h"
+#include "TCanvas.h"
+
+#include "./AculCalPars.h"
+
+using std::cout;
+using std::endl;
+using std::cerr;
+
+class AculCalib {
+
+protected:
+	vector<Double_t> fA;	//calibration parameter A
+	vector<Double_t> fB;	//calibration parameter A
+
+	TString fParFileName;	//name of file with parameters
+
+	AculCalPars *fPars;		//parameters used for calibration
+
+public:
+	//Default constructor.
+	AculCalib();
+
+	//Destructor.
+	virtual ~AculCalib();
+	ClassDef(AculCalib,1);
+
+	virtual void Init();
+
+	void SetParFile(const char* parfile);
+	const char* GetParFileName() {return fParFileName.Data();}
+
+	//Print parameters used for calibration.
+	void PrintParameters(const char* option = "");
+	//Print calibration parameters.
+	void PrintCalibParameters();
+
+	//Get calibration parameter A.
+	Double_t GetA(Int_t i);
+	//Get calibration parameter B.
+	Double_t GetB(Int_t i);
+
+protected:
+	void CanDivider(TCanvas *c, Int_t noPads, Int_t columns = 0, Int_t rows = 0);
+
+};
+
+#endif

AculCalib/AculCalib.mk

+################################################################################
+# AculData input with some variables
+################################################################################
+
+# ACULCALIBLIBS := -lCore -lCint -lRIO -lTree -lNet -lThread -lHist -lMatrix -lMathCore -lGpad -lGraf -lSpectrum #-lTELoss
+ACULCALIBLIBS := -lCore -lRIO -lTree -lNet -lThread -lHist -lMatrix -lMathCore -lGpad -lGraf -lSpectrum #-lTELoss
+
+# Add inputs and outputs from these tool invocations to the build variables 
+ACULCALIB_HEADERS += \
+$(ACULCALIB)/AculCalib.h \
+$(ACULCALIB)/AculCalibScint.h \
+$(ACULCALIB)/AculCalibSi.h \
+$(ACULCALIB)/AculCalPars.h \
+$(ACULCALIB)/AculCalParsScint.h \
+$(ACULCALIB)/AculCalParsScintFile.h \
+$(ACULCALIB)/AculCalParsSi.h \
+$(ACULCALIB)/AculCalibLinkDef.h
+
+ACULCALIBCPP_SRCS += \
+$(ACULCALIB)/AculCalib.cpp \
+$(ACULCALIB)/AculCalibScint.cpp \
+$(ACULCALIB)/AculCalibSi.cpp \
+$(ACULCALIB)/AculCalPars.cpp \
+$(ACULCALIB)/AculCalParsScint.cpp \
+$(ACULCALIB)/AculCalParsScintFile.cpp \
+$(ACULCALIB)/AculCalParsSi.cpp \
+$(ACULCALIB)/AculCalibDict.cpp
+
+ACULCALIBOBJS += \
+$(ACULCALIB)/AculCalib.o \
+$(ACULCALIB)/AculCalibScint.o \
+$(ACULCALIB)/AculCalibSi.o \
+$(ACULCALIB)/AculCalPars.o \
+$(ACULCALIB)/AculCalParsScint.o \
+$(ACULCALIB)/AculCalParsScintFile.o \
+$(ACULCALIB)/AculCalParsSi.o \
+$(ACULCALIB)/AculCalibDict.o
+
+ACULCALIBCPP_DEPS += \
+$(ACULCALIB)/AculCalib.d \
+$(ACULCALIB)/AculCalibScint.d \
+$(ACULCALIB)/AculCalibSi.d \
+$(ACULCALIB)/AculCalPars.d \
+$(ACULCALIB)/AculCalParsScint.d \
+$(ACULCALIB)/AculCalParsScintFile.d \
+$(ACULCALIB)/AculCalParsSi.d \
+$(ACULCALIB)/AculCalibDict.d
\ No newline at end of file

AculCalib/AculCalibLinkDef.h

+#ifdef __CINT__
+#pragma link off all globals;
+#pragma link off all classes;
+#pragma link off all functions;
+
+//#pragma link C++ class AculRaw;
+//#pragma link C++ class AculConvert;
+#pragma link C++ class AculCalib;
+#pragma link C++ class AculCalibScint;
+#pragma link C++ class AculCalibSi;
+#pragma link C++ class AculCalPars;
+#pragma link C++ class AculCalParsScint;
+#pragma link C++ class AculCalParsScintFile;
+#pragma link C++ class AculCalParsSi;
+
+#endif
+

AculCalib/AculCalibScint.h

+//////////////////////////////////////////////////////////////////////////////
+//                                                            				//
+// This class is intended for ...                             				//
+//                                                            				//
+// It work like this... User may use such functions ... in such steps.      //
+//
+// Keywords in parameter file and possible comments
+//
+// Something about order of keywords
+//
+// Example of parameter file (with explanations)
+//
+//			energies	4	#number of energy points
+//			crystals	16	#number of crystals in detector
+//			files 4
+//			#fileID		fileName
+//			#fileID not implemented yet
+//			data/csi_13_Ealpha16.root
+//			data/csi_13_Ealpha21.root
+//			data/csi_13_Ealpha26.root
+//			data/csi_13_Ealpha30.root
+//			#keyword	detector	particle
+//			detector	SQ13  Alpha
+//			#keyword	energy [MeV/A]
+//			energy 66.542
+//			#keyword;	filename;	number of cuts in file
+//			cutFile cuts/cutsSQ13Alpha.root	2
+//			cutsSQ13Alpha16
+//			cutSQ13Alpha16Amp
+//			#channel	minimum	maximum
+//			0	650		830
+//			1	920		1150
+//\			...
+//			15	800		1000
+//			#CsI2, energy ~ 21 MeV/A, Alpha
+//			energy 85.437
+//			#keyword;	filename;	number of cuts in file
+//			cutFile cuts/cutsSQ13Alpha.root	2
+//			cutSQ13Alpha21
+//			cutSQ13Alpha21Amp
+//			#channel	minimum	maximum
+//			0	1050	1200
+//\			\...
+//			15	1150	1350
+//			#CsI2, energy ~ 26 MeV/A, Alpha
+//			energy 105.5
+//			...
+//
+//asdasd
+//////////////////////////////////////////////////////////////////////////////
+
+
+#pragma once
+
+//#include "TObject.h"
+//#include "TROOT.h"
+#include <iostream>
+#include <fstream>
+//#include <vector>
+
+#include "TFile.h"
+#include "TTree.h"
+//#include "TCanvas.h"
+#include "TH1I.h"
+#include "TGraphErrors.h"
+//#include "TArrayD.h"
+#include "TF1.h"
+
+#include "./AculCalib.h"
+
+using std::cout;
+using std::endl;
+//using std::vector;
+
+class AculCalibScint : public AculCalib {
+
+private:
+//
+	//todo delete this strange double array somewhere
+	TFile **fInFiles;	//! doc of class member
+	TTree **fTrees;		//!
+
+	TFile *fCutFile;
+
+	vector< vector<TH1I*> > fHistFull;
+	vector< vector<TH1I*> > fHistCut;
+//
+	vector< vector<Double_t> > fMeanPeakPos; //doc of class member
+	vector< vector<Double_t> > fMeanPeakRMS;
+//
+	//todo make vector of graphs
+	TGraphErrors *gCal[16];
+//	TFile *fGraphs;
+
+public:
+	AculCalibScint();
+	//default constructor
+
+	AculCalibScint(const char* parfile);
+	virtual ~AculCalibScint();
+	ClassDef (AculCalibScint,1);	//decription right after ClassDef
+
+	virtual void Init();
+
+	void PrintTrees();
+
+	//Description of the function. I think it does not work.
+	void DrawVariable(const char* variable, Int_t treeID, TCanvas *canvas, Int_t lowRange = 0, Int_t upRange = 4096);
+
+	//Description of the function. I think it does not work.
+	void DrawBeam(TCanvas *canvas, Int_t file, const char* variable);
+
+	//One of the crucial function. It founds the mean of the peak related to our particle.
+	void GetPeakMean(const char* variable, Int_t treeID, TCanvas *canvas,
+			const char* beamcut, const Int_t nbins = 4096, Int_t lowRange = 0);
+	void Calibrate(TCanvas *canvas, Bool_t savefile = 0, const char* filename = "", const char* option = "READ");
+
+	void WriteClbParameters(const char* filename);
+
+	TTree* GetTree(Int_t treeID);
+
+//private functions:
+//	void LoadCuts();
+
+private:
+	void OpenFiles();
+	void LoadTrees();
+
+	void SaveClbGraphs(const char* filename, const char* option = "READ");
+	void FillGraph(TGraphErrors *g, Int_t npoints, /*Double_t *energies,*/ Int_t graphNumber, const char* option = "");
+
+
+//	void SetPars();
+};

AculCalib/AculCalibSi.cpp

+/*
+ * AculCalibSi.cpp
+ *
+ *  Created on: Oct 26, 2016
+ *      Author: vratik
+ */
+
+#include "AculCalibSi.h"
+#include "AculCalParsSi.h"
+
+ClassImp(AculCalibSi);
+
+AculCalibSi::AculCalibSi() {
+	printf("AculCalibScint::Default constructor called.\n");
+//	fInFiles = 0;
+//	fTrees = 0;
+//	fCutFile = 0;
+}
+
+AculCalibSi::AculCalibSi(const char* parfile) {
+	printf("AculCalibScint::Constructor called.\n");
+
+	SetParFile(parfile);
+	Init();
+}
+
+AculCalibSi::~AculCalibSi() {
+
+	printf("AculCalibScint::Destructor called.\n");
+
+}
+
+void AculCalibSi::Init() {
+	fPars = new AculCalParsSi(fParFileName.Data());
+}

AculCalib/AculCalibSi.h

+/*
+ * AculCalibSi.h
+ *
+ *  Created on: Oct 26, 2016
+ *      Author: vratik
+ */
+
+#ifndef ACULCALIB_ACULCALIBSI_H_
+#define ACULCALIB_ACULCALIBSI_H_
+
+#include "AculCalib.h"
+
+class AculCalibSi: public AculCalib {
+private:
+
+//	Double_t something;
+
+public:
+	AculCalibSi();
+	AculCalibSi(const char* parfile);
+	virtual ~AculCalibSi();
+	ClassDef(AculCalibSi, 1);
+
+	void Init();
+
+//	Bool_t	CalculateCalibParameters(const char* inputfile, const char* block,
+//			const char* treename, Int_t lowerchannel = 0,
+//			Int_t upperchannel = 4095, Int_t nEBins = 1000, Int_t lowersubaddress = 0,
+//			Int_t uppersubaddress = ADDRESSNUMBER-1); //calculate calibration parameters for given block in given file
+	//function is not completely ready to use
+	//
+	//function for calculation of calibrate parameters for DAQ system based on "Go4"
+	//
+	//  inputfile: root file with calibration spectra
+	//  block: block name to be calibrated
+	//  lowerchannel: minimal channel from which the spectrum will be analysed
+	//  upperchannel: maximal channel up to which the spectrum will be analysed
+	//  lowersubaddress: block subaddress
+	//  uppersubaddress: block subbaddress
+
+
+};
+
+#endif /* ACULCALIB_ACULCALIBSI_H_ */

AculCalib/CMakeLists.txt

+############################################################################
+# CMakeLists.txt file for building AculCalib package
+############################################################################
+
+ROOT_STANDARD_LIBRARY_PACKAGE(AculCalib
+  HEADERS
+    AculCalib.h
+    AculCalibScint.h
+    AculCalibSi.h
+    AculCalPars.h
+    AculCalParsScintFile.h
+    AculCalParsScint.h
+    AculCalParsSi.h
+  SOURCES
+    AculCalib.cpp
+    # AculCalibDict.cpp
+    AculCalibScint.cpp
+    AculCalibSi.cpp
+    AculCalPars.cpp
+    AculCalParsScint.cpp
+    AculCalParsScintFile.cpp
+    AculCalParsSi.cpp
+#   DEPENDENCIES
+#     MathCore
+#     Matrix
+#     RIO
+   LINKDEF
+     AculCalibLinkDef.h
+)
+
+# ROOT_ADD_TEST_SUBDIRECTORY(test)
+
+# install(FILES ${CMAKE_CURRENT_BINARY_DIR}/G__AculCalib.cxx DESTINATION ${CMAKE_BINARY_DIR}/include)
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libAculCalib.rootmap DESTINATION ${CMAKE_BINARY_DIR}/lib)
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libAculCalib_rdict.pcm DESTINATION ${CMAKE_BINARY_DIR}/lib)
+install(TARGETS AculCalib LIBRARY DESTINATION ${CMAKE_BINARY_DIR}/lib ARCHIVE DESTINATION ${CMAKE_BINARY_DIR}/lib)
\ No newline at end of file

AculData/AculCalibCsI.h

@@ -44,8 +44,8 @@ private:
 	Int_t nCuts;				//number of cuts
 	TClonesArray cutsCol;
 
-	TH1I *hfull[NOCALFILES][16];
-	TH1I *hcut[NOCALFILES][16];
+	TH1I *hfull[NOCALFILES][16];	//!
+	TH1I *hcut[NOCALFILES][16];		//!
 
 	Int_t peakMin[NOCALFILES][16];
 	Int_t peakMax[NOCALFILES][16];

AculData/AculCalibration.cpp

@@ -393,7 +393,7 @@ Bool_t AculCalibration::SetCalibrationParameters(const char* calparfile)
 	char	cA[40], cB[40], cC[40], cD[40];
 
 	//open file with calibration parameters
-	ifstream calFileR;
+	std::ifstream calFileR;
 	calFileR.open(calparfile);
 
 
@@ -439,10 +439,10 @@ void AculCalibration::ShowRawSpectra(const char* filename, const Int_t block, TC
 	//  xaxismax: maximal channel, which will be displayed
 	//  subaddress:
 
-	Char_t address[40];
-	Char_t histName[40];
-	Char_t fillCommand[40];
-	Char_t fillCondition[40];
+	TString address;
+	TString histName;
+	TString command;
+	TString condition;
 
 
 	if (!rawCanvas) {
@@ -453,11 +453,8 @@ void AculCalibration::ShowRawSpectra(const char* filename, const Int_t block, TC
 
 	rawCanvas->Clear();
 
-//	cout << "hovno" << endl;
-
 	rawCanvas->SetFillColor(10);
 
-//	cout << "hovno" << endl;
 	TFile *fr = new TFile(filename);
 	if (fr->IsOpen() == 0) {
 		cout << endl << "File " << filename << " was not opened and won't be processed" << endl << endl;
@@ -465,23 +462,21 @@ void AculCalibration::ShowRawSpectra(const char* filename, const Int_t block, TC
 	}
 	TH1I *hRead = 0;
 	TTree *tr = (TTree*)fr->Get("RAW");
-//	cout << "hovno" << endl;
-
 
 	if (subaddress > 15) {
 		rawCanvas->Divide(4, 4);
 		rawCanvas->SetFillColor(10);
-//		cout << "hovno" << endl;
 		for (Int_t i = 0; i < 16; i++) {
 			cout << i << endl;
 			rawCanvas->cd(i+1);
 			hRead = new TH1I("name", "title", 4096, 0, 4095);
-			sprintf(address, "C3[%d][%d]", block, i);
-			sprintf(histName, "H3[%d][%d]", block, i);
+			address.Form("C3[%d][%d]", block, i);
+			histName.Form("H3[%d][%d]", block, i);
 			hRead->SetName(histName);
-			sprintf(fillCommand, "%s >> %s", address, hRead->GetName());
-			sprintf(fillCondition, "%s > 0", address);
-			tr->Draw(fillCommand, fillCondition, "");
+			command.Form("%s >> %s", address.Data(), hRead->GetName());
+			// sprintf(fillCondition, "%s > 0", address);
+			condition.Form("%s > 0", address.Data());
+			tr->Draw(command, condition, "");
 			if (hRead) {
 				hRead->SetDirectory(0);
 //				cout << hRead->GetEntries() << endl;
@@ -496,13 +491,14 @@ void AculCalibration::ShowRawSpectra(const char* filename, const Int_t block, TC
 	else {
 		fr->cd();
 		hRead = new TH1I("name", "title", 4096, 0, 4095);
-		sprintf(address, "C3[%d][%d]", block, subaddress);
-		sprintf(histName, "H3[%d][%d]", block, subaddress);
+		address.Form("C3[%d][%d]", block, subaddress);
+		histName.Form("H3[%d][%d]", block, subaddress);
 		hRead->SetName(histName);
-		sprintf(fillCommand, "%s >> %s", address, hRead->GetName());
-		sprintf(fillCondition, "%s > 0", address);
+		command.Form("%s >> %s", address.Data(), hRead->GetName());
+		// sprintf(fillCondition, "%s > 0", address);
+		condition.Form("%s > 0", address.Data());
 //		cout << fillCommand << setw(20) << fillCondition << endl;
-		tr->Draw(fillCommand, fillCondition, "goff");
+		tr->Draw(command, condition, "goff");
 		if (hRead) {
 			hRead->SetDirectory(0);
 //			if (fHRawList) {
@@ -621,11 +617,16 @@ void AculCalibration::FillRawSpectraFile(const char* rawdatafile, const char* bl
 		return;
 	}
 
-	char address[40];
-	char histName[40];
-	char histTitle[40];
-	char fillCommand[40];
-	char fillCondition[40];
+	// char address[40];
+	// char histName[40];
+	// char histTitle[40];
+	// char fillCommand[40];
+	// char fillCondition[40];
+	TString address;
+	TString histName;
+	TString histTitle;
+	TString command;
+	TString condition;
 
 	fw.cd();
 	TH1I *hRead = 0;
@@ -633,14 +634,16 @@ void AculCalibration::FillRawSpectraFile(const char* rawdatafile, const char* bl
 	for (Int_t i = 0; i < 16; i++) {	//zkontrolovat hranice
 		cout << i << endl;	//predelat na info
 		hRead = new TH1I("name", "title", 4096, 0, 4095);
-		sprintf(address, "%s[%d]", block, i);
-		sprintf(histName, "%s[%d]", block, i);
-		sprintf(histTitle, "%s : %s", rawdatafile, histName);
+		address.Form("%s[%d]", block, i);
+		histName.Form("%s[%d]", block, i);
+		histTitle.Form("%s : %s", rawdatafile, histName.Data());
 		hRead->SetName(histName);
 		hRead->SetTitle(histTitle);
-		sprintf(fillCommand, "%s >> %s", address, hRead->GetName());
-		sprintf(fillCondition, "%s > 0", address);
-		tr->Draw(fillCommand, fillCondition, "goff");		//prozkoumat goff
+		// sprintf(fillCommand, "%s >> %s", address, hRead->GetName());
+		command.Form("%s >> %s", address.Data(), hRead->GetName());
+		// sprintf(fillCondition, "%s > 0", address);
+		condition.Form("%s > 0", address.Data());
+		tr->Draw(command, condition, "goff");		//prozkoumat goff
 		hRead->Write();
 	}//for
 
@@ -679,7 +682,7 @@ Bool_t AculCalibration::CalculateCalibParameters(const char* inputfile, const ch
 		else { oFileName.Form("%s[%d-%d].cal", block, lowersubaddress, uppersubaddress); }
 	}//if
 
-	ofstream outcalfile;
+	std::ofstream outcalfile;
 	outcalfile.open(oFileName.Data());
 	if (!outcalfile.is_open()) {
 		Error("CalculateCalibParameters", "Output file %s was not opened", oFileName.Data());
@@ -1087,7 +1090,7 @@ void AculCalibration::FindEnergyPeaks(TCanvas *c1, const char* ifile, const char
 
 	//creation of output text file with positions of peaks in MeV
 	TString workFile = outfile;
-	ofstream ofile;
+	std::ofstream ofile;
 	ofile.open(workFile.Data());
 	if (!ofile.is_open()) {
 		Error("PeaksFitting", "Output file %s was not opened", workFile.Data());
@@ -1128,7 +1131,7 @@ void AculCalibration::FindAverageEnergies(const char* ifile, const char* outfile
 
 	//creation of output text file with average values of peak energies in MeV
 	TString workFile = outfile;
-	ofstream ofile;
+	std::ofstream ofile;
 	ofile.open(workFile.Data());
 	if (!ofile.is_open()) {
 		Error("PeaksFitting", "Output file %s was not opened", workFile.Data());
@@ -1380,7 +1383,7 @@ void AculCalibration::SetInputParameters() {
 	Char_t	identificator[100];
 
 
-	ifstream fipr;
+	std::ifstream fipr;
 	fipr.open(fParFileName.Data());
 	if (!fipr.is_open()) {
 		Error("AculCalibration::SetInputsParameters", "File with input parameters \"%s\" was not opened.", fParFileName.Data());

AculData/AculData.mk

@@ -2,25 +2,25 @@
 # AculData input with some variables
 ################################################################################
 
-ACULDATALIBS := -lCore -lCint -lRIO -lTree -lNet -lThread -lHist -lMatrix -lMathCore -lGpad -lGraf -lSpectrum #-lTELoss
+ACULDATALIBS := -lCore -lRIO -lTree -lNet -lThread -lHist -lMatrix -lMathCore -lGpad -lGraf -lSpectrum #-lTELoss
 
 # Add inputs and outputs from these tool invocations to the build variables 
 ACULDATA_HEADERS += \
 $(ACULDATA)/AculCalibration.h \
 $(ACULDATA)/AculCalibCsI.h \
-$(ACULDATA)/linkdef.h
+$(ACULDATA)/AculDataLinkDef.h
 
 ACULDATACPP_SRCS += \
 $(ACULDATA)/AculCalibration.cpp \
 $(ACULDATA)/AculCalibCsI.cpp \
-$(ACULDATA)/AculDataCint.cpp
+$(ACULDATA)/AculDataDict.cpp
 
 ACULDATAOBJS += \
 $(ACULDATA)/AculCalibration.o \
 $(ACULDATA)/AculCalibCsI.o \
-$(ACULDATA)/AculDataCint.o
+$(ACULDATA)/AculDataDict.o
 
 ACULDATACPP_DEPS += \
 $(ACULDATA)/AculCalibration.d \
 $(ACULDATA)/AculCalibCsI.d \
-$(ACULDATA)/AculDataCint.d
\ No newline at end of file
+$(ACULDATA)/AculDataDict.d
\ No newline at end of file

AculData/linkdef.h → AculData/AculDataLinkDef.h

-#ifdef __CINT__
+#ifdef __CLING__
 #pragma link off all globals;
 #pragma link off all classes;
 #pragma link off all functions;
@@ -9,6 +9,4 @@
 #pragma link C++ class AculCalibCsI;
 //#pragma link C++ class ConfigDictionary;
 
-
 #endif
\ No newline at end of file
-

AculData/CMakeLists.txt

+############################################################################
+# CMakeLists.txt file for building AculData package
+############################################################################
+
+ROOT_STANDARD_LIBRARY_PACKAGE(AculData
+  HEADERS
+    AculCalibCsI.h
+    AculCalibration.h
+  SOURCES
+    AculCalibCsI.cpp
+    AculCalibration.cpp
+#   DEPENDENCIES
+#     MathCore
+#     Matrix
+#     RIO
+   LINKDEF
+     AculDataLinkDef.h
+)
+
+# ROOT_ADD_TEST_SUBDIRECTORY(test)
+
+# install(FILES ${CMAKE_CURRENT_BINARY_DIR}/G__AculData.cxx DESTINATION ${CMAKE_BINARY_DIR}/include)
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libAculData.rootmap DESTINATION ${CMAKE_BINARY_DIR}/lib)
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libAculData_rdict.pcm DESTINATION ${CMAKE_BINARY_DIR}/lib)
+install(TARGETS AculData LIBRARY DESTINATION ${CMAKE_BINARY_DIR}/lib ARCHIVE DESTINATION ${CMAKE_BINARY_DIR}/lib)
\ No newline at end of file

AculData/ConfigDictionary.h

-#ifndef CONFIGDICTIONARY_H
-#define CONFIGDICTIONARY_H
-
-
-#include "TObject.h"
-#include "ReturnCodes.h"
-#include "TStopwatch.h"
-#include "TROOT.h"
-#include <string>
-#include <map>
-#include <sstream>
-#include "TLorentzVector.h"
-#include <iostream>
-#include "TMath.h"
-#include "TString.h"
-#include "TTree.h"
-
-
-class ConfigDictionary{
-public:
-	typedef std::map<std::string,std::string>::iterator CDIter;
-	ConfigDictionary();
-	ConfigDictionary(std::string);
-	virtual ~ConfigDictionary(){};//empty virtual destructor
-
-	ClassDef(ConfigDictionary,1);
-	std::string ToString();
-	void FromString(std::string);
-
-	//These throw errors if couldn't find key:
-	std::string GetString(std::string)throw(std::string);
-	int	GetInt(std::string)throw(std::string);
-	double GetDouble(std::string)throw(std::string);
-	bool GetBool(std::string)throw(std::string);
-
-	//These will always set 'something' into map:
-	void SetString(std::string,std::string);
-	void SetDouble(std::string,double);
-	void SetInt(std::string,int);
-	void SetBool(std::string,bool);
-	
-	CDIter Begin(){return configMap.begin();};
-	CDIter End(){return configMap.end();};
-
-private:
-	std::map<std::string,std::string> configMap;
-};
-
-#endif

CMakeLists.txt

+cmake_minimum_required(VERSION 3.0)
+project(AculUtils)
+
+# Find ROOT package
+find_package(ROOT REQUIRED)
+
+# Set installation prefix
+# set(CMAKE_INSTALL_PREFIX "..")
+
+# Set output directories for built targets
+# set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
+# set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
+
+message(STATUS "CMAKE_LIBRARY_OUTPUT_DIRECTORY is: ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}")
+
+
+# file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/lib) # prevent mkdir races
+# set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
+# set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
+# set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
+
+# message(STATUS "ROOT Configuration \n
+# System          ${CMAKE_SYSTEM}
+# Processor       ${PROCESSOR} (${CMAKE_SYSTEM_PROCESSOR})
+# Build type      ${CMAKE_BUILD_TYPE}
+# Install path    ${CMAKE_INSTALL_PREFIX}
+# Compiler        ${CMAKE_CXX_COMPILER_ID} ${CMAKE_CXX_COMPILER_VERSION}
+# Compiler flags:
+# C               ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${_BUILD_TYPE_UPPER}}
+# C++             ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${_BUILD_TYPE_UPPER}}
+# Linker flags:
+# Executable      ${CMAKE_EXE_LINKER_FLAGS}
+# Module          ${CMAKE_MODULE_LINKER_FLAGS}
+# Shared          ${CMAKE_SHARED_LINKER_FLAGS}\n")
+
+# Add include directories for ROOT
+include_directories(${ROOT_INCLUDE_DIRS})
+# Print the value of ROOT_INCLUDE_DIRS
+message(STATUS "ROOT include directories: ${ROOT_INCLUDE_DIRS}")
+message(STATUS "ROOT_GET_INSTALL_DIR: ${ROOT_GET_INSTALL_DIR}")
+# ROOT_GET_INSTALL_DIR
+ROOT_GET_INSTALL_DIR(shared_lib_install_dir)
+
+# Add the subdirectories
+add_subdirectory(TELoss)
+add_subdirectory(AculCalib)
+add_subdirectory(AculData)
+add_subdirectory(Utilities)
+
+
+# install(FILES ${CMAKE_CURRENT_BINARY_DIR}/G__AculData.cxx DESTINATION include)
+# install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libAculData.rootmap DESTINATION lib)
+# install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libAculData_rdict.pcm DESTINATION lib)
+# install(TARGETS AculData LIBRARY DESTINATION lib ARCHIVE DESTINATION lib)
+
+
+# Set the output directory for the dictionary files
+# set(GEN_DICT_OUTPUT_DIR ${CMAKE_CURRENT_BINARY_DIR})
+# set(GEN_DICT_OUTPUT_DIR ${CMAKE_BINARY_DIR})
+message(STATUS "GEN_DICT_OUTPUT_DIR: ${GEN_DICT_OUTPUT_DIR}")
+message(STATUS "CMAKE_CURRENT_BINARY_DIR: ${CMAKE_CURRENT_BINARY_DIR}")
+message(STATUS "CMAKE_BINARY_DIR: ${CMAKE_BINARY_DIR}")
+message(STATUS "GEN_DICT_OUTPUT_DIR: ${GEN_DICT_OUTPUT_DIR}")
+message(STATUS "CMAKE_COMMAND: ${CMAKE_COMMAND}")
+
+# set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
+# message(STATUS "CMAKE_LIBRARY_OUTPUT_DIRECTORY: ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}")
+# message(STATUS "shared_lib_install_dir: ${shared_lib_install_dir}")
\ No newline at end of file

README

-  1) set path in makefile according to your operating system
+Tested with 
+root_6.28_04 (precompiled binaries for Ubuntu 20.04)
+root-6.22.08 (compiled from source at nra161: /LynxOS/mbsusr/mbsdaq/analysis/root/root-6.22.08)
+
+I. Use with GNU make
+
+1) set path in makefile according to your operating system
 
 2) type in terminal:
 
@@ -7,3 +13,23 @@
 	make install
 
 3) add the install folder to LD_LIBRARY_PATH
+
+II. Use with cmake
+
+1) mkdir build
+
+2) cd build
+
+3) cmake ..
+
+4) make install
+
+III. Test of compiled libraries
+
+1) cd macros
+
+2) modify libraries paths in rootlogon.C if needed
+
+3) rootlogon.C will automatically load compiled libraries libTELoss.so and libAculData.so, then
+	root -l testOfAculData.cxx
+	root -l testOfTELoss.cxx
\ No newline at end of file

TELoss/CMakeLists.txt

+############################################################################
+# CMakeLists.txt file for building TELoss package
+############################################################################
+
+# include_directories(TELoss)
+
+# Get the list of include directories
+get_property(INCLUDE_DIRS DIRECTORY PROPERTY INCLUDE_DIRECTORIES)
+
+# Print the include directories
+message(STATUS "Include directories: ${INCLUDE_DIRS}")
+message(STATUS "CMAKE_CURRENT_SOURCE_DIR: ${CMAKE_CURRENT_SOURCE_DIR}")
+message(STATUS "CMAKE_CURRENT_BINARY_DIR: ${CMAKE_CURRENT_BINARY_DIR}")
+
+# Add the source files specific to the TELoss module
+set(SOURCES
+    TELoss.cpp
+    TELoss.h
+    TELossLinkDef.h
+)
+
+# Add the Fortran source file
+set(FORTRAN_SOURCES
+    ELOSS.f90
+)
+
+# Generate dictionary for TELoss class
+ROOT_GENERATE_DICTIONARY(
+    G__TELoss
+        ${CMAKE_CURRENT_SOURCE_DIR}/TELoss.h 
+    LINKDEF 
+        ${CMAKE_CURRENT_SOURCE_DIR}/TELossLinkDef.h)
+
+# Add the dictionary source file to the sources list
+list(APPEND SOURCES ${CMAKE_CURRENT_BINARY_DIR}/G__TELoss.cxx)
+
+# Create a library target for the TELoss module
+add_library(TELoss SHARED ${SOURCES} ${FORTRAN_SOURCES})
+
+# Link against ROOT libraries
+target_link_libraries(TELoss ${ROOT_LIBRARIES})
+
+# Set compiler flags for Fortran source
+enable_language(Fortran)
+set_source_files_properties(${FORTRAN_SOURCES} PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/modules)
+
+# install(FILES ${CMAKE_CURRENT_BINARY_DIR}/G__AculData.cxx DESTINATION ${CMAKE_BINARY_DIR}/include)
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libTELoss.rootmap DESTINATION ${CMAKE_BINARY_DIR}/lib)
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libTELoss_rdict.pcm DESTINATION ${CMAKE_BINARY_DIR}/lib)
+install(TARGETS TELoss LIBRARY DESTINATION ${CMAKE_BINARY_DIR}/lib ARCHIVE DESTINATION ${CMAKE_BINARY_DIR}/lib)
\ No newline at end of file

TELoss/TELoss.mk

@@ -2,19 +2,24 @@
 # TELoss input with some variables
 ################################################################################
 
-TELOSSLIBS := -lCore -lCint -lMathCore -lMatrix -lHist -lgfortran
+# TELOSSLIBS := -lCore -lCint -lMathCore -lMatrix -lHist -lgfortran
+TELOSSLIBS := -lCore -lMathCore -lMatrix -lHist -lgfortran
 
 # Add inputs and outputs from these tool invocations to the build variables 
 
+TELOSS_HEADERS += \
+$(TELOSS)/TELoss.h \
+$(TELOSS)/TELossLinkDef.h
+
 TELOSSCPP_SRCS += \
 $(TELOSS)/TELoss.cpp \
-$(TELOSS)/TELossCint.cpp
+$(TELOSS)/TELossDict.cpp
 
 TELOSSOBJS += \
 $(TELOSS)/ELOSS.o \
 $(TELOSS)/TELoss.o \
-$(TELOSS)/TELossCint.o
+$(TELOSS)/TELossDict.o
 
 TELOSSCPP_DEPS += \
 $(TELOSS)/TELoss.d \
-$(TELOSS)/TELossCint.d
+$(TELOSS)/TELossDict.d

TELoss/linkdef.h → TELoss/TELossLinkDef.h

-#ifdef __CINT__
+#ifdef __CLING__
 #pragma link off all globals;
 #pragma link off all classes;
 #pragma link off all functions;
 
 #pragma link C++ class TELoss;
 
-
 #endif
\ No newline at end of file

Utilities/CMakeLists.txt

+############################################################################
+# CMakeLists.txt file for building Utilities package
+############################################################################
+
+ROOT_STANDARD_LIBRARY_PACKAGE(Utilities
+  HEADERS
+    CalPars.h
+    ConfigDictionary.h
+    CsICalib.h
+    ReturnCodes.h
+  SOURCES
+    CalPars.cpp
+    ConfigDictionary.cpp
+    CsICalib.cpp
+#   DEPENDENCIES
+#     MathCore
+#     Matrix
+#     RIO
+   LINKDEF
+     UtilitiesLinkDef.h
+)
+
+# ROOT_ADD_TEST_SUBDIRECTORY(test)
+
+# install(FILES ${CMAKE_CURRENT_BINARY_DIR}/G__Utilities.cxx DESTINATION ${CMAKE_BINARY_DIR}/include)
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libUtilities.rootmap DESTINATION ${CMAKE_BINARY_DIR}/lib)
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libUtilities_rdict.pcm DESTINATION ${CMAKE_BINARY_DIR}/lib)
+install(TARGETS Utilities LIBRARY DESTINATION ${CMAKE_BINARY_DIR}/lib ARCHIVE DESTINATION ${CMAKE_BINARY_DIR}/lib)
\ No newline at end of file

Utilities/CalPars.cpp

+#include "CalPars.h"
+
+ClassImp(CalPars);
+
+
+CalPars::CalPars(const char* clbfile) {
+
+	ReadParFile(clbfile);
+
+}
+
+CalPars::~CalPars() {
+
+	printf("CalPars::Destructor called.\n");
+
+}
+
+Double_t CalPars::GetA(Int_t i) {
+
+	if (i >= fA.GetSize()) {
+		return 0.;
+	}
+	return fA[i];
+}
+
+Double_t CalPars::GetB(Int_t i) {
+
+	if (i >= fB.GetSize()) {
+		return 0.;
+	}
+	return fB[i];
+}
+
+Double_t CalPars::GetC(Int_t i) {
+
+	if (i >= fC.GetSize()) {
+		return 0.;
+	}
+	return fC[i];
+}
+
+void CalPars::ReadParFile(const char* clbfile) {
+
+	clbFile = clbfile;	
+
+	std::ifstream infile(clbfile);
+	if ( !infile.is_open() ) {
+		printf("CalPars::ReadParFile: File %s was not open.\n", clbfile);
+		printf("CalPars::ReadParFile: Calibration parameters are empty!!!\n");
+		return;
+	}	
+
+	TString line;
+	Int_t nopars;
+	Double_t a, b;
+	Int_t c;		//threshold
+
+	printf("CalPars::ReadParFile: File %s was open.\n", clbfile);
+
+	line.ReadLine(infile);
+	sscanf(line.Data(), "%*d %d", &nopars);
+//	Info("CalPars::ReadParFile", "%d calibration parameters will be loaded", nopars);
+	printf("CalPars::ReadParFile: %d calibration parameters will be loaded\n", nopars);
+
+	fA.Set(nopars);
+	fB.Set(nopars);
+	fC.Set(nopars);
+
+	for (Int_t i = 0; i <nopars; i++) {
+		line.ReadLine(infile);
+
+//		if ( line.BeginsWith("#") ) continue;
+
+//		cout << line.Data() << endl;
+		sscanf(line.Data(), "%lf %lf %d", &b, &a, &c);
+		fA[i] = a;
+		fB[i] = b;
+		fC[i] = c;
+//		printf("fA[%d]: %f,\tfB[%d]: %f\n", i, fA[i], i, fB[i]);
+//		printf("fA[%d]: %f,\tfB[%d]: %f\n\n", i, a, i, b);
+	}
+
+}
+
+void CalPars::PrintClbPars() {
+
+	printf("CalPars::PrintClbPars: %d calibration parameters from %s file.\n", fA.GetSize(), clbFile.Data());
+	
+	for (Int_t i = 0; i<fA.GetSize(); i++) {
+		printf("%d\t%f\t%f\t%f\n", i, GetA(i), GetB(i), GetC(i));
+	}
+
+}

Utilities/CalPars.h

+#pragma once
+
+#include <iostream>
+#include <fstream>
+
+#include "TArrayD.h"
+#include "TArrayI.h"
+#include "TString.h"
+#include "TObject.h"
+
+using std::cout;
+using std::endl;
+
+class CalPars /*: TObject*/ {
+
+private:
+	TArrayD fA;
+	TArrayD fB;
+	TArrayI fC;
+
+	TString clbFile;
+
+public:
+
+	CalPars() : fA(0), fB(0), fC(0) {};
+	CalPars(const char* clbfile);
+	virtual ~CalPars();
+
+	Double_t GetA(Int_t i);
+	Double_t GetB(Int_t i);
+	Double_t GetC(Int_t i);
+
+	void ReadParFile(const char* clbfile);
+	void PrintClbPars();
+
+	ClassDef(CalPars, 1);
+};

AculData/ConfigDictionary.cpp → Utilities/ConfigDictionary.cpp

@@ -100,17 +100,24 @@ ClassImp(ConfigDictionary);
 //  Info("Some optional variables wasn't read!");
 //}
 //--------------------</pre>
+//
+// ADDED 21.03.2012:
+//
+// With use of templates, now ConfigDictionary can handle complex objects
+// reading and writing instantly as long as proper >> and << operators are
+// provided for an object initialization.
+//
 //	END_HTML
 //////////////////////////////////////////////////////////////////////////////
 
 //_____________________________________________________________________________
 ConfigDictionary::ConfigDictionary(){
-	//just empty map...
+	//Empty map...
 }
 
 //_____________________________________________________________________________
 ConfigDictionary::ConfigDictionary(std::string params){
-	//Just creates dictionary using FromString method
+	//Creates dictionary using FromString method
 	FromString(params);
 }
 
@@ -154,63 +161,61 @@ void ConfigDictionary::FromString(std::string params){
 }
 
 //_____________________________________________________________________________
-std::string ConfigDictionary::GetString(std::string key)throw(std::string){
+std::string ConfigDictionary::GetString(std::string key){
 	//Extracts string from given key
 	//(if it exist, otherwise raises exception)
-
+	//This works also for long strings with white spaces in it!
 	if (configMap.find(key) == configMap.end()){
 		Error("ConfigDictionary::GetString",
 				"Couldn't find the key: %s!",key.c_str());
-		throw(key);
+		// throw(key);
+		throw std::runtime_error("Couldn't find the key: " + key);
 	}
 	return configMap[key];
 }
 
 //_____________________________________________________________________________
-int	ConfigDictionary::GetInt(std::string key)throw(std::string){
-	//Extracts integer from given key
-	//(if it exist, otherwise raises exception)
-	if (configMap.find(key) == configMap.end()){
-		Error("ConfigDictionary::GetInt",
-				"Couldn't find the key: %s!",key.c_str());
-		throw(key);
+int ConfigDictionary::GetInt(std::string key) {
+    // Extracts integer from given key
+    // (if it exists, otherwise raises exception)
+    try {
+        return Get<int>(key);
+    } catch (const std::string& message) {
+        // Catch the exception thrown by Get<int> and re-throw it as std::runtime_error
+        throw std::runtime_error(message);
     }
-	int returned=0;
-	//Convert string to int:
-	std::stringstream ss(configMap[key]);
-	ss>>returned;
-	return returned;
 }
 
 //_____________________________________________________________________________
-double ConfigDictionary::GetDouble(std::string key)throw(std::string){
-	//Extracts integer from given key
+double ConfigDictionary::GetDouble(std::string key){
+	//Extracts double precision floating number from given key
 	//(if it exist, otherwise raises exception)
-	if (configMap.find(key) == configMap.end()){
-		Error("ConfigDictionary::GetDouble",
-				"Couldn't find the key: %s!",key.c_str());
-		throw(key);
+	try
+	{
+		return Get<double>(key);
+	} catch (const std::string& message) {
+        // Catch the exception thrown by Get<int> and re-throw it as std::runtime_error
+        throw std::runtime_error(message);
     }
-	double returned=0.0;
-	//Convert string to double:
-	std::stringstream ss(configMap[key]);
-	ss>>returned;
-	return returned;
 }
 
 //_____________________________________________________________________________
-bool ConfigDictionary::GetBool(std::string key)throw(std::string){
+bool ConfigDictionary::GetBool(std::string key){
 	//Extracts boolean from given key
 	//(if it exist, otherwise raises exception)
+	//Differs from template to make it more readable.
+	
+	// Check if the key exists in the config map
 	if (configMap.find(key) == configMap.end()){
 		Error("ConfigDictionary::GetBool",
 				"Couldn't find the key: %s!",key.c_str());
-		throw(key);
+		throw std::runtime_error("Couldn't find the key: " + key);
 	}
 	//Convert string to bool:
 	if (configMap[key].compare("true") == 0)
 		return true;
-	else return false;
+	else
+		return false;
 }
 
 //_____________________________________________________________________________
@@ -221,23 +226,19 @@ void ConfigDictionary::SetString(std::string key,std::string value){
 
 //_____________________________________________________________________________
 void ConfigDictionary::SetDouble(std::string key,double value){
-	//Sets value to key, converts double to string first
-	std::stringstream ss;
-	ss<<value;
-	configMap[key] = ss.str();
+	Set<double>(key,value);
 }
 
 //_____________________________________________________________________________
 void ConfigDictionary::SetInt(std::string key,int value){
 	//Sets value to key, converts int to string first
-	std::stringstream ss;
-	ss<<value;
-	configMap[key] = ss.str();
+	Set<int>(key,value);
 }
 
 //_____________________________________________________________________________
 void ConfigDictionary::SetBool(std::string key,bool value){
 	//Sets value to key, converts bool to string first
+	//Differs from template to make it more readable.
 	if (value == true)	configMap[key] = "true";
 	else				configMap[key] = "false";
 }

Utilities/ConfigDictionary.h

+#ifndef CONFIGDICTIONARY_H
+#define CONFIGDICTIONARY_H
+
+
+#include "TObject.h"
+#include "ReturnCodes.h"
+#include "TStopwatch.h"
+#include "TROOT.h"
+#include <string>
+#include <map>
+#include <sstream>
+#include <vector>
+#include "TLorentzVector.h"
+#include <iostream>
+#include "TMath.h"
+#include "TString.h"
+#include "TTree.h"
+
+
+#define ARRAY_DELIM '$'
+
+class ConfigDictionary{
+public:
+	typedef std::map<std::string,std::string>::iterator CDIter;
+	ConfigDictionary();
+	ConfigDictionary(std::string);
+	virtual ~ConfigDictionary(){};//empty virtual destructor
+
+	ClassDef(ConfigDictionary,1);
+	std::string ToString();
+	void FromString(std::string);
+
+	//These throw errors if couldn't find key:
+	//Most of methods below are just using templates to
+	//make them usable in Cint.
+	std::string GetString(std::string);
+	int	GetInt(std::string);
+	double GetDouble(std::string);
+	bool GetBool(std::string);
+
+	//These will always set 'something' into map:
+	void SetString(std::string,std::string);
+	void SetDouble(std::string,double);
+	void SetInt(std::string,int);
+	void SetBool(std::string,bool);
+	
+	CDIter Begin(){return configMap.begin();};
+	CDIter End(){return configMap.end();};
+
+
+	//_________________________________________________________________________
+	template <class T>
+	T Get(std::string key) {
+		//This method will get object of any class
+		//that was - presumably - stored before in string format in CD.
+		//Object needs to have proper >> operator.
+		//If operation fails, returned item should have default value
+		//depending on its empty constructor.
+		//For strings containing spaces it won't work properly, as it
+		//would extract only first space followed item!
+		if (configMap.find(key) == configMap.end()) {
+			Error(	"ConfigDictionary::Get",
+					"Couldn't find the key: %s!",
+					key.c_str());
+			throw std::runtime_error("Couldn't find the key: " + key);
+		}
+		// Use std::istringstream to convert the string to the desired type
+		std::istringstream inStream(configMap[key]);
+		T item;
+		// Extract the value from the stringstream
+		inStream >> item;
+		// Check if extraction failed
+		if (inStream.fail()) {
+			// Throw std::runtime_error with an informative message
+			throw std::runtime_error("Failed to extract value for key: " + key);
+		}
+
+		// Return the extracted item
+		return item;
+	}
+
+
+	//_____________________________________________________________________________
+	template <class T>
+	void Set(std::string key,T value){
+		//Sets value to key, converts T to string first with << operator.
+		std::stringstream ss;
+		ss<<value;
+		configMap[key] = ss.str();
+	}
+
+
+	//_________________________________________________________________________
+	template <class T>
+	int GetArray(std::string key,std::vector<T> & output){
+		//Preconditions: T must have >> operator
+		//Effect: searches for key in map and pushes values stored in it into output vector
+		//Returns: number of elements pushed into vector
+		
+		int retNumber = 0;	// Counter for the number of elements pushed into the vector
+		
+		// Check if the key exists in the config map
+		if (configMap.find(key) == configMap.end()){
+			Error(	"ConfigDictionary::GetInt",
+					"Couldn't find the key: %s!",key.c_str());
+			throw std::runtime_error("Couldn't find the key: " + key);
+		}
+
+		// Create a string stream from the value associated with the key
+		std::istringstream arrayString(configMap[key]);
+		// Temporary string to hold each item from the string stream
+		std::string itemString;
+
+		//Dangerous - maybe? - exceptions for ss not handled...
+		// Loop to extract each item from the string stream
+		while (std::getline(arrayString,itemString,ARRAY_DELIM)){
+			std::stringstream itemStream(itemString); // Create a string stream from the item string
+			if (!itemString.empty()) { // Check if the item string is not empty
+				T item; // Temporary variable to hold the converted item
+				itemStream >> item; // Extract the item from the string stream
+				output.push_back(item); // Push the item into the output vector
+				retNumber++; // Increment the counter
+			}
+			
+		}
+
+		// Return the number of elements pushed into the vector
+		return retNumber;
+	}
+
+	//_________________________________________________________________________
+	template <class T>
+	void SetArray(std::string key,std::vector<T> & input){
+		std::ostringstream arrayString;
+		for (unsigned int i=0;i<input.size();i++){
+			arrayString<<input[i]<<ARRAY_DELIM;
+		}
+		configMap[key] = arrayString.str();
+	}
+
+
+
+private:
+	std::map<std::string,std::string> configMap;
+};
+
+#endif

Utilities/CsICalib.h

+#pragma once
+
+//#include "TObject.h"
+//#include "TROOT.h"
+#include <iostream>
+#include <fstream>
+
+#include "TFile.h"
+#include "TTree.h"
+#include "TCutG.h"
+#include "TCanvas.h"
+#include "TClonesArray.h"
+#include "TH1I.h"
+#include "TGraphErrors.h"
+#include "TArrayD.h"
+#include "TF1.h"
+
+#define NOCALFILES 5
+
+using std::cout;
+using std::endl;
+
+class CsICalib {
+	private:
+
+	TString detName;
+	TString partName;
+	
+	TClonesArray fr;		//TFile
+//	TFile *fData;
+	TClonesArray tr;
+	TClonesArray colFiles;
+	TClonesArray colTrees;
+	Int_t nofiles;
+	TString fileNames[100];
+	TString cutNames[100];
+
+	Int_t energyPoints;
+	TArrayD fE;
+
+	TFile *fCuts;
+	TString cutsFileName;
+	Int_t nCuts;				//number of cuts
+	TClonesArray cutsCol;
+
+	TH1I *hfull[NOCALFILES][16];	//!
+	TH1I *hcut[NOCALFILES][16];		//!
+
+	Int_t peakMin[NOCALFILES][16];
+	Int_t peakMax[NOCALFILES][16];
+	Double_t mean[NOCALFILES][16];
+	Double_t meanRMS[NOCALFILES][16];
+
+	TGraphErrors *gCal[16];
+	TFile *fGraphs;
+	TArrayD fA;
+	TArrayD fB;
+
+	public:
+//	CsICalib() : a(0), b(0), c(0), p(0){};
+	CsICalib();
+	CsICalib(const char* parfile);
+	virtual ~CsICalib();
+
+
+
+	void OpenTrees();
+	void LoadCuts();
+
+	void ReadParFile(const char* parfile);
+	void PrintParameters(const char* option = "");
+	void PrintPeakRanges();
+
+	void DrawVariable(const char* variable, Int_t tree, TCanvas *canvas, Int_t lowRange = 0, Int_t upRange = 4096);
+	void DrawBeam(TCanvas *canvas, Int_t files, const char* variable);
+//	void DrawdEE(const char* variable, Int_t tree, TCanvas *canvas);
+	void DrawVariableCut(const char* variable, Int_t tree, TCanvas *canvas, const char* cut1, const char* cut2 = "", Int_t lowRange = 0);
+	void GetPeakMean(const char* variable, Int_t tree, Int_t energy, TCanvas *canvas, const char* beamcut, const Int_t nbins = 4096, Int_t lowRange = 0);
+
+	void Calibrate(TCanvas *canvas, Bool_t savefile = 0, const char* filename = "", const char* option = "READ");
+	void FillGraph(TGraphErrors *g, Int_t npoints, Double_t *energies, Int_t graphNumber, const char* option = "");
+	void WriteClbParameters(const char* filename);
+	void SaveClbGraphs(const char* filename, const char* option = "READ");
+	void ReadClbParameters(const char* filename);
+	void DrawClbGraphs(const char* filename, const char* graphname, TCanvas *canvas);
+	void DrawEnergyDeposite(const char* variable, TCanvas *canvas, Int_t tree, const char* option = "");
+
+	void PrintTrees();
+	void PrintFiles();
+	void PrintCuts();
+
+	Double_t GetA(Int_t i) {return fA[i];};
+	Double_t GetB(Int_t i) {return fB[i];};
+
+
+	// Define the class for the cint dictionary
+	ClassDef (CsICalib,1);
+};

Utilities/Utilities.mk

+################################################################################
+# AculData input with some variables
+################################################################################
+
+# UTILITIESLIBS := -lCore -lCint -lRIO -lTree -lNet -lThread -lHist -lMatrix -lMathCore -lGpad -lGraf
+UTILITIESLIBS := -lCore -lRIO -lTree -lNet -lThread -lHist -lMatrix -lMathCore -lGpad -lGraf
+#UTILITIESLIBS := -lGui -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -pthread -lm -ldl -rdynamic
+
+# Add inputs and outputs from these tool invocations to the build variables 
+UTILITIES_HEADERS += \
+$(UTILITIES)/CalPars.h \
+$(UTILITIES)/CsICalib.h \
+$(UTILITIES)/ConfigDictionary.h \
+$(UTILITIES)/UtilitiesLinkDef.h
+
+UTILITIESCPP_SRCS += \
+$(UTILITIES)/CalPars.cpp \
+$(UTILITIES)/CsICalib.cpp \
+$(UTILITIES)/ConfigDictionary.cpp \
+$(UTILITIES)/UtilitiesDict.cpp
+
+UTILITIESOBJS += \
+$(UTILITIES)/CalPars.o \
+$(UTILITIES)/CsICalib.o \
+$(UTILITIES)/ConfigDictionary.o \
+$(UTILITIES)/UtilitiesDict.o
+
+UTILITIESCPP_DEPS += \
+$(UTILITIES)/CalPars.d \
+$(UTILITIES)/CsICalib.d \
+$(UTILITIES)/ConfigDictionary.d \
+$(UTILITIES)/UtilitiesDict.d
+

Utilities/UtilitiesLinkDef.h

+#ifdef __CINT__
+#pragma link off all globals;
+#pragma link off all classes;
+#pragma link off all functions;
+
+#pragma link C++ class CalPars;
+#pragma link C++ class CsICalib;
+#pragma link C++ class ConfigDictionary;
+
+#endif
+

html.cxx → htmldoc.cxx

+#include "THtml.h"
+
+void htmldoc()
 {
-	gSystem->Load("./libAculData.so");
 	gSystem->Load("./libTELoss.so");
+	gSystem->Load("./libAculCalib.so");
+	gSystem->Load("./libAculData.so");
 
 	THtml h;
 
 	h.SetInputDir(".");
+	h.SetOutputDir("htmldoc");
+	h.SetProductName("AculUtils");
+
 
 	h.MakeAll();
 

load.cxx

 {
-	gSystem->Load("~/workspace/Utilities/libAculData.so");
+	gSystem->Load("libTELoss.so");
+	gSystem->Load("libAculData.so");
 
 }

macros/calibration_CsI/calibrationSQ13Alpha.cxx

@@ -33,8 +33,14 @@
 
 //	cal.DrawBeam(myCanv, 4, "SQ13");
 //return;
+// <<<<<<< HEAD
 //	cal.DrawVariableCut("SQ13", 0, c2, "cutsSQ13Alpha16");
 //	cal.DrawVariableCut("SQ13", 0, c2, "cutsSQ13Alpha16", "cutSQ13Alpha16Amp");
+// =======
+	cal.DrawVariableCut("SQ13", 0, c1, "cutsSQ13Alpha16");
+	return;
+	cal.DrawVariableCut("SQ13", 0, c1, "cutsSQ13Alpha16", "cutSQ13Alpha16Amp");
+// >>>>>>> newArch
 //return;
 //	cal.DrawVariableCut("SQ13", 1, c2, "cutSQ13Alpha21", "cutSQ13Alpha21Amp");
 //	cal.DrawVariableCut("SQ13", 2, c3, "cutSQ13Alpha26", "cutSQ13Alpha26Amp");

macros/myMacros/SQ13Alpha.par

+energies	4	#number of energy points
+crystals	16	#number of crystals in detector
+files 4
+#fileID		fileName
+#fileID not implemented yet
+data/csi_13_Ealpha16.root
+data/csi_13_Ealpha21.root
+data/csi_13_Ealpha26.root
+data/csi_13_Ealpha30.root
+#keyword	detector	particle
+detector	SQ13  Alpha
+#keyword	energy [MeV/A]
+energy 66.542
+#keyword;	filename;	number of cuts in file
+cutFile cuts/cutsSQ13Alpha.root	2
+cutsSQ13Alpha16
+cutSQ13Alpha16Amp
+#channel	minimum	maximum
+0	650		830
+1	920		1150
+2	850		1000
+3	1200	1400
+4	960		1100
+5	700		850
+6	650		800
+7	1040	1240
+8	850		1050
+9	650		850
+10	950		1200
+11	900		1100
+12	740		860
+13	1140	1380
+14	420		500
+15	800		1000
+#CsI2, energy ~ 21 MeV/A, Alpha
+energy 85.437
+#keyword;	filename;	number of cuts in file
+cutFile cuts/cutsSQ13Alpha.root	2
+cutSQ13Alpha21
+cutSQ13Alpha21Amp
+#channel	minimum	maximum
+0	1050	1200
+1	1350	1550
+2	1190	1400
+3	1650	1950
+4	1300	1500
+5	950		1100
+6	900		1050
+7	1450	1700
+8	1150	1400
+9	900		1100
+10	1350	1600
+11	1250	1500
+12	950		1200
+13	1600	1860
+14	550		640
+15	1150	1350
+#CsI2, energy ~ 26 MeV/A, Alpha
+energy 105.5
+#keyword;	filename;	number of cuts in file
+cutFile cuts/cutsSQ13Alpha.root	2
+cutSQ13Alpha26
+cutSQ13Alpha26Amp
+#channel	minimum	maximum
+0	1300	1600
+1	1750	2050
+2	1560	1800
+3	2250	2500
+4	1720	2000
+5	1200	1450
+6	1160	1400
+7	1800	2200
+8	1600	1850
+9	1200	1400
+10	1750	2100
+11	1650	1900
+12	1250	1600
+13	2150	2450
+14	690		900
+15	1500	1700
+#CsI2, energy ~ 30 MeV/A, Alpha
+energy 119.54
+#keyword;	filename;	number of cuts in file
+cutFile cuts/cutsSQ13Alpha.root	2
+cutSQ13Alpha30
+cutSQ13Alpha30Amp
+#channel	minimum	maximum
+0	1450	1750
+1	2200	2450
+2	1900	2150
+3	2590	3000
+4	2100	2350
+5	1500	1650
+6	1400	1600
+7	2250	2550
+8	1900	2150
+9	1400	1600
+10	2050	2600
+11	1950	2200
+12	1580	1710
+13	2550	2900
+14	1100	1250
+15	1800	2000
\ No newline at end of file

macros/myMacros/cuts

+../calibration_CsI/cuts/
\ No newline at end of file

macros/myMacros/data

+../calibration_CsI/data/
\ No newline at end of file

macros/myMacros/parTest.cxx

+//#include "../../AculCalib/AculCalPars.h"
+//#include "../../AculCalib/AculCalibScint.h"
+//#include "../../AculCalib/AculCalibSi.h"
+//#include "TSystem.h"
+//#include <iostream>
+//
+using std::cout;
+using std::endl;
+
+void parTest()
+{
+	gSystem->Load("../../libTELoss.so");
+	gSystem->Load("../../libAculCalib.so");
+
+/*	AculCalibSi ps;
+	ps.SetParFile("parforcal.par");
+	ps.Init();
+	ps.PrintParameters();
+	return;
+*/
+
+//	AculCalParsScintFile pp;
+//	pp.SetNoCrystals(16);
+//	pp.Init();
+//	return;
+
+	cout << "-----------------------" << endl;
+
+	AculCalParsScint p;
+	p.SetParFile("SQ13Alpha.par");
+	p.Init();
+//	cout << p.GetFileName(0) << endl;
+//	cout << p.GetFileName(1) << endl;
+//	cout << p.GetFileName(2) << endl;
+//	cout << p.GetFileName(3) << endl;
+//	cout << p.GetFileName(4) << endl;
+//	p.PrintParameters("");
+	p.PrintParameters("all");
+//	return;
+	p.Reset();
+//	p.PrintParameters("");
+//	return;
+
+	cout << "-----------------------" << endl;
+
+	AculCalibScint c;
+	c.SetParFile("SQ13Alpha.par");
+	c.Init();
+	c.PrintParameters();
+//	return;
+
+//	c.PrintParameters("all");
+
+//	c.OpenFiles();
+
+//	c.LoadTrees();
+	c.PrintTrees();
+
+	TCanvas *c1 = new TCanvas("c1", "Plain");
+	TCanvas *c2 = new TCanvas("c2", "Plain");
+	TCanvas *c3 = new TCanvas("c3", "Plain");
+	TCanvas *c4 = new TCanvas("c4", "Plain");
+//	c.DrawVariable("SQ13", 2, c1);
+//	c.DrawBeam(c1, 4, "SQ13");
+
+//	c.GetPeakMean("SQ13", 0, c1, "cutSQ13Alpha16Amp", 256);
+	c.GetPeakMean("SQ13", 0, c1, "cutSQ13Ala16Amp", 256);
+	c.GetPeakMean("SQ13", 1, c2, "cutSQ13Alpha21Amp", 256);
+	c.GetPeakMean("SQ13", 2, c3, "cutSQ13Alpha26Amp", 256);
+	c.GetPeakMean("SQ13", 3, c4, "cutSQ13Alpha30Amp", 256);
+
+//return;
+//	c.PrintFiles();
+//	c.PrintCuts();
+
+//	TCanvas *c1 = new TCanvas("c1", "Plain");
+//	c.GetPeakMean("SQ13", 0, 0, c1, "cutSQ13Alpha16Amp", 256);
+
+	TCanvas *cCal = new TCanvas("cCal", "calibration Alpha");
+	c.Calibrate(cCal);
+
+	return;
+}

macros/parforcal.par

+//226Ra
+//relative units are normalized to 1
+
+4					noPeaks	//number of peaks// число пиков, по которым происходит калибровка
+4.751				E1	//in MeV including dead layer of alpha source//энергии альфа источника
+5.459 				E2	//in MeV//
+5.972				E3	//in MeV//
+7.661				E4	//in MeV//
+2.3 				deadLayer
+0 					lowersubaddress
+15 				uppersubaddress
+ANS				block
+AnalysisxTree		treename
+400	lowerChannel			//in channels//каналы,
+2000	upperChannel			//in channels//каналы
+0.5	lowerPeakHight			//in relative units; minimal range of the peak//
+0.5	upperPeakHight			//in relative units; minimal range of the peak//
+0.1	peakPositionTolerance	//in relative units; for check of the peaks positions in channels//
+2	fitFunctionLineWidth	//integer 1 - 10; graphics//
+20	minFitSigma				//minimal sigma of the peaks to be fitted//
+0.3	fitHightThreshold		//in relative units; the minimal height of the treated peak//

macros/rootlogon.C

+{
+    TString pathToLibs = "../build/lib/";
+    // TString pathToLibs = "../";
+    
+    TString pathToTELoss = pathToLibs + "libTELoss.so";
+    TString pathToAculData = pathToLibs + "libAculData.so";
+    TString pathToUtilities = pathToLibs + "libUtilities.so";
+    TString pathToAculCalib = pathToLibs + "libAculCalib.so";
+
+    //libTELoss.so loading
+    Int_t teloss = gSystem->Load(pathToTELoss);
+    if (teloss==0) Info("rootlogon.C", "Library %s was successfully loaded.", pathToTELoss.Data());
+    else Error("rootlogon.C", "Some error with %s loading", pathToTELoss.Data());
+
+    //libAculData.so loading
+    Int_t aculdata = gSystem->Load(pathToAculData);
+    if (aculdata==0) Info("rootlogon.C", "Library %s was successfully loaded.", pathToAculData.Data());
+    else Error("rootlogon.C", "Some error with %s loading", pathToAculData.Data());
+
+    //libUtilities.so loading
+    Int_t utilities = gSystem->Load(pathToUtilities);
+    if (utilities==0) Info("rootlogon.C", "Library %s was successfully loaded.", pathToUtilities.Data());
+    else Error("rootlogon.C", "Some error with %s loading", pathToUtilities.Data());
+
+    //libAculCalib.so loading
+    Int_t aculcalib = gSystem->Load(pathToAculCalib);
+    if (aculcalib==0) Info("rootlogon.C", "Library %s was successfully loaded.", pathToAculCalib.Data());
+    else Error("rootlogon.C", "Some error with %s loading", pathToAculCalib.Data());
+    
+}
\ No newline at end of file

macros/testOfAculData.cxx

+#include "../AculData/AculCalibration.h"
+
+void testOfAculData()
+{
+	// gSystem->Load("/home/aculina/AculUt/libAculData.so");
+	// gSystem->Load("/home/aculina/AculUt/libTELoss.so");
+
+	AculCalibration cal;
+	
+    cal.SetParFileName("./parforcal.par");	
+    cal.Init();	//takes parameters from .par
+	cal.PrintInputParameters();
+	
+    cal.PrintCalibrationParameters();
+
+}

macros/testOfTELoss.cxx

+#include "TSystem.h"
+
+#include "../TELoss/TELoss.h"
+
+void testOfTELoss() {
+
+    //creating two object for combination particle-material
+    TELoss	mSi_4He;
+	TELoss	mSi_1H;
+
+    //setting tables for alphas in silicon
+	mSi_4He.SetEL(1, 2.321);            //general properties of material (silicon)
+	mSi_4He.AddEL(14., 28.086, 1);      //add Si element to material
+	mSi_4He.SetZP(2., 4.);		        //set 4He particles
+	mSi_4He.SetEtab(100000, 200.);	    //set table with ranges
+	mSi_4He.SetDeltaEtab(300);          //some other table
+
+    //setting tables for protons in silicon
+	mSi_1H.SetEL(1, 2.321);             //general properties of material (silicon)
+	mSi_1H.AddEL(14., 28.086, 1);       //add Si element to material        
+	mSi_1H.SetZP(1., 1.);		        //set 4He particles        
+	mSi_1H.SetEtab(100000, 200.);       //set table with ranges        
+	mSi_1H.SetDeltaEtab(300);           //some other table    
+
+    cout << "Remaining energy of proton with energy of 20 MeV after penetration 1 mm of silicon is:" << endl;
+    cout << "expected (according to LISE++):\t14.604 MeV" << endl;
+    cout << "calculated:\t\t\t" << mSi_1H.GetE(20, 1000) << " MeV" << endl << endl;
+
+    cout << "Remaining energy of alpha with energy of 50 MeV after penetration 1 mm of silicon is:" << endl << endl;
+    cout << "expected (according to LISE++):\t5.447 MeV" << endl;
+    cout << "calculated:\t\t\t" << mSi_4He.GetE(50, 1000) << " MeV" << endl << endl;
+
+    cout << "Remaining energy of alpha with energy of 70 MeV after penetration 1 mm of silicon is:" << endl << endl;
+    cout << "expected (according to LISE++):\t45.076 MeV" << endl;
+    cout << "calculated:\t\t\t" << mSi_4He.GetE(70, 1000) << " MeV" << endl << endl;
+
+}
\ No newline at end of file

makefile

@@ -25,42 +25,86 @@ ROOTCFLAGS = $(shell root-config --cflags)
 PWD = $(shell pwd)
 #INSTALLFOLDER = $(HOME)/AculLib
 
+UTILITIES = $(PWD)/Utilities
 ACULDATA = $(PWD)/AculData
+ACULCALIB = $(PWD)/AculCalib
 TELOSS = $(PWD)/TELoss
 
+-include $(UTILITIES)/Utilities.mk
 -include $(ACULDATA)/AculData.mk
+-include $(ACULCALIB)/AculCalib.mk
 -include $(TELOSS)/TELoss.mk
 
-all: libAculData.so \
+all: libUtilities.so \
+	libAculData.so \
+	libAculCalib.so \
 	libTELoss.so
 
 #ROOT html documentation, it will be done as a program which will be alsa compiled by this makefile, program will be as a last condition after all of the libraries
-htmldoc: libAculData.so
+htmldoc: libAculData.so libAculCalib.so libTELoss.so
 	-$(RM) htmldoc
-	root -l -q html.cxx	
+	root -l -q htmldoc.cxx	
+
+clean_htmldoc:
+	-$(RM) htmldoc
+	-@echo ' '
 
 clean:
+	-$(RM) $(UTILITIESOBJS) $(UTILITIESCPP_DEPS) 
+	-$(RM) $(UTILITIES)/UtilitiesDict.* libUtilities.so $(UTILITIES)/*.pcm
+	-@echo ' '
 	-$(RM) $(ACULDATAOBJS) $(ACULDATACPP_DEPS) 
-	-$(RM) $(ACULDATA)/AculDataCint.* libAculData.so
+	-$(RM) $(ACULDATA)/AculDataDict.* *.pcm $(ACULDATA)/*.pcm
+	 -$(RM) libAculData.so
+	-@echo ' '
+	-$(RM) $(ACULCALIBOBJS) $(ACULCALIBCPP_DEPS) 
+	-$(RM) $(ACULCALIB)/AculCalibDict.* libAculCalib.so $(ACULCALIB)/*.pcm
 	-@echo ' '
 	-$(RM) $(TELOSSOBJS) $(TELOSSCPP_DEPS)
-	-$(RM) $(TELOSS)/TELossCint.* libTELoss.so
+	-$(RM) $(TELOSS)/TELossDict.* *.pcm $(TELOSS)/*.pcm $(TELOSS)/*.pcm
+	-$(RM) libTELoss.so
 	-@echo ' '
 	-$(RM) htmldoc
 	-@echo ' '
 
-# Those *Cint* files below need special treating:
-$(ACULDATA)/AculDataCint.cpp:
-	-@echo 'Pre-building AculDataCint.cpp and AculDataCint.h files'
-	-rootcint -f $(ACULDATA)/AculDataCint.cpp -c -p $(ACULDATA_HEADERS)
+# Those *Dictionary* files below need special treating:
+$(UTILITIES)/UtilitiesDict.cpp:
+	-@echo 'Pre-building UtilitiesDict.cpp and UtilitiesDict.h files'
+	-rootcling -f $(UTILITIES)/UtilitiesDict.cpp -p $(UTILITIES_HEADERS)
+	-@echo 'Creating: link to UtilitiesDict_rdict.pcm'
+	-ln -s $(UTILITIES)/UtilitiesDict_rdict.pcm .
+	-@echo ' '
+
+$(ACULDATA)/AculDataDict.cpp:
+	-@echo 'Pre-building AculDataDict.cpp and AculDataCint.h files'
+	-rootcling -f $(ACULDATA)/AculDataDict.cpp -p $(ACULDATA_HEADERS)
+	-@echo 'Creating: link to AculDataDict_rdict.pcm'
+	-ln -s $(ACULDATA)/AculDataDict_rdict.pcm .
+	-@echo ' '
+
+$(ACULCALIB)/AculCalibDict.cpp:
+	-@echo 'Pre-building AculCalibDict.cpp and AculCalibDict.h files'
+	-rootcling -f $(ACULCALIB)/AculCalibDict.cpp -p $(ACULCALIB_HEADERS)
+	-@echo 'Creating: link to AculCalibDict_rdict.pcm'
+	-ln -s $(ACULCALIB)/AculCalibDict_rdict.pcm .
 	-@echo ' '
 	
-$(TELOSS)/TELossCint.cpp:
-	-@echo 'Pre-building TELossCint.cpp and TELossCint.h files'
-	-rootcint -f $(TELOSS)/TELossCint.cpp -c -p $(TELOSS)/TELoss.h $(TELOSS)/linkdef.h
+$(TELOSS)/TELossDict.cpp:
+	-@echo 'Pre-building TELossDict.cpp and TELossDict_rdict.pcm files'
+	@echo 
+	-rootcling -f $@ -c $(CXXFLAGS) -p $(TELOSS_HEADERS)
+	-@echo 'Creating: link to TELossDict_rdict.pcm'
+	-ln -s $(TELOSS)/TELossDict_rdict.pcm .
 	-@echo ' '	
 
 #*.so files
+libUtilities.so: $(UTILITIESOBJS)
+	@echo 'Building target: $@'
+	@echo 'Invoking: $(CC) Linker'
+	$(CC) -L $(ROOTLIBS) -shared -o"libUtilities.so" $(UTILITIESOBJS) $(UTILITIESLIBS)
+	@echo 'Finished building target: $@'
+	@echo ' '
+
 libAculData.so: libTELoss.so $(ACULDATAOBJS)
 	@echo 'Building target: $@'
 	@echo 'Invoking: GCC C++ Linker'
@@ -68,6 +112,13 @@ libAculData.so: libTELoss.so $(ACULDATAOBJS)
 	@echo 'Finished building target: $@'
 	@echo ' '
 	
+libAculCalib.so: libTELoss.so $(ACULCALIBOBJS)
+	@echo 'Building target: $@'
+	@echo 'Invoking: GCC C++ Linker'
+	$(CC) -L . -L $(ROOTLIBS) -shared -o"libAculCalib.so" $(ACULCALIBOBJS) $(ACULCALIBLIBS)
+	@echo 'Finished building target: $@'
+	@echo ' '
+
 libTELoss.so: $(TELOSSOBJS)
 	@echo 'Building target: $@'
 	@echo 'Invoking: GCC C++ Linker'
@@ -83,7 +134,6 @@ libTELoss.so: $(TELOSSOBJS)
 	@echo 'Building file: $@'
 	@echo 'Invoking: $(CC) Compiler'
 	$(CC) -I$(ROOTINCS) -O0 -g3 -Wall -c -fmessage-length=0 -fPIC $(ROOTCFLAGS) -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o"$@" "$<"
-#	$(CC) -I$(ROOTINCS) -O2 -Wall -mmmx -msse -msse2 -msse3 -mfpmath=sse,387 -march=nocona -mtune=nocona -c -fmessage-length=0 -fPIC -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o"$@" "$<"
 	@echo 'Finished building: $@'
 	@echo ' '