.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.cpp

+#include "AculCalibScint.h"
+#include "AculCalParsScint.h"
+
+ClassImp(AculCalibScint);
+
+AculCalibScint::AculCalibScint() {
+
+	printf("AculCalibScint::Default constructor called.\n");
+	fInFiles = 0;
+	fTrees = 0;
+	fCutFile = 0;
+
+
+}
+
+AculCalibScint::AculCalibScint(const char* parfile) {
+	printf("AculCalibScint::Constructor called.\n");
+
+	SetParFile(parfile);
+	Init();
+//	cout << "nofiles: " << nofiles << endl;
+//	OpenTrees();
+//	LoadCuts();
+
+//	fr.Print();
+//	fr.At(0);
+	
+
+}
+
+AculCalibScint::~AculCalibScint() {
+
+	printf("AculCalibScint::Destructor called.\n");
+
+}
+
+void AculCalibScint::Init() {
+	fPars = new AculCalParsScint(fParFileName.Data());
+	OpenFiles();
+	LoadTrees();
+
+	fHistFull.resize(fPars->GetNoRawFiles());
+	fHistCut.resize(fPars->GetNoRawFiles());
+
+	fMeanPeakPos.resize(fPars->GetNoRawFiles());
+	fMeanPeakRMS.resize(fPars->GetNoRawFiles());
+//	SetPars();
+}
+
+void AculCalibScint::PrintTrees() {
+
+	if (!fTrees) {
+		cerr << "\"AculCalibScint::PrintTrees\" Probably no tree was open." << endl;
+		return;
+	}
+
+//	TTree *curTree = 0;
+	cout << " AculCalibScint::PrintTrees:" << endl;
+	for (Int_t i = 0; i < fPars->GetNoRawFiles(); i++) {
+//		curTree = fTrees[i];
+		if (fTrees[i]) {
+			printf("\tTree No. %d; File: %s; Name: %s\n", i, fTrees[i]->GetDirectory()->GetName(), fTrees[i]->GetName());
+		} else {
+			printf("\tTree No. %d was not loaded. Maximal number of trees is %d\n", i, fPars->GetNoRawFiles());
+		}
+	}
+
+	return;
+}
+
+void AculCalibScint::OpenFiles() {
+
+	if (!fPars) {
+		cerr << "\"AculCalibScint::OpenFiles\" parameters were not initialized." << endl;
+		return;
+	}
+
+	fPars->GetNoRawFiles();
+	fInFiles = new TFile* [fPars->GetNoRawFiles()];
+	for (Int_t i = 0; i < fPars->GetNoRawFiles(); i++) {
+		fInFiles[i] = new TFile(fPars->GetFileName(i), "READ");
+//		cout << "\"AculCalibScint::OpenFiles\" File \"" << fInFiles[i]->GetName() << "\" was opened." << endl;
+	}
+
+}
+
+void AculCalibScint::LoadTrees() {
+
+	if (!fInFiles) {
+		cerr << "\"AculCalibScint::LoadTrees\" Input files were not open." << endl;
+		return;
+	}
+
+	fTrees = new TTree* [fPars->GetNoRawFiles()];
+	for (Int_t i = 0; i < fPars->GetNoRawFiles(); i++) {
+		fTrees[i] = (TTree*)fInFiles[i]->Get("AnalysisxTree");
+//		cout << "\"AculCalibScint::LoadTrees\" Tree \"" << fTrees[i]->GetName()
+//				<< "\" from file \"" << fInFiles[i]->GetName() << "\" was loaded." << endl;
+	}
+
+}
+
+TTree* AculCalibScint::GetTree(Int_t treeID) {
+	if (treeID >= fPars->GetNoRawFiles()) {
+		cerr << "\"AculCalibScint::DrawVariable\" Tree number " << treeID
+				<< " cannot exist. Maximal treeID is " << fPars->GetNoRawFiles() - 1 << "." << endl;
+		return 0;
+	}
+
+	return fTrees[treeID];
+}
+
+void AculCalibScint::DrawVariable(const char* variable, Int_t treeID, TCanvas *canvas, Int_t lowRange, Int_t upRange) {
+
+
+	if (!canvas) {
+		cerr << "\"AculCalibScint::DrawVariable\" Canvas pointer was NULL" << endl;
+		return;
+	}
+
+	//todo change 16 to parameter
+	const Int_t nPads = 16;
+	CanDivider(canvas, nPads);
+
+	TString canvasTitle;
+	TString var;
+	TString con;
+
+	TTree *curTree = 0;
+	curTree = GetTree(treeID);
+	if (!curTree) {
+		printf("AculCalibScint::DrawVariable: Tree No. %d was not found.\n", treeID);
+		return;
+	}
+
+	canvasTitle.Form("variable: %s; tree: %d", variable, treeID);
+	canvas->SetTitle(canvasTitle.Data());
+
+	for (Int_t i = 0; i < nPads; i++) {
+		var.Form("%s[%d]", variable, i);
+		con.Form("%s[%d]>%d && %s[%d]<%d", variable, i, lowRange, variable, i, upRange);
+		canvas->cd(i+1);
+		curTree->Draw(var.Data(), con.Data());
+		canvas->Update();
+	}
+
+}
+
+void AculCalibScint::DrawBeam(TCanvas *canvas, Int_t file, const char* variable) {
+
+	canvas->SetTitle("Beam");
+
+	const Int_t noFiles = file;
+
+	//todo delet parameter "files"
+	CanDivider(canvas, 0, noFiles, 3);
+
+	TTree *curTree = 0;
+	TCutG *curCutG = 0;
+	TString var;
+	TString con;
+
+//	cout << "cuts " << fPars->GetNoCuts() << endl;
+	cout << "this function has to be checked" << endl;
+	return;
+
+	for (Int_t i = 0; i < noFiles; i++) {
+		canvas->cd(i+1);
+		curTree = GetTree(i);
+		if (!curTree) {
+			printf("AculCalibCsI::DrawBeam: Tree No. %d was not found.\n", i);
+			continue;
+		}
+		curTree->Draw("QDC[0]:TDC[0]", "TDC[0]<1000 && QDC[0]<2000", "cont");
+//		curTree->Draw("QDC[0]+QDC[1]:(TDC[2]+TDC[3])/2. - (TDC[0]+TDC[1])/2.", "", "cont");
+//		cout << "aksjda\t" << energyPoints << endl;
+		for (Int_t j = 0; j < fPars->GetNoRawFiles(); j++) {
+//			if ( fPars->GetCut(j) ) {
+	//			TCutG *cutTemp = fPars->GetCut(j);
+	//			curCutG = new TCutG(*cutTemp);
+				curCutG->Draw("same");
+//				printf("AculCalibCsI::DrawBeam: cTOF cut No. %d cannot be drawn, need to repair this function.\n", j);
+//			}
+		}
+
+		canvas->cd(noFiles+1+i);
+		curTree->Draw("QDC[0]:QDC[1]", "", "cont");
+		for (Int_t j = 0; j < fPars->GetNoRawFiles(); j++) {
+//			if ( fPars->GetCut(noFiles + j) ) {
+//				TCutG *cutTemp = fPars->GetCut(noFiles + j);
+//				curCutG = new TCutG(*cutTemp);
+				curCutG->Draw("same");
+//				printf("AculCalibCsI::DrawBeam: cQCD cut No. %d cannot be drawn, need to repair this function.\n", j);
+//			}
+		}
+
+		canvas->cd(2*noFiles+1+i);
+		var.Form("%s[5]:TDC[0]", variable);
+		con.Form("%s[5]>200", variable);
+		curTree->Draw(var.Data(), con.Data(), "cont");
+		for (Int_t j = 0; j < fPars->GetNoRawFiles(); j++) {
+//			if ( cutsCol.At(files + j) ) {
+//				curCutG = (TCutG*)cutsCol.At(files + j);
+//				curCutG->Draw("same");
+//				printf("AculCalibCsI::DrawBeam: cQCD cut No. %d cannot be drawn, need to repair this function.\n", j);
+//			}
+		}
+		canvas->Update();
+	}
+}
+
+void AculCalibScint::GetPeakMean(const char* variable, Int_t treeID, /*Int_t energy,*/ TCanvas *canvas, const char* beamcut, const Int_t nbins, Int_t lowRange) {
+
+//	todo: change this parameter as nonconstant
+	const Int_t noCrystals = 16;
+	CanDivider(canvas, noCrystals);
+
+	TString var;
+	TString con;
+	TString hname;
+	TString canvasTitle;
+	TCutG *currCut = fPars->GetCut(beamcut, treeID);
+
+//	if (!fPars->GetCut(beamcut, treeID)) {
+//		cout << "\"AculCalibScint::GetPeakMean\" cut with name \"" << beamcut << "\" was not found." << endl;
+//	} else {
+//		currCut =
+//	}
+
+//	todo manage the canvas name using cut name
+	if (currCut) {
+		canvasTitle.Form("variable: %s; tree: %d; cut: %s;", variable, treeID, currCut->GetName());
+		canvas->SetTitle(canvasTitle.Data());
+	} else {
+		canvasTitle.Form("variable: %s; tree: %d; no cut;", variable, treeID);
+		canvas->SetTitle(canvasTitle.Data());
+	}
+
+	TTree *curTree = 0;
+	curTree = GetTree(treeID);
+	if (!curTree) {
+		printf("AculCalibCsI::GetPeakMean: Tree No. %d was not found.\n", treeID);
+		return;
+	}
+
+	TString sVariable = variable;
+	sVariable.ToLower();
+	Int_t channel = 0;
+
+	for (Int_t i = 0; i < noCrystals; i++) {
+
+		if (sVariable.Contains("anc")) {
+			channel = i+1;
+		} else {
+			channel = i;
+		}
+
+		var.Form("%s[%d]>>hfull[%d][%d]", variable, channel, treeID, i);
+		if (currCut) {
+			con.Form("%s[%d]>%d && %s", variable, channel, lowRange, currCut->GetName());
+		}
+		else {
+//			cout << "\"AculCalibScint::GetPeakMean\" cut with name \"" << beamcut << "\" was not found." << endl;
+			con.Form("%s[%d]>%d", variable, channel, lowRange);
+		}
+		canvas->cd(i+1);
+		hname.Form("hfull[%d][%d]", treeID, i);
+		fHistFull[treeID].push_back( new TH1I(hname.Data(), "title", nbins, 0, 4096) );
+		curTree->SetLineColor(1);
+		curTree->Draw(var.Data(), con.Data());
+
+		var.Form("%s[%d]>>hcut[%d][%d]", variable, channel, treeID, i);
+		if (currCut) {
+			con.Form("%s[%d]>%d && %s[%d]<%d && %s",
+					variable, channel, fPars->GetMinChannel(treeID, i),
+					variable, channel, fPars->GetMaxChannel(treeID, i),
+					fPars->GetCut(beamcut, treeID)->GetName());
+		}
+		else {
+			con.Form("%s[%d]>%d && %s[%d]<%d",
+					variable, channel, fPars->GetMinChannel(treeID, i),
+					variable, channel, fPars->GetMaxChannel(treeID, i));
+		}
+
+		hname.Form("hcut[%d][%d]", treeID, i);
+		fHistCut[treeID].push_back( new TH1I(hname.Data(), "title", nbins, 0, 4096) );
+		fHistCut[treeID][i]->SetLineColor(3);
+		curTree->Draw(var.Data(), con.Data(), "same");
+
+		gPad->Update();
+		fMeanPeakPos[treeID].push_back(fHistCut[treeID][i]->GetMean());
+//		cout << fMeanPeakPos[treeID][i] << endl;
+		fMeanPeakRMS[treeID].push_back(fHistCut[treeID][i]->GetRMS());
+	}
+
+
+//	cout << fMeanPeakPos.size() << "\t" << fMeanPeakPos[treeID].size() << endl;
+//	cout << fMeanPeakPos.size() << "\t" << fMeanPeakPos[0].size() << endl;
+//	cout << fMeanPeakPos.size() << "\t" << fMeanPeakPos[1].size() << endl;
+//	cout << fMeanPeakPos.size() << "\t" << fMeanPeakPos[2].size() << endl;
+//	cout << fMeanPeakPos.size() << "\t" << fMeanPeakPos[3].size() << endl;
+
+	canvas->Update();
+
+}
+
+void AculCalibScint::Calibrate(TCanvas *canvas, Bool_t savefile, const char* filename, const char* option) {
+
+	//todo change this parameter as nonconstant
+	//e.g. the number of found fPeakMeans
+	const Int_t noChannels = 16;
+
+	//todo
+	if (!canvas) return;
+	CanDivider(canvas, noChannels);
+
+	for (Int_t i = 0; i < fPars->GetNoRawFiles(); i++) {
+		cout << i << "\t" << fMeanPeakPos[i].size() << endl;
+		if (fMeanPeakPos[i].size() < noChannels || fMeanPeakRMS[i].size() < noChannels) {
+//			cout << i << "\t" << fMeanPeakPos[i].size() << endl;
+			cout << "\"AculCalibScint::Calibrate\" something bad here" << endl;
+			return;
+		}
+	}
+
+//	cout << alphas2.GetSize()+1 << endl;
+//	cout << energyPoints+1 << endl;
+	cout << fPars->GetNoEPoints() << endl;
+	const Int_t energyPoints = fPars->GetNoEPoints();
+
+	TString gName;
+	TString gTitle;
+
+//	if (savefile) fGraphs->Open(filename, "RECREATE");
+
+	TF1 *fnc;
+
+	for (Int_t i = 0; i < noChannels; i++) {
+		canvas->cd(i+1);
+		gCal[i] = new TGraphErrors(energyPoints+1);
+//		FillGraph(gCal[i], energies.GetSize()+1, energies.GetArray(), i);
+		FillGraph(gCal[i], energyPoints+1, i);
+//		if (savefile) gCal[i]->Write();
+//		gCal[i]->Draw("Al*");
+		gCal[i]->Draw("A*");
+		gName.Form("g%s%s%d\n", fPars->GetDetName(), fPars->GetParticleName(), i);
+		gTitle.Form("%s %s\n", fPars->GetDetName(), fPars->GetParticleName());
+//		gCal[i]->SetTitle(gTitle.Data());
+		gCal[i]->SetName(gName.Data());
+		gCal[i]->Fit("pol1");
+		fnc = gCal[i]->GetFunction("pol1");
+		fnc->SetLineColor(kRed);
+		fA.push_back(fnc->GetParameter(1));
+		fB.push_back(fnc->GetParameter(0));
+		canvas->Update();
+	}
+	if (savefile) SaveClbGraphs(filename, option);
+
+}
+
+void AculCalibScint::FillGraph(TGraphErrors *g, Int_t npoints, /*Double_t *energies,*/ Int_t graphNumber, const char* option) {
+
+	TString opt = option;
+
+	//todo check if fMeanPeakPos is full
+
+	//all available energy points and (0,0)
+	g->SetPoint(0, 0., 0.);
+	for (Int_t i = 0; i < npoints-1; i++) {
+//		g->SetPoint(i+1, energies[i], mean[i][graphNumber]);
+//		g->SetPointError(i+1, 0, meanRMS[i][graphNumber]);
+//		cout << "Graph number: " << graphNumber << endl;
+//		cout << graphNumber << "\t" << fMeanPeakPos[i][graphNumber] << endl;
+		g->SetPoint(i+1, fMeanPeakPos[i][graphNumber], fPars->GetCalEnergy(i));
+		g->SetPointError(i+1, fMeanPeakRMS[i][graphNumber], 0);
+	}
+
+//	for (Int_t j = 1; j < 4; j++) {
+//			g->SetPoint(j, 0., 0.);
+//	}
+
+
+}
+
+void AculCalibScint::SaveClbGraphs(const char* filename, const char* option) {
+
+//	cout << "asdasd" << endl;
+//	cout << fGraphs << endl;
+	TFile fGraphs(filename, option);
+
+//	if (fGraphs) fGraphs->Close();
+
+//	cout << "asdasd" << endl;
+//	fGraphs = new TFile(filename, option);
+	cout << fGraphs.IsOpen() << endl;
+		cout << fGraphs.GetName() << endl;
+	fGraphs.Print();
+//	if (!fGraphs->IsOpen()) {
+//		printf("AculCalibCsI::SaveClbGraphs: file %s was not open.\n", filename);
+//		return;
+//	}
+
+	for (Int_t i = 0; i<16; i++) {
+		fGraphs.cd();
+		gCal[i]->Write();
+	}
+	fGraphs.Close();
+	return;
+}
+
+void AculCalibScint::WriteClbParameters(const char* filename) {
+
+	std::ofstream outfile(filename);
+	if ( !outfile.is_open() ) {
+		printf("AculCalibCsI::WriteClbParameters: File %s was not open.\n", filename);
+		return;
+	}
+
+	outfile << "#detector:\t" << fPars->GetDetName() << ",\tparticle:\t" << fPars->GetParticleName() << endl;
+	outfile << "#channel\tfA\tfB" << endl;
+	for (Int_t i = 0; i < (Int_t)fA.size(); i++) {
+		outfile << i << "\t" << fA[i] << "\t" << fB[i] << endl;
+	}
+
+	outfile.close();
+}

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

@@ -23,11 +23,11 @@ AculCalibration::AculCalibration() : fEnergy(0), fEnergyInput(0), fA(0), fB(0),
 
 	fCurrentHStack = NULL;
 	fCurrentHistList.IsOwner();
-//	todo: change size of fA and fB in some other place
+//	todo: change size of fA and fB in some other place
 	fA.Set(32);
-	fB.Set(32);
-//	fEnergy.Set(4);
-//	fEnergyInput.Set(4);
+	fB.Set(32);
+//	fEnergy.Set(4);
+//	fEnergyInput.Set(4);
 
 	kRaNOPEAKS = 0;
 	fLowerPeakRelativeHight = 0.;
@@ -171,7 +171,7 @@ Int_t AculCalibration::PeaksFitting(TH1* hSpectrum, Option_t* option, Double_t s
 	if (peaksNumber != kRaNOPEAKS) {
 		Info("PeaksFitting", "In histogram %s was found %d peaks", hSpectrum->GetName(), peaksNumber);
 		return 1;
-	}
+	}
 	//should be optional output
 	Info("PeaksFitting", "Number of peaks in %s: %d", hSpectrum->GetName(), peaksNumber);
 
@@ -258,7 +258,7 @@ Int_t AculCalibration::PeaksFitting(TH1* hSpectrum, Option_t* option, Double_t s
 	TMath::Sort(peaksNumber, peak, j, kFALSE);
 	fPeak.Set(peaksNumber);
 	for (Int_t i = 0; i < peaksNumber; i++) {
-		fPeak[i] = peak[j[i]];
+		fPeak[i] = peak[j[i]];
 		//printf("\tPeak peak\t%f\n", fPeak[i]);
 	}
 
@@ -267,23 +267,23 @@ Int_t AculCalibration::PeaksFitting(TH1* hSpectrum, Option_t* option, Double_t s
 		for (Int_t i = 0; i < peaksNumber; i++) {
 			printf("\tPeak position is\t%f\n", fPeak[i]);
 		}
-	}
-
+	}
+
 	//	provest kontrolu pomerne polohy piku,
 	//	jestli jsou spatne, provest urcita opatreni,
 	//	napr. zapis daneho histogramu do souboru,
 	//	zapis do souboru s chybama, vypis na obrazovku, ...
-	for (Int_t i = 0; i < peaksNumber; i++) {
+	for (Int_t i = 0; i < peaksNumber; i++) {
 			if ( !( (((1-fPeakPositionTolerance)*(fEnergy[0]/fEnergy[i])) < (fPeak[0]/fPeak[i])) && (((1+fPeakPositionTolerance)*(fEnergy[0]/fEnergy[i])) > (fPeak[0]/fPeak[i])) ) ) {
-			//printf("\tPeaksFitt fEnergy\t%f\n", fEnergy[i]);		
+			//printf("\tPeaksFitt fEnergy\t%f\n", fEnergy[i]);		
 			if (fCalInformation /* && opt.Contains("writebad")*/) {
 				fCalInformation->cd();
 				hSpectrum->Write();
 			}
 			//return 2;*/
 		}
-	}//for
-
+	}//for
+
 	return 0;
 }
 
@@ -358,27 +358,27 @@ void AculCalibration::PrintInputParameters()
 
 	return;
 
-}
-
-
+}
+
+
 Double_t AculCalibration::GetA(Int_t i) 
 {
-	if (i >= fA.GetSize()) //if i >= number of array element
+	if (i >= fA.GetSize()) //if i >= number of array element
 	{
 		return 0.;
 	}
 	return fA[i];
-}
-
+}
+
 Double_t AculCalibration::GetB(Int_t i) 
 {
-	if (i >= fB.GetSize()) 
+	if (i >= fB.GetSize()) 
 	{
 		return 0.;
 	}
 	return fB[i];
-}
-
+}
+
 
 
 Bool_t AculCalibration::SetCalibrationParameters(const char* calparfile)
@@ -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());
@@ -783,7 +786,7 @@ Bool_t AculCalibration::CalculateCalibParameters(const char* inputfile, const ch
 
 		//calibration parameters calculation																//ok
 		for (Int_t j = 0; j < kRaNOPEAKS; j++) {		//delat podle poctu zkoumanych piku
-			calGraph->SetPoint(j, fPeak[j], fEnergy[j]);  //calibration graph filling
+			calGraph->SetPoint(j, fPeak[j], fEnergy[j]);  //calibration graph filling
 			printf("\tPeak\t%f and energy\t%f\n", fPeak[j], fEnergy[j]);
 		}//for
 		calGraph->Fit(calFunction, "Q", "goff", 0, 4096);  //omezit hlasitost fitovani, udelat volitelne, dodelat volby rozsahu
@@ -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());
@@ -1103,17 +1106,17 @@ void AculCalibration::FindEnergyPeaks(TCanvas *c1, const char* ifile, const char
 		c1->cd(i+1);
 		PeaksFitting(hWork);
 		hWork->Draw();
-		ofile<<i<<"\t";
+		ofile<<i<<"\t";
 		for(Int_t j=0; j<kRaNOPEAKS; j++) {
-			ofile << fPeak[j] <<"\t";
-		}
+			ofile << fPeak[j] <<"\t";
+		}
 		ofile<<endl;
 
 	}
 
 	ofile.close();
-}
-
+}
+
 void AculCalibration::FindAverageEnergies(const char* ifile, const char* outfile) {
 
 	TString iFile = ifile;
@@ -1128,51 +1131,51 @@ 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());
 		return;
 	}
 
-	TH1 *hWork = 0;
-	Double_t hArray[histList->GetEntries()][kRaNOPEAKS];
-	//TString hSumName;
-	Double_t hSumE1 = 0.;
-	Double_t hAvrE1 = 0.;
-	Double_t hSumE2 = 0.;
-	Double_t hAvrE2 = 0.;
-	Double_t hSumE3 = 0.;
-	Double_t hAvrE3 = 0.;
-	Double_t hSumE4 = 0.;
+	TH1 *hWork = 0;
+	Double_t hArray[histList->GetEntries()][kRaNOPEAKS];
+	//TString hSumName;
+	Double_t hSumE1 = 0.;
+	Double_t hAvrE1 = 0.;
+	Double_t hSumE2 = 0.;
+	Double_t hAvrE2 = 0.;
+	Double_t hSumE3 = 0.;
+	Double_t hAvrE3 = 0.;
+	Double_t hSumE4 = 0.;
 	Double_t hAvrE4 = 0.;
 //	c1->Clear();
 //	c1->Divide(6, 6);
 
-	for (Int_t i = 0; i < histList->GetEntries(); i++) {
+	for (Int_t i = 0; i < histList->GetEntries(); i++) {
 		fr->GetObject(histList->At(i)->GetName(), hWork);
-		PeaksFitting(hWork);
-		for(Int_t j = 0; j < kRaNOPEAKS; j++) {
+		PeaksFitting(hWork);
+		for(Int_t j = 0; j < kRaNOPEAKS; j++) {
 			hArray[i][j] = fPeak[j];
-			if(fPeak[j]==0.){
-				Error("FindAverageEnergies", "No peak in channel %i !", histList->GetEntries());			
-			}
+			if(fPeak[j]==0.){
+				Error("FindAverageEnergies", "No peak in channel %i !", histList->GetEntries());			
+			}
 			//hSumName.Form("hSumE%i",j);
-		}
-
-		hSumE1 += hArray[i][0];
-		hSumE2 += hArray[i][1];
-		hSumE3 += hArray[i][2];
-		hSumE4 += hArray[i][3];
+		}
+
+		hSumE1 += hArray[i][0];
+		hSumE2 += hArray[i][1];
+		hSumE3 += hArray[i][2];
+		hSumE4 += hArray[i][3];
 //		std::cout<<"i "<<i<<" hSumE1 "<<hSumE1<<std::endl;
 	}
-	hAvrE1 = hSumE1/histList->GetEntries();
-	hAvrE2 = hSumE2/histList->GetEntries();
-	hAvrE3 = hSumE3/histList->GetEntries();
-	hAvrE4 = hSumE4/histList->GetEntries();
+	hAvrE1 = hSumE1/histList->GetEntries();
+	hAvrE2 = hSumE2/histList->GetEntries();
+	hAvrE3 = hSumE3/histList->GetEntries();
+	hAvrE4 = hSumE4/histList->GetEntries();
 	ofile <<"Average energies are:\t"<<hAvrE1<<"\t"<<hAvrE2<<"\t"<<hAvrE3<<"\t"<<hAvrE4<<std::endl;
 	ofile.close();
-}
+}
 
 
 void AculCalibration::ShowAnalyzedSpectra(const char *filename, TCanvas* fittedRawCanvas, Int_t xaxismin, Int_t xaxismax, Int_t subaddress)
@@ -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());
@@ -1400,8 +1403,8 @@ void AculCalibration::SetInputParameters() {
 
 		if ( strcmp(identificator, "noPeaks") == 0 ) {
 			kRaNOPEAKS = static_cast<Int_t>(atoi(parameter));
-			fEnergyInput.Set(kRaNOPEAKS);
-			fEnergy.Set(kRaNOPEAKS);
+			fEnergyInput.Set(kRaNOPEAKS);
+			fEnergy.Set(kRaNOPEAKS);
 			fPeak.Set(kRaNOPEAKS);
 			for (Int_t i = 0; i < kRaNOPEAKS; i++) {
 				fipr.getline(line, lineLength);

AculData/AculCalibration.h

@@ -74,7 +74,7 @@ private:
 
 	//these variables are the main for the class
 	TArrayD fA;		//calibration parameter, f(x) = fA*x + fB
-	TArrayD fB;		//calibration parameter, f(x) = fA*x + fB
+	TArrayD fB;		//calibration parameter, f(x) = fA*x + fB
 
 	TArrayD fPeak;	//v teto promenne je ulozena momentalni hodnota piku v kanalech, zejmena v jedne fci, mozno udelat ji jako lokalni, bude navratovou hodnotou fce PeaksFitting, predelat delku pole
 
@@ -83,7 +83,7 @@ private:
 	TString fParFileName;
 
 	//it is very doubtful that we need this class variable
-	TFile		*fCalInformation;
+	TFile		*fCalInformation;
 
 	
 
@@ -144,7 +144,7 @@ public:
 	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
+			Int_t uppersubaddress = ADDRESSNUMBER-1); //calculate calibration parameters for given block in given file
 
 	//function is not completely ready to use
 	//
@@ -176,13 +176,13 @@ public:
 
 	void CalibrateRawSpectra(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);
 
-	void FindEnergyPeaks(TCanvas *c1, const char* ifile, const char* outfile); 
+	void FindEnergyPeaks(TCanvas *c1, const char* ifile, const char* outfile); 
 	// Outputs calibrated energies for each channel in txt file 
 	//
 	// 
-	//  
-
-	void FindAverageEnergies(const char* ifile, const char* outfile);
+	//  
+
+	void FindAverageEnergies(const char* ifile, const char* outfile);
 	// Outputs average values of calibrated energies for the whole detector in txt file
 	//
 	// 

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
-
+#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/ELOSS.f90

@@ -4,320 +4,256 @@
 !== File: ELOSS.f90
 !== Date: 08/12/2000
 !======================================================================
-!  ELOSS.f90 
+!  ELOSS.f90
 !
 !  FUNCTIONS/SUBROUTINES exported from ELOSS.dll:
-!	ELOSS      - subroutine 
+!  ELOSS      - subroutine
+!======================================================================
+!== Date 2024-05-03
+!   Some reworking of code:
 !
-subroutine ELOSS(NEL,ZEL,AEL,WEL,DEN,ZP,AP,NE,ETAB,RE,ZW,AW)
+! * remove obsolete fortran instructions;
+! * replace common block with module;
+! * change precision to standard C double;
+! * remove restriction for 5 elements in material.
+
+module m_eloss
+  use iso_c_binding, only: c_int,c_double
+
+  real(c_double),allocatable,dimension(:),private:: adj,as,z,f,um
+  real(c_double),private:: oz,ro,azm,aj,zion,aion, zmed,amed
+  integer,private :: jc
+
+contains
+  subroutine ELOSS(NEL,ZEL,AEL,WEL,DEN,ZP,AP,NE,ETAB,RE,ZW,AW)&
+       bind(C,name='eloss_')
 
-  ! Expose subroutine ELOSS to users of this DLL
-  !
-  !DEC$ ATTRIBUTES DLLEXPORT::ELOSS
 
-	IMPLICIT REAL*8(A-H,O-Z)
-	INTERFACE
-	SUBROUTINE rde(E, R, R1, R2, IRE)
-		REAL*8   E, R, R1, R2
-		INTEGER  IRE
-	END SUBROUTINE rde
-	END INTERFACE
+  IMPLICIT none
 
   ! Variables
 
   ! Input:
-	INTEGER NEL, NE
-	REAL*8  ZEL(NEL),AEL(NEL),WEL(NEL), DEN,ZP,AP, ETAB(NE)
+  INTEGER(c_int),intent(in) ::NEL ! number of elements in the material
+  INTEGER(c_int) ::NE ! number of points in E -- Range table
+  real(c_double),dimension(nel),intent(in):: zel
+  real(c_double),dimension(nel),intent(in):: ael
+  real(c_double),dimension(nel),intent(in):: wel
+  real(c_double),intent(in) :: den
+  real(c_double),intent(in) :: ZP,AP
+  real(c_double),dimension(ne),intent(in):: Etab
 
   ! Output:
-	REAL*8  RE(NE),ZW,AW
-
-  ! Local
-	COMMON adj(5),as(5),z(5),f(5),um(5),oz,ro,azm,aj,zion,aion,&
-	       zmed,amed,jc
+  real(c_double),dimension(ne),intent(out) :: RE
+  REAL(c_double),intent(out) :: ZW,AW
 
+!!$ local variables
+  integer :: i,j,ire
+  real(c_double) :: rel,rel1,uma,umed,zam,zme
   ! Body of ELOSS
 
-	zion = ZP
-	aion = AP
-	jc   = NEL
-	ro   = DEN
-	
-	!== two parameters with question
-	ire  = 1
-	oz   = 1.
-	DO i = 1, NEL
-		as(i) = AEL(i)
-		z(i)  = ZEL(i)
-		um(i) = WEL(i)
-		IF(z(i) .LE. 13.) THEN
-			adj(i) = 12.*z(i) + 7.
-		ELSE
-			adj(i) = 9.76*z(i) + 58.8 / z(i)**0.19
-		END IF
-	END DO
-
-	uma=0.
-	zam=0.
-	umed=0.
-	zme=0.
-	aj=0.
-	DO i = 1, jc
-		uma=uma+um(i)*as(i)
-		umed=umed+um(i)
-		zme=zme+um(i)*z(i)
-	END DO
-
-	amed=uma/umed
-	zmed=zme/umed
-	
-	DO i = 1, jc
-		f(i)=um(i)*as(i)/uma
-	END DO
-
-	DO i = 1, jc
-		zam=zam+f(i)*z(i)/as(i)
-	END DO
-
-	azm=1./zam
-	aj=0.
-	
-	DO i = 1, jc
-		aj=aj+f(i)*z(i)*log(adj(i))/as(i)
-	END DO
-	
-	aj=aj*azm
-	aj=exp(aj)
-	ZW = zmed
-	AW = amed
-
-	DO j = 1, NE
-		!== result [mg/cm^2]
-		CALL rde(ETAB(j), RE(j), rel1, rel, ire)
-	END DO
+  zion = ZP
+  aion = AP
+  jc   = NEL
+  ro   = DEN
+  allocate(adj(jc),as(jc),z(jc),f(jc),um(jc))
+
+  !== two parameters with question
+  ire  = 1
+  oz   = 1.
+
+  as=ael;z = ZEL; um = WEL
+  DO concurrent (i = 1:jc)
+     IF(z(i) .LE. 13.) THEN
+        adj(i) = 12.*z(i) + 7.
+     ELSE
+        adj(i) = 9.76*z(i) + 58.8 / z(i)**0.19
+     END IF
+  END DO
+
+  uma=sum(um*as)
+  zme=sum(um*z)
+  zam=zme/uma;  azm=1./zam
+  umed=sum(um)
+  aj=exp(sum(um*z*log(adj))/uma*azm)
+
+  amed=uma/umed
+  zmed=zme/umed
+
+  f=um*as/uma
+
+  ZW = zmed
+  AW = amed
+
+  DO j = 1, NE
+     !== result [mg/cm^2]
+     CALL rde(ETAB(j), RE(j), rel1, rel, ire)
+  END DO
+  deallocate(adj,as,z,f,um)
 end subroutine ELOSS
 
 SUBROUTINE rde(e,range,rel1,rel,ix)
-	IMPLICIT REAL*8(A-H,O-Z)
-
-	INTERFACE 
-		REAL*8 FUNCTION c(x)
-			REAL*8 x
-		END FUNCTION c
-
-		REAL*8 FUNCTION c1(x)
-			REAL*8 x
-		END FUNCTION c1
-	END INTERFACE
-
-
-
-! calculates range and de/dx for compounds
-	dimension ala(3),ala1(3)
-	dimension a(3,3),a1(4,4),a2(4,4),b(2,3),cc(5)
-	common	adj(5),as(5),z(5),f(5),um(5),oz,ro,azm,aj,zion,aion,&
-			zmed,amed,jc
-	dimension alaj1(4),altau1(4)
-
-	data a/	-.75265, .073736, .040556, 2.5398,-.312,.018664, &
-			-.24598, .11548, -.0099661/
-
-	data a1/-8.0155,     0.36916,    -1.4307e-02,  3.4718e-03,	&
-			 1.8371,    -1.452e-02,  -3.0142e-02,  2.3603e-03,	&
-			 0.045233,  -9.5873e-04,  7.1303e-03, -6.8538e-04,	&
-			-5.9898e-03,-5.2315e-04, -3.3802e-04,  3.9405e-05/
-
-	data a2/-8.725,		 0.8309,	 -0.13396,	    0.012625,	&
-			 1.8797,	 0.11139,	 -0.064808,		0.0054043,	&
-			 0.74192,	-0.528805,	  0.1264232,   -0.00934142,	&
-			 0.752005,  -0.5558937,   0.12843119,  -0.009306336/
-
-	data b/	0.422377e-06,   3.858019e-09, 0.0304043e-06, -0.1667989e-09, &
-           -0.00038106e-06, 0.00157955e-09/
-
-	if(e.le.0.002)then
-		range=0.
-		rel1=0.
-		rel=0.
-		return
-	endif
-
-! this a flag
-	ibis=-1
-
-	en	=	e/aion
-	tau	=	en*1.008
-
-	altau	=	log(tau)
-	alaj	=	log(aj)
-	alaj1(1)=	1.
-	altau1(1)=	1.
-	DO kk = 2,4
-		alaj1(kk)=alaj**(kk-1)
-		altau1(kk)=altau**(kk-1)
-	END DO
-	t	=	tau/938.256
-	tt	=	2.*t + t*t
-	beta=	sqrt(tt)/(1.+t)
-
-
-	s1=0.
-	DO i=1,4
-		DO j=1,4
-			s1	=	s1 + a2(j,i)*alaj1(j)*altau1(i)
-		END DO
-	END DO
-
-	ala(1) = azm*exp(s1)
-	
-	s2=0.
-	DO i=2,4
-		DO j=1,4
-			s2	=	s2 + (i-1)*a2(j,i)*alaj1(j)*altau1(i-1)
-		END DO
-	END DO
-	ala1(1)=ala(1)*s2/tau
-
-	s1=0.
-	DO i=1,4
-		DO j=1,4
-			s1	=	s1 + a1(j,i)*alaj1(j)*altau1(i)
-		END DO
-	END DO
-
-	ala(3) = azm*exp(s1)
-
-	s2=0.
-	DO i=2,4
-		DO j=1,4
-			s2	=	s2 + (i-1)*a1(j,i)*alaj1(j)*altau1(i-1)
-		END DO
-	END DO
-	ala1(3)=ala(3)*s2/tau
-
-	s1=0.
-	DO i=1,3
-		DO j=1,3
-			s1	=	s1	+	a(j,i)*alaj1(j)*altau1(i)
-		END DO
-	END DO
-	ala(2)=azm*exp(s1)/1000.
-
-	s2=0.
-	DO i=2,3
-		DO j=1,3
-			s2	=	s2 + (i-1)*a(j,i)*alaj1(j)*altau1(i-1)
-		END DO
-	END DO
-	ala1(2)=ala(2)*s2/tau
-
-25	continue
-	coefa=3.
-	coefb=1.
-
-	alaa=(ala(1)*(tanh(coefa*(.98 - en))+1.)/2.			&
-		+ ala(2)*(tanh(coefa*(en - .98))+1.)/2.)		&
-		*        (tanh(coefb*(8.0 - en))+1.)/2.			&
-		+ ala(3)*(tanh(coefb*(en  - 8.))+1.)/2.
-
-
-	alim1=0.
-	alim2=0.
-	if(coefa*(en-.98).lt.85)then
-		alim1=1.008/cosh(coefa*(.98-en))/cosh(coefa*(.98-en))
-	endif
-	if(coefb*(en-8.).lt.85)then
-		alim2=1.008/cosh(coefb*(8.-en))/cosh(coefb*(8.-en))
-	endif
-
-	alaa1=(ala1(1)*(tanh(coefa*(.98-en))+1.)/2.+		&
-		ala1(2)*(tanh(coefa*(en-.98))+1.)/2.)*			&
-		(tanh(coefb*(8.-en))+1.)/2.+					&
-		ala1(3)*(tanh(coefb*(en-8.))+1.)/2.+			&
-		coefa/2.*(tanh(coefb*(8.-en))+1.)/2.*			&
-		(ala(2)*alim1-ala(1)*alim1)+					&
-		coefb/2.*(ala(3)*alim2-							&
-		(ala(1)*(tanh(coefa*(.98-en))+1.)/2.+			&
-		ala(2)*(tanh(coefa*(en-.98))+1.)/2.)*alim2)
-
-
-	hi=137.*beta/zion
-	bz=(31.8+3.86*(aj**.625))*azm*.000001
-	bz=bz*(zion**2.666667)*c(hi)
-	bz1=(4.357+.5288*(aj**.625))*azm*.001
-	bz1=bz1*(zion**1.666667)*c1(hi)
-	bep=beta*beta
-	rel1=zion*zion/(alaa1+bz1*((1.-bep)**1.5)/931.141/beta)
-	rel1=rel1/1000.
-	range=(alaa+bz)*aion/1.008/zion/zion
-	range=range*1000.
-
-! Atention!! this version do not work correctly for ix.ne.1
-	if(ix.ne.1)return
-	ank=.153574*ro/azm
-	z23=zion**.666667
-	abet=beta*125./z23
-	zef=zion*(1.-exp(-abet))
-	zef2=zef*zef
-	om=1022000.*bep/(1.-bep)
-	cbet=0.
-	DO k=1,jc
-		cc(k)=0.
-		DO i=1,2
-			DO j=1,3
-				cc(k)=cc(k)+b(i,j)*((1./bep-1.)**j)*((adj(k)**(i+1)))
-			END DO
-		END DO
-		cbet=cbet+f(k)*cc(k)/as(k)
-	END DO
-	cbet=cbet*azm
-	del1=ank*zef2*(log(om/oz)-bep)/bep
-	del1=del1/ro
-	del2=2.*ank*zef2*(log(oz/aj)-cbet)/bep
-	del2=del2/ro
-	rel2=rel1-del1
-	rel3=rel1-rel2+del2
-	if(del1)8,8,9
-8	rel=rel1
-	goto 12
-9	if(del1+del2-rel2)10,10,11
-10	rel=rel3
-	goto 12
-11	if(del1.lt.rel1)then
-	 rel=rel2
-	 else
-	 rel=rel1
-	endif
-12	return
-	END
-
-
-	REAL*8 FUNCTION c(x) 
-	REAL*8 x
-	IF(x .LE. 0.2) THEN
-		c = -0.00006 + (0.05252 + 0.12857*x)*x
-	ELSE IF(x .LE. 2.) THEN
-		c = -0.00185 + (0.07355 + (0.07172 - 0.02723*x)*x)*x
-	ELSE IF(x .LE. 3.) THEN
-		c = -0.0793  + (0.3323  - (0.1234  - 0.0153*x)*x)*x
-	ELSE
-		c = 0.22
-	END IF
-	END
-
-	REAL*8 FUNCTION c1(x)
-	REAL*8 x
-
-	IF(x .LE. 0.2) THEN
-		c1 = 0.05252+.25714*x
-	ELSE IF(x .LE. 2.0) THEN
-		c1 = 0.07355 + (0.14344 - 0.08169*x)*x
-	ELSE IF(x .LE. 3.0) THEN
-		c1 = 0.3323  - (0.2468  - 0.0459*x)*x
-	ELSE
-		c1 = 0.
-	END IF
-	
-	END
-
-
+  ! calculates range and de/dx for compounds
+  IMPLICIT none !REAL(c_double) (A-H,O-Z)
+
+  real(c_double),intent(in) ::E
+  integer,intent(in) ::ix
+  real(c_double),intent(out) ::range
+  real(c_double),intent(out) ::rel1
+  real(c_double),intent(out) ::rel
+
+  integer :: i,j,k,kk
+
+  real(c_double),parameter,dimension(3,3)::a=reshape([&
+       -0.75265, .073736, .040556,&
+       +2.53980,-.312000, .018664, &
+       -0.24598, .115480,-.0099661],shape=[3,3])
+  real(c_double),parameter,dimension(4,4)::a1=reshape([&
+       -8.0155   , 0.36916  ,-1.4307e-2, 3.4718e-3, &
+       +1.8371   ,-1.4520e-2,-3.0142e-2, 2.3603e-3, &
+       -4.5233e-2,-9.5873e-4, 7.1303e-3,-6.8538e-4, &
+       -5.9898e-3,-5.2315e-4,-3.3802e-4, 3.9405e-5],shape=[4,4])
+  real(c_double),parameter,dimension(4,4)::a2=reshape([&
+       -8.725000, 0.8309000,-0.13396000, 0.012625, &
+       -1.879700, 0.1113900,-0.06480800, 0.0054043, &
+       -0.741920,-0.5288050, 0.12642320,-9.341420e-3,&
+       -0.752005,-0.5558937, 0.12843119,-9.306336e-3 ],shape=[4,4])
+  real(c_double),parameter,dimension(2,3)::b=reshape([&
+       +4.223770e-07, 3.858019e-09, 3.04043e-08,&
+       -1.667989e-10,-3.810600e-10, 1.57955e-12],shape=[2,3])
+
+  real(c_double),allocatable,dimension(:) :: cc
+  real(c_double),dimension(3) :: ala, ala1
+  real(c_double) :: alaa,alaa1
+  real(c_double),dimension(4) :: alaj1, altau1
+  real(c_double) :: abet, alaj, altau, ank, bep, beta, bz, bz1,cbet, t, tau, tt
+  real(c_double),parameter ::  coefa=3.,  coefb=1.
+  real(c_double) :: alim1, alim2, del1, del2, en, hi, om, rel2, rel3, zef, zef2
+
+  if(e.le.0.002)then
+     range=0.
+     rel1=0.
+     rel=0.
+     return
+  endif
+
+  en = e/aion
+  tau = en*1.008
+
+  altau = log(tau)
+  alaj = log(aj)
+  DO concurrent (kk = 1:4)
+     alaj1(kk)=alaj**(kk-1)
+     altau1(kk)=altau**(kk-1)
+  END DO
+  t = tau/938.256
+  tt = 2.*t + t*t
+  beta= sqrt(tt)/(1.+t)
+
+
+  ala(1) = azm*exp(dot_product(alaj1,matmul(a2,altau1)))
+  ala(2) = azm*exp(dot_product(alaj1(1:3),matmul(a,altau1(1:3))))/1000.
+  ala(3) = azm*exp(dot_product(alaj1,matmul(a1,altau1)))
+
+  ala1(1)=ala(1)*dot_product(alaj1,matmul(a2(:,2:4),altau1(1:3)*[1,2,3]))/tau
+  ala1(2)=ala(2)*dot_product(alaj1(1:3),matmul(a(:,2:3),altau1(1:2)*[1,2]))/tau
+  ala1(3)=ala(3)*dot_product(alaj1,matmul(a1(:,2:4),altau1(1:3)*[1,2,3]))/tau
+
+  associate(ca=>coefa*(.98 - en),cb=>coefb*(8.0 - en))
+    associate(tca=>(1+tanh(ca))/2.,tcb=>(1+tanh(cb))/2.)
+      alaa=(ala(1)*tca + ala(2)*(1.0-tca))*tcb + ala(3)*(1.0-tcb)
+
+      alim1=0.; alim2=0.
+      if(-ca.lt.85)then
+         alim1=1.008*(cosh(ca)**(-2))
+      endif
+      if(-cb.lt.85)then
+         alim2=1.008*(cosh(cb)**(-2))
+      endif
+
+      alaa1=(ala1(1)*tca+ ala1(2)*(1.0-tca))*tcb + ala1(3)*(1.0-tcb)+&
+           coefa*tcb* (ala(2)-ala(1))*alim1/2.+   &
+           coefb*(ala(3)-(ala(1)*tca+ala(2)*(1.-tca)))*alim2/2.
+    end associate
+  end associate
+
+  hi=137.*beta/zion
+  bz=(31.8+3.86*(aj**.625))*azm* 1e-6 *(zion**2.666667)*c(hi)
+  bz1=(4.357+.5288*(aj**.625))*azm* .001 *(zion**1.666667)*c1(hi)
+  bep=beta*beta
+  rel1=zion*zion/(alaa1+bz1*((1.- beta**2)**1.5)/931.141/beta)/1000.
+  range=(alaa+bz)*aion/(1.008*zion**2)*1000.
+
+  ! Atention!! this version do not work correctly for ix.ne.1
+  if(ix.ne.1) then
+     return
+  end if
+
+  allocate(cc(size(as)))
+
+  ank=.153574*ro/azm
+!  z23=zion**.666667
+  abet=beta*125.*(zion** (-2.0/3.0))
+  zef=zion*(1.-exp(-abet))
+  zef2=zef*zef
+  om= 1022000. *bep/(1.-bep)
+  cbet=0.
+  DO k=1,jc
+     cc(k)=0.
+     DO i=1,2
+        DO j=1,3
+           cc(k)=cc(k)+b(i,j)*((1./bep-1.)**j)*((adj(k)**(i+1)))
+        END DO
+     END DO
+     cbet=cbet+f(k)*cc(k)/as(k)
+  END DO
+  cbet=cbet*azm
+  del1=ank*zef2*(log(om/oz)-bep)/bep/ro
+  del2=2.*ank*zef2*(log(oz/aj)-cbet)/bep/ro
+  rel2=rel1-del1
+  rel3=rel1-rel2+del2
+!!$ here is a replasement for an Arithmetic IF construct
+  if (del1 <=0.0 ) then
+     rel=rel1
+  else if (del1+del2-rel2<=0) then
+     rel=rel3
+  else if(del1.lt.rel1)then
+     rel=rel2
+  else
+     rel=rel1
+  endif
+  deallocate(cc)
+  return
+END SUBROUTINE rde
+
+
+pure FUNCTION c(x) result(res)
+   REAL(c_double),intent(in) :: x
+   real(c_double) :: res
+  IF(x .LE. 0.2) THEN
+     res = -0.00006 + (0.05252 + 0.12857*x)*x
+  ELSE IF(x .LE. 2.) THEN
+     res = -0.00185 + (0.07355 + (0.07172 - 0.02723*x)*x)*x
+  ELSE IF(x .LE. 3.) THEN
+     res = -0.0793  + (0.3323  - (0.1234  - 0.0153*x)*x)*x
+  ELSE
+     res = 0.22
+  END IF
+END FUNCTION c
+
+pure FUNCTION c1(x) result(res)
+  REAL(c_double),intent(in) :: x
+  real(c_double) :: res
+  IF(x .LE. 0.2) THEN
+     res = 0.05252+.25714*x
+  ELSE IF(x .LE. 2.0) THEN
+     res = 0.07355 + (0.14344 - 0.08169*x)*x
+  ELSE IF(x .LE. 3.0) THEN
+     res = 0.3323  - (0.2468  - 0.0459*x)*x
+  ELSE
+     res = 0.
+  END IF
+
+END FUNCTION c1
+
+end module m_eloss

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 returned=0;
-	//Convert string to int:
-	std::stringstream ss(configMap[key]);
-	ss>>returned;
-	return returned;
+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);
+    }
 }
 
 //_____________________________________________________________________________
-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);
-	}
-	double returned=0.0;
-	//Convert string to double:
-	std::stringstream ss(configMap[key]);
-	ss>>returned;
-	return returned;
+	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);
+    }
 }
 
 //_____________________________________________________________________________
-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.cpp

+#include "CsICalib.h"
+
+ClassImp(CsICalib);
+
+CsICalib::CsICalib() : fr("TFile", 5), tr("TTree", 5), cutsCol("TCutG"), fA(16), fB(16) {
+
+	printf("CsICalib::Default constructor called.\n");
+
+
+}
+
+CsICalib::CsICalib(const char* parfile) : fr("TFile", 5), tr("TTree", 5), cutsCol("TCutG", 10), fA(16), fB(16) {
+	printf("CsICalib::Constructor called.\n");
+
+	ReadParFile(parfile);
+//	PrintParameters();
+	cout << "nofiles: " << nofiles << endl;
+	OpenTrees();
+	LoadCuts();
+
+//	fr.Print();
+//	fr.At(0);
+	
+
+}
+
+CsICalib::~CsICalib() {
+
+	printf("CsICalib::Destructor called.\n");
+
+}
+
+void CsICalib::OpenTrees() {
+
+	TFile *file;
+	for (Int_t i = 0; i < nofiles; i++) {	
+		fr[i] = new TFile(fileNames[i], "READ");
+		file = (TFile*)fr.At(i);
+		cout << file->GetName() << endl;
+		tr[i] = (TTree*)file->Get("AnalysisxTree");
+	}
+}
+
+void CsICalib::LoadCuts() {
+
+	if (cutsFileName == "") {
+		printf("CsICalib::LoadCuts: Name of file (*.root) with cuts was not provided.\n");
+		printf("CsICalib::LoadCuts: No cuts has been loaded.\n");
+		return;
+	}
+	fCuts = new TFile(cutsFileName.Data(), "READ");
+	for (Int_t i = 0; i < nCuts; i++) {
+		cutsCol[i] = (TCutG*)fCuts->Get(cutNames[i]);
+	}
+
+}
+
+void CsICalib::ReadParFile(const char* parfile) {
+	
+	std::ifstream infile(parfile);
+	if ( !infile.is_open() ) {
+		printf("CsICalib::ReadParFile: File %s was not open.\n", parfile);
+		return;
+	}
+
+	energyPoints = 0;
+
+	TString line;
+
+	Int_t i, min, max;
+	char det[100], part[100], fname[500], cname[100];	
+
+	double en;	//energy
+
+	while (!infile.eof()) {
+		line.ReadLine(infile);
+
+		if ( line.BeginsWith("#") ) continue;
+
+		if ( line.BeginsWith("energies") ) {
+			sscanf(line.Data(), "%*s %d", &i);
+			fE.Set(i);
+			continue;
+		}
+
+		if ( line.BeginsWith("files") ) {
+			sscanf(line.Data(), "%*s %d", &i);
+			nofiles = i;
+			printf("CsICalib::ReadParFile: %d files will be loaded:\n", nofiles);
+			for (Int_t j = 0; j < nofiles; j++) {
+				line.ReadLine(infile);
+				sscanf(line, "%s", fname);
+				fileNames[j] = fname;
+				cout << fileNames[j] << endl;
+			}
+			continue;
+		}
+
+		if ( line.BeginsWith("cutFile") ) {
+			sscanf(line.Data(), "%*s %s %d", fname, &nCuts);
+			cutsFileName = fname;
+			for (Int_t j = 0; j < nCuts; j++) {
+				line.ReadLine(infile);
+				sscanf(line, "%s", cname);
+				cutNames[j] = cname;
+				cout << cutNames[j] << endl;
+			}
+			continue;
+		}
+
+		if ( line.BeginsWith("detector") ) {
+			sscanf(line.Data(), "%*s %s %s", det, part);
+			detName = det;
+			partName = part;
+			printf("%s %s\n", detName.Data(), partName.Data());
+			continue;
+		}
+
+		if ( line.BeginsWith("energy") ) {
+			sscanf(line.Data(), "%*s %lf", &en);
+			fE[energyPoints] = en;
+			printf("%f\n", fE[energyPoints]);
+			energyPoints++;
+			continue;
+		}
+
+		sscanf(line.Data(), "%d %d %d", &i, &min, &max);
+		peakMin[energyPoints-1][i] = min;
+		peakMax[energyPoints-1][i] = max;
+//		printf("%d %d %d\n", i, peakMin[energyPoints-1][i], peakMax[energyPoints-1][i]);
+	}//while
+
+	printf("energyPoints: %d\n", energyPoints);
+
+	infile.close();
+	return;
+}
+
+void CsICalib::PrintParameters(const char* option) {
+	
+	TString opt = option;
+
+	printf("Energy points: %d\n", energyPoints);
+//	printf("Detector: %s, Particle: %s\n", ????);
+	for (Int_t i = 0; i < energyPoints; i++) {	
+		printf("Peak ranges for energy %f:\n", fE[i]);
+		if ( opt.Contains("v") ) {
+			for (Int_t j = 0; j < 16; j++) {
+				printf("ch: %d\tmin: %d\tmax: %d\n", j, peakMin[i][j], peakMax[i][j]);
+			}
+		}//if
+	}//for
+
+}
+
+
+void CsICalib::PrintPeakRanges() {
+	for (Int_t i = 0; i < 16; i++) {
+		printf("%d\t%d\t%d\n", i, peakMin[0][i], peakMax[0][i]);
+	}
+}
+
+void CsICalib::PrintTrees() {
+
+	TTree *curTree = 0;
+	for (Int_t i = 0; i < tr.GetEntries(); i++) {
+		curTree = (TTree*)tr.At(i);
+		if (curTree) {
+			printf("Tree No. %d; File: %s; Name: %s\n", i, curTree->GetDirectory()->GetName(), curTree->GetName());
+		} else {
+			printf("Tree No. %d was not loaded. Maximal number of trees is %d\n", i, NOCALFILES);
+		}
+	}
+
+	return;
+}
+
+void CsICalib::PrintFiles() {
+
+	printf("Number of loaded files: %d\n", fr.GetEntries());
+
+
+	TFile *curFile = 0;
+	for (Int_t i = 0; i < fr.GetEntries(); i++) {
+		curFile = (TFile*)fr.At(i);
+		if (curFile) {
+			printf("File No. %d: \"%s\"\n", i, curFile->GetName());
+		}
+//		else {
+//			printf("File No. %d was not loaded. Maximal number of files is %d\n", i, NOCALFILES);
+//		}
+	}
+
+	return;
+}
+
+void CsICalib::PrintCuts() {
+	
+//	printf("CsICalib::PrintCuts: works wrong\n");
+//	return;
+	if (fCuts) printf("Cuts loaded from file \"%s\"\n", fCuts->GetName());
+
+	/*for (Int_t i = 0; i < NOCALFILES; i++) {
+		if (cTOF[i]) {
+			printf("TOF cut No. %d; Name: \"%s\"\n", i, cutsCol[i]->GetName());
+			cout << "asdjasd" << endl;
+		}
+		else {
+			printf("TOF cut No. %d was not loaded. Maximal number of cuts is %d\n", i, NOCALFILES);
+		}
+	}//for */
+
+	TCutG *curCut = 0;
+	//cutsCol
+
+	for (Int_t i = 0; i < cutsCol.GetEntries(); i++) {
+		curCut = (TCutG*)cutsCol.At(i);
+		if (curCut) {
+			printf("Cut No. %d; Name: \"%s\"\n", i, curCut->GetName());
+		} /*else {
+			printf("TOF cut No. %d was not loaded. Maximal number of cuts is %d\n", i, NOCALFILES);
+		}*/
+	}
+
+/*	for (Int_t i = 0; i < NOCALFILES; i++) {
+		if (cQCD[i]) {
+			printf("QCD cut No. %d; Name: \"%s\"\n", i, cQCD[i]->GetName());
+//			cout << "kasjhd" << endl;
+		} else {
+//			cout << "bhajskd" << endl;
+			printf("QCD cut No. %d was not loaded. Maximal number of cuts is %d\n", i, NOCALFILES);
+//			cout << "vsdfjks" << endl;
+		}
+	}
+
+	printf("CsICalib::PrintCuts: End of function.\n");
+*/
+	return;
+}
+
+void CsICalib::DrawVariable(const char* variable, Int_t tree, TCanvas *canvas, Int_t lowRange, Int_t upRange) {
+
+//	if (!canvas) TCanvas *c = new TCanvas();
+	if (!canvas) return;
+
+	canvas->Clear();
+	canvas->Divide(4,4);
+	
+	TString canvasTitle;
+	TString var;
+	TString con;
+
+	TTree *curTree = 0;
+	curTree = (TTree*)tr.At(tree);
+	if (!curTree) {
+		printf("CsICalib::DrawVariable: Tree No. %d was not found.\n", tree);
+		return;
+	}
+
+	canvasTitle.Form("variable: %s; tree: %d", variable, tree);	
+	canvas->SetTitle(canvasTitle.Data());
+
+	for (Int_t i = 0; i < 16; i++) {
+		var.Form("%s[%d]", variable, i);
+		con.Form("%s[%d]>%d && %s[%d]<%d", variable, i, lowRange, variable, i, upRange);
+		canvas->cd(i+1);
+		curTree->Draw(var.Data(), con.Data());
+		canvas->Update();
+	}
+
+}
+
+void CsICalib::DrawBeam(TCanvas *canvas, Int_t files, const char* variable) {
+
+	canvas->SetTitle("Beam");
+	canvas->Clear();
+//	canvas->Divide(files, 2);
+	canvas->Divide(files, 3);
+
+	TTree *curTree = 0;
+	TCutG *curCutG = 0;
+	TString var;
+	TString con;
+	
+	for (Int_t i = 0; i < files; i++) {
+		canvas->cd(i+1);
+		curTree = (TTree*)tr.At(i);
+		if (!curTree) {
+			printf("CsICalib::DrawBeam: Tree No. %d was not found.\n", i);
+			continue;
+		}
+		curTree->Draw("QDC[0]:TDC[0]", "TDC[0]<1000 && QDC[0]<2000", "cont");
+//		curTree->Draw("QDC[0]+QDC[1]:(TDC[2]+TDC[3])/2. - (TDC[0]+TDC[1])/2.", "", "cont");
+//		cout << "aksjda\t" << energyPoints << endl;
+		for (Int_t j = 0; j < energyPoints; j++) {		
+			if ( cutsCol.At(j) ) {
+				curCutG = (TCutG*)cutsCol.At(j);
+				curCutG->Draw("same");
+//				printf("CsICalib::DrawBeam: cTOF cut No. %d cannot be drawn, need to repair this function.\n", j);
+			}
+		}
+
+		canvas->cd(files+1+i);
+		curTree->Draw("QDC[0]:QDC[1]", "", "cont");
+		for (Int_t j = 0; j < energyPoints; j++) {		
+			if ( cutsCol.At(files + j) ) {
+				curCutG = (TCutG*)cutsCol.At(files + j);
+				curCutG->Draw("same");
+//				printf("CsICalib::DrawBeam: cQCD cut No. %d cannot be drawn, need to repair this function.\n", j);
+			}
+		}
+
+		canvas->cd(2*files+1+i);
+		var.Form("%s[5]:TDC[0]", variable);
+		con.Form("%s[5]>200", variable);
+		curTree->Draw(var.Data(), con.Data(), "cont");
+		for (Int_t j = 0; j < energyPoints; j++) {		
+//			if ( cutsCol.At(files + j) ) {
+//				curCutG = (TCutG*)cutsCol.At(files + j);
+//				curCutG->Draw("same");
+//				printf("CsICalib::DrawBeam: cQCD cut No. %d cannot be drawn, need to repair this function.\n", j);
+//			}
+		}
+		canvas->Update();
+	}
+}
+
+void CsICalib::DrawVariableCut(const char* variable, Int_t tree, TCanvas *canvas, const char* cut1, const char* cut2, Int_t lowRange) {
+
+//	cout << "kjashbdfjka ajsdbf jakhsdb askjdhb" << endl;
+
+	if (!cutsCol.FindObject(cut1)) {
+		printf("Cut %s was not found.\n", cut1);
+		return;
+	}
+
+	canvas->Clear();
+	canvas->Divide(4,4);
+
+	TString canvasTitle;
+	TString var;
+	TString con;
+	TString sVariable = variable;
+	sVariable.ToLower();
+	Int_t channel = 0;
+
+//	cout << cutsCol.FindObject(cut1)->GetName() << endl;
+
+	canvasTitle.Form("variable: %s; cut1: %s; cut2: %s; tree: %d", variable, cutsCol.FindObject(cut1)->GetName(), cut2 , tree);	
+	canvas->SetTitle(canvasTitle.Data());
+
+	TTree *curTree = 0;
+	curTree = (TTree*)tr.At(tree);
+	if (!curTree) {
+		printf("CsICalib::DrawVariableCut: Tree No. %d was not found.\n", tree);
+		return;
+	}
+
+	for (Int_t i = 0; i<16; i++) {
+		if (sVariable.Contains("anc")) {
+			channel = i+1;
+		} else {
+			channel = i;
+		}
+//		cout << channel << endl;
+		var.Form("%s[%d]", variable, channel);
+		con.Form("%s[%d]>%d", variable, channel, lowRange);
+
+		canvas->cd(i+1);
+		curTree->SetLineColor(1);
+		curTree->Draw(var.Data(), con.Data());
+		curTree->SetLineColor(3);
+		con.Form("%s[%d]>0 && %s", variable, channel, cutsCol.FindObject(cut1)->GetName());
+		curTree->Draw(var.Data(), con.Data(), "same");
+
+		TString scut2 = cut2;
+		if (scut2.Length() != 0) {
+			if (!cutsCol.FindObject(cut2)) {
+				printf("Cut %s was not found.\n", cut2);
+				continue;
+			}
+			curTree->SetLineColor(4);
+			con.Form("%s[%d]>0 && %s", variable, channel, cutsCol.FindObject(cut2)->GetName());
+			curTree->Draw(var.Data(), con.Data(), "same");
+		}
+		canvas->Update();
+	}	
+
+}
+
+void CsICalib::GetPeakMean(const char* variable, Int_t tree, Int_t energy, TCanvas *canvas, const char* beamcut, const Int_t nbins, Int_t lowRange) {
+
+	canvas->Clear();
+	canvas->Divide(4,4);
+
+	TString var;
+	TString con;
+	TString hname;
+	TString canvasTitle;
+
+	canvasTitle.Form("variable: %s; tree: %d; cut: %s;", variable, tree, cutsCol.FindObject(beamcut)->GetName());	
+	canvas->SetTitle(canvasTitle.Data());
+
+	TTree *curTree = 0;
+	curTree = (TTree*)tr.At(tree);
+	if (!curTree) {
+		printf("CsICalib::GetPeakMean: Tree No. %d was not found.\n", tree);
+		return;
+	}
+
+	TString sVariable = variable;
+	sVariable.ToLower();
+	Int_t channel = 0;
+
+	for (Int_t i = 0; i<16; i++) {
+
+		if (sVariable.Contains("anc")) {
+			channel = i+1;
+		} else {
+			channel = i;
+		}		
+		
+		var.Form("%s[%d]>>hfull[%d][%d]", variable, channel, tree, i);
+		con.Form("%s[%d]>%d && %s", variable, channel, lowRange, cutsCol.FindObject(beamcut)->GetName());
+		canvas->cd(i+1);
+		hname.Form("hfull[%d][%d]", tree, i);
+		hfull[tree][i] = new TH1I(hname.Data(), "title", nbins, 0, 4096);
+		curTree->SetLineColor(1);
+		curTree->Draw(var.Data(), con.Data());
+
+		var.Form("%s[%d]>>hcut[%d][%d]", variable, channel, tree, i);
+		con.Form("%s[%d]>%d && %s[%d]<%d && %s", variable, channel, peakMin[energy][i], variable, channel, peakMax[energy][i], cutsCol.FindObject(beamcut)->GetName());
+		hname.Form("hcut[%d][%d]", tree, i);
+		hcut[tree][i] = new TH1I(hname.Data(), "title", nbins, 0, 4096);
+		hcut[tree][i]->SetLineColor(3);
+		curTree->Draw(var.Data(), con.Data(), "same");
+
+		gPad->Update();
+		mean[tree][i] = hcut[tree][i]->GetMean();
+		meanRMS[tree][i] = hcut[tree][i]->GetRMS();
+//		cout << meanRMS[tree][i] << endl;
+//		cout << hcut[tree][i]->GetMean() << "\t" << hcut[tree][i]->GetRMS() << endl << endl;
+		
+		
+	}	
+
+	canvas->Update();
+
+}
+
+void CsICalib::Calibrate(TCanvas *canvas, Bool_t savefile, const char* filename, const char* option) {
+
+	canvas->Clear();
+	canvas->Divide(4,4);
+
+//	cout << alphas2.GetSize()+1 << endl;
+	cout << energyPoints+1 << endl;
+
+	TString gName;
+	TString gTitle;
+
+//	if (savefile) fGraphs->Open(filename, "RECREATE");
+
+	TF1 *fnc;
+
+	for (Int_t i = 0; i<16; i++) {
+		canvas->cd(i+1);
+		gCal[i] = new TGraphErrors(energyPoints+1);
+//		FillGraph(gCal[i], energies.GetSize()+1, energies.GetArray(), i);
+		FillGraph(gCal[i], energyPoints+1, fE.GetArray(), i);
+//		if (savefile) gCal[i]->Write();
+//		gCal[i]->Draw("Al*");
+		gCal[i]->Draw("A*");
+		gName.Form("g%s%s%d\n", detName.Data(), partName.Data(), i);
+		gTitle.Form("%s %s\n", detName.Data(), partName.Data());
+//		gCal[i]->SetTitle(gTitle.Data());
+		gCal[i]->SetName(gName.Data());
+		gCal[i]->Fit("pol1");
+		fnc = gCal[i]->GetFunction("pol1");
+		fnc->SetLineColor(kRed);
+		fA[i] = fnc->GetParameter(1);
+		fB[i] = fnc->GetParameter(0);
+		canvas->Update();
+	}
+	if (savefile) SaveClbGraphs(filename, option);
+
+}
+
+void CsICalib::FillGraph(TGraphErrors *g, Int_t npoints, Double_t *energies, Int_t graphNumber, const char* option) {
+
+	TString opt = option;
+
+	//all available energy points and (0,0)
+	g->SetPoint(0, 0., 0.);
+	for (Int_t i = 0; i < npoints-1; i++) {
+//		g->SetPoint(i+1, energies[i], mean[i][graphNumber]);
+//		g->SetPointError(i+1, 0, meanRMS[i][graphNumber]);
+		g->SetPoint(i+1, mean[i][graphNumber], energies[i]);
+		g->SetPointError(i+1, meanRMS[i][graphNumber], 0);
+	}
+
+//	for (Int_t j = 1; j < 4; j++) {
+//			g->SetPoint(j, 0., 0.);
+//	}
+	
+
+}
+
+void CsICalib::WriteClbParameters(const char* filename) {
+
+	std::ofstream outfile(filename);
+	if ( !outfile.is_open() ) {
+		printf("CsICalib::WriteClbParameters: File %s was not open.\n", filename);
+		return;
+	}	
+	
+	outfile << "#detector:\t" << detName << ",\tparticle:\t" << partName << endl;
+	outfile << "#channel\tfA\tfB" << endl;
+	for (Int_t i = 0; i < 16; i++) {
+		outfile << i << "\t" << fA[i] << "\t" << fB[i] << endl;
+	}
+}
+
+void CsICalib::SaveClbGraphs(const char* filename, const char* option) {	
+
+	cout << "asdasd" << endl;	
+	cout << fGraphs << endl;
+	if (fGraphs) fGraphs->Close();
+	cout << "asdasd" << endl;
+	fGraphs = new TFile(filename, option);
+	cout << fGraphs->IsOpen() << endl;
+		cout << fGraphs->GetName() << endl;
+	fGraphs->Print();
+//	if (!fGraphs->IsOpen()) {
+//		printf("CsICalib::SaveClbGraphs: file %s was not open.\n", filename);
+//		return;
+//	}
+
+	for (Int_t i = 0; i<16; i++) {
+		fGraphs->cd();
+		gCal[i]->Write();
+	}
+	fGraphs->Close();
+	return;
+}
+
+void CsICalib::ReadClbParameters(const char* filename) {
+
+	std::ifstream infile(filename);
+	if ( !infile.is_open() ) {
+		printf("CsICalib::ReadClbParameters: File %s was not open.\n", filename);
+		return;
+	}	
+
+	TString line;
+	Int_t i;
+	Double_t a, b;
+
+	while (!infile.eof()) {
+		line.ReadLine(infile);
+
+		if ( line.BeginsWith("#") ) continue;
+
+//		cout << line.Data() << endl;
+		sscanf(line.Data(), "%d %lf %lf", &i, &a, &b);
+		fA[i] = a;
+		fB[i] = b;
+//		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 CsICalib::DrawClbGraphs(const char* filename, const char* graphname, TCanvas *canvas) {
+
+	printf("CsICalib::DrawClbGraphs: does not work\n");
+	return;
+
+	TFile gfile(filename);
+	
+	TString gName;
+//	TGraph *gr;
+
+	for (Int_t i = 0; i < 16; i++) {
+		gName.Form("%s%d", graphname, i);
+		gCal[i] = (TGraphErrors*)gfile.Get(gName.Data());
+		canvas->cd(i+1);
+		gCal[i]->Draw("A*");
+	}
+}
+
+void CsICalib::DrawEnergyDeposite(const char* variable, TCanvas *canvas, Int_t tree, const char* option) {
+	if (!canvas) return;
+
+	canvas->Divide(4,4);
+	
+	TString opt;
+	opt = option;
+	opt.ToLower();
+
+	TString canvasTitle;
+	TString var;
+	TString con;
+
+	TTree *curTree = 0;
+	curTree = (TTree*)tr.At(tree);
+	if (!curTree) {
+		printf("CsICalib::DrawVariable: Tree No. %d was not found.\n", tree);
+		return;
+	}
+
+	canvasTitle.Form("variable: %s [MeV]; tree: %d", variable, tree);	
+	canvas->SetTitle(canvasTitle.Data());
+
+	if (!opt.Contains("same")) canvas->Divide(4,4);
+	for (Int_t i = 0; i < 16; i++) {
+		var.Form("%s[%d]*%f + %f", variable, i, fB[i], fA[i]);
+//		var.Form("%s[%d]*%f + %f", variable, i, fA[i], fB[i]);
+		con.Form("%s[%d]>0", variable, i);
+		
+		if (opt.Contains("same")) {
+			if (i==0) curTree->Draw(var.Data(), con.Data());			
+			curTree->Draw(var.Data(), con.Data(), "same");
+		}
+		else {
+			canvas->cd(i+1);
+			curTree->Draw(var.Data(), con.Data());
+		}
+		canvas->Update();
+	}
+
+	
+}

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

@@ -25,48 +25,99 @@ 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'
 	$(CC) -L . -L $(ROOTLIBS) -shared -o"libAculData.so" $(ACULDATAOBJS) $(ACULDATALIBS)
 	@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: $@'
@@ -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 ' '