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MCA_data.cxx
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MCA_data.cxx
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// started by C. Krauss in 2008
// updated to include calibration and analysis in 2012
//
// Compare spectra
// database of background lines
#include "sstream"
#include "math.h"
#include "TMath.h"
#include "MCA_data.h"
#include "TCanvas.h"
#include "TRegexp.h"
#include "TFile.h"
#include "TLegend.h"
#include "TF1.h"
#include "iostream"
#include "fstream"
#include "iomanip"
#include "TSpectrum.h"
#include "TString.h"
#include "TPolyMarker.h"
#include "TGraphErrors.h"
using namespace std;
// define reference times for source strength
#define JAN2011 1293904800 // (Jan 1 2011, 12:00 MT)
#define NOV2010 1288634400 // (Nov 1 2010, 12:00 MT)
#define APR1974 134049600 // (Apr 1 1974, 12:00 GMT)
#define DAYSINYEAR 365.2425
#define SECONDSINDAY (3600.0*24.0)
#define SECONDSINYEAR (DAYSINYEAR*SECONDSINDAY)
ClassImp(MCA_data);
ClassImp(CalMCA_data);
ClassImp(GeCalibrate);
ClassImp(SourceData);
MCA_data::MCA_data(const char *name):TNamed(name, "MCA data"){
hdata = 0;
};
MCA_data::~MCA_data(){
// if (hdata!=0)
// delete hdata;
};
int MCA_data::Read(char *filename){
SetName(filename);
char* ext = strrchr(filename,'.');
if (ext !=0){
if (!strcmp(ext,".CNF")||!strcmp(ext,".cnf"))
Read_CNF(filename);
else
if (!strcmp(ext,".IEC")||!strcmp(ext,".iec"))
Read_IEC(filename);
else {
cout << "File format unknown as input type." << endl;
return -1;
}
}
else{
cout << " filename needs to have an extension." << endl;
return -1;
}
return 0;
}
int MCA_data::Read_CNF(char *filename){
static int instance = 0;
instance++;
// char basename[300];
// char outfilename[300];
soutfilename = new char[300];
sshortname = new char[300];
strncpy(sshortname,filename,300);
char *ext = strrchr(sshortname,'.');
if (!strcmp(ext,".CNF")||!strcmp(ext,".cnf")){
ext[0] = 0;
cout<< " opening CNF file: "<<sshortname<<endl;
strcpy(soutfilename,sshortname);
strncpy(soutfilename+strlen(soutfilename),".root",10);
}
if (strrchr(sshortname,'/')){
strncpy(sshortname,strrchr(sshortname,'/')+1,strlen(sshortname)-(sshortname-strrchr(sshortname,'/')));
}
SetName(sshortname);
ifstream inf(filename,ios::binary);
unsigned short header[8];
inf.read((char*)header,16);
// header[3] = (header[3] & 0xF) >> 4 |(header[3]&0xF0)>>4| (header[3]&0xF00)<<4 | (header[3]&0xF000)>>4;
cout << " 1: " << header[0] << " 2: " << header[1] << " 3: " << header[2] << endl;
cout << " 4: " << header[3] << " 5: " << header[4] << " 6: " << header[5] << endl;
// int channels = header[3];
int channels = 0;
if (header[5] == 38400){
cout << " 32768 channels in file !?" << endl;
channels = 32768;
}
if (header[5] == 37888){
cout << " 32768 channels in file !?" << endl;
channels = 32768;
}
if (header[5] == 39936){
cout << " 32768 channels in file !?" << endl;
channels = 32768;
}
if (header[5] == 5632){
cout << " 8192 channels in file !?" << endl;
channels = 32768/4.;// 8k file
header[5] = 38400;
}
if (channels == 0){
cerr << " unkonwn file type! aborting." << endl;
exit(0);
}
// if (header[1] == 4 && header[2] == 1028) {
// channels = 32768/4.;
// header[5] = 38400;
// }
// if (header[1] == 0 && header[2] == 1024) {
// channels = 32768;
// }
cout << " number of channels: " << channels << " " << " data offset: " << header[5]<< endl;
// int channel = 32768;
int date_offs = 0xb07; // Current version of CNF file has date and time info start here, time is consecutive
int realt_offs = 0xb0f;
int livet_offs = 0xb17;
inf.seekg(date_offs);
unsigned long long date, livet, realt;
inf.read((char*)&date,8);
double ddate = double(date)/1e7;
double realdate = ddate - 3506691600; // date in CNF file is in seconds since 1858, Nov 16, 7:00 GMT, the offset to unix time is given here. (time in Mountain time)
// realdate -= 2* 3600; // convert to eastern time
time_t real_date_t = (time_t(realdate));
SetStartTime(real_date_t);
char *time_c = ctime(&real_date_t);
cout << " converted, extracted time: " << time_c;
char *tmp_c = strchr(time_c,'\n');
tmp_c[0]= '\0';
inf.read((char*)&realt,8);
inf.read((char*)&livet,8);
double drealt = double(~(realt)+1)/1e7; // Calculate 2's complement and convert to seconds...
SetRealTime(drealt);
double dlivet = double(~(livet)+1)/1e7;
SetLiveTime(dlivet);
SetChannels(channels);
cout << " data taking time (real): " << setprecision(10)<< drealt << "s, (live): " << dlivet << "s" << endl;
inf.seekg(header[5]);
unsigned int mydata[channels];
inf.read((char*)mydata,channels*4);
char title[400];
sprintf(title,"MCA Data, %s, %7.2lf s live time",time_c, GetLiveTime());
char hn[400];
sprintf(hn,"data_%d",instance-1);
SetData(new TH1I(hn,title, GetChannels(),0,GetChannels()+1));
int entries = 0;
for (int i = 0 ; i<channels ; i++){
GetData()->SetBinContent(1+i,mydata[i]);
entries += mydata[i];
}
GetData()->SetEntries(entries);
inf.close();
// TFile yo(outfilename,"recreate");
// h->Write();
// yo.Close();
cout << " Done, success." << endl;
return 1;
}
int MCA_data::Read_IEC(char *filename){
static int instance = 0;
instance++;
char buffer[1000];
ifstream inf(filename);
if (!inf.is_open()) {
cout << " file " << filename << " not found " << endl;
return 0;
}
// char outname[300],shortname[300];
soutfilename = new char[300];
sshortname = new char[300];
if (strrchr(filename,'.')!=0){
strncpy(sshortname,filename,strrchr(filename,'.')-filename);
sshortname[strrchr(filename,'.')-filename] = '\0';
// cout << "DEBUG: " << sshortname << " " << filename<< " " << strchr(filename,'.')-filename<< endl;
}
else
strncpy(sshortname,filename,strlen(filename));
// cout << " DEBUG: " << sshortname << endl;
sprintf(soutfilename,"%s.root",sshortname);
// TFile *yo = new TFile(soutfilename,"recreate");
// remove leading path
if (strrchr(sshortname,'/')){
strncpy(sshortname,strrchr(sshortname,'/')+1,strlen(sshortname)-(sshortname-strrchr(sshortname,'/')));
}
SetName(sshortname);
// MCA_data mydata(sshortname);
// first line contains system information,
inf.getline(buffer,999);
// second line contains live time, real time and channel number
inf.getline(buffer,999);
char tmp[50], *tmp2;
strncpy(tmp,buffer+4,14);
tmp[14] = '\0';
SetLiveTime(strtod(tmp,&tmp2));
strncpy(tmp,buffer+18,14);
tmp[14] = '\0';
SetRealTime(strtod(tmp,&tmp2));
strncpy(tmp,buffer+32,strlen(buffer)-32);
SetChannels(atoi(tmp));
// third line contains start time and date
inf.getline(buffer,999);
struct tm tdate;
tdate.tm_mday = atoi(buffer+4); // day
tdate.tm_mon = atoi(buffer+7)-1; // month
tdate.tm_year = atoi(buffer+10)+100; // year
tdate.tm_hour = atoi(buffer+13); //hour
tdate.tm_min = atoi(buffer+16); // minutes
tdate.tm_sec = atoi(buffer+19); //seconds
SetStartTime(mktime(&tdate));
time_t tmp_t = GetStartTime();
char *time_c = ctime(&tmp_t);
char *tmp_c = strchr(time_c,'\n');
tmp_c[0]= '\0';
cout << " got time: " << time_c << endl;
// fourth line contains energy calibration (unused here)
inf.getline(buffer,999);
cout << " got channels: " << GetChannels() << endl;
sprintf(buffer,"MCA Data, %s, %7.2lf s live time",time_c, GetLiveTime());
char hn[400];
sprintf(hn,"data_%d",instance-1);
SetData(new TH1I(hn,buffer, GetChannels(),0,GetChannels()+1));
bool found = false;
while (!inf.eof()){
inf.getline(buffer,999);
// cout << buffer << endl;
if (!strncmp(buffer,"A004USERDEFINED",15)) {
found = true;
break;
}
}
if (found){
// data entries start here
int data[5];
int channel = 0;
int entries = 0;
while (!inf.eof() && channel+5<GetChannels()){
inf.getline(buffer,999);
// cout << buffer << endl;
sscanf(buffer+4,"%d %d %d %d %d %d",&channel,&data[0],&data[1],&data[2],&data[3],&data[4]);
GetData()->SetBinContent(channel+1,data[0]);
GetData()->SetBinContent(channel+2,data[1]);
GetData()->SetBinContent(channel+3,data[2]);
GetData()->SetBinContent(channel+4,data[3]);
GetData()->SetBinContent(channel+5,data[4]);
entries += data[0] + data[1] + data[2] + data[3] + data[4];
if (inf.eof()) break;
}
GetData()->SetEntries(entries);
// mydata.Write();
cout << " done, success." << endl;
}
else{
cout << " data elements not found, no output." << endl;
return 0;
}
// yo->Close();
return 1;
}
TH1D* MCA_data::GetNormalizedData(){
hdata->Sumw2();
TH1D* rv = new TH1D("data_norm",hdata->GetTitle(),hdata->GetNbinsX(),hdata->GetXaxis()->GetXmin(),hdata->GetXaxis()->GetXmax());
for (int i = 0 ; i < hdata->GetNbinsX()+2 ; i++){ // include under- and overflow bins.
rv->SetBinContent(i,hdata->GetBinContent(i)/dreal_time);
rv->SetBinError(i,hdata->GetBinError(i)/dreal_time);
}
rv->SetEntries(double(hdata->GetEntries()));
return rv;
}
void SourceData::InitCo60(TString filename, bool old){
// Data from http://nucleardata.nuclear.lu.se/nucleardata/toi/nuclide.asp?iZA=270060
//Eg (keV) Ig (%) Decay mode
//346.93 7 0.0076 5 b-
//826.06 3 0.0076 8 b-
//1173.237 4 99.9736 7 b-
//1332.501 5 99.9856 4 b-
//2158.57 10 0.00111 18 b-
//2505 2.0E-6 4 b-
vdGammaEnergy.push_back(346.93);
vdLineIntensity.push_back(0.0076);
vdGammaEnergy.push_back(826.06);
vdLineIntensity.push_back(0.0076);
vdGammaEnergy.push_back(1173.237);
vdLineIntensity.push_back(99.9736);
vdGammaEnergy.push_back(1332.501);
vdLineIntensity.push_back(99.9856);
vdGammaEnergy.push_back(2158.57);
vdLineIntensity.push_back(0.00111);
vdGammaEnergy.push_back(3505);
vdLineIntensity.push_back(2.0E-6);
if (old){
dSourceStrength = 0.39701; // source stength in MBq (10.73uCi)
tReferenceDate = APR1974;
}
else{
dSourceStrength = 0.037; // source stength in MBq
tReferenceDate = JAN2011;
}
dHalfLife = 1925.28*SECONDSINDAY; // in seconds, 1925.28d (NNDC)
for (int i = 0 ; i<vdGammaEnergy.size(); i++)
vdChannelNumber.push_back(0);
sFileName = filename;
sIsotopeName = TString("Co60");
if (!GetFile() ) cerr << " File not opened. Error" <<endl;
}
void SourceData::InitAm241(TString filename, bool old){
// Data from http://nucleardata.nuclear.lu.se/nucleardata/toi/nuclide.asp?iZA=95024
// list truncated, only 60keV line implemented...
//Eg (keV) Ig (%) Decay mode
//13.81 2 a
//26.3448 2 2.40 2 a
//27.03 a
//31.4 a
//32.183 0.0174 4 a
//33.1964 3 0.126 3 a
//38.54 3 a
//42.73 5 0.0055 11 a
//43.423 10 0.073 8 a
//51.01 3 0.000026 12 a
//54.0 a
//55.56 2 0.0181 18 a
//56.8 a
//57.85 5 0.0052 15 a
//59.5412 2 35.9 4 a
//61.46 a
//64.83 2 0.000145 18 a
//67.45 5 0.00042 10 a
//69.76 3 0.0029 4 a
//75.8 2 ~0.0006 a
//78.1 a
vdGammaEnergy.push_back(59.5412);
vdLineIntensity.push_back(39.9);
if (old){
dSourceStrength = 0.43216; // source stength in MBq (11.68uCi)
tReferenceDate = APR1974;
}
else {
cerr << " new Am241 Source does not exist in our inventory." << endl;
exit(0);
}
dHalfLife = 432.6*SECONDSINYEAR; // in seconds, 432.6y (NNDC)
for (int i = 0 ; i<vdGammaEnergy.size(); i++)
vdChannelNumber.push_back(0);
sFileName = filename;
sIsotopeName = TString("Am241");
if (!GetFile() ) cerr << " File not opened. Error" <<endl;
}
void SourceData::InitCo57(TString filename){
//Eg (keV) Ig (%) Decay mode
//14.41300 15 9.16 15 e
//122.0614 4 85.60 17 e
//136.4743 5 10.68 8 e
//230.29 2 0.0004 4 e
//339.54 18 0.0139 3 e
//352.36 1 0.0132 3 e
//366.75 1 0.0013 3 e
//569.92 4 0.017 1 e
//692.03 2 0.157 9 e
//706.40 20 0.0253 5 e
vdGammaEnergy.push_back(14.413);
vdLineIntensity.push_back(9.16);
vdGammaEnergy.push_back(122.0614);
vdLineIntensity.push_back(85.6);
vdGammaEnergy.push_back(136.4743);
vdLineIntensity.push_back(10.68);
vdGammaEnergy.push_back(230.29);
vdLineIntensity.push_back(0.0004);
vdGammaEnergy.push_back(339.54);
vdLineIntensity.push_back(0.0139);
vdGammaEnergy.push_back(352.36);
vdLineIntensity.push_back(0.0132);
vdGammaEnergy.push_back(366.75);
vdLineIntensity.push_back(0.0013);
vdGammaEnergy.push_back(569.92);
vdLineIntensity.push_back(0.017);
vdGammaEnergy.push_back(692.03);
vdLineIntensity.push_back(0.157);
vdGammaEnergy.push_back(706.40);
vdLineIntensity.push_back(0.0253);
dSourceStrength = 0.037; // source stength in MBq
tReferenceDate = JAN2011;
dHalfLife = 271.74*SECONDSINDAY; // in seconds, 271.74d (NNDC)
for (int i = 0 ; i<vdGammaEnergy.size(); i++)
vdChannelNumber.push_back(0);
sFileName = filename;
sIsotopeName = TString("Co57");
if (!GetFile() ) cerr << " File not opened. Error" <<endl;
}
void SourceData::InitBa133(TString filename, bool old){
// Data from http://nucleardata.nuclear.lu.se/nucleardata/toi/nuclide.asp?iZA=560133
// Eg (keV) Ig (%) Decay mode
// 53.161 1 2.199 22 e
// 79.6139 26 2.62 6 e
// 80.9971 14 34.06 27 e
// 160.613 8 0.645 8 e
// 223.234 12 0.450 4 e
// 276.398 2 7.164 22 e
// 302.853 1 18.33 6 e
// 356.017 2 62.05 19 e
// 383.851 3 8.94 3 e
vdGammaEnergy.push_back(53.161);
vdLineIntensity.push_back(2.199);
vdGammaEnergy.push_back(79.6139);
vdLineIntensity.push_back(2.62);
vdGammaEnergy.push_back(80.9971);
vdLineIntensity.push_back(34.06);
vdGammaEnergy.push_back(160.613);
vdLineIntensity.push_back(0.645);
vdGammaEnergy.push_back(223.234);
vdLineIntensity.push_back(0.450);
vdGammaEnergy.push_back(276.394);
vdLineIntensity.push_back(7.164);
vdGammaEnergy.push_back(302.853);
vdLineIntensity.push_back(18.33);
vdGammaEnergy.push_back(356.017);
vdLineIntensity.push_back(62.05);
vdGammaEnergy.push_back(383.851);
vdLineIntensity.push_back(8.94);
if (old){
tReferenceDate = APR1974;
dSourceStrength = 0.39627; // source stength in MBq (10.71uCi)
}
else{
tReferenceDate = JAN2011;
dSourceStrength = 0.037; // source stength in MBq
}
dHalfLife = 10.551*SECONDSINYEAR; // in seconds, 10.551y (NNDC)
for (int i = 0 ; i<vdGammaEnergy.size(); i++)
vdChannelNumber.push_back(0);
sFileName = filename;
sIsotopeName = TString("Ba133");
if (!GetFile() ) cerr << " File not opened. Error" <<endl;
}
bool SourceData::GetFile(){
if (sFileName.Contains(".root")){
TFile y(sFileName);
if (y.IsZombie()) cerr<< "File is zombie!" << endl;
sFileName.Resize(sFileName.Last('.'));
if (sFileName.Last('/')!=0)
sFileName.Replace(0,1+sFileName.Last('/'),0,0);
// cout << sFileName << endl;
MCA_data *pdata = (MCA_data*) y.Get(sFileName);
if (pdata != 0){
data = *pdata;
return true;
}
}
else{
if (sFileName.Contains(".IEC") || sFileName.Contains(".iec")){
MCA_data *pdata = new MCA_data();
char *fn = new char[300];
strncpy(fn,sFileName.Data(),300);
if (pdata->Read_IEC(fn)!=0){
data = *pdata;//small memory leak here. ignore.
return true;
}
}
if (sFileName.Contains(".CNF") || sFileName.Contains(".cnf")){
MCA_data *pdata = new MCA_data();
char *fn = new char[300];
strncpy(fn,sFileName.Data(),300);
if (pdata->Read_CNF(fn)!=0){
data = *pdata;//small memory leak here. ignore.
return true;
}
}
}
return false;
}
void SourceData::InitMn54(TString filename){
// Data from http://nucleardata.nuclear.lu.se/nucleardata/toi/nuclide.asp?iZA=250054
//Eg (keV) Ig (%) Decay mode
//834.848 3 99.976 1 e+b+
vdGammaEnergy.push_back(834.848);
vdLineIntensity.push_back(99.976);
dSourceStrength = 0.037; // source stength in MBq
tReferenceDate = JAN2011;
dHalfLife = 312.12*SECONDSINDAY; // in seconds, 312.12d (NNDC)
for (int i = 0 ; i<vdGammaEnergy.size(); i++)
vdChannelNumber.push_back(0);
sFileName = filename;
sIsotopeName = TString("Mn54");
if (!GetFile() ) cerr << " File not opened. Error" <<endl;
}
void SourceData::InitCs137(TString filename, bool old){
//Eg (keV) Ig (%) Decay mode
//283.53 4 0.00058 8 b-
//661.657 3 85.1 2 b-
vdGammaEnergy.push_back(283.53);
vdLineIntensity.push_back(0.00058);
vdGammaEnergy.push_back(661.657);
vdLineIntensity.push_back(85.1);
if (old){
dSourceStrength = 0.41033; // source stength in MBq (11.09uCi)
tReferenceDate = APR1974;
}
else{
dSourceStrength = 0.037; // source stength in MBq
tReferenceDate = JAN2011;
}
dHalfLife = 30.8*SECONDSINYEAR; // in seconds, 30.8y (NNDC)
for (int i = 0 ; i<vdGammaEnergy.size(); i++)
vdChannelNumber.push_back(0);
sFileName = filename;
sIsotopeName = TString("Cs137");
if (!GetFile() ) cerr << " File not opened. Error" <<endl;
}
void SourceData::InitCd109(TString filename){
//Eg (keV) Ig (%) Decay mode
//88.04 5 3.61 10 e
vdGammaEnergy.push_back(88.04);
vdLineIntensity.push_back(3.61);
dSourceStrength = 0.037; // source stength in MBq
tReferenceDate = JAN2011;
dHalfLife = 461.4*SECONDSINDAY; // in seconds, 461.4 days (NNDC)
for (int i = 0 ; i<vdGammaEnergy.size(); i++)
vdChannelNumber.push_back(0);
sFileName = filename;
sIsotopeName = TString("Cd109");
if (!GetFile() ) cerr << " File not opened. Error" <<endl;
}
void SourceData::InitSr90(TString filename){
cerr << " Not implemented. " << endl;
}
void SourceData::InitTl204(TString filename){
//XR l 9.99 0.81 % 3 8.1E-5 3
//XR kα2 68.894 0.469 % 15 3.23E-4 10
//XR kα1 70.818 0.789 % 24 5.59E-4 17
//XR kβ3 79.824 0.095 % 3 7.60E-5 24
//XR kβ1 80.225 0.182 % 6 1.46E-4 5
//XR kβ2 82.473 0.0659 % 21 5.44E-5 17
// from NNDC database....
vdGammaEnergy.push_back(9.99);
vdLineIntensity.push_back(0.810);
vdGammaEnergy.push_back(68.894);
vdLineIntensity.push_back(0.469);
vdGammaEnergy.push_back(70.818);
vdLineIntensity.push_back(0.789);
vdGammaEnergy.push_back(79.824);
vdLineIntensity.push_back(0.095);
vdGammaEnergy.push_back(80.225);
vdLineIntensity.push_back(0.182);
vdGammaEnergy.push_back(82.473);
vdLineIntensity.push_back(0.0659);
dSourceStrength = 0.037; // source stength in MBq
tReferenceDate = NOV2010;
dHalfLife = 3.783*365.2425*SECONDSINDAY; // in seconds, 3.783y (NNDC)
for (int i = 0 ; i<vdGammaEnergy.size(); i++)
vdChannelNumber.push_back(0);
sFileName = filename;
sIsotopeName = TString("Tl204");
if (!GetFile() ) cerr << " File not opened. Error" <<endl;
}
void SourceData::InitZn65(TString filename){
//344.95 20 0.0030 3 e+b+
//770.6 2 0.0030 3 e+b+
//1115.546 4 50.60 24 e+b+
vdGammaEnergy.push_back(344.95);
vdLineIntensity.push_back(0.0030);
vdGammaEnergy.push_back(770.6);
vdLineIntensity.push_back(0.0030);
vdGammaEnergy.push_back(1115.546);
vdLineIntensity.push_back(50.60);
dSourceStrength = 0.037; // source stength in MBq
tReferenceDate = JAN2011;
dHalfLife = 243.93*SECONDSINDAY; // in seconds, 243.93d (NNDC)
for (int i = 0 ; i<vdGammaEnergy.size(); i++)
vdChannelNumber.push_back(0);
sFileName = filename;
sIsotopeName = TString("Zn65");
if (!GetFile() ) cerr << " File not opened. Error" <<endl;
}
void SourceData::InitFe55(TString filename){
cerr << " Not implemented. " << endl;
}
void GeCalibrate::Init(vector<TString> filenames){
for (vector<TString>::iterator i=filenames.begin() ; i!=filenames.end();i++){
cout << "File: " << *i << endl;
// file must start with isotope name:
if ((*i).Contains("Co-60")){
cout << "found Co60 file" << endl;
SourceData *d = new SourceData();
if ((*i).Contains("old"))
d->InitCo60(*i, true);
else
d->InitCo60(*i);
vpData.push_back(d);
char tmp[60];
strcpy(tmp,(*i).Data()+6);
char* t2 = strrchr(tmp,'.');
t2[0] = 0;
cal_date = TString(tmp);
}
if ((*i).Contains("Am-241")){
cout << "found Am241 file" << endl;
SourceData *d = new SourceData();
if ((*i).Contains("old"))
d->InitAm241(*i, true);
else
d->InitAm241(*i);
vpData.push_back(d);
char tmp[60];
strcpy(tmp,(*i).Data()+6);
char* t2 = strrchr(tmp,'.');
t2[0] = 0;
cal_date = TString(tmp);
}
if ((*i).Contains("Mn-54")){
cout << "found Mn54 file" << endl;
SourceData *d = new SourceData();
d->InitMn54(*i);
vpData.push_back(d);
char tmp[60];
strcpy(tmp,(*i).Data()+6);
char* t2 = strrchr(tmp,'.');
t2[0] = 0;
cal_date = TString(tmp);
}
if ((*i).Contains("Ba-133")){
cout << "found Ba133 file" << endl;
SourceData *d = new SourceData();
if ((*i).Contains("old"))
d->InitBa133(*i, true);
else
d->InitBa133(*i);
vpData.push_back(d);
char tmp[60];
strcpy(tmp,(*i).Data()+7);
char* t2 = strrchr(tmp,'.');
t2[0] = 0;
cal_date = TString(tmp);
}
if ((*i).Contains("Zn-65")){
cout << "found Zn65 file" << endl;
SourceData *d = new SourceData();
d->InitZn65(*i);
vpData.push_back(d);
char tmp[60];
strcpy(tmp,(*i).Data()+6);
char* t2 = strrchr(tmp,'.');
t2[0] = 0;
cal_date = TString(tmp);
}
if ((*i).Contains("Cd-109")){
cout << "found Cd109 file" << endl;
SourceData *d = new SourceData();
d->InitCd109(*i);
vpData.push_back(d);
}
if ((*i).Contains("Co-57")){
cout << "found Co-57 file" << endl;
SourceData *d = new SourceData();
d->InitCo57(*i);
vpData.push_back(d);
}
if ((*i).Contains("Cs-137")){
cout << "found Cs-137 file" << endl;
SourceData *d = new SourceData();
if ((*i).Contains("old"))
d->InitCs137(*i, true);
else
d->InitCs137(*i);
vpData.push_back(d);
}
if ((*i).Contains("Tl-204")){
cout << "found Tl-204 file" << endl;
SourceData *d = new SourceData();
d->InitTl204(*i);
vpData.push_back(d);
}
if ((*i).Contains("Fe-55")){
cout << "found Fe-55 file" << endl;
SourceData *d = new SourceData();
d->InitFe55(*i);
vpData.push_back(d);
}
}
if (vpData.size()==0){
cerr<< " Error: no source run data found. Aborting." << endl;
exit(0);
}
if (vpData.size()<filenames.size()){
cerr<< " Error: some source run data not found. Aborting. Check file name format (has to start with NN-xxx, e.g. Mn-54 or Ba-133)! " << endl;
exit(0);
}
}
CalMCA_data::CalMCA_data(MCA_data &dat) : MCA_data(dat) {
hCalData=0;
}
void CalMCA_data::Analyse(){
// ...
TCanvas *cc = new TCanvas("cc","Spectra");
cc->Divide(1,2);
cc->cd(1);
hCalData->Draw();
TSpectrum *s = new TSpectrum(160);
TH1D *b = (TH1D*) s->Background(hCalData,20,"Compton");
TH1D* d = (TH1D*)hCalData->Clone("diff");
d->Add(b,-1);
d->Rebin(16);
s->Search(d,10);
s->Search(hCalData,10);
hCalData->Draw();
b->Draw("same");
gPad->SetLogy(1);
cc->cd(2);
d->Draw();
TList *functions = hCalData->GetListOfFunctions();
TPolyMarker *pm = (TPolyMarker*)functions->FindObject("TPolyMarker");
double *X;
double *Y;
X= pm->GetX();
Y= pm->GetY();
for (int i = 0 ; i<pm->GetN() ; i++){
cout << i << " " << X[i] << " " << Y[i] << endl;
}
}
CalMCA_data* GeCalibrate::ApplyCalibration(TString filename){
// Calculate livetime corrected and calibrated histogram from raw (root) datafile.
if (!valid_calibration) {
cerr << "calibration in file is not valid!" << endl;
exit(0);
}
MCA_data *pdata = 0;
if (filename.Contains(".root")){
TFile y(filename);
if (y.IsZombie()) {
cerr<< "File is zombie!" << endl;
exit(0);
}
filename.Resize(filename.Last('.'));
if (filename.Last('/')!=0)
filename.Replace(0,1+filename.Last('/'),0,0);
// cout << sFileName << endl;
pdata = (MCA_data*) y.Get(filename);
}
else{
if (filename.Contains(".IEC") || filename.Contains(".iec")){
pdata = new MCA_data(filename.Data());
char *fn = new char[200];
strncpy(fn,filename.Data(),filename.Length());
if (pdata->Read_IEC(fn)==0){
cerr << " File " << filename << " could not be read."<< endl;
exit(0);
}
}
if (filename.Contains(".CNF") || filename.Contains(".cnf")){
pdata = new MCA_data(filename.Data());
char *fn = new char[200];
strncpy(fn,filename.Data(),filename.Length());
if (pdata->Read_CNF(fn)==0){
cerr << " File " << filename << " could not be read."<< endl;
exit(0);
}
}
}
CalMCA_data *caldat = 0;
if (pdata != 0){
// got the raw data...
TH1D *hist = pdata->GetNormalizedData();
// time corrected data
caldat = new CalMCA_data(*pdata);
int bins = hist->GetNbinsX();
double bmin = GetEnergyfromChannel(hist->GetXaxis()->GetXmin());
double bmax = GetEnergyfromChannel(hist->GetXaxis()->GetXmax());
if (bmin==bmax) return 0;
caldat->SetCalData(new TH1D("cal_data",hist->GetTitle(),bins,bmin,bmax));
for (int i = 0; i < bins+2 ; i++){
caldat->GetCalData()->SetBinContent(i,hist->GetBinContent(i));
caldat->GetCalData()->SetBinError(i,hist->GetBinError(i));
}
caldat->GetCalData()->SetEntries(hist->GetEntries());
TString outfilename(filename+TString("_cal.root"));
cout << " Trying to write file to : " << outfilename << endl;
TFile yo(outfilename,"recreate");
caldat->Write();
yo.Close();
}
return caldat;
}
void GeCalibrate::Calibrate(){
int num_peaks[vpData.size()];
int alllines = 0;
TCanvas *c[vpData.size()];
for (int source = 0 ; source < vpData.size() ; source++){
char idn[20],name[300];
sprintf(idn,"can_%d",source);
sprintf(name,"Spectrum %s",vpData[source]->GetIsotopeName().Data());
c[source] = new TCanvas(idn,name);
TSpectrum ts(vpData[source]->GetNumLines(),2);
ts.SetResolution(6);
int peaks = ts.Search(vpData[source]->GetData()->GetData(),6,"",0.01);
vpData[source]->GetData()->GetData()->Draw();
cout << peaks << " peaks found for source " << vpData[source]->GetIsotopeName()<< endl;
num_peaks[source] = peaks;
alllines += num_peaks[source];
}
cout << " using " << alllines << " lines for calibration " << endl;
int min_peaks = 1000;
int i_min = -1;
for (int i = 0 ; i<vpData.size();i++){
if (num_peaks[i]<min_peaks) {min_peaks = num_peaks[i];i_min = i;}
}
SourceData *firstI = vpData[i_min];// get isotope data
cout << "Starting calibration with " << firstI->GetIsotopeName() << endl;
int max_intensity=0;
int max_line = -1;
for (int ii = 0; ii < firstI->GetNumLines() ;ii++){//loop over all lines to find larges intensity
if (firstI->GetIntensity(ii)>max_intensity){
max_intensity = firstI->GetIntensity(ii);
max_line = ii;
}
}
MCA_data* firstD = firstI->GetData();// get measured spectrum
TH1I *firstH = firstD->GetData(); // get histogram
firstH->Draw();
TList *functions = firstH->GetListOfFunctions();
TPolyMarker *pm = (TPolyMarker*)functions->FindObject("TPolyMarker");
double *X;
double *Y;
X= pm->GetX();
Y= pm->GetY();
int dmax_intensity = 0;
int max_marker = -1;
for (int i = 0 ; i < pm->GetN(); i++){
cout << i << " " << X[i] << " " << Y[i] << endl;
if (Y[i]>dmax_intensity) {
dmax_intensity = Y[i];
max_marker = i;
}
}
cout << " marker " << max_marker << " " << max_line << endl;
if (max_marker>=0 && max_line >= 0){// found match..
if (firstI->GetChannelNumber(max_line)>0) cout << "DOUBLE ASSIGNMENT OF LINE. Fix me."<< endl;
else
firstI->SetChannelNumber(max_line,X[max_marker]);
}
// now calculate two point estimate for calibration trough 0,0
double initialoffset = 0;
double initialslope = firstI->GetEnergy(max_line)/firstI->GetChannelNumber(max_line);
cout << "initial guess: E = 0 + " << initialslope << " * ch " << endl;
int line = 0;
double energies[alllines], intensities[alllines];
double channels[alllines], peakh[alllines];
double ch_e[alllines], rel_int[alllines];
double eff[alllines];
// energies[line] = firstI->GetEnergy(max_line);
// channels[line] = firstI->GetChannelNumber(max_line);
// ch_e[line] = sqrt(channels[line]);
// line++;
// now process all other lines, but only when the points are close to the initial calibration line...
for (int isotope = 0; isotope<vpData.size();isotope++){
SourceData* source = vpData[isotope];
cout << " *****************************************************************"<< endl;
cout << source->GetIsotopeName() << endl;
MCA_data* dat = source ->GetData();// get measured spectrum
TH1I *hist = dat->GetData(); // get histogram
hist->Draw();
functions = hist->GetListOfFunctions();
pm = (TPolyMarker*)functions->FindObject("TPolyMarker");
X= pm->GetX();
Y= pm->GetY();
bool used[pm->GetN()];
for (int i = 0; i < pm->GetN() ; i++){ used[i] = false;}// initialize array
for (int iline = 0 ; iline < source->GetNumLines() ; iline++){
if (source->GetEnergy(iline) < 20) continue;
cout << " processing line " << iline <<" " << source->GetEnergy(iline)<<"keV Intensity: "<< source->GetIntensity(iline)<< endl;
// calculate the channel range for this line:
double ch = source->GetEnergy(iline) * 1/initialslope;
double min_ch = ch - (12 + 18*ch/1000);
double max_ch = ch + (12 + 18*ch/1000);
cout << " Search window: " << min_ch << " " << max_ch << endl;
if (iline==0){
char newtitle[300];
sprintf (newtitle,"%s(%d) %s", source->GetIsotopeName().Data(),source->GetNumLines(),hist->GetTitle());
hist->SetTitle(newtitle);
}
// if (isotope == i_min && iline == max_line) continue;//already used this line for initial guess
double intensity = 0;
bool match = false;
for (int i = 0 ; i < pm->GetN(); i++){
if (X[i]<max_ch && X[i]>min_ch) {
intensity = Y[i];
// match
match = true;
if (used[i] == true){
cout << "DOUBLE ASSIGNMENT OF MARKER. FIX ME." << endl;
continue;
}
used[i] = true;
energies[line] = source->GetEnergy(iline);
intensities[line] = source->GetIntensity(iline);
double fit_min = X[i] - (12 + 18*ch/10000);
double fit_max = X[i] + (12 + 18*ch/10000);
double fwhm = FindFWHM(hist, X[i], Y[i]);
double area = fwhm/2.35482 * Y[i] * sqrt(2.0*TMath::Pi());
double delta_t = dat->GetStartTime() - source->GetReferenceDate();
double exp_rate = dat->GetLiveTime()*source->GetSourceStrength()*1e6*exp(-delta_t*log(2)/source->GetHalfLife())*source->GetIntensity(iline);
double efficiency = area/exp_rate;
eff[line] = efficiency;
cout << "&&& *** $$$ fwhm: " << fwhm << " area: " << area<<" exp: " <<exp_rate<< " " << efficiency<< endl;
channels[line] = X[i];
if (source->GetChannelNumber(iline)>0)
cout << " DOUBLE ASSIGNMENT OF LINE " << source->GetIsotopeName() << " "
<< source->GetEnergy(iline) << " keV (#"<< iline << "). Fix me." << endl;
else
source->SetChannelNumber(iline,X[i]);
peakh[line] = Y[i];
rel_int[line] = source->GetIntensity(iline)/double(Y[i]);
hist->Fit("gaus","Q+","",fit_min,fit_max);//X[i]-15,X[i]+15);// fit gaussian in narrow window around peak
TF1 *ff = hist->GetFunction("gaus");
ch_e[line] = ff->GetParError(2);//(X[i]-min_ch)+(max_ch-X[i])/2.;
// channels[line] = ff->GetParameter(1);
line++;
cout << "Match! " << i << " ch: " << X[i] << " cts: " << Y[i] << " min ch: " << min_ch << " max ch: " << max_ch<< endl;
if ((fabs(X[i]-ff->GetParameter(1))/X[i])>.1)
cout << " LARGE difference between gaussian and tspectrum peak pos: " << X[i] << " " << ff->GetParameter(1) << endl;
break;
}
}
if (match = false) {
cout << " No match for line " << source->GetEnergy(iline) << " keV (" << source->GetIntensity(iline) << "%) found"<< endl;
}
}
}
cout << " found " << line << " matches" << endl;
// Add double match removal here:
//
calplot = new TGraphErrors (line,channels,energies,ch_e,0);
TCanvas *cc = new TCanvas("Cal","Calibration");
cc->Divide(1,3);
cc->cd(1);
calplot->Draw("a*");
calplot->GetXaxis()->SetTitle("Channel");
calplot->GetYaxis()->SetTitle("Energy [keV]");
calplot->Fit("pol1");
TF1* f = (TF1*) calplot->GetFunction("pol1");
if (f!=0){
dSlope = f->GetParameter(1);
dOffset = f->GetParameter(0);
cout << " final function: " << dOffset << " + " << dSlope << " * ch" << endl;
valid_calibration = true;
}
// Add efficiency curve here!
TGraph *gi = new TGraph(line,intensities,peakh);