merge in Bastian M. Wojek's cpp-version of msr2data. This should help to step towards a real platform independent musrfit package.
This commit is contained in:
nemu
parent
9ac709451c
commit
060192488c
799
src/classes/PMsr2Data.cpp
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799
src/classes/PMsr2Data.cpp
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/***************************************************************************
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PMsr2Data.cpp
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Author: Bastian M. Wojek / Andreas Suter
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e-mail: andreas.suter@psi.ch
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$Id$
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***************************************************************************/
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/***************************************************************************
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* Copyright (C) 2009 by Bastian M. Wojek / Andreas Suter *
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* andreas.suter@psi.ch *
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* *
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* This program is free software; you can redistribute it and/or modify *
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* it under the terms of the GNU General Public License as published by *
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* the Free Software Foundation; either version 2 of the License, or *
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* (at your option) any later version. *
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* *
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* This program is distributed in the hope that it will be useful, *
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* but WITHOUT ANY WARRANTY; without even the implied warranty of *
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
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* GNU General Public License for more details. *
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* *
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* You should have received a copy of the GNU General Public License *
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* along with this program; if not, write to the *
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* Free Software Foundation, Inc., *
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* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
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***************************************************************************/
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#include <cctype>
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#include <sstream>
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#include <fstream>
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#include <iomanip>
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using namespace std;
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#include <boost/algorithm/string/trim.hpp> // for stripping leading whitespace in std::string
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#include <boost/algorithm/string/case_conv.hpp> // for to_lower() in std::string
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#include <boost/algorithm/string/split.hpp> // split strings at certain characters
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using namespace boost::algorithm;
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#include "PMsr2Data.h"
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//-------------------------------------------------------------
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/**
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* <p> Write formatted output to file
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*/
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void writeValues(ofstream &outFile, const double &value, const unsigned int &width)
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{
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if (fabs(value) >= 1.0e6 || (fabs(value) < 1.0e-4 && fabs(value) > 0.0))
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outFile << scientific << setprecision(width - 8);
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else
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outFile.setf(ios::floatfield);
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outFile << setw(width) << left << value;
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return;
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}
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//-------------------------------------------------------------
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/**
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* <p>
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*/
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PMsr2Data::PMsr2Data(const string &ext) : fFileExtension(ext), fRunListFile(false)
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{
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fRunVector.clear();
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fRunVectorIter = fRunVector.end();
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fRunListFileStream = 0;
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fSaxParser = 0;
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fStartupHandler = 0;
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fDataHandler = 0;
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fMsrHandler = 0;
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}
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//-------------------------------------------------------------
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/**
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* <p>
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*/
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PMsr2Data::~PMsr2Data()
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{
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fRunVector.clear();
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fRunVectorIter = fRunVector.end();
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fIndVar.clear();
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if (fRunListFileStream) {
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fRunListFileStream->close();
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delete fRunListFileStream;
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fRunListFileStream = 0;
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}
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if (fSaxParser) {
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delete fSaxParser;
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fSaxParser = 0;
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}
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if (fStartupHandler) {
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delete fStartupHandler;
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fStartupHandler = 0;
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}
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if (fDataHandler) {
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delete fDataHandler;
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fDataHandler = 0;
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}
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if (fMsrHandler) {
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delete fMsrHandler;
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fMsrHandler = 0;
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}
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}
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//-------------------------------------------------------------
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/**
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* <p>
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*/
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unsigned int PMsr2Data::GetPresentRun() const
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{
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if (fRunVectorIter != fRunVector.end())
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return *fRunVectorIter;
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else
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return 0;
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}
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//-------------------------------------------------------------
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/**
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* <p>
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*/
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int PMsr2Data::SetRunNumbers(unsigned int runNo)
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{
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if (runNo > 9999 || runNo < 1)
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return 1;
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fRunVector.clear();
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fRunVector.push_back(runNo);
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fRunVectorIter = fRunVector.begin();
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return 0;
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}
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//-------------------------------------------------------------
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/**
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* <p>
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*/
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int PMsr2Data::SetRunNumbers(unsigned int runNoStart, unsigned int runNoEnd)
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{
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if ((runNoStart > 9999) || (runNoEnd > 9999) || (runNoStart < 1) || (runNoEnd < 1))
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return 1;
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fRunVector.clear();
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if (runNoStart <= runNoEnd) {
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for (unsigned int i(runNoStart); i<=runNoEnd; ++i)
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fRunVector.push_back(i);
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} else {
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for (unsigned int i(runNoStart); i>=runNoEnd; --i)
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fRunVector.push_back(i);
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}
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fRunVectorIter = fRunVector.begin();
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return 0;
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}
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//-------------------------------------------------------------
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/**
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* <p>
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*/
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int PMsr2Data::SetRunNumbers(const vector<unsigned int> &runListVector)
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{
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if (runListVector.empty())
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return -1;
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for (vector<unsigned int>::const_iterator iter(runListVector.begin()); iter!=runListVector.end(); iter++) {
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if (*iter > 9999 || *iter < 1)
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return 1;
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}
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fRunVector = runListVector;
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fRunVectorIter = fRunVector.begin();
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return 0;
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}
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//-------------------------------------------------------------
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/**
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* <p>
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*/
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int PMsr2Data::SetRunNumbers(const string &runListFile)
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{
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fRunVector.clear();
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ifstream in(runListFile.c_str());
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if (!in) {
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cout << endl;
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cout << ">> msr2data: **ERROR** The runlist file " << runListFile << " cannot be opened! Please check!" << endl;
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return -1;
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}
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string line, indvar;
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istringstream strLine;
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vector<string> splitVec;
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unsigned int cntr(0);
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unsigned int runNo;
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while (getline(in, line)) {
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trim(line);
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if (line.empty())
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continue;
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else if (line.at(0) == '#')
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continue;
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else
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cntr++;
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split( splitVec, line, is_any_of("#") ); // split the string if any comments appear on the line
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if (cntr == 1) { // Read in the names of the independent variables in the runlist file
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strLine.clear();
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strLine.str(splitVec[0]);
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strLine >> indvar; // "RUN"
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if (indvar.compare("RUN")) {
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cout << endl;
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cout << ">> msr2data: **ERROR** The format of the runlist file " << runListFile << " is not correct! Please check!" << endl;
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}
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while (strLine >> indvar)
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fIndVar.push_back(indvar);
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}
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if (cntr > 1) {
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strLine.clear();
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strLine.str(splitVec[0]);
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strLine >> runNo;
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if (runNo > 9999 || runNo < 1)
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return 1;
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fRunVector.push_back(runNo);
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}
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splitVec.clear();
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}
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in.close();
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fRunVectorIter = fRunVector.begin();
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fRunListFile = true;
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fRunListFileStream = new ifstream(runListFile.c_str());
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return 0;
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}
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//-------------------------------------------------------------
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/**
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* <p>
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*/
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int PMsr2Data::ParseXmlStartupFile()
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{
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int status;
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fSaxParser = new TSAXParser();
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fStartupHandler = new PStartupHandler();
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string startup_path_name(fStartupHandler->GetStartupFilePath().Data());
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fSaxParser->ConnectToHandler("PStartupHandler", fStartupHandler);
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status = fSaxParser->ParseFile(startup_path_name.c_str());
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// check for parse errors
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if (status) { // error
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cout << endl << ">> msr2data: **WARNING** reading/parsing musrfit_startup.xml." << endl;
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// clean up
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if (fSaxParser) {
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delete fSaxParser;
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fSaxParser = 0;
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}
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if (fStartupHandler) {
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delete fStartupHandler;
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fStartupHandler = 0;
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}
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}
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return status;
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}
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//-------------------------------------------------------------
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/**
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* <p>
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*/
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int PMsr2Data::ReadMsrFile(const string &infile)
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{
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int status;
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fMsrHandler = new PMsrHandler(infile.c_str());
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status = fMsrHandler->ReadMsrFile();
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if (status != PMUSR_SUCCESS) {
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switch (status) {
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case PMUSR_MSR_FILE_NOT_FOUND:
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cout << endl << ">> msr2data: **ERROR** Could not find " << infile << endl;
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break;
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case PMUSR_MSR_SYNTAX_ERROR:
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cout << endl << ">> msr2data: **SYNTAX ERROR** in file " << infile << ", full stop here." << endl;
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break;
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default:
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cout << endl << ">> msr2data: **UNKOWN ERROR** when trying to read the msr-file" << endl;
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break;
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}
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}
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return status;
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}
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//-------------------------------------------------------------
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/**
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* <p>
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*/
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bool PMsr2Data::ReadRunDataFile()
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{
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if (fStartupHandler)
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fDataHandler = new PRunDataHandler(fMsrHandler, fStartupHandler->GetDataPathList());
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else
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fDataHandler = new PRunDataHandler(fMsrHandler);
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bool success = fDataHandler->IsAllDataAvailable();
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if (!success) {
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cout << endl << ">> msr2data: **WARNING** Could not read all data files, will continue without the data file information..." << endl;
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delete fDataHandler;
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fDataHandler = 0;
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}
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return success;
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}
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//-------------------------------------------------------------
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/**
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* <p>
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*/
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bool PMsr2Data::PrepareNewInputFile(unsigned int tempRun) const
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{
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if (fRunVectorIter == fRunVector.end())
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return false;
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if (*fRunVectorIter == tempRun)
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return true;
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const int N(4); // number of digits for the runnumber
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ostringstream strInfile;
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strInfile << tempRun << fFileExtension << ".msr";
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ifstream in(strInfile.str().c_str());
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if (!in) {
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cout << endl;
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cout << ">> msr2data: **ERROR** The template msr-file " << strInfile.str() << " cannot be opened! Please check!" << endl;
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return false;
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}
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ostringstream strOutfile;
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strOutfile << *fRunVectorIter << fFileExtension << ".msr";
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ofstream out(strOutfile.str().c_str());
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if (!out) {
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cout << endl;
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cout << ">> msr2data: **ERROR** The new msr file " << strOutfile.str() << " cannot be opened! Please check!" << endl;
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return false;
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}
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ostringstream tempRunNumber;
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tempRunNumber.fill('0');
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tempRunNumber.setf(ios::internal, ios::adjustfield);
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tempRunNumber.width(N);
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tempRunNumber << tempRun;
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ostringstream newRunNumber;
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newRunNumber.fill('0');
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newRunNumber.setf(ios::internal, ios::adjustfield);
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newRunNumber.width(N);
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newRunNumber << *fRunVectorIter;
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cout << endl << ">> msr2data: **INFO** Generating new input msr file " << strOutfile.str() << endl;
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string line, firstOnLine;
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istringstream strLine;
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// write the run number in the TITLE line of the msr-file (is overwritten later by musrfit if called with the -t option)
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getline(in, line);
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out << *fRunVectorIter << endl;
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while (getline(in, line)) {
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if (line.empty()) {
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out << endl;
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continue;
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}
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if (!line.compare("SET BATCH") || !line.compare("END RETURN"))
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continue;
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strLine.clear();
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strLine.str(line);
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strLine >> firstOnLine;
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if (!firstOnLine.compare("RUN")) {
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string::size_type loc = line.rfind(tempRunNumber.str());
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if ( loc != string::npos ) {
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line.replace(loc, N, newRunNumber.str());
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} else {
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cout << endl;
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cout << ">> msr2data: **WARNING** The template run file number does not match the \"file index\"" << endl;
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cout << ">> msr2data: **WARNING** Unexpected things may happen... (for sure)" << endl;
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}
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}
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out << line << endl;
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}
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in.close();
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out.close();
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return true;
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}
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//-------------------------------------------------------------
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/**
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* <p>
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*/
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void PMsr2Data::WriteOutput(const string &outfile, bool db, bool withHeader) const
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{
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if (!to_lower_copy(outfile).compare("none")) {
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fRunVectorIter++;
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return;
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}
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string msrTitle(fMsrHandler->GetMsrTitle()->Data());
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string msrFileName(fMsrHandler->GetFileName().Data());
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unsigned int msrNoOfParams(fMsrHandler->GetNoOfParams());
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PMsrParamList *msrParamList(fMsrHandler->GetMsrParamList());
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vector<string> dataParamNames;
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vector<string> dataParamLabels;
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vector<double> dataParam, dataParamErr;
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if (fDataHandler) {
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PMsrRunList *msrRunList(fMsrHandler->GetMsrRunList());
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PRawRunData *rawRunData(fDataHandler->GetRunData((*msrRunList)[0].fRunName[0]));
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switch (rawRunData->fTemp.size()) {
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case 1:
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dataParamNames.push_back("dataT");
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dataParamLabels.push_back("T (K)");
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dataParam.push_back(rawRunData->fTemp[0].first);
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dataParamErr.push_back(rawRunData->fTemp[0].second);
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break;
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default:
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ostringstream oss;
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for (unsigned int i(0); i<rawRunData->fTemp.size(); i++) {
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oss << "dataT" << i;
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dataParamNames.push_back(oss.str());
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oss.str("");
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oss << "T" << i << " (K)";
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dataParamLabels.push_back(oss.str());
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oss.str("");
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dataParam.push_back(rawRunData->fTemp[i].first);
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dataParamErr.push_back(rawRunData->fTemp[i].second);
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}
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break;
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}
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double value;
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value = rawRunData->fField;
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if (value != -9.9e99) {
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dataParamNames.push_back("dataB");
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dataParamLabels.push_back("mu0 H (G)");
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dataParam.push_back(value);
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}
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value = rawRunData->fEnergy;
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if (value != -999.0) {
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dataParamNames.push_back("dataE");
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dataParamLabels.push_back("Implantation Energy (keV)");
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dataParam.push_back(value);
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}
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value = rawRunData->fTransport;
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if (value != -999.0) {
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dataParamNames.push_back("dataTr");
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dataParamLabels.push_back("Transport (kV)");
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dataParam.push_back(value);
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}
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vector<double> ra(rawRunData->fRingAnode);
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if (ra.size() > 1) {
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dataParamNames.push_back("dataRALRAR");
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dataParamLabels.push_back("RAL-RAR (kV)");
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dataParam.push_back(ra[0]-ra[1]);
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}
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if (ra.size() == 4) {
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dataParamNames.push_back("dataRATRAB");
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dataParamLabels.push_back("RAT-RAB (kV)");
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dataParam.push_back(ra[2]-ra[3]);
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}
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}
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// get the independent variable values from the runlist file if needed
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vector<double> indVarValues;
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if (fRunListFile) {
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string line;
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vector<string> splitVec;
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unsigned int runNo;
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double val;
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istringstream strLine;
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while (getline(*fRunListFileStream, line)) {
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trim(line);
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if (line.empty())
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continue;
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else if (line.at(0) == '#' || !line.substr(0,3).compare("RUN"))
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continue;
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else {
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split( splitVec, line, is_any_of("#") ); // split the string if any comments appear on the line
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strLine.clear();
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strLine.str(splitVec[0]);
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strLine >> runNo;
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if (runNo != *fRunVectorIter) {
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cout << endl;
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cout << ">> msr2data: **ERROR** The run number in the runlist file does not match the one which should be processed..." << endl;
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cout << ">> msr2data: **ERROR** Something is very strange... Please report this bug!" << endl;
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fRunVectorIter = fRunVector.end();
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return;
|
||||
}
|
||||
while (strLine >> val) {
|
||||
indVarValues.push_back(val);
|
||||
}
|
||||
if (indVarValues.size() != fIndVar.size()) {
|
||||
cout << endl;
|
||||
cout << ">> msr2data: **ERROR** The number of data entries in the runlist file for the run number " << runNo << endl;
|
||||
cout << ">> msr2data: **ERROR** does not match the number of labels given in the RUN-line! Please check the file!" << endl;
|
||||
fRunVectorIter = fRunVector.end();
|
||||
return;
|
||||
}
|
||||
break;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// The RUNLIST file stream and the run vector iterator might get out of synchronization, if the following check is placed before the above block...
|
||||
PMsrStatisticStructure *msrStatistic(fMsrHandler->GetMsrStatistic());
|
||||
if (!msrStatistic->fValid) {
|
||||
cout << endl;
|
||||
cout << ">> msr2data: **WARNING** The fit of run " << *fRunVectorIter << " has not converged!" << endl;
|
||||
cout << ">> msr2data: **WARNING** Its parameter data have not been appended to the output file " << outfile << endl;
|
||||
fRunVectorIter++;
|
||||
|
||||
delete fMsrHandler;
|
||||
fMsrHandler = 0;
|
||||
|
||||
if (fDataHandler) {
|
||||
delete fDataHandler;
|
||||
fDataHandler = 0;
|
||||
}
|
||||
|
||||
// clean up some vectors
|
||||
dataParamNames.clear();
|
||||
dataParamLabels.clear();
|
||||
dataParam.clear();
|
||||
dataParamErr.clear();
|
||||
indVarValues.clear();
|
||||
|
||||
return;
|
||||
}
|
||||
|
||||
// open the DB or dat file and write the data
|
||||
|
||||
ofstream outFile(outfile.c_str(), ios::app);
|
||||
if (!outFile) {
|
||||
cout << endl;
|
||||
cout << ">> msr2data: The output file " << outfile << " cannot be opened! Please check!" << endl;
|
||||
fRunVectorIter = fRunVector.end();
|
||||
return;
|
||||
}
|
||||
|
||||
if (db) {
|
||||
|
||||
if (withHeader && (fRunVectorIter == fRunVector.begin())) {
|
||||
outFile << "TITLE" << endl;
|
||||
outFile << ">>>Put your title here<<<" << endl << endl;
|
||||
outFile << "Abstract" << endl;
|
||||
outFile << ">>>Put your abstract here<<<" << endl << endl;
|
||||
outFile << "LABELS" << endl;
|
||||
|
||||
if (fDataHandler) {
|
||||
for (unsigned int i(0); i < dataParamLabels.size(); ++i) {
|
||||
outFile << dataParamLabels[i] << endl;
|
||||
}
|
||||
}
|
||||
|
||||
if (fRunListFile) {
|
||||
for (unsigned int i(0); i < fIndVar.size(); ++i) {
|
||||
outFile << fIndVar[i] << endl;
|
||||
}
|
||||
}
|
||||
|
||||
for (unsigned int i(0); i < msrNoOfParams; ++i) {
|
||||
outFile << (*msrParamList)[i].fName.Data() << endl;
|
||||
}
|
||||
|
||||
if (msrStatistic->fChisq)
|
||||
outFile << "CHISQ" << endl;
|
||||
else
|
||||
outFile << "maxLH" << endl;
|
||||
|
||||
outFile << "NDF" << endl;
|
||||
|
||||
if (msrStatistic->fChisq)
|
||||
outFile << "CHISQred" << endl;
|
||||
else
|
||||
outFile << "maxLHred" << endl;
|
||||
|
||||
outFile << "RUN" << endl;
|
||||
|
||||
outFile << endl << "Data";
|
||||
|
||||
if (fDataHandler) {
|
||||
for (unsigned int i(0); i < dataParamNames.size(); ++i) {
|
||||
outFile << " " << dataParamNames[i];
|
||||
}
|
||||
}
|
||||
|
||||
if (fRunListFile) {
|
||||
for (unsigned int i(0); i < fIndVar.size(); ++i) {
|
||||
outFile << " " << fIndVar[i];
|
||||
}
|
||||
}
|
||||
|
||||
for (unsigned int i(0); i < msrNoOfParams; ++i) {
|
||||
outFile << " " << (*msrParamList)[i].fName.Data();
|
||||
}
|
||||
|
||||
if (msrStatistic->fChisq)
|
||||
outFile << " " << "CHISQ";
|
||||
else
|
||||
outFile << " " << "maxLH";
|
||||
|
||||
outFile << " " << "NDF";
|
||||
|
||||
if (msrStatistic->fChisq)
|
||||
outFile << " " << "CHISQred";
|
||||
else
|
||||
outFile << " " << "maxLHred";
|
||||
|
||||
outFile << " " << "RUN" << endl;
|
||||
|
||||
outFile << "\\-e" << endl;
|
||||
}
|
||||
|
||||
if (fDataHandler) {
|
||||
for (unsigned int i(0); i < dataParam.size(); ++i) {
|
||||
if (i < dataParamErr.size())
|
||||
outFile << dataParamNames[i] << " = " << dataParam[i] << ", " \
|
||||
<< dataParamErr[i] << ", " << dataParamErr[i] << ",\\" << endl;
|
||||
else
|
||||
outFile << dataParamNames[i] << " = " << dataParam[i] << ", 0, 0,\\" << endl;
|
||||
}
|
||||
}
|
||||
|
||||
if (fRunListFile) {
|
||||
for (unsigned int i(0); i < indVarValues.size(); ++i) {
|
||||
outFile << fIndVar[i] << " = " << indVarValues[i] << ", 0, 0,\\" << endl;
|
||||
}
|
||||
}
|
||||
|
||||
for (unsigned int i(0); i < msrNoOfParams; ++i) {
|
||||
outFile << (*msrParamList)[i].fName.Data() << " = " << (*msrParamList)[i].fValue << ", ";
|
||||
if ((*msrParamList)[i].fPosErrorPresent)
|
||||
outFile << (*msrParamList)[i].fPosError << ", ";
|
||||
else
|
||||
outFile << fabs((*msrParamList)[i].fStep) << ", ";
|
||||
outFile << fabs((*msrParamList)[i].fStep) << ",\\" << endl;
|
||||
}
|
||||
|
||||
if (msrStatistic->fChisq)
|
||||
outFile << "CHISQ = " << msrStatistic->fMin << ", 0, 0,\\" << endl;
|
||||
else
|
||||
outFile << "maxLH = " << msrStatistic->fMin << ", 0, 0,\\" << endl;
|
||||
|
||||
outFile << "NDF = " << msrStatistic->fNdf << ", 0, 0,\\" << endl;
|
||||
|
||||
if (msrStatistic->fChisq)
|
||||
outFile << "CHISQred = " << msrStatistic->fMin/msrStatistic->fNdf << ", 0, 0,\\" << endl;
|
||||
else
|
||||
outFile << "maxLHred = " << msrStatistic->fMin/msrStatistic->fNdf << ", 0, 0,\\" << endl;
|
||||
|
||||
outFile << *fRunVectorIter << ",,, " << msrTitle << endl;
|
||||
|
||||
} else { // no DB file but ASCII file with data columns
|
||||
|
||||
unsigned int length(0), maxlength(12);
|
||||
for (unsigned int i(0); i < dataParamNames.size(); ++i) {
|
||||
length = dataParamNames[i].length();
|
||||
if (length > maxlength)
|
||||
maxlength = length;
|
||||
}
|
||||
for (unsigned int i(0); i < fIndVar.size(); ++i) {
|
||||
length = fIndVar[i].length();
|
||||
if (length > maxlength)
|
||||
maxlength = length;
|
||||
}
|
||||
string s;
|
||||
for (unsigned int i(0); i < msrNoOfParams; ++i) {
|
||||
s = (*msrParamList)[i].fName.Data();
|
||||
length = s.length();
|
||||
if (length > maxlength)
|
||||
maxlength = length;
|
||||
}
|
||||
|
||||
if (maxlength < 13)
|
||||
maxlength = 13; // will use a minimum field width of 13 which corresponds to: -1.23456e-07 + ' '
|
||||
else
|
||||
maxlength += 1; // maximum length of parameter names + ' '
|
||||
|
||||
if (withHeader && (fRunVectorIter == fRunVector.begin())) {
|
||||
|
||||
if (fDataHandler) {
|
||||
for (unsigned int i(0); i < dataParamNames.size(); ++i) {
|
||||
s = dataParamNames[i];
|
||||
if (i < dataParamErr.size()) {
|
||||
outFile << setw(maxlength) << left << s << setw(maxlength + 3) << left << s + "Err";
|
||||
} else
|
||||
outFile << setw(maxlength) << left << s;
|
||||
}
|
||||
}
|
||||
|
||||
if (fRunListFile) {
|
||||
for (unsigned int i(0); i < fIndVar.size(); ++i) {
|
||||
outFile << setw(maxlength) << left << fIndVar[i];
|
||||
}
|
||||
}
|
||||
|
||||
for (unsigned int i(0); i < msrNoOfParams; ++i) {
|
||||
s = (*msrParamList)[i].fName.Data();
|
||||
outFile << setw(maxlength) << left << s \
|
||||
<< setw(maxlength + 6) << left << s + "PosErr" \
|
||||
<< setw(maxlength + 6) << left << s + "NegErr";
|
||||
}
|
||||
s.clear();
|
||||
|
||||
if (msrStatistic->fChisq)
|
||||
outFile << setw(maxlength) << left << "CHISQ";
|
||||
else
|
||||
outFile << setw(maxlength) << left << "maxLH";
|
||||
|
||||
outFile << setw(maxlength) << left << "NDF";
|
||||
|
||||
if (msrStatistic->fChisq)
|
||||
outFile << setw(maxlength) << left << "CHISQred";
|
||||
else
|
||||
outFile << setw(maxlength) << left << "maxLHred";
|
||||
|
||||
outFile << setw(maxlength) << left << "RUN" << endl;
|
||||
}
|
||||
|
||||
if (fDataHandler) {
|
||||
for (unsigned int i(0); i < dataParam.size(); ++i) {
|
||||
if (i < dataParamErr.size()) {
|
||||
writeValues(outFile, dataParam[i], maxlength);
|
||||
writeValues(outFile, dataParamErr[i], maxlength + 3);
|
||||
} else {
|
||||
writeValues(outFile, dataParam[i], maxlength);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (fRunListFile) {
|
||||
for (unsigned int i(0); i < indVarValues.size(); ++i) {
|
||||
writeValues(outFile, indVarValues[i], maxlength);
|
||||
}
|
||||
}
|
||||
|
||||
for (unsigned int i(0); i < msrNoOfParams; ++i) {
|
||||
writeValues(outFile, (*msrParamList)[i].fValue, maxlength);
|
||||
|
||||
if ((*msrParamList)[i].fPosErrorPresent)
|
||||
writeValues(outFile, (*msrParamList)[i].fPosError, maxlength + 6);
|
||||
else
|
||||
writeValues(outFile, fabs((*msrParamList)[i].fStep), maxlength + 6);
|
||||
|
||||
writeValues(outFile, fabs((*msrParamList)[i].fStep), maxlength + 6);
|
||||
}
|
||||
|
||||
writeValues(outFile, msrStatistic->fMin, maxlength);
|
||||
|
||||
writeValues(outFile, msrStatistic->fNdf, maxlength);
|
||||
|
||||
writeValues(outFile, msrStatistic->fMin/msrStatistic->fNdf, maxlength);
|
||||
|
||||
writeValues(outFile, *fRunVectorIter, maxlength);
|
||||
outFile << endl;
|
||||
|
||||
}
|
||||
|
||||
cout << endl << ">> msr2data: **INFO** Parameter data of file " << msrFileName << " have been appended to " << outfile << endl;
|
||||
|
||||
fRunVectorIter++;
|
||||
|
||||
if (fRunVectorIter == fRunVector.end())
|
||||
outFile << endl << endl;
|
||||
outFile.close();
|
||||
|
||||
delete fMsrHandler;
|
||||
fMsrHandler = 0;
|
||||
|
||||
if (fDataHandler) {
|
||||
delete fDataHandler;
|
||||
fDataHandler = 0;
|
||||
}
|
||||
|
||||
// clean up some vectors
|
||||
dataParamNames.clear();
|
||||
dataParamLabels.clear();
|
||||
dataParam.clear();
|
||||
dataParamErr.clear();
|
||||
indVarValues.clear();
|
||||
|
||||
return;
|
||||
|
||||
}
|
||||
|
||||
81
src/include/PMsr2Data.h
Normal file
81
src/include/PMsr2Data.h
Normal file
@ -0,0 +1,81 @@
|
||||
/***************************************************************************
|
||||
|
||||
PMsr2Data.h
|
||||
|
||||
Author: Bastian M. Wojek / Andreas Suter
|
||||
e-mail: andreas.suter@psi.ch
|
||||
|
||||
$Id$
|
||||
|
||||
***************************************************************************/
|
||||
|
||||
/***************************************************************************
|
||||
* Copyright (C) 2009 by Bastian M. Wojek / Andreas Suter *
|
||||
* andreas.suter@psi.ch *
|
||||
* *
|
||||
* This program is free software; you can redistribute it and/or modify *
|
||||
* it under the terms of the GNU General Public License as published by *
|
||||
* the Free Software Foundation; either version 2 of the License, or *
|
||||
* (at your option) any later version. *
|
||||
* *
|
||||
* This program is distributed in the hope that it will be useful, *
|
||||
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
|
||||
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
|
||||
* GNU General Public License for more details. *
|
||||
* *
|
||||
* You should have received a copy of the GNU General Public License *
|
||||
* along with this program; if not, write to the *
|
||||
* Free Software Foundation, Inc., *
|
||||
* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
|
||||
***************************************************************************/
|
||||
|
||||
#ifndef _PMSR2DATA_H_
|
||||
#define _PMSR2DATA_H_
|
||||
|
||||
#include <string>
|
||||
using namespace std;
|
||||
|
||||
#include "PRunDataHandler.h"
|
||||
#include "PStartupHandler.h"
|
||||
|
||||
#include <TSAXParser.h>
|
||||
|
||||
//-------------------------------------------------------------
|
||||
/**
|
||||
* <p>
|
||||
*/
|
||||
class PMsr2Data
|
||||
{
|
||||
public:
|
||||
PMsr2Data(const string&); // File extension
|
||||
~PMsr2Data();
|
||||
|
||||
int SetRunNumbers(unsigned int); // single run given
|
||||
int SetRunNumbers(unsigned int, unsigned int); // run list specified through first and last run number
|
||||
int SetRunNumbers(const string&); // run list file given
|
||||
int SetRunNumbers(const vector<unsigned int>&); // explicit run list specified using [ ]
|
||||
unsigned int GetPresentRun() const;
|
||||
|
||||
int ParseXmlStartupFile();
|
||||
int ReadMsrFile(const string&);
|
||||
bool ReadRunDataFile();
|
||||
|
||||
bool PrepareNewInputFile(unsigned int) const; // template
|
||||
|
||||
void WriteOutput(const string&, bool, bool) const;
|
||||
|
||||
private:
|
||||
string fFileExtension;
|
||||
vector<unsigned int> fRunVector;
|
||||
mutable vector<unsigned int>::const_iterator fRunVectorIter;
|
||||
bool fRunListFile;
|
||||
vector<string> fIndVar;
|
||||
ifstream *fRunListFileStream;
|
||||
TSAXParser *fSaxParser;
|
||||
PStartupHandler *fStartupHandler;
|
||||
mutable PRunDataHandler *fDataHandler;
|
||||
mutable PMsrHandler *fMsrHandler;
|
||||
};
|
||||
|
||||
|
||||
#endif // _PMSR2DATA_H_
|
||||
435
src/msr2data.cpp
Normal file
435
src/msr2data.cpp
Normal file
@ -0,0 +1,435 @@
|
||||
/***************************************************************************
|
||||
|
||||
msr2data.cpp
|
||||
|
||||
Author: Bastian M. Wojek / Andreas Suter
|
||||
e-mail: andreas.suter@psi.ch
|
||||
|
||||
$Id$
|
||||
|
||||
***************************************************************************/
|
||||
|
||||
/***************************************************************************
|
||||
* Copyright (C) 2009 by Bastian M. Wojek / Andreas Suter *
|
||||
* andreas.suter@psi.ch *
|
||||
* *
|
||||
* This program is free software; you can redistribute it and/or modify *
|
||||
* it under the terms of the GNU General Public License as published by *
|
||||
* the Free Software Foundation; either version 2 of the License, or *
|
||||
* (at your option) any later version. *
|
||||
* *
|
||||
* This program is distributed in the hope that it will be useful, *
|
||||
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
|
||||
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
|
||||
* GNU General Public License for more details. *
|
||||
* *
|
||||
* You should have received a copy of the GNU General Public License *
|
||||
* along with this program; if not, write to the *
|
||||
* Free Software Foundation, Inc., *
|
||||
* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
|
||||
***************************************************************************/
|
||||
|
||||
#include "PMsr2Data.h"
|
||||
|
||||
#include <algorithm>
|
||||
#include <sstream>
|
||||
#include <iostream>
|
||||
using namespace std;
|
||||
|
||||
#include <boost/algorithm/string/case_conv.hpp> // for to_lower() in std::string
|
||||
using namespace boost::algorithm;
|
||||
|
||||
//--------------------------------------------------------------------------
|
||||
/**
|
||||
* <p>
|
||||
* std::string
|
||||
*/
|
||||
bool isNumber(const string &s)
|
||||
{
|
||||
unsigned int number;
|
||||
istringstream iss;
|
||||
ostringstream oss;
|
||||
iss.str(s);
|
||||
iss >> number;
|
||||
oss << number;
|
||||
if (iss.str().compare(oss.str()))
|
||||
return false;
|
||||
return true;
|
||||
}
|
||||
|
||||
//--------------------------------------------------------------------------
|
||||
/**
|
||||
* <p>
|
||||
*/
|
||||
void msr2data_syntax()
|
||||
{
|
||||
cout << endl << "usage 1: msr2data <run> <extension> [-o<outputfile>] [data] [noheader] [nosummary] [fit-<template>[!]] [-k] [-t]";
|
||||
cout << endl << "usage 2: msr2data <run1> <run2> <extension> [-o<outputfile>] [data] [noheader] [nosummary] [fit-<template>[!]] [-k] [-t]";
|
||||
cout << endl << "usage 3: msr2data \\[<run1> <run2> ... <runN>\\] <extension> [-o<outputfile> ] [data] [noheader] [nosummary] [fit-<template>[!]] [-k] [-t]";
|
||||
cout << endl << "usage 4: msr2data <runlist> <extension> [-o<outputfile>] [data] [noheader] [nosummary] [fit-<template>[!]] [-k] [-t]";
|
||||
cout << endl;
|
||||
cout << endl << " <run>, <run1>, <run2>, ... <runN> : run numbers";
|
||||
cout << endl << " <extension> : msr-file extension, e.g. _tf_h13 for the file name 8472_tf_h13.msr";
|
||||
cout << endl << " -o<outputfile> : specify the name of the DB or column data output file; default: out.db/out.dat";
|
||||
cout << endl << " data : instead of to a DB file the data are written to a simple column structure";
|
||||
cout << endl << " noheader : no file header is written to the output file";
|
||||
cout << endl << " nosummary : no additional data from the run data file is written to the output file";
|
||||
cout << endl << " fit-<template>! : generate msr-files for the runs to be processed from the <template>-run";
|
||||
cout << endl << " and call musrfit for fitting these runs";
|
||||
cout << endl << " fit-<template> : same as above, but the <template>-run is only used for the first file creation - ";
|
||||
cout << endl << " the succeding files are generated using the musrfit-output from the last runs";
|
||||
cout << endl << " -k : if fitting is used, pass the option --keep-mn2-output to musrfit";
|
||||
cout << endl << " -t : if fitting is used, pass the option --title-from-data-file to musrfit";
|
||||
cout << endl;
|
||||
cout << endl << " For further information please refer to";
|
||||
cout << endl << " https://wiki.intranet.psi.ch/MUSR/Msr2Data";
|
||||
cout << endl << endl;
|
||||
}
|
||||
|
||||
//--------------------------------------------------------------------------
|
||||
/**
|
||||
* <p>
|
||||
* std::vector of std::string
|
||||
* bool (DB file ore not)
|
||||
*/
|
||||
string msr2data_outputfile(vector<string> &arg, bool db = true)
|
||||
{
|
||||
string outputFile;
|
||||
if (db)
|
||||
outputFile = "out.db";
|
||||
else
|
||||
outputFile = "out.dat";
|
||||
|
||||
vector<string>::iterator iterNext(arg.begin());
|
||||
for (vector<string>::iterator iter(arg.begin()); iter != arg.end(); iter++) {
|
||||
iterNext = iter + 1;
|
||||
if (!iter->substr(0,2).compare("-o")) {
|
||||
if (!iter->compare("-o")) {
|
||||
if ((iterNext != arg.end()) && (iterNext->compare("noheader")) && (iterNext->compare("nosummary")) \
|
||||
&& (iterNext->substr(0,3).compare("fit")) && (iterNext->compare("-k")) && (iterNext->compare("-t")) \
|
||||
&& (iterNext->compare("data")) ) {
|
||||
outputFile = *iterNext;
|
||||
arg.erase(iterNext);
|
||||
arg.erase(iter);
|
||||
break;
|
||||
} else {
|
||||
cout << endl;
|
||||
cout << ">> msr2data: **WARNING** You did not specify an output file! The default one (" << outputFile << ") will be used." << endl;
|
||||
arg.erase(iter);
|
||||
break;
|
||||
}
|
||||
} else {
|
||||
outputFile = iter->substr(2);
|
||||
arg.erase(iter);
|
||||
break;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
return outputFile;
|
||||
}
|
||||
|
||||
//--------------------------------------------------------------------------
|
||||
/**
|
||||
* <p>
|
||||
* std::vector of std::string
|
||||
* string
|
||||
*/
|
||||
bool msr2data_useOption(vector<string> &arg, const string &s)
|
||||
{
|
||||
bool option(true);
|
||||
|
||||
vector<string>::iterator iter;
|
||||
iter = find(arg.begin(), arg.end(), s);
|
||||
|
||||
if (iter != arg.end()) {
|
||||
option = false;
|
||||
arg.erase(iter);
|
||||
}
|
||||
return option;
|
||||
}
|
||||
|
||||
//--------------------------------------------------------------------------
|
||||
/**
|
||||
* <p>
|
||||
* std::vector of std::string
|
||||
* bool
|
||||
*/
|
||||
unsigned int msr2data_doFitting(vector<string> &arg, bool &chainfit)
|
||||
{
|
||||
unsigned int temp(0);
|
||||
|
||||
string s;
|
||||
istringstream iss;
|
||||
for (vector<string>::iterator iter(arg.begin()); iter != arg.end(); iter++) {
|
||||
if (!iter->substr(0,4).compare("fit-")) {
|
||||
s = iter->substr(4);
|
||||
string::size_type loc = s.rfind('!');
|
||||
if (loc != string::npos)
|
||||
chainfit = false;
|
||||
else
|
||||
chainfit = true;
|
||||
iss.str(s);
|
||||
iss >> temp;
|
||||
arg.erase(iter);
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
return temp;
|
||||
}
|
||||
|
||||
//--------------------------------------------------------------------------
|
||||
/**
|
||||
* <p>
|
||||
*
|
||||
* \param argc
|
||||
* \param argv
|
||||
*/
|
||||
int main(int argc, char *argv[])
|
||||
{
|
||||
// check the number of arguments
|
||||
if (argc < 3) {
|
||||
msr2data_syntax();
|
||||
return 0;
|
||||
}
|
||||
|
||||
// use a string-vector for the arguments to get rid of god damn char* as far as possible...
|
||||
vector<string> arg;
|
||||
for (int i(1); i<argc; i++) {
|
||||
arg.push_back(argv[i]);
|
||||
}
|
||||
|
||||
unsigned int runTAG;
|
||||
vector<unsigned int> run_vec;
|
||||
string run_list;
|
||||
string msrExtension;
|
||||
|
||||
if (arg[0].at(0) == '[') { // In case a list of runs is given by [...]
|
||||
runTAG = 1;
|
||||
|
||||
unsigned int firstRunNumberInArg(0), lastRunNumberInArg(0);
|
||||
unsigned int rightbracket(999);
|
||||
|
||||
if (!arg[0].compare("["))
|
||||
firstRunNumberInArg = 1;
|
||||
else
|
||||
arg[0]=arg[0].substr(1);
|
||||
|
||||
for (unsigned int i(firstRunNumberInArg); i<arg.size(); i++) {
|
||||
string::size_type loc = arg[i].rfind(']');
|
||||
if ( loc != string::npos ) {
|
||||
rightbracket = i;
|
||||
if (!arg[i].compare("]") && i > 0)
|
||||
lastRunNumberInArg = i-1;
|
||||
else {
|
||||
arg[i]=arg[i].substr(0,loc);
|
||||
lastRunNumberInArg = i;
|
||||
}
|
||||
break;
|
||||
}
|
||||
}
|
||||
if (rightbracket == 999) {
|
||||
cout << endl;
|
||||
cout << ">> msr2data: **ERROR** You used the list specification without closing bracket (])! Quitting now." << endl;
|
||||
return 0;
|
||||
}
|
||||
|
||||
for (unsigned int i(firstRunNumberInArg); i<=lastRunNumberInArg; ++i)
|
||||
run_vec.push_back(atoi(arg[i].c_str()));
|
||||
|
||||
msrExtension = arg[rightbracket + 1];
|
||||
|
||||
vector<string>::iterator iter(arg.begin());
|
||||
for (unsigned int i(0); i<rightbracket + 2; i++) {
|
||||
arg.erase(iter);
|
||||
iter = arg.begin();
|
||||
}
|
||||
|
||||
} else {
|
||||
bool argOneIsNumber(isNumber(arg[0])), argTwoIsNumber(isNumber(arg[1]));
|
||||
|
||||
if (argOneIsNumber && argTwoIsNumber) { // the first two arguments are numbers: an interval of numbers is given
|
||||
runTAG = 2;
|
||||
|
||||
if (arg.size() < 3) {
|
||||
cout << endl;
|
||||
cout << ">> msr2data: **ERROR** No msr-file extension specified! Quitting now..." << endl;
|
||||
run_vec.clear();
|
||||
arg.clear();
|
||||
return 0;
|
||||
}
|
||||
|
||||
run_vec.push_back(atoi(arg[0].c_str()));
|
||||
run_vec.push_back(atoi(arg[1].c_str()));
|
||||
|
||||
msrExtension = arg[2];
|
||||
|
||||
vector<string>::iterator iter(arg.begin());
|
||||
for (unsigned int i(0); i < 3; i++) {
|
||||
arg.erase(iter);
|
||||
iter = arg.begin();
|
||||
}
|
||||
} else if (argOneIsNumber && !argTwoIsNumber) { // only one run number is given
|
||||
runTAG = 3;
|
||||
run_vec.push_back(atoi(arg[0].c_str()));
|
||||
msrExtension = arg[1];
|
||||
|
||||
vector<string>::iterator iter(arg.begin());
|
||||
for (unsigned int i(0); i < 2; i++) {
|
||||
arg.erase(iter);
|
||||
iter = arg.begin();
|
||||
}
|
||||
} else { // assume a runlist-file with "independent variables" is given
|
||||
runTAG = 4;
|
||||
run_list = arg[0];
|
||||
msrExtension = arg[1];
|
||||
|
||||
vector<string>::iterator iter(arg.begin());
|
||||
for (unsigned int i(0); i < 2; i++) {
|
||||
arg.erase(iter);
|
||||
iter = arg.begin();
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// check if the output format is DB or data
|
||||
bool db(msr2data_useOption(arg, "data"));
|
||||
|
||||
// check the arguments for the "-o" option and set the output filename
|
||||
string outputFile(msr2data_outputfile(arg, db));
|
||||
|
||||
// introduce check, if no output should be generated - in that case we do not need msrfile and rundata handlers later
|
||||
bool realOutput(true);
|
||||
if (!to_lower_copy(outputFile).compare("none"))
|
||||
realOutput = false;
|
||||
|
||||
// create the msr2data-object and set the run numbers according to the runTAG above
|
||||
PMsr2Data msr2dataHandler(msrExtension);
|
||||
|
||||
int status;
|
||||
|
||||
switch(runTAG) {
|
||||
case 1:
|
||||
status = msr2dataHandler.SetRunNumbers(run_vec);
|
||||
break;
|
||||
case 2:
|
||||
status = msr2dataHandler.SetRunNumbers(run_vec[0], run_vec[1]);
|
||||
break;
|
||||
case 3:
|
||||
status = msr2dataHandler.SetRunNumbers(run_vec[0]);
|
||||
break;
|
||||
case 4:
|
||||
status = msr2dataHandler.SetRunNumbers(run_list);
|
||||
break;
|
||||
default:
|
||||
cout << endl;
|
||||
cout << ">> msr2data: **ERROR** None of the possible run list specifications has been detected! Quitting now..." << endl;
|
||||
run_vec.clear();
|
||||
arg.clear();
|
||||
return 0;
|
||||
}
|
||||
|
||||
if (status == 1) {
|
||||
cout << endl;
|
||||
cout << ">> msr2data: **ERROR** The run numbers are out of range! Quitting..." << endl;
|
||||
run_vec.clear();
|
||||
arg.clear();
|
||||
return status;
|
||||
}
|
||||
|
||||
run_vec.clear();
|
||||
|
||||
// check if fitting should be done and in case, which template run number to use
|
||||
unsigned int temp(0);
|
||||
bool chainfit(true);
|
||||
string musrfitOptions;
|
||||
|
||||
temp = msr2data_doFitting(arg, chainfit);
|
||||
|
||||
// check if any options should be passed to musrfit
|
||||
if (temp) {
|
||||
if (!msr2data_useOption(arg, "-k"))
|
||||
musrfitOptions.append("-k ");
|
||||
if (!msr2data_useOption(arg, "-t"))
|
||||
musrfitOptions.append("-t ");
|
||||
}
|
||||
|
||||
bool writeHeader(false), writeSummary(false);
|
||||
|
||||
if (realOutput) {
|
||||
// check the arguments for the "noheader" option
|
||||
writeHeader = msr2data_useOption(arg, "noheader");
|
||||
|
||||
// check the arguments for the "nosummary" option
|
||||
writeSummary = msr2data_useOption(arg, "nosummary");
|
||||
}
|
||||
|
||||
// read musrfit startup file
|
||||
if (writeSummary) {
|
||||
status = msr2dataHandler.ParseXmlStartupFile();
|
||||
}
|
||||
|
||||
// Processing the run list, do the fitting and write the data to the DB or data output file
|
||||
bool firstrun(true);
|
||||
unsigned int oldtemp(temp);
|
||||
|
||||
while (msr2dataHandler.GetPresentRun()) {
|
||||
ostringstream strInfile;
|
||||
strInfile << msr2dataHandler.GetPresentRun() << msrExtension << ".msr";
|
||||
|
||||
// if fitting should be done, prepare a new input file
|
||||
if (temp) {
|
||||
bool success(true);
|
||||
if (firstrun || !chainfit)
|
||||
success = msr2dataHandler.PrepareNewInputFile(temp);
|
||||
else
|
||||
success = msr2dataHandler.PrepareNewInputFile(oldtemp);
|
||||
if (firstrun)
|
||||
firstrun = false;
|
||||
oldtemp = msr2dataHandler.GetPresentRun();
|
||||
|
||||
if (!success) {
|
||||
cout << endl << ">> msr2data: **ERROR** Input file generation has not been successful! Quitting..." << endl;
|
||||
arg.clear();
|
||||
return -1;
|
||||
}
|
||||
|
||||
// and do the fitting
|
||||
ostringstream oss;
|
||||
oss << "musrfit" << " " << strInfile.str() << " " << musrfitOptions;
|
||||
cout << endl << ">> msr2data: **INFO** Calling " << oss.str() << endl;
|
||||
system(oss.str().c_str());
|
||||
}
|
||||
|
||||
// read msr-file
|
||||
if (realOutput) {
|
||||
status = msr2dataHandler.ReadMsrFile(strInfile.str());
|
||||
if (status != PMUSR_SUCCESS) {
|
||||
arg.clear();
|
||||
return status;
|
||||
}
|
||||
}
|
||||
|
||||
// read data files
|
||||
if (writeSummary)
|
||||
writeSummary = msr2dataHandler.ReadRunDataFile();
|
||||
|
||||
// write DB or dat file
|
||||
msr2dataHandler.WriteOutput(outputFile, db, writeHeader);
|
||||
|
||||
}
|
||||
|
||||
if (!arg.empty()) {
|
||||
cout << endl << ">> msr2data: **INFO** The following command line arguments have been specified but not been used: " << endl;
|
||||
cout << ">> msr2data: **INFO**";
|
||||
for (unsigned int i(0); i<arg.size(); i++)
|
||||
cout << " " << arg[i];
|
||||
cout << endl;
|
||||
arg.clear();
|
||||
}
|
||||
|
||||
cout << endl << ">> msr2data: done ..." << endl;
|
||||
|
||||
return 1;
|
||||
}
|
||||
Loading…
x
Reference in New Issue
Block a user