LMU/musrfit
5
0
Fork 0
Code Issues 5 Pull Requests Actions Packages Projects Releases 4 Activity

modernized code to C++11 and newer.

Browse Source 
This allows to analyze the code by external code analyzers. Since a lot is adopted,
the version is changed to 1.4.3

Conflicts:
	src/classes/PFitter.cpp
	src/classes/PFourier.cpp
	src/classes/PMsrHandler.cpp
	src/classes/PMusrCanvas.cpp
	src/classes/PRunAsymmetry.cpp
	src/classes/PRunAsymmetryRRF.cpp
	src/classes/PRunListCollection.cpp
	src/classes/PRunSingleHisto.cpp
	src/classes/PRunSingleHistoRRF.cpp
	src/classes/PStartupHandler.cpp
	src/include/PFourier.h
	src/include/PRunListCollection.h
	src/musrFT.cpp
This commit is contained in:
suter_a
2019-04-16 15:34:49 +02:00
parent 1c5069bc48
commit c64c74dbf8
138 changed files with 7017 additions and 7230 deletions
Download Patch File Download Diff File Expand all files Collapse all files

389
src/msr2data.cpp
View File

@@ -8,7 +8,7 @@
***************************************************************************/
/***************************************************************************
* Copyright (C) 2009-2014 by Bastian M. Wojek / Andreas Suter *
* Copyright (C) 2009-2019 by Bastian M. Wojek / Andreas Suter *
* andreas.suter@psi.ch *
* *
* This program is free software; you can redistribute it and/or modify *
@@ -46,15 +46,12 @@
#include <fstream>
#include <cstdlib>
#include <limits>
using namespace std;
#include <string>
#include <boost/algorithm/string.hpp>
#include <boost/algorithm/string/case_conv.hpp> // for to_lower() in std::string
using namespace boost::algorithm;
#include <boost/lexical_cast.hpp> // for atoi-replacement
// #include <boost/filesystem.hpp> // for a clean way to check if a file exists
//--------------------------------------------------------------------------
/**
@@ -66,7 +63,7 @@ using namespace boost::algorithm;
*
* \param s string
*/
bool isNumber(const string &s)
bool isNumber(const std::string &s)
{
unsigned int number(0);
try {
@@ -84,86 +81,86 @@ bool isNumber(const string &s)
*/
void msr2data_syntax()
{
cout << endl << "usage 0: msr2data [--version] | [--help]";
cout << endl << "usage 1: msr2data <run> <extension> options";
cout << endl << "usage 2: msr2data <run1> <run2> <extension> options";
cout << endl << "usage 3: msr2data \\[<runList>\\] <extension> options";
cout << endl << "usage 4: msr2data <runListFileName> <extension> options";
cout << endl;
cout << endl << " <runList> can be:";
cout << endl << " (i) <run0>, <run1>, <run2>, ... <runN> : run numbers, e.g. 123 124";
cout << endl << " (ii) <run0>-<runN> : a range, e.g. 123-125 -> 123 124 125";
cout << endl << " (iii) <run0>:<runN>:<step> : a sequence, e.g. 123:127:2 -> 123 125 127";
cout << endl << " <step> will give the step width and has to be a positive number!";
cout << endl << " a <runList> can also combine (i)-(iii), e.g. 123 128-130 133, etc.";
cout << endl << " <runListFileName> : an ASCII file containing a list of run numbers and optional";
cout << endl << " external parameters is passed to msr2data. For details see";
cout << endl << " the online documentation: http://lmu.web.psi.ch/musrfit/user/MUSR/Msr2Data.html";
cout << endl << " <extension> : msr-file extension, e.g. _tf_h13 for the file name 8472_tf_h13.msr";
cout << endl;
cout << endl << "options:";
cout << endl << " -o<outputfile> : specify the name of the DB or column-data output file; default: out.db/out.dat";
cout << endl << " if the option '-o none' is used, no output file will be written.";
cout << endl << " new : before writing a new output file, delete the contents of any existing file with the same name";
cout << endl << " data : instead of to a DB file the data are written to a simple column structure";
cout << endl << " header : force writing of the file header to the output file";
cout << endl << " noheader : no file header is written to the output file";
cout << endl << " If either none or both of the header options are given, the file header will be written";
cout << endl << " if a new file is created, but not if the output file exists already!";
cout << endl << " nosummary : no additional data from the run data file is written to the output file";
cout << endl << " paramList <param> : option used to select the parameters which shall be exported.";
cout << endl << " <param> is a list of parameter numbers to be exported. Allowed lists are:";
cout << endl << " 1-16 will export parameters 1 to 16. 1 3 5 will export parameters 1 3 5.";
cout << endl << " A combination of both is possible, e.g. 1-16 19 31 62, and so on.";
cout << endl << " fit : invoke musrfit to fit the specified runs";
cout << endl << " All msr input files are assumed to be present, none is newly generated!";
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 successive files are generated using the musrfit output from the preceding runs";
cout << endl << " msr-<template> : same as above without calling musrfit";
cout << endl << " In case any fitting option is present, this option is ignored!";
cout << endl << " -k, --keep-mn2-output : if fitting is used, pass the option --keep-mn2-output to musrfit";
cout << endl << " -t, --title-from-data-file : if fitting is used, pass the option --title-from-data-file to musrfit";
cout << endl << " -e, --estimateN0: estimate N0 for single histogram fits.";
cout << endl << " -p, --per-run-block-chisq: will per run block chisq to the msr-file.";
cout << endl;
cout << endl << " global : switch on the global-fit mode";
cout << endl << " Within that mode all specified runs will be united in a single msr file!";
cout << endl << " The fit parameters can be either run specific or common to all runs.";
cout << endl << " For a complete description of this feature please refer to the manual.";
cout << endl;
cout << endl << " global+[!] : operate in the global-fit mode, however, in case a global input file is created";
cout << endl << " all specified runs are pre-analyzed first one by one using the given template.";
cout << endl << " For the generation of the global input file, the run-specific parameter values are taken";
cout << endl << " from this pre-analysis for each run---they are not just copied from the template.";
cout << endl << " The specification of '!' determines which fit mode (see above) is used for this pre-analysis.";
cout << endl;
cout << endl << " Typical examples:";
cout << endl;
cout << endl << " msr2data 2047 2050 _tf_histo fit-2046";
cout << endl << " will use 2046_tf_histo.msr as templete, and subsequently generating 2047_tf_histo.msr until";
cout << endl << " 2050_tf_histo.msr and fit them.";
cout << endl;
cout << endl << " msr2data 2047 2050 _tf_histo msr-2046";
cout << endl << " will use 2046_tf_histo.msr as templete, and subsequently generating 2047_tf_histo.msr until";
cout << endl << " 2050_tf_histo.msr, but NO fitting will be done.";
cout << endl;
cout << endl << " msr2data 2046 2050 _tf_histo -o fitParam.db";
cout << endl << " will collect the fit parameters from runs 2046-2050 (msr-files 2046_tf_histo.msr etc.) and";
cout << endl << " write them to the file fitParam.db (DB-format).";
cout << endl;
cout << endl << " msr2data [2047:2053:2 2056] _tf_histo fit-2045";
cout << endl << " will use 2045_tf_histo.msr as templete, and subsequently generating msr-files from the run-list:";
cout << endl << " 2047 2049 2051 2053 2056 (2047_tf_histo.msr etc.) and fit them.";
cout << endl;
cout << endl << " msr2data 2046 2058 _tf_histo paramList 1-12 data -o fitParam.dat";
cout << endl << " will export the parameters number 1 trough 12 in a column like fashion of the runs 2046 to 2058,";
cout << endl << " collected form the msr-files 2046_tf_histo.msr and so on.";
cout << endl;
cout << endl << " For further information please refer to";
cout << endl << " http://lmu.web.psi.ch/musrfit/user/html/msr2data.html#msr2data";
cout << endl << endl;
std::cout << std::endl << "usage 0: msr2data [--version] | [--help]";
std::cout << std::endl << "usage 1: msr2data <run> <extension> options";
std::cout << std::endl << "usage 2: msr2data <run1> <run2> <extension> options";
std::cout << std::endl << "usage 3: msr2data \\[<runList>\\] <extension> options";
std::cout << std::endl << "usage 4: msr2data <runListFileName> <extension> options";
std::cout << std::endl;
std::cout << std::endl << " <runList> can be:";
std::cout << std::endl << " (i) <run0>, <run1>, <run2>, ... <runN> : run numbers, e.g. 123 124";
std::cout << std::endl << " (ii) <run0>-<runN> : a range, e.g. 123-125 -> 123 124 125";
std::cout << std::endl << " (iii) <run0>:<runN>:<step> : a sequence, e.g. 123:127:2 -> 123 125 127";
std::cout << std::endl << " <step> will give the step width and has to be a positive number!";
std::cout << std::endl << " a <runList> can also combine (i)-(iii), e.g. 123 128-130 133, etc.";
std::cout << std::endl << " <runListFileName> : an ASCII file containing a list of run numbers and optional";
std::cout << std::endl << " external parameters is passed to msr2data. For details see";
std::cout << std::endl << " the online documentation: http://lmu.web.psi.ch/musrfit/user/MUSR/Msr2Data.html";
std::cout << std::endl << " <extension> : msr-file extension, e.g. _tf_h13 for the file name 8472_tf_h13.msr";
std::cout << std::endl;
std::cout << std::endl << "options:";
std::cout << std::endl << " -o<outputfile> : specify the name of the DB or column-data output file; default: out.db/out.dat";
std::cout << std::endl << " if the option '-o none' is used, no output file will be written.";
std::cout << std::endl << " new : before writing a new output file, delete the contents of any existing file with the same name";
std::cout << std::endl << " data : instead of to a DB file the data are written to a simple column structure";
std::cout << std::endl << " header : force writing of the file header to the output file";
std::cout << std::endl << " noheader : no file header is written to the output file";
std::cout << std::endl << " If either none or both of the header options are given, the file header will be written";
std::cout << std::endl << " if a new file is created, but not if the output file exists already!";
std::cout << std::endl << " nosummary : no additional data from the run data file is written to the output file";
std::cout << std::endl << " paramList <param> : option used to select the parameters which shall be exported.";
std::cout << std::endl << " <param> is a list of parameter numbers to be exported. Allowed lists are:";
std::cout << std::endl << " 1-16 will export parameters 1 to 16. 1 3 5 will export parameters 1 3 5.";
std::cout << std::endl << " A combination of both is possible, e.g. 1-16 19 31 62, and so on.";
std::cout << std::endl << " fit : invoke musrfit to fit the specified runs";
std::cout << std::endl << " All msr input files are assumed to be present, none is newly generated!";
std::cout << std::endl << " fit-<template>! : generate msr files for the runs to be processed from the <template> run";
std::cout << std::endl << " and call musrfit for fitting these runs";
std::cout << std::endl << " fit-<template> : same as above, but the <template> run is only used for the first file creation---";
std::cout << std::endl << " the successive files are generated using the musrfit output from the preceding runs";
std::cout << std::endl << " msr-<template> : same as above without calling musrfit";
std::cout << std::endl << " In case any fitting option is present, this option is ignored!";
std::cout << std::endl << " -k, --keep-mn2-output : if fitting is used, pass the option --keep-mn2-output to musrfit";
std::cout << std::endl << " -t, --title-from-data-file : if fitting is used, pass the option --title-from-data-file to musrfit";
std::cout << std::endl << " -e, --estimateN0: estimate N0 for single histogram fits.";
std::cout << std::endl << " -p, --per-run-block-chisq: will per run block chisq to the msr-file.";
std::cout << std::endl;
std::cout << std::endl << " global : switch on the global-fit mode";
std::cout << std::endl << " Within that mode all specified runs will be united in a single msr file!";
std::cout << std::endl << " The fit parameters can be either run specific or common to all runs.";
std::cout << std::endl << " For a complete description of this feature please refer to the manual.";
std::cout << std::endl;
std::cout << std::endl << " global+[!] : operate in the global-fit mode, however, in case a global input file is created";
std::cout << std::endl << " all specified runs are pre-analyzed first one by one using the given template.";
std::cout << std::endl << " For the generation of the global input file, the run-specific parameter values are taken";
std::cout << std::endl << " from this pre-analysis for each run---they are not just copied from the template.";
std::cout << std::endl << " The specification of '!' determines which fit mode (see above) is used for this pre-analysis.";
std::cout << std::endl;
std::cout << std::endl << " Typical examples:";
std::cout << std::endl;
std::cout << std::endl << " msr2data 2047 2050 _tf_histo fit-2046";
std::cout << std::endl << " will use 2046_tf_histo.msr as templete, and subsequently generating 2047_tf_histo.msr until";
std::cout << std::endl << " 2050_tf_histo.msr and fit them.";
std::cout << std::endl;
std::cout << std::endl << " msr2data 2047 2050 _tf_histo msr-2046";
std::cout << std::endl << " will use 2046_tf_histo.msr as templete, and subsequently generating 2047_tf_histo.msr until";
std::cout << std::endl << " 2050_tf_histo.msr, but NO fitting will be done.";
std::cout << std::endl;
std::cout << std::endl << " msr2data 2046 2050 _tf_histo -o fitParam.db";
std::cout << std::endl << " will collect the fit parameters from runs 2046-2050 (msr-files 2046_tf_histo.msr etc.) and";
std::cout << std::endl << " write them to the file fitParam.db (DB-format).";
std::cout << std::endl;
std::cout << std::endl << " msr2data [2047:2053:2 2056] _tf_histo fit-2045";
std::cout << std::endl << " will use 2045_tf_histo.msr as templete, and subsequently generating msr-files from the run-list:";
std::cout << std::endl << " 2047 2049 2051 2053 2056 (2047_tf_histo.msr etc.) and fit them.";
std::cout << std::endl;
std::cout << std::endl << " msr2data 2046 2058 _tf_histo paramList 1-12 data -o fitParam.dat";
std::cout << std::endl << " will export the parameters number 1 trough 12 in a column like fashion of the runs 2046 to 2058,";
std::cout << std::endl << " collected form the msr-files 2046_tf_histo.msr and so on.";
std::cout << std::endl;
std::cout << std::endl << " For further information please refer to";
std::cout << std::endl << " http://lmu.web.psi.ch/musrfit/user/html/msr2data.html#msr2data";
std::cout << std::endl << std::endl;
}
//--------------------------------------------------------------------------
@@ -175,10 +172,10 @@ void msr2data_syntax()
* \param arg vector containing the command line arguments
*
*/
void msr2data_cleanup(PMsr2Data *msr2dataHandler, vector<unsigned int> &run_vec, vector<string> &arg)
void msr2data_cleanup(PMsr2Data *msr2dataHandler, std::vector<unsigned int> &run_vec, std::vector<std::string> &arg)
{
delete msr2dataHandler;
msr2dataHandler = 0;
msr2dataHandler = nullptr;
run_vec.clear();
arg.clear();
return;
@@ -192,7 +189,7 @@ void msr2data_cleanup(PMsr2Data *msr2dataHandler, vector<unsigned int> &run_vec,
* \param arg vector containing the command line arguments
*
*/
void msr2data_cleanup(PMsr2Data *msr2dataHandler, vector<string> &arg)
void msr2data_cleanup(PMsr2Data *msr2dataHandler, std::vector<std::string> &arg)
{
delete msr2dataHandler;
msr2dataHandler = 0;
@@ -211,11 +208,11 @@ void msr2data_cleanup(PMsr2Data *msr2dataHandler, vector<string> &arg)
* \param arg list of arguments
*
*/
string msr2data_validArguments(const vector<string> &arg)
std::string msr2data_validArguments(const std::vector<std::string> &arg)
{
string word;
std::string word;
for (vector<string>::const_iterator iter(arg.begin()); iter != arg.end(); ++iter) {
for (std::vector<std::string>::const_iterator iter(arg.begin()); iter != arg.end(); ++iter) {
if ( (!iter->compare("header")) || (!iter->compare("noheader")) || (!iter->compare("nosummary")) \
|| (!iter->substr(0,3).compare("fit")) || (!iter->compare("-k")) || (!iter->compare("--keep-mn2-output")) \
|| (!iter->compare("-t")) || (!iter->compare("--title-from-data-file")) \
@@ -254,16 +251,16 @@ string msr2data_validArguments(const vector<string> &arg)
* \param arg argument string list from the msr2data call
* \param db true if output file is a db-file
*/
string msr2data_outputfile(vector<string> &arg, bool db = true)
std::string msr2data_outputfile(std::vector<std::string> &arg, bool db = true)
{
string outputFile;
std::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) {
std::vector<std::string>::iterator iterNext(arg.begin());
for (std::vector<std::string>::iterator iter(arg.begin()); iter != arg.end(); ++iter) {
iterNext = iter + 1;
if (!iter->substr(0,2).compare("-o")) {
if (!iter->compare("-o")) {
@@ -277,8 +274,8 @@ string msr2data_outputfile(vector<string> &arg, bool db = true)
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;
std::cout << std::endl;
std::cout << ">> msr2data: **WARNING** You did not specify an output file! The default one (" << outputFile << ") will be used." << std::endl;
arg.erase(iter);
break;
}
@@ -304,11 +301,11 @@ string msr2data_outputfile(vector<string> &arg, bool db = true)
* \param arg list of arguments
* \param s option string
*/
bool msr2data_useOption(vector<string> &arg, const string &s)
bool msr2data_useOption(std::vector<std::string> &arg, const std::string &s)
{
bool option(true);
vector<string>::iterator iter;
std::vector<std::string>::iterator iter;
iter = find(arg.begin(), arg.end(), s);
if (iter != arg.end()) {
@@ -333,12 +330,12 @@ bool msr2data_useOption(vector<string> &arg, const string &s)
* \param chainfit if true
*
*/
int msr2data_doFitting(vector<string> &arg, bool &chainfit)
int msr2data_doFitting(std::vector<std::string> &arg, bool &chainfit)
{
int temp(0);
string s;
vector<string>::iterator iter(arg.begin());
std::string s;
std::vector<std::string>::iterator iter(arg.begin());
while (iter != arg.end()) {
if (!iter->compare("fit")) { // fit found
if (temp) { // temp already found previously
@@ -353,8 +350,8 @@ int msr2data_doFitting(vector<string> &arg, bool &chainfit)
return -2; // fatal error - another fit option is specified
}
s = iter->substr(4);
string::size_type loc = s.rfind('!');
if (loc != string::npos) {
std::string::size_type loc = s.rfind('!');
if (loc != std::string::npos) {
chainfit = false;
s.erase(loc);
}
@@ -386,12 +383,12 @@ int msr2data_doFitting(vector<string> &arg, bool &chainfit)
* \param arg list of arguments
* \param inputOnly flag, if true create msr-files only (no fitting)
*/
int msr2data_doInputCreation(vector<string> &arg, bool &inputOnly)
int msr2data_doInputCreation(std::vector<std::string> &arg, bool &inputOnly)
{
int temp(0);
string s;
for (vector<string>::iterator iter(arg.begin()); iter != arg.end(); ++iter) {
std::string s;
for (std::vector<std::string>::iterator iter(arg.begin()); iter != arg.end(); ++iter) {
if (!iter->substr(0,4).compare("msr-")) {
s = iter->substr(4);
try {
@@ -414,7 +411,7 @@ int msr2data_doInputCreation(vector<string> &arg, bool &inputOnly)
* <p>
*
*/
int msr2data_paramList(vector<string> &arg, vector<unsigned int> &paramList)
int msr2data_paramList(std::vector<std::string> &arg, std::vector<unsigned int> &paramList)
{
paramList.clear(); // make sure paramList is empty
@@ -433,24 +430,24 @@ int msr2data_paramList(vector<string> &arg, vector<unsigned int> &paramList)
// make sure there are parameter list elements to follow
if (idx == arg.size()) {
cerr << endl << "**ERROR** found paramList without any arguments!" << endl;
std::cerr << std::endl << "**ERROR** found paramList without any arguments!" << std::endl;
msr2data_syntax();
return -1;
}
// paramList tag present and further elements present: collect them
vector<string> str;
std::vector<std::string> str;
unsigned int idx_end=0;
size_t pos=string::npos;
size_t pos=std::string::npos;
for (unsigned int i=idx; i<arg.size(); i++) {
pos = arg[i].find("-");
if (pos == 0) { // likely something like -o, -k, etc.
idx_end = i;
break;
} else if (pos != string::npos) { // looks like a parameter list like n0-n1
} else if (pos != std::string::npos) { // looks like a parameter list like n0-n1
boost::split(str, arg[i], boost::is_any_of("-"));
if (str.size() != 2) { // something is wrong, since the structure n0-n1 is expected
cerr << endl << "**ERROR** found token " << arg[i] << " in paramList command which cannot be handled." << endl;
std::cerr << std::endl << "**ERROR** found token " << arg[i] << " in paramList command which cannot be handled." << std::endl;
msr2data_syntax();
return -1;
}
@@ -459,7 +456,7 @@ int msr2data_paramList(vector<string> &arg, vector<unsigned int> &paramList)
break;
}
if (!isNumber(str[0]) || !isNumber(str[1])) {
cerr << endl << "**ERROR** found token " << arg[i] << " in paramList command which cannot be handled." << endl;
std::cerr << std::endl << "**ERROR** found token " << arg[i] << " in paramList command which cannot be handled." << std::endl;
msr2data_syntax();
return -1;
}
@@ -484,7 +481,7 @@ int msr2data_paramList(vector<string> &arg, vector<unsigned int> &paramList)
for (unsigned int i=0; i<paramList.size(); i++) {
for (unsigned int j=i+1; j<paramList.size(); j++) {
if (paramList[i] == paramList[j]) {
cerr << endl << "**ERROR** the parameter list numbers have to be unique. Found " << paramList[i] << " at least 2 times." << endl;
std::cerr << std::endl << "**ERROR** the parameter list numbers have to be unique. Found " << paramList[i] << " at least 2 times." << std::endl;
msr2data_syntax();
return -1;
}
@@ -501,7 +498,7 @@ int msr2data_paramList(vector<string> &arg, vector<unsigned int> &paramList)
* \htmlonly <a href="http://lmu.web.psi.ch/musrfit/user/html/msr2data.html#msr2data">musr2data online help</a>
* \endhtmlonly
* \latexonly msr2data online help: \texttt{http://lmu.web.psi.ch/musrfit/user/html/msr2data.html#msr2data}
* \endlatexonly
* \std::endlatexonly
*
* \param argc number of arguments
* \param argv list of arguments
@@ -515,9 +512,9 @@ int main(int argc, char *argv[])
return 0;
} else if (!strcmp(argv[1], "--version")) {
#ifdef HAVE_CONFIG_H
cout << endl << "msr2data version: " << PACKAGE_VERSION << ", git-branch: " << GIT_BRANCH << ", git-rev: " << GIT_CURRENT_SHA1 << endl << endl;
std::cout << std::endl << "msr2data version: " << PACKAGE_VERSION << ", git-branch: " << GIT_BRANCH << ", git-rev: " << GIT_CURRENT_SHA1 << std::endl << std::endl;
#else
cout << endl << "msr2data git-branch: " << GIT_BRANCH << ", git-rev: " << GIT_CURRENT_SHA1 << endl << endl;
std::cout << std::endl << "msr2data git-branch: " << GIT_BRANCH << ", git-rev: " << GIT_CURRENT_SHA1 << std::endl << std::endl;
#endif
return 0;
} else {
@@ -533,23 +530,23 @@ int main(int argc, char *argv[])
}
// use a string-vector for the arguments to get rid of char* as far as possible...
vector<string> arg;
std::vector<std::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;
vector<unsigned int> param_vec;
std::vector<unsigned int> run_vec;
std::string run_list;
std::string msrExtension;
std::vector<unsigned int> param_vec;
try {
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(numeric_limits<unsigned int>::max());
unsigned int rightbracket(std::numeric_limits<unsigned int>::max());
if (!arg[0].compare("["))
firstRunNumberInArg = 1;
@@ -557,8 +554,8 @@ int main(int argc, char *argv[])
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 ) {
std::string::size_type loc = arg[i].rfind(']');
if ( loc != std::string::npos ) {
rightbracket = i;
if (!arg[i].compare("]") && i > 0)
lastRunNumberInArg = i-1;
@@ -569,9 +566,9 @@ int main(int argc, char *argv[])
break;
}
}
if (rightbracket == numeric_limits<unsigned int>::max()) {
cerr << endl;
cerr << ">> msr2data: **ERROR** You used the list specification without closing bracket (])! Quitting now." << endl;
if (rightbracket == std::numeric_limits<unsigned int>::max()) {
std::cerr << std::endl;
std::cerr << ">> msr2data: **ERROR** You used the list specification without closing bracket (])! Quitting now." << std::endl;
return 0;
}
@@ -582,14 +579,14 @@ int main(int argc, char *argv[])
// parse run_list string
PStringNumberList *nl = new PStringNumberList(run_list);
if (nl == 0) { // couldn't invoke object
cerr << endl;
cerr << ">> msr2data: **ERROR** Couldn't invoke run_list parser object! Quitting now." << endl;
std::cerr << std::endl;
std::cerr << ">> msr2data: **ERROR** Couldn't invoke run_list parser object! Quitting now." << std::endl;
return 0;
}
string errorMsg("");
std::string errorMsg("");
if (!nl->Parse(errorMsg)) {
cerr << endl;
cerr << ">> msr2data: " << errorMsg << " - Quitting now." << endl;
std::cerr << std::endl;
std::cerr << ">> msr2data: " << errorMsg << " - Quitting now." << std::endl;
return 0;
}
// get run list vector
@@ -598,7 +595,7 @@ int main(int argc, char *argv[])
msrExtension = arg[rightbracket + 1];
vector<string>::iterator iter(arg.begin());
std::vector<std::string>::iterator iter(arg.begin());
for (unsigned int i(0); i<rightbracket + 2; ++i) {
arg.erase(iter);
iter = arg.begin();
@@ -611,8 +608,8 @@ int main(int argc, char *argv[])
runTAG = 2;
if (arg.size() < 3) {
cerr << endl;
cerr << ">> msr2data: **ERROR** No msr-file extension specified! Quitting now..." << endl;
std::cerr << std::endl;
std::cerr << ">> msr2data: **ERROR** No msr-file extension specified! Quitting now..." << std::endl;
run_vec.clear();
arg.clear();
return 0;
@@ -623,7 +620,7 @@ int main(int argc, char *argv[])
msrExtension = arg[2];
vector<string>::iterator iter(arg.begin());
std::vector<std::string>::iterator iter(arg.begin());
for (unsigned int i(0); i < 3; i++) {
arg.erase(iter);
iter = arg.begin();
@@ -633,7 +630,7 @@ int main(int argc, char *argv[])
run_vec.push_back(boost::lexical_cast<unsigned int>(arg[0]));
msrExtension = arg[1];
vector<string>::iterator iter(arg.begin());
std::vector<std::string>::iterator iter(arg.begin());
for (unsigned int i(0); i < 2; i++) {
arg.erase(iter);
iter = arg.begin();
@@ -643,7 +640,7 @@ int main(int argc, char *argv[])
run_list = arg[0];
msrExtension = arg[1];
vector<string>::iterator iter(arg.begin());
std::vector<std::string>::iterator iter(arg.begin());
for (unsigned int i(0); i < 2; i++) {
arg.erase(iter);
iter = arg.begin();
@@ -652,8 +649,8 @@ int main(int argc, char *argv[])
}
}
catch(boost::bad_lexical_cast &) {
cerr << endl;
cerr << ">> msr2data: **ERROR** At least one given run number is out of range! Quitting..." << endl;
std::cerr << std::endl;
std::cerr << ">> msr2data: **ERROR** At least one given run number is out of range! Quitting..." << std::endl;
run_vec.clear();
arg.clear();
return -1;
@@ -667,10 +664,10 @@ int main(int argc, char *argv[])
}
// check the validity of the command line given command line arguments
string wrongArgument(msr2data_validArguments(arg));
std::string wrongArgument(msr2data_validArguments(arg));
if (!wrongArgument.empty()) {
cerr << endl;
cerr << ">> msr2data: **ERROR** Unknown argument: " << wrongArgument << ". Quitting..." << endl;
std::cerr << std::endl;
std::cerr << ">> msr2data: **ERROR** Unknown argument: " << wrongArgument << ". Quitting..." << std::endl;
run_vec.clear();
arg.clear();
return -1;
@@ -680,11 +677,11 @@ int main(int argc, char *argv[])
bool db(msr2data_useOption(arg, "data"));
// check the arguments for the "-o" option and set the output filename
string outputFile(msr2data_outputfile(arg, db));
std::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"))
if (!boost::algorithm::to_lower_copy(outputFile).compare("none"))
realOutput = false;
// create the msr2data-object and set the run numbers according to the runTAG above
@@ -706,15 +703,15 @@ int main(int argc, char *argv[])
status = msr2dataHandler->SetRunNumbers(run_list);
break;
default:
cerr << endl;
cerr << ">> msr2data: **ERROR** None of the possible run list specifications has been detected! Quitting now..." << endl;
std::cerr << std::endl;
std::cerr << ">> msr2data: **ERROR** None of the possible run list specifications has been detected! Quitting now..." << std::endl;
msr2data_cleanup(msr2dataHandler, run_vec, arg);
return 0;
}
if (status == 1) {
cerr << endl;
cerr << ">> msr2data: **ERROR** The run numbers are out of range! Quitting..." << endl;
std::cerr << std::endl;
std::cerr << ">> msr2data: **ERROR** The run numbers are out of range! Quitting..." << std::endl;
msr2data_cleanup(msr2dataHandler, run_vec, arg);
return status;
} else if (status == -1) {
@@ -727,18 +724,18 @@ int main(int argc, char *argv[])
// check if fitting should be done and in case, which template run number to use
int temp(0);
bool chainfit(true), onlyInputCreation(false);
string musrfitOptions;
std::string musrfitOptions;
temp = msr2data_doFitting(arg, chainfit);
if (temp == -2) {
cerr << endl;
cerr << ">> msr2data: **ERROR** More than one fitting options are specified! Quitting..." << endl;
std::cerr << std::endl;
std::cerr << ">> msr2data: **ERROR** More than one fitting options are specified! Quitting..." << std::endl;
msr2data_cleanup(msr2dataHandler, arg);
return temp;
} else if (temp == -3) {
cerr << endl;
cerr << ">> msr2data: **ERROR** The given template has not a valid run number! Quitting..." << endl;
std::cerr << std::endl;
std::cerr << ">> msr2data: **ERROR** The given template has not a valid run number! Quitting..." << std::endl;
msr2data_cleanup(msr2dataHandler, arg);
return temp;
}
@@ -765,8 +762,8 @@ int main(int argc, char *argv[])
outputFile = "none";
}
if (temp == -3) {
cerr << endl;
cerr << ">> msr2data: **ERROR** The given template has not a valid run number! Quitting..." << endl;
std::cerr << std::endl;
std::cerr << ">> msr2data: **ERROR** The given template has not a valid run number! Quitting..." << std::endl;
msr2data_cleanup(msr2dataHandler, arg);
return temp;
}
@@ -800,8 +797,8 @@ int main(int argc, char *argv[])
// Check if all given run numbers are covered by the formatting of the data file name
status = msr2dataHandler->CheckRunNumbersInRange();
if(status) {
cerr << endl;
cerr << ">> msr2data: **ERROR** At least one given run number is out of range! Quitting..." << endl;
std::cerr << std::endl;
std::cerr << ">> msr2data: **ERROR** At least one given run number is out of range! Quitting..." << std::endl;
msr2data_cleanup(msr2dataHandler, arg);
return status;
}
@@ -812,7 +809,7 @@ int main(int argc, char *argv[])
// 1 - write header explicitly (even if the file is present already)
// 2 - write header automatically if a new file is created and do not if the data is appended to an existing file
fstream *fileOutput = 0;
std::fstream *fileOutput = nullptr;
if (realOutput) {
// check the arguments for the "header" and "noheader" options
if (!msr2data_useOption(arg, "header")) {
@@ -830,15 +827,15 @@ int main(int argc, char *argv[])
// delete old db/data file if the "new" option is given
if (!msr2data_useOption(arg, "new")) {
fileOutput = new fstream;
fileOutput->open(outputFile.c_str(), ios::in);
fileOutput = new std::fstream;
fileOutput->open(outputFile.c_str(), std::ios::in);
if (fileOutput->is_open()) {
cout << endl << ">> msr2data: **INFO** Deleting output file " << outputFile << endl;
std::cout << std::endl << ">> msr2data: **INFO** Deleting output file " << outputFile << std::endl;
fileOutput->close();
fileOutput->open(outputFile.c_str(), ios::out | ios::trunc);
fileOutput->open(outputFile.c_str(), std::ios::out | std::ios::trunc);
fileOutput->close();
} else {
cout << endl << ">> msr2data: **INFO** Ignoring the 'new' option since " << outputFile << " does not exist yet." << endl;
std::cout << std::endl << ">> msr2data: **INFO** Ignoring the 'new' option since " << outputFile << " does not exist yet." << std::endl;
}
delete fileOutput;
fileOutput = 0;
@@ -850,7 +847,7 @@ int main(int argc, char *argv[])
// GLOBAL MODE
if (!setNormalMode) {
ostringstream strInfile;
std::ostringstream strInfile;
strInfile << msr2dataHandler->GetPresentRun() << "+global" << msrExtension << ".msr";
// if fitting should be done, prepare a new input file
@@ -859,7 +856,7 @@ int main(int argc, char *argv[])
bool success(msr2dataHandler->PrepareGlobalInputFile(temp, strInfile.str(), globalMode));
if (!success) {
cerr << endl << ">> msr2data: **ERROR** Input file generation has not been successful! Quitting..." << endl;
std::cerr << std::endl << ">> msr2data: **ERROR** Input file generation has not been successful! Quitting..." << std::endl;
msr2data_cleanup(msr2dataHandler, arg);
return -1;
}
@@ -868,23 +865,23 @@ int main(int argc, char *argv[])
// and do the fitting
if (!onlyInputCreation) {
// check if MUSRFITPATH is set, if not issue a warning
string path("");
std::string path("");
bool pathSet(false);
char *pathPtr(getenv("MUSRFITPATH"));
if (pathPtr) {
path = boost::lexical_cast<string>(pathPtr);
path = boost::lexical_cast<std::string>(pathPtr);
if (!path.empty()) {
pathSet = true;
path.append("/");
}
}
if (!pathSet) {
cerr << endl << ">> msr2data: **WARNING** The MUSRFITPATH environment variable is not set!";
cerr << endl << ">> msr2data: **WARNING** Please set it or at least ensure that musrfit can be found on the PATH!" << endl;
std::cerr << std::endl << ">> msr2data: **WARNING** The MUSRFITPATH environment variable is not set!";
std::cerr << std::endl << ">> msr2data: **WARNING** Please set it or at least ensure that musrfit can be found on the PATH!" << std::endl;
}
ostringstream oss;
std::ostringstream oss;
oss << path << "musrfit" << " " << strInfile.str() << " " << musrfitOptions;
cout << endl << ">> msr2data: **INFO** Calling " << oss.str() << endl;
std::cout << std::endl << ">> msr2data: **INFO** Calling " << oss.str() << std::endl;
system(oss.str().c_str());
}
}
@@ -928,7 +925,7 @@ int main(int argc, char *argv[])
// Processing the run list, do the fitting and write the data to the DB or data output file
bool firstrun(true);
unsigned int oldtemp(0); // should be accessed only when updated before...
ostringstream strInfile;
std::ostringstream strInfile;
while (msr2dataHandler->GetPresentRun()) {
strInfile.clear();
@@ -948,7 +945,7 @@ int main(int argc, char *argv[])
oldtemp = msr2dataHandler->GetPresentRun();
if (!success) {
cerr << endl << ">> msr2data: **ERROR** Input file generation has not been successful! Quitting..." << endl;
std::cerr << std::endl << ">> msr2data: **ERROR** Input file generation has not been successful! Quitting..." << std::endl;
msr2data_cleanup(msr2dataHandler, arg);
return -1;
}
@@ -957,23 +954,23 @@ int main(int argc, char *argv[])
// and do the fitting
if (!onlyInputCreation) {
// check if MUSRFITPATH is set, if not issue a warning
string path("");
std::string path("");
bool pathSet(false);
char *pathPtr(getenv("MUSRFITPATH"));
if (pathPtr) {
path = boost::lexical_cast<string>(pathPtr);
path = boost::lexical_cast<std::string>(pathPtr);
if (!path.empty()) {
pathSet = true;
path.append("/");
}
}
if (!pathSet) {
cerr << endl << ">> msr2data: **WARNING** The MUSRFITPATH environment variable is not set!";
cerr << endl << ">> msr2data: **WARNING** Please set it or at least ensure that musrfit can be found on the PATH!" << endl;
std::cerr << std::endl << ">> msr2data: **WARNING** The MUSRFITPATH environment variable is not set!";
std::cerr << std::endl << ">> msr2data: **WARNING** Please set it or at least ensure that musrfit can be found on the PATH!" << std::endl;
}
ostringstream oss;
std::ostringstream oss;
oss << path << "musrfit" << " " << strInfile.str() << " " << musrfitOptions;
cout << endl << ">> msr2data: **INFO** Calling " << oss.str() << endl;
std::cout << std::endl << ">> msr2data: **INFO** Calling " << oss.str() << std::endl;
system(oss.str().c_str());
}
}
@@ -1012,37 +1009,37 @@ int main(int argc, char *argv[])
// Unfortunately, there are also problems with boost::filesystem::exists(outputFile)
// Therefore, first try to open the file for reading and if this works, write to it - not clean but it works
if (realOutput) {
fileOutput = new fstream;
fileOutput->open(outputFile.c_str(), ios::in);
fileOutput = new std::fstream;
fileOutput->open(outputFile.c_str(), std::ios::in);
if (fileOutput->is_open()) {
fileOutput->close();
fileOutput->open(outputFile.c_str(), ios::out | ios::app);
fileOutput->open(outputFile.c_str(), std::ios::out | std::ios::app);
if (fileOutput->is_open()) {
*fileOutput << endl << endl;
*fileOutput << std::endl << std::endl;
fileOutput->close();
} else {
cerr << endl << ">> msr2data: **ERROR** The output file " << outputFile << " cannot be opened! Please check!";
cerr << endl;
std::cerr << std::endl << ">> msr2data: **ERROR** The output file " << outputFile << " cannot be opened! Please check!";
std::cerr << std::endl;
}
} else {
cerr << endl << ">> msr2data: **WARNING** No output has been written to the file " << outputFile << "!";
cerr << endl << ">> msr2data: **WARNING** Please check the range of runs and the specified options!" << endl;
std::cerr << std::endl << ">> msr2data: **WARNING** No output has been written to the file " << outputFile << "!";
std::cerr << std::endl << ">> msr2data: **WARNING** Please check the range of runs and the specified options!" << std::endl;
}
delete fileOutput;
fileOutput = 0;
}
if (!arg.empty()) {
cout << endl << ">> msr2data: **INFO** The following command line arguments have been specified but not been used: " << endl;
cout << ">> msr2data: **INFO**";
std::cout << std::endl << ">> msr2data: **INFO** The following command line arguments have been specified but not been used: " << std::endl;
std::cout << ">> msr2data: **INFO**";
for (unsigned int i(0); i<arg.size(); ++i)
cout << " " << arg[i];
cout << endl;
std::cout << " " << arg[i];
std::cout << std::endl;
}
msr2data_cleanup(msr2dataHandler, arg);
cout << endl << ">> msr2data: done ..." << endl;
std::cout << std::endl << ">> msr2data: done ..." << std::endl;
return 1;
}