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
435
src/msr2data.cpp
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435
src/msr2data.cpp
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/***************************************************************************
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msr2data.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 "PMsr2Data.h"
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#include <algorithm>
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#include <sstream>
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#include <iostream>
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using namespace std;
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#include <boost/algorithm/string/case_conv.hpp> // for to_lower() in std::string
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using namespace boost::algorithm;
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//--------------------------------------------------------------------------
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/**
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* <p>
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* std::string
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*/
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bool isNumber(const string &s)
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{
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unsigned int number;
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istringstream iss;
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ostringstream oss;
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iss.str(s);
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iss >> number;
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oss << number;
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if (iss.str().compare(oss.str()))
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return false;
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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 msr2data_syntax()
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{
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cout << endl << "usage 1: msr2data <run> <extension> [-o<outputfile>] [data] [noheader] [nosummary] [fit-<template>[!]] [-k] [-t]";
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cout << endl << "usage 2: msr2data <run1> <run2> <extension> [-o<outputfile>] [data] [noheader] [nosummary] [fit-<template>[!]] [-k] [-t]";
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cout << endl << "usage 3: msr2data \\[<run1> <run2> ... <runN>\\] <extension> [-o<outputfile> ] [data] [noheader] [nosummary] [fit-<template>[!]] [-k] [-t]";
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cout << endl << "usage 4: msr2data <runlist> <extension> [-o<outputfile>] [data] [noheader] [nosummary] [fit-<template>[!]] [-k] [-t]";
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cout << endl;
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cout << endl << " <run>, <run1>, <run2>, ... <runN> : run numbers";
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cout << endl << " <extension> : msr-file extension, e.g. _tf_h13 for the file name 8472_tf_h13.msr";
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cout << endl << " -o<outputfile> : specify the name of the DB or column data output file; default: out.db/out.dat";
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cout << endl << " data : instead of to a DB file the data are written to a simple column structure";
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cout << endl << " noheader : no file header is written to the output file";
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cout << endl << " nosummary : no additional data from the run data file is written to the output file";
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cout << endl << " fit-<template>! : generate msr-files for the runs to be processed from the <template>-run";
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cout << endl << " and call musrfit for fitting these runs";
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cout << endl << " fit-<template> : same as above, but the <template>-run is only used for the first file creation - ";
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cout << endl << " the succeding files are generated using the musrfit-output from the last runs";
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cout << endl << " -k : if fitting is used, pass the option --keep-mn2-output to musrfit";
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cout << endl << " -t : if fitting is used, pass the option --title-from-data-file to musrfit";
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cout << endl;
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cout << endl << " For further information please refer to";
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cout << endl << " https://wiki.intranet.psi.ch/MUSR/Msr2Data";
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cout << endl << endl;
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}
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//--------------------------------------------------------------------------
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/**
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* <p>
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* std::vector of std::string
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* bool (DB file ore not)
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*/
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string msr2data_outputfile(vector<string> &arg, bool db = true)
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{
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string outputFile;
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if (db)
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outputFile = "out.db";
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else
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outputFile = "out.dat";
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vector<string>::iterator iterNext(arg.begin());
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for (vector<string>::iterator iter(arg.begin()); iter != arg.end(); iter++) {
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iterNext = iter + 1;
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if (!iter->substr(0,2).compare("-o")) {
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if (!iter->compare("-o")) {
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if ((iterNext != arg.end()) && (iterNext->compare("noheader")) && (iterNext->compare("nosummary")) \
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&& (iterNext->substr(0,3).compare("fit")) && (iterNext->compare("-k")) && (iterNext->compare("-t")) \
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&& (iterNext->compare("data")) ) {
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outputFile = *iterNext;
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arg.erase(iterNext);
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arg.erase(iter);
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break;
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} else {
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cout << endl;
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cout << ">> msr2data: **WARNING** You did not specify an output file! The default one (" << outputFile << ") will be used." << endl;
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arg.erase(iter);
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break;
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}
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} else {
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outputFile = iter->substr(2);
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arg.erase(iter);
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break;
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}
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}
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}
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return outputFile;
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}
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//--------------------------------------------------------------------------
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/**
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* <p>
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* std::vector of std::string
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* string
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*/
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bool msr2data_useOption(vector<string> &arg, const string &s)
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{
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bool option(true);
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vector<string>::iterator iter;
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iter = find(arg.begin(), arg.end(), s);
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if (iter != arg.end()) {
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option = false;
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arg.erase(iter);
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}
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return option;
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}
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//--------------------------------------------------------------------------
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/**
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* <p>
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* std::vector of std::string
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* bool
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*/
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unsigned int msr2data_doFitting(vector<string> &arg, bool &chainfit)
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{
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unsigned int temp(0);
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string s;
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istringstream iss;
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for (vector<string>::iterator iter(arg.begin()); iter != arg.end(); iter++) {
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if (!iter->substr(0,4).compare("fit-")) {
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s = iter->substr(4);
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string::size_type loc = s.rfind('!');
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if (loc != string::npos)
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chainfit = false;
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else
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chainfit = true;
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iss.str(s);
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iss >> temp;
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arg.erase(iter);
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break;
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}
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}
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return temp;
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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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* \param argc
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* \param argv
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*/
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int main(int argc, char *argv[])
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{
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// check the number of arguments
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if (argc < 3) {
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msr2data_syntax();
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return 0;
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}
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// use a string-vector for the arguments to get rid of god damn char* as far as possible...
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vector<string> arg;
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for (int i(1); i<argc; i++) {
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arg.push_back(argv[i]);
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}
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unsigned int runTAG;
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vector<unsigned int> run_vec;
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string run_list;
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string msrExtension;
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if (arg[0].at(0) == '[') { // In case a list of runs is given by [...]
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runTAG = 1;
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unsigned int firstRunNumberInArg(0), lastRunNumberInArg(0);
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unsigned int rightbracket(999);
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if (!arg[0].compare("["))
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firstRunNumberInArg = 1;
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else
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arg[0]=arg[0].substr(1);
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for (unsigned int i(firstRunNumberInArg); i<arg.size(); i++) {
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string::size_type loc = arg[i].rfind(']');
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if ( loc != string::npos ) {
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rightbracket = i;
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if (!arg[i].compare("]") && i > 0)
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lastRunNumberInArg = i-1;
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else {
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arg[i]=arg[i].substr(0,loc);
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lastRunNumberInArg = i;
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}
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break;
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}
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}
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if (rightbracket == 999) {
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cout << endl;
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cout << ">> msr2data: **ERROR** You used the list specification without closing bracket (])! Quitting now." << endl;
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return 0;
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}
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for (unsigned int i(firstRunNumberInArg); i<=lastRunNumberInArg; ++i)
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run_vec.push_back(atoi(arg[i].c_str()));
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msrExtension = arg[rightbracket + 1];
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vector<string>::iterator iter(arg.begin());
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for (unsigned int i(0); i<rightbracket + 2; i++) {
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arg.erase(iter);
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iter = arg.begin();
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}
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} else {
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bool argOneIsNumber(isNumber(arg[0])), argTwoIsNumber(isNumber(arg[1]));
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if (argOneIsNumber && argTwoIsNumber) { // the first two arguments are numbers: an interval of numbers is given
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runTAG = 2;
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if (arg.size() < 3) {
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cout << endl;
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cout << ">> msr2data: **ERROR** No msr-file extension specified! Quitting now..." << endl;
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run_vec.clear();
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arg.clear();
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return 0;
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}
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run_vec.push_back(atoi(arg[0].c_str()));
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run_vec.push_back(atoi(arg[1].c_str()));
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msrExtension = arg[2];
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vector<string>::iterator iter(arg.begin());
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for (unsigned int i(0); i < 3; i++) {
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arg.erase(iter);
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iter = arg.begin();
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}
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} else if (argOneIsNumber && !argTwoIsNumber) { // only one run number is given
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runTAG = 3;
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run_vec.push_back(atoi(arg[0].c_str()));
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msrExtension = arg[1];
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vector<string>::iterator iter(arg.begin());
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for (unsigned int i(0); i < 2; i++) {
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arg.erase(iter);
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iter = arg.begin();
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}
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} else { // assume a runlist-file with "independent variables" is given
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runTAG = 4;
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run_list = arg[0];
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msrExtension = arg[1];
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vector<string>::iterator iter(arg.begin());
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for (unsigned int i(0); i < 2; i++) {
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arg.erase(iter);
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iter = arg.begin();
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}
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}
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}
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// check if the output format is DB or data
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bool db(msr2data_useOption(arg, "data"));
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// check the arguments for the "-o" option and set the output filename
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string outputFile(msr2data_outputfile(arg, db));
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// introduce check, if no output should be generated - in that case we do not need msrfile and rundata handlers later
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bool realOutput(true);
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if (!to_lower_copy(outputFile).compare("none"))
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realOutput = false;
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// create the msr2data-object and set the run numbers according to the runTAG above
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PMsr2Data msr2dataHandler(msrExtension);
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int status;
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switch(runTAG) {
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case 1:
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status = msr2dataHandler.SetRunNumbers(run_vec);
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break;
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case 2:
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status = msr2dataHandler.SetRunNumbers(run_vec[0], run_vec[1]);
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break;
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case 3:
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status = msr2dataHandler.SetRunNumbers(run_vec[0]);
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break;
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case 4:
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status = msr2dataHandler.SetRunNumbers(run_list);
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break;
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default:
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cout << endl;
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cout << ">> msr2data: **ERROR** None of the possible run list specifications has been detected! Quitting now..." << endl;
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run_vec.clear();
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arg.clear();
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return 0;
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}
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if (status == 1) {
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cout << endl;
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cout << ">> msr2data: **ERROR** The run numbers are out of range! Quitting..." << endl;
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run_vec.clear();
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arg.clear();
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return status;
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}
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run_vec.clear();
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// check if fitting should be done and in case, which template run number to use
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unsigned int temp(0);
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bool chainfit(true);
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string musrfitOptions;
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temp = msr2data_doFitting(arg, chainfit);
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// check if any options should be passed to musrfit
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if (temp) {
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if (!msr2data_useOption(arg, "-k"))
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musrfitOptions.append("-k ");
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if (!msr2data_useOption(arg, "-t"))
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musrfitOptions.append("-t ");
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}
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bool writeHeader(false), writeSummary(false);
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if (realOutput) {
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// check the arguments for the "noheader" option
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writeHeader = msr2data_useOption(arg, "noheader");
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// check the arguments for the "nosummary" option
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writeSummary = msr2data_useOption(arg, "nosummary");
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}
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// read musrfit startup file
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if (writeSummary) {
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status = msr2dataHandler.ParseXmlStartupFile();
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}
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// Processing the run list, do the fitting and write the data to the DB or data output file
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bool firstrun(true);
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unsigned int oldtemp(temp);
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while (msr2dataHandler.GetPresentRun()) {
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ostringstream strInfile;
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strInfile << msr2dataHandler.GetPresentRun() << msrExtension << ".msr";
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// if fitting should be done, prepare a new input file
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if (temp) {
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bool success(true);
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if (firstrun || !chainfit)
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success = msr2dataHandler.PrepareNewInputFile(temp);
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else
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success = msr2dataHandler.PrepareNewInputFile(oldtemp);
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if (firstrun)
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firstrun = false;
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oldtemp = msr2dataHandler.GetPresentRun();
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if (!success) {
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cout << endl << ">> msr2data: **ERROR** Input file generation has not been successful! Quitting..." << endl;
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arg.clear();
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return -1;
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}
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// and do the fitting
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ostringstream oss;
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oss << "musrfit" << " " << strInfile.str() << " " << musrfitOptions;
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cout << endl << ">> msr2data: **INFO** Calling " << oss.str() << endl;
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system(oss.str().c_str());
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}
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// read msr-file
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if (realOutput) {
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status = msr2dataHandler.ReadMsrFile(strInfile.str());
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if (status != PMUSR_SUCCESS) {
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arg.clear();
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return status;
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}
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}
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// read data files
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if (writeSummary)
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writeSummary = msr2dataHandler.ReadRunDataFile();
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// write DB or dat file
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msr2dataHandler.WriteOutput(outputFile, db, writeHeader);
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}
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if (!arg.empty()) {
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cout << endl << ">> msr2data: **INFO** The following command line arguments have been specified but not been used: " << endl;
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cout << ">> msr2data: **INFO**";
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for (unsigned int i(0); i<arg.size(); i++)
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cout << " " << arg[i];
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cout << endl;
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arg.clear();
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}
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cout << endl << ">> msr2data: done ..." << endl;
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return 1;
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}
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