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musrfit/src/any2many.cpp

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/***************************************************************************
any2many.cpp
Author: Andreas Suter
e-mail: andreas.suter@psi.ch
***************************************************************************/
/***************************************************************************
* Copyright (C) 2007-2021 by 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. *
***************************************************************************/
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include <iostream>
#include <fstream>
#include <TString.h>
#include <TSAXParser.h>
#include "git-revision.h"
#include "PMusr.h"
#include "PStartupHandler.h"
#include "PRunDataHandler.h"
//--------------------------------------------------------------------------
/**
* <p>Sends the usage description to the standard output.
*/
void any2many_syntax()
{
std::cout << std::endl << "usage: any2many [--help] : will show this help.";
std::cout << std::endl << " any2many --version : will show the git version.";
std::cout << std::endl << " any2many -f <filenameList-input> | -r <runList-input>";
std::cout << std::endl << " -c <convert-options> [-p <output-path>] [-y <year>]";
std::cout << std::endl << " [-o <outputFileName> | -t <in-template> <out-template>] [-s]";
std::cout << std::endl << " [-rebin <n>] [-z <compressed>]";
std::cout << std::endl << " -f <filenameList-input> : where <filenameList-input> is space";
std::cout << std::endl << " separeted a list of file names (not starting with a '-'),";
std::cout << std::endl << " e.g. 2010/lem10_his_0111.root 2010/lem10_his_0112.root";
std::cout << std::endl << " -o <outputFileName> : this option only makes sense, if <filenameList-input>";
std::cout << std::endl << " is a single input file name!";
std::cout << std::endl << " -r <runList-input> : where <runList-input> is a list of run numbers";
std::cout << std::endl << " separated by spaces ' ' of the form: <run1> <run2> <run3>";
std::cout << std::endl << " etc., or a sequence of runs <runStart>-<runEnd>, e.g. 111-222";
std::cout << std::endl << " -t <in-template> <out-template> : ";
std::cout << std::endl << " <in-/out-template> : template file name. Needed for run-lists in";
std::cout << std::endl << " order to generate the proper file names. The following template";
std::cout << std::endl << " tags can be used: [yy] for year, and [rrrr] for the run number.";
std::cout << std::endl << " If the run number tag is used, the number of 'r' will give the";
std::cout << std::endl << " number of digits used with leading zeros, e.g. [rrrrrr] and run";
std::cout << std::endl << " number 123 will result in 000123. The same is true for the";
std::cout << std::endl << " year, i.e. [yyyy] will result in something like 1999.";
std::cout << std::endl << " -c <convert-options> : <inFormat> <outFormat>";
std::cout << std::endl << " <inFormat> : input data file format. Supported formats are:";
std::cout << std::endl << " MusrRoot, PSI-BIN, ROOT (LEM), MUD, NeXus, PSI-MDU, WKM";
std::cout << std::endl << " <outFormat> : ouput data file format. Supported formats are:";
std::cout << std::endl << " PSI-BIN, MusrRoot, ROOT, MUD, NeXus1-HDF4, NeXus1-HDF5, NeXus1-XML,";
std::cout << std::endl << " NeXus2-HDF4, NeXus2-HDF5, NeXus2-XML, WKM, ASCII";
std::cout << std::endl << " Comment: ROOT is superseeded by MusrRoot. If there is not a very good";
std::cout << std::endl << " reason, avoid it!";
std::cout << std::endl << " -h <histo-group-list> : This option is for MusrRoot input files only!";
std::cout << std::endl << " Select the the histo groups to be exported. <histo-group-list> is a space";
std::cout << std::endl << " separated list of the histo group, e.g. -h 0, 20 will try to export the histo";
std::cout << std::endl << " 0 (NPP) and 20 (PPC).";
std::cout << std::endl << " -p <output-path> : where <output-path> is the output path for the";
std::cout << std::endl << " converted files. If nothing is given, the current directory";
std::cout << std::endl << " will be used, unless the option '-s' is used.";
std::cout << std::endl << " -y <year> : if the option -y is used, here a year in the form 'yy' or 'yyyy' can";
std::cout << std::endl << " be given, if this is the case, any automatic file name";
std::cout << std::endl << " generation needs a year, this number will be used.";
std::cout << std::endl << " -s : with this option the output data file will be sent to the stdout.";
std::cout << std::endl << " -rebin <n> : where <n> is the number of bins to be packed";
std::cout << std::endl << " -z [g|b] <compressed> : where <compressed> is the output file name";
std::cout << std::endl << " (without extension) of the compressed data collection, and";
std::cout << std::endl << " 'g' will result in .tar.gz, and 'b' in .tar.bz2 files.";
std::cout << std::endl;
std::cout << std::endl << " If the template option '-t' is absent, the output file name will be";
std::cout << std::endl << " generated according to the input data file name, and the output data";
std::cout << std::endl << " format.";
std::cout << std::endl;
std::cout << std::endl << "examples:" << std::endl;
std::cout << std::endl << " any2many -f 2010/lem10_his_0123.root -c ROOT ASCII -rebin 25";
std::cout << std::endl << " Will take the LEM ROOT file '2010/lem10_his_0123.root' rebin it with 25";
std::cout << std::endl << " and convert it to ASCII. The output file name will be";
std::cout << std::endl << " lem10_his_0123.ascii, and the file will be saved in the current directory." << std::endl;
std::cout << std::endl << " any2many -f 2010/lem10_his_0123.root -c MusrRoot NEXUS2-HDF5 -o 2010/lem10_his_0123_v2.nxs";
std::cout << std::endl << " Will take the MusrRoot file '2010/lem10_his_0123.root' ";
std::cout << std::endl << " and convert it to NeXus IDF V2. The output file name will be";
std::cout << std::endl << " lem10_his_0123_v2.nxs, and the file will be saved in the current directory." << std::endl;
std::cout << std::endl << " any2many -r 123 137 -c PSI-BIN MUD -t d[yyyy]/deltat_tdc_gps_[rrrr].bin \\";
std::cout << std::endl << " [rrrrrr].msr -y 2001";
std::cout << std::endl << " Will take the run 123 and 137, will generate the input file names:";
std::cout << std::endl << " d2001/deltat_tdc_gps_0123.bin and d2001/deltat_tdc_gps_0137.bin, and";
std::cout << std::endl << " output file names 000123.msr and 000137.msr" << std::endl;
std::cout << std::endl << " any2many -r 100-117 -c PSI-MDU ASCII -t d[yyyy]/deltat_tdc_alc_[rrrr].mdu \\";
std::cout << std::endl << " [rrr].ascii -y 2011 -s";
std::cout << std::endl << " Will take the runs 100 through 117 and convert the PSI-MDU input files to";
std::cout << std::endl << " ASCII output and instead of saving them into a file, they will be spit to";
std::cout << std::endl << " the standard output." << std::endl;
std::cout << std::endl << " any2many -r 100-117 -c NEXUS MusrRoot -t d[yyyy]/psi_gps_[rrrr].NXS \\";
std::cout << std::endl << " psi_[yyyy]_gps_[rrrr].root -z b psi_gps_run_100to117";
std::cout << std::endl << " Will take the runs 100 through 117 and convert the NEXUS input files";
std::cout << std::endl << " to MusrRoot output. Afterwards these new files will be collected in a";
std::cout << std::endl << " compressed archive psi_gps_run_100to117.tar.bz2." << std::endl;
std::cout << std::endl << " any2many -f 2010/lem10_his_0123.root 2010/lem10_his_0012.root -c MusrRoot MusrRoot -rebin 25";
std::cout << std::endl << " Will read the two files '2010/lem10_his_0123.root' and '2010/lem10_his_0012.root',";
std::cout << std::endl << " rebin them with 25 and export them as LEM ROOT files with adding rebin25 to the";
std::cout << std::endl << " name, e.g. 2010/lem10_his_0123_rebin25.root";
std::cout << std::endl << std::endl;
}
//--------------------------------------------------------------------------
/**
* <p>any2many is used to convert any musr-data-file format in any other including ascii.
*
* <b>return:</b>
* - PMUSR_SUCCESS if everthing went smooth
* - PMUSR_WRONG_STARTUP_SYNTAX if syntax error is encountered
*
* \param argc number of input arguments
* \param argv list of input arguments
*/
int main(int argc, char *argv[])
{
bool show_syntax = false;
int status;
PAny2ManyInfo info;
PStringVector inputFormat;
PStringVector outputFormat;
TString outputFileName = TString("");
// init inputFormat
inputFormat.push_back("musrroot");
inputFormat.push_back("psi-bin");
inputFormat.push_back("root");
inputFormat.push_back("mud");
inputFormat.push_back("nexus");
inputFormat.push_back("psi-mdu");
inputFormat.push_back("wkm");
// init outputFormat
outputFormat.push_back("psi-bin");
outputFormat.push_back("musrroot");
outputFormat.push_back("root");
outputFormat.push_back("mud");
outputFormat.push_back("nexus1-hdf4");
outputFormat.push_back("nexus1-hdf5");
outputFormat.push_back("nexus1-xml");
outputFormat.push_back("nexus2-hdf4");
outputFormat.push_back("nexus2-hdf5");
outputFormat.push_back("nexus2-xml");
outputFormat.push_back("wkm");
outputFormat.push_back("ascii");
// init info structure
info.useStandardOutput = false;
info.rebin = 1;
info.compressionTag = 0; // no compression as default
info.idf = 0; // undefined
info.inTemplate = TString("");
info.outTemplate = TString("");
info.outFileName = TString("");
// call any2many without arguments
if (argc == 1) {
any2many_syntax();
return PMUSR_SUCCESS;
}
// call any2many --help or any2many --version
if (argc == 2) {
if (!strncmp(argv[1], "--help", 128))
any2many_syntax();
else if (strstr(argv[1], "--v")) {
#ifdef HAVE_CONFIG_H
std::cout << std::endl << "any2many version: " << PACKAGE_VERSION << ", git-branch: " << GIT_BRANCH << ", git-rev: " << GIT_CURRENT_SHA1 << " (" << BUILD_TYPE << "), ROOT version: " << ROOT_VERSION_USED << std::endl << std::endl;
#else
std::cout << std::endl << "any2many git-branch: " << GIT_BRANCH << ", git-rev: " << GIT_CURRENT_SHA1 << std::endl << std::endl;
#endif
} else {
any2many_syntax();
return PMUSR_WRONG_STARTUP_SYNTAX;
}
return PMUSR_SUCCESS;
}
info.outPath = TString("./");
// handle the other command options
Int_t ival;
for (int i=1; i<argc; i++) {
if (!strcmp(argv[i], "-y")) { // handle year option
if (i+1 < argc) {
// check that date if it is either of the form 'yy' or 'yyyy'
if ((strlen(argv[i+1]) != 2) && (strlen(argv[i+1]) != 4)) {
std::cerr << std::endl << ">> any2many **ERROR** found in option '-y' the argument '" << argv[i+1] << "' which is neither of the form 'yy' nor 'yyyy'." << std::endl;
show_syntax = true;
break;
}
ival=0;
status = sscanf(argv[i+1], "%d", &ival);
if (status == 1) {
info.year = argv[i+1];
i++;
} else {
std::cerr << std::endl << ">> any2many **ERROR** found in option '-y' the argument '" << argv[i+1] << "' which is not a number." << std::endl;
show_syntax = true;
break;
}
} else {
show_syntax = true;
break;
}
} else if (!strcmp(argv[i], "-s")) { // handle standard output option '-s'
info.useStandardOutput = true;
} else if (!strcmp(argv[i], "-f")) { // set input option tag
if (i+1 < argc) {
bool done = false;
int j = i+1;
do {
if (argv[j][0] == '-') { // assuming the next option is found
done = true;
} else {
info.inFileName.push_back(argv[j]);
j++; // shift input to the proper place
}
} while (!done && (j<argc));
i = j-1;
if (j >= argc) // make sure that counter is still in range
break;
} else {
std::cerr << std::endl << ">> any2many **ERROR** found input option '-f' without any arguments" << std::endl;
show_syntax = true;
break;
}
} else if (!strcmp(argv[i], "-o")) { // handle output file name option '-o'
if (i+1 < argc) {
outputFileName = argv[i+1];
i++;
} else {
std::cerr << std::endl << ">> any2many **ERROR** found output file name option '-o' without any arguments" << std::endl;
show_syntax = true;
break;
}
} else if (!strcmp(argv[i], "-r")) {
if (i+1 < argc) {
// first check for run list sequence of the form <runStartNo>-<runEndNo>
int startNo, endNo;
status = sscanf(argv[i+1], "%d-%d", &startNo, &endNo);
if (status == 2) { // this is run list sequence
if (endNo < startNo) {
ival = startNo;
startNo = endNo;
endNo = ival;
}
for (int j=startNo; j<=endNo; j++)
info.runList.push_back(j);
i++;
} else { // check for run list of the form <run1> <run2> ... <runN>
bool done = false;
int j = i+1;
do {
status = sscanf(argv[j], "%d", &ival);
if (status == 1) {
info.runList.push_back(ival);
j++;
} else {
done = true;
}
} while (!done && (j<argc));
i = j-1;
if (j >= argc) // make sure that counter is still in range
break;
}
} else {
std::cerr << std::endl << ">> any2many **ERROR** found input option '-r' without any arguments" << std::endl;
show_syntax = true;
break;
}
// check if any valid input option was found
if (info.runList.size() == 0) {
std::cerr << std::endl << ">> any2many **ERROR** found input option '-r' without any valid arguments" << std::endl;
show_syntax = true;
break;
}
} else if (!strcmp(argv[i], "-c")) { // set convert option tag
bool found = false;
std::string sval;
if (i+2 < argc) {
sval = argv[i+1];
found = false;
for (unsigned int j=0; j<inputFormat.size(); j++) {
if (!inputFormat[j].CompareTo(sval, TString::kIgnoreCase)) {
info.inFormat = sval;
found = true;
break;
}
}
if (!found) {
std::cerr << std::endl << ">> any2many **ERROR** found unkown input data file format option '" << sval << "'" << std::endl;
show_syntax = true;
break;
}
sval = argv[i+2];
found = false;
for (unsigned int j=0; j<outputFormat.size(); j++) {
if (!outputFormat[j].CompareTo(sval, TString::kIgnoreCase)) {
info.outFormat = sval;
found = true;
break;
}
}
if (!found) {
std::cerr << std::endl << ">> any2many **ERROR** found unkown output data file format option '" << sval << "'" << std::endl;
show_syntax = true;
break;
}
i += 2; // shift argument position
} else {
std::cerr << std::endl << ">> any2many **ERROR** found option '-c' with missing arguments" << std::endl;
show_syntax = true;
break;
}
} else if (!strcmp(argv[i], "-h")) { // filter histo group list (for MusrRoot and ROOT (LEM) only!)
bool done = false;
int j = i+1;
do {
status = sscanf(argv[j], "%d", &ival);
if (status == 1) {
info.groupHistoList.push_back(ival);
j++;
} else {
done = true;
}
} while (!done && (j<argc));
i = j-1;
if (j >= argc) // make sure that counter is still in range
break;
} else if (!strcmp(argv[i], "-p")) { // filter output path name flag
if (i+1 < argc) {
info.outPath = argv[i+1];
if (!info.outPath.EndsWith("/"))
info.outPath += "/";
i++;
} else {
std::cerr << std::endl << ">> any2many **ERROR** found output option '-p' without any argument." << std::endl;
show_syntax = true;
break;
}
} else if (!strcmp(argv[i], "-rebin")) { // filter out rebinning option
if (i+1 < argc) {
status = sscanf(argv[i+1], "%d", &ival);
if (status == 1) {
info.rebin = ival;
i++;
} else {
std::cerr << std::endl << ">> any2many **ERROR** found in option '-rebin " << argv[i+1] << "' which doesn't make any sense." << std::endl;
show_syntax = true;
break;
}
} else {
std::cerr << std::endl << ">> any2many **ERROR** found output option '-rebin' without any argument." << std::endl;
show_syntax = true;
break;
}
} else if (!strcmp(argv[i], "-t")) { // filter out the input/output file template
if (i+2 < argc) {
if ((argv[i+1][0] == '-') || (argv[i+2][0] == '-')) {
std::cerr << std::endl << ">> any2many **ERROR** found invalid template in option '-t'" << std::endl;
show_syntax = true;
break;
}
info.inTemplate = argv[i+1];
info.outTemplate = argv[i+2];
i += 2; // shift argument position
} else {
std::cerr << std::endl << ">> any2many **ERROR** found option '-t' with missing arguments" << std::endl;
show_syntax = true;
break;
}
} else if (!strcmp(argv[i], "-z")) { // filter out if compression is whished
if (i+2 < argc) {
if ((argv[i+1][0] == '-') || (argv[i+2][0] == '-')) {
std::cerr << std::endl << ">> any2many **ERROR** found invalid template in option '-t'" << std::endl;
show_syntax = true;
break;
}
if (argv[i+1][0] == 'g') {
info.compressionTag = 1;
} else if (argv[i+1][0] == 'b') {
info.compressionTag = 2;
} else {
std::cerr << std::endl << ">> any2many **ERROR** found in option '-z' compression tag '" << argv[i+1] << "' which is not supported." << std::endl;
show_syntax = true;
break;
}
info.compressFileName = argv[i+2];
i += 2; // shift argument position
} else {
std::cerr << std::endl << ">> any2many **ERROR** found option '-z' with missing arguments" << std::endl;
show_syntax = true;
break;
}
} else { // unrecognized command
std::cerr << std::endl << ">> any2many **ERROR** found unrecognized option " << argv[i] << std::endl;
show_syntax = true;
break;
}
}
// make sure that either a filenameList or a runList has been provided
if ((info.inFileName.size()==0) && (info.runList.size()==0)) {
std::cerr << std::endl << ">> any2many **ERROR** neither a input filename list, nor a run list was given." << std::endl;
show_syntax = true;
}
// make sure that in/out formats are given
if ((info.inFormat.Length() == 0) || (info.outFormat.Length() == 0)) {
std::cerr << std::endl << ">> any2many **ERROR** conversion information is missing." << std::endl;
show_syntax = true;
}
// check if the output format is nexus
if (info.outFormat.Contains("nexus1", TString::kIgnoreCase))
info.idf = 1;
if (info.outFormat.Contains("nexus2", TString::kIgnoreCase))
info.idf = 2;
// in case the '-o' is present, make sure that inFileName is only a single file name
if (outputFileName.Length() > 0) {
if (info.inFileName.size() == 1) {
// make sure there is not in addition the template option given
if ((info.inTemplate.Length() == 0) && (info.outTemplate.Length() == 0)) {
info.outFileName = outputFileName;
} else {
std::cerr << std::endl << ">> any2many **ERROR** found option '-o' cannot be combined with option '-t'." << std::endl;
show_syntax = true;
}
} else {
std::cerr << std::endl << ">> any2many **ERROR** found option '-o' with multiple input file names, which doesn't make any sense." << std::endl;
show_syntax = true;
}
}
if (show_syntax) {
info.runList.clear();
any2many_syntax();
return PMUSR_WRONG_STARTUP_SYNTAX;
}
if (!info.inFormat.CompareTo(info.outFormat, TString::kIgnoreCase) && (info.rebin == 1)) {
info.runList.clear();
std::cerr << std::endl << ">> any2many **ERROR** input data format == output data format, only allowed if rebin != 1.";
std::cerr << std::endl << " will ignore the request." << std::endl << std::endl;
return PMUSR_SUCCESS;
}
// read startup file
char startup_path_name[128];
TSAXParser *saxParser = new TSAXParser();
PStartupHandler *startupHandler = new PStartupHandler();
if (!startupHandler->StartupFileFound()) {
std::cerr << std::endl << ">> any2many **WARNING** couldn't find " << startupHandler->GetStartupFilePath().Data();
std::cerr << std::endl;
// clean up
if (saxParser) {
delete saxParser;
saxParser = nullptr;
}
if (startupHandler) {
delete startupHandler;
startupHandler = nullptr;
}
} else {
strcpy(startup_path_name, startupHandler->GetStartupFilePath().Data());
saxParser->ConnectToHandler("PStartupHandler", startupHandler);
//status = saxParser->ParseFile(startup_path_name);
// parsing the file as above seems to lead to problems in certain environments;
// use the parseXmlFile function instead (see PStartupHandler.cpp for the definition)
status = parseXmlFile(saxParser, startup_path_name);
// check for parse errors
if (status) { // error
std::cerr << std::endl << ">> any2many **WARNING** Reading/parsing musrfit_startup.xml failed.";
std::cerr << std::endl;
// clean up
if (saxParser) {
delete saxParser;
saxParser = nullptr;
}
if (startupHandler) {
delete startupHandler;
startupHandler = nullptr;
}
}
}
// read all the necessary runs (raw data)
PRunDataHandler *dataHandler;
if (startupHandler)
dataHandler = new PRunDataHandler(&info, startupHandler->GetDataPathList());
else
dataHandler = new PRunDataHandler(&info);
// read and convert all data
dataHandler->ConvertData();
// check if it has been successfull
bool success = dataHandler->IsAllDataAvailable();
if (!success) {
std::cerr << std::endl << ">> any2many **ERROR** Couldn't read all data files, will quit ..." << std::endl;
}
// clean up
info.runList.clear();
if (saxParser) {
delete saxParser;
saxParser = nullptr;
}
if (startupHandler) {
delete startupHandler;
startupHandler = nullptr;
}
if (dataHandler) {
delete dataHandler;
dataHandler = nullptr;
}
return PMUSR_SUCCESS;
}
// end ---------------------------------------------------------------------
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