musrfit.cpp

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/***************************************************************************
 
  musrfit.cpp
 
  Author: Andreas Suter
  e-mail: andreas.suter@psi.ch
 
***************************************************************************/
 
/***************************************************************************
 *   Copyright (C) 2007-2026 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
 
#ifdef HAVE_GOMP
#include <omp.h>
#endif
 
#include <cstdio>
#include <cstdlib>
//#include <string.h>
#include <sys/types.h>
#include <unistd.h>
#include <signal.h>
 
#include <iostream>
#include <fstream>
#include <memory>
 
#include <TSAXParser.h>
#include <TString.h>
#include <TFile.h>
#include <TCanvas.h>
#include <TH1.h>
#include <TSystem.h>
#include <TSystemFile.h>
#include <TThread.h>
 
#ifdef HAVE_GIT_REV_H
#include "git-revision.h"
#endif
 
#include "PMusr.h"
#include "PStartupHandler.h"
#include "PMsrHandler.h"
#include "PRunDataHandler.h"
#include "PRunListCollection.h"
#include "PFitter.h"
 
//--------------------------------------------------------------------------
 
static int timeout = 3600; // given in (sec)
 
//--------------------------------------------------------------------------
void* musrfit_timeout(void *args)
{
  pid_t *pid = (pid_t*)(args);
 
  sleep(timeout);
 
  std::cerr << std::endl << ">> **FATAL ERROR** musrfit_timeout for task pid=" << *pid << " called! Will kill it!" << std::endl << std::endl;
 
  kill(*pid, SIGKILL);
 
  return (void*)nullptr;
}
 
//--------------------------------------------------------------------------
void musrfit_syntax()
{
  std::cout << std::endl << "usage: musrfit [<msr-file> [-k, --keep-mn2-ouput] [-c, --chisq-only] [-t, --title-from-data-file]";
  std::cout << std::endl << "                            [-e, --estimateN0] [-p, --per-run-block-chisq]";
  std::cout << std::endl << "                            [--dump <type>] [--timeout <timeout_tag>] |";
  std::cout << std::endl << "                            -n, --no-of-cores-avail | -u, --use-no-of-threads <number> |";
  std::cout << std::endl << "                            --nexus-support | --show-dynamic-path | --version | --help";
  std::cout << std::endl << "       <msr-file>: msr input file";
  std::cout << std::endl << "       'musrfit <msr-file>' will execute musrfit";
  std::cout << std::endl << "       'musrfit' or 'musrfit --help' will show this help";
  std::cout << std::endl << "       'musrfit --version' will print the musrfit version";
  std::cout << std::endl << "       'musrfit --nexus-support' will print if NeXus support is available.";
  std::cout << std::endl << "       'musrfit --show-dynamic-path' will print the internal dynamic library search paths.";
  std::cout << std::endl << "       -k, --keep-mn2-output: will rename the files MINUIT2.OUTPUT and ";
  std::cout << std::endl << "              MINUIT2.root to <msr-file>-mn2.output and <msr-file>-mn2.root,";
  std::cout << std::endl << "              respectively,";
  std::cout << std::endl << "              e.g. <msr-file> = 147.msr -> 147-mn2.output, 147-mn2.root";
  std::cout << std::endl << "       -c, --chisq-only: instead of fitting the data, chisq is just calculated";
  std::cout << std::endl << "              once and the result is set to the stdout. This feature is useful";
  std::cout << std::endl << "              to adjust initial parameters.";
  std::cout << std::endl << "       -t, --title-from-data-file: will replace the <msr-file> run title by the";
  std::cout << std::endl << "              run title of the FIRST run of the <msr-file> run block, if a run title";
  std::cout << std::endl << "              is present in the data file.";
  std::cout << std::endl << "       -e, --estimateN0: estimate N0 for single histogram fits.";
  std::cout << std::endl << "       -p, --per-run-block-chisq: will write per run block chisq to the msr-file.";
  std::cout << std::endl << "       -n, --no-of-cores-avail: print out how many cores are available (only vaild for OpenMP)";
  std::cout << std::endl << "       -u, --use-no-of-threads <number>:";
  std::cout << std::endl << "              <number>: number of threads to be used (OpenMP). Needs to be <= max. number of cores.";
  std::cout << std::endl << "              If OpenMP is enable, the maximal number of cores is used, if it is not limited by this option.";
  std::cout << std::endl << "       -r, --reset: reset startup musrfit_startup.xml, i.e. rewrite a default, and quit.";
  std::cout << std::endl << "                    The order of which musrfit_startup.xml is reset is:";
  std::cout << std::endl << "                       (i)   if present in the current dir.";
  std::cout << std::endl << "                       (ii)  if present under $HOME/.musrfit/";
  std::cout << std::endl << "                       (iii) if present under $MUSRFITPATH/";
  std::cout << std::endl << "                       (iv)  if present under $ROOTSYS/";
  std::cout << std::endl << "       -y, --yaml: write fit results (MINUIT2.OUTPUT) into a yaml-file. Output <msr-file>.yaml";
  std::cout << std::endl << "       --dump <type> is writing a data file with the fit data and the theory";
  std::cout << std::endl << "              <type> can be 'ascii', 'root'";
  std::cout << std::endl << "       --timeout <timeout_tag>: overwrites to predefined timeout of " << timeout << " (sec).";
  std::cout << std::endl << "              <timeout_tag> <= 0 means timeout facility is not enabled. <timeout_tag> = nn";
  std::cout << std::endl << "              will set the timeout to nn (sec).";
  std::cout << std::endl;
  std::cout << std::endl << "       At the end of a fit, musrfit writes the fit results into an <mlog-file> and";
  std::cout << std::endl << "       swaps them, i.e. in the <msr-file> you will find the fit results and in the";
  std::cout << std::endl << "       <mlog-file> your initial guess values.";
  std::cout << std::endl << std::endl;
}
 
//--------------------------------------------------------------------------
void musrfit_write_ascii(TString fln, PRunData *data, int runCounter)
{
  // generate dump file name
  TString count("_");
  count += runCounter;
  Ssiz_t index = fln.Last('.');
  fln.Insert(index, count);
 
  std::ofstream f;
 
  // open dump-file
  f.open(fln.Data(), std::iostream::out);
  if (!f.is_open()) {
    std::cout << std::endl << "Couldn't open dump (" << fln.Data() << ") file for writting, sorry ...";
    std::cout << std::endl;
    return;
  }
 
  // dump data
  f << "% number of data values = " << data->GetValue()->size() << std::endl;
  f << "% time (us), value, error, theory" << std::endl;
  double time;
  for (unsigned int i=0; i<data->GetValue()->size(); i++) {
    time = data->GetDataTimeStart() + (double)i*data->GetDataTimeStep();
    f << time << ", " << data->GetValue()->at(i) << ", " << data->GetError()->at(i) << ", " << data->GetTheory()->at(i) << std::endl;
  }
 
  // close file
  f.close();
}
 
//--------------------------------------------------------------------------
void musrfit_dump_ascii(char *fileName, PRunListCollection *runList)
{
  TString fln(fileName);
  fln.ReplaceAll(".msr", ".dat");
 
  // go through the run list, get the data and dump it in a file
 
  int runCounter = 0;
  PRunData *data;
 
  // single histos
  unsigned int size = runList->GetNoOfSingleHisto();
  if (size > 0) {
    for (unsigned int i=0; i<size; i++) {
      data = runList->GetSingleHisto(i);
      if (data) {
        // dump data
        musrfit_write_ascii(fln, data, runCounter);
        runCounter++;
      }
    }
  }
 
  // single histos
  size = runList->GetNoOfSingleHistoRRF();
  if (size > 0) {
    for (unsigned int i=0; i<size; i++) {
      data = runList->GetSingleHistoRRF(i);
      if (data) {
        // dump data
        musrfit_write_ascii(fln, data, runCounter);
        runCounter++;
      }
    }
  }
 
  // asymmetry
  size = runList->GetNoOfAsymmetry();
  if (size > 0) {
    for (unsigned int i=0; i<size; i++) {
      data = runList->GetAsymmetry(i);
      if (data) {
        // dump data
        musrfit_write_ascii(fln, data, runCounter);
        runCounter++;
      }
    }
  }
 
  // asymmetry RRF
  size = runList->GetNoOfAsymmetryRRF();
  if (size > 0) {
    for (unsigned int i=0; i<size; i++) {
      data = runList->GetAsymmetryRRF(i);
      if (data) {
        // dump data
        musrfit_write_ascii(fln, data, runCounter);
        runCounter++;
      }
    }
  }
 
  // muMinus
  size = runList->GetNoOfMuMinus();
  if (size > 0) {
    for (unsigned int i=0; i<size; i++) {
      data = runList->GetMuMinus(i);
      if (data) {
        // dump data
        musrfit_write_ascii(fln, data, runCounter);
        runCounter++;
      }
    }
  }
 
  // nonMusr
  size = runList->GetNoOfNonMusr();
  if (size > 0) {
    for (unsigned int i=0; i<size; i++) {
      data = runList->GetNonMusr(i);
      if (data) {
        // dump data
        musrfit_write_ascii(fln, data, runCounter);
        runCounter++;
      }
    }
  }
}
 
//--------------------------------------------------------------------------
void musrfit_write_root(TFile &f, TString fln, PRunData *data, int runCounter)
{
  char name[128];
 
  TString title = fln.Copy();
  snprintf(name, sizeof(name), "_%d", runCounter);
  title.ReplaceAll(".root", name);
 
  snprintf(name, sizeof(name),"c%d", runCounter);
 
  std::unique_ptr<TCanvas> c = std::make_unique<TCanvas>(name, title.Data(), 10, 10, 800, 600);
 
  // create histos
  Double_t diff = data->GetDataTimeStep();
  Double_t start = -diff/2.0;
  Double_t end = data->GetDataTimeStep()*data->GetValue()->size();
  std::unique_ptr<TH1F> hdata = std::make_unique<TH1F>("hdata", "run data", data->GetValue()->size(), start, end);
  std::unique_ptr<TH1F> htheo = std::make_unique<TH1F>("htheo", "run theory", data->GetValue()->size(), start, end);
 
  // fill data
  for (unsigned int i=0; i<data->GetValue()->size(); i++) {
    hdata->SetBinContent(i+1, data->GetValue()->at(i));
    hdata->SetBinError(i+1, data->GetError()->at(i));
    htheo->SetBinContent(i+1, data->GetTheory()->at(i));
  }
 
  hdata->SetMarkerStyle(20);
  hdata->Draw("*H HIST E1");
 
  htheo->SetLineColor(2);
  htheo->SetLineWidth(3);
  htheo->Draw("C SAME");
 
  f.WriteTObject(c.get());
}
 
//--------------------------------------------------------------------------
void musrfit_dump_root(char *fileName, PRunListCollection *runList)
{
  TString fln(fileName);
  fln.ReplaceAll(".msr", ".root");
 
  TFile f(fln.Data(), "recreate");
 
  // go through the run list, get the data and dump it in a file
 
  int runCounter = 0;
  PRunData *data;
 
  // single histos
  unsigned int size = runList->GetNoOfSingleHisto();
  if (size > 0) {
    for (unsigned int i=0; i<size; i++) {
      data = runList->GetSingleHisto(i);
      if (data) {
        // dump data
        musrfit_write_root(f, fln, data, runCounter);
        runCounter++;
      }
    }
  }
 
  // single histo RRF
  size = runList->GetNoOfSingleHistoRRF();
  if (size > 0) {
    for (unsigned int i=0; i<size; i++) {
      data = runList->GetSingleHistoRRF(i);
      if (data) {
        // dump data
        musrfit_write_root(f, fln, data, runCounter);
        runCounter++;
      }
    }
  }
 
  // asymmetry
  size = runList->GetNoOfAsymmetry();
  if (size > 0) {
    for (unsigned int i=0; i<size; i++) {
      data = runList->GetAsymmetry(i);
      if (data) {
        // dump data
        musrfit_write_root(f, fln, data, runCounter);
        runCounter++;
      }
    }
  }
 
  // asymmetry RRF
  size = runList->GetNoOfAsymmetryRRF();
  if (size > 0) {
    for (unsigned int i=0; i<size; i++) {
      data = runList->GetAsymmetryRRF(i);
      if (data) {
        // dump data
        musrfit_write_root(f, fln, data, runCounter);
        runCounter++;
      }
    }
  }
 
  // muMinus
  size = runList->GetNoOfMuMinus();
  if (size > 0) {
    for (unsigned int i=0; i<size; i++) {
      data = runList->GetMuMinus(i);
      if (data) {
        // dump data
        musrfit_write_root(f, fln, data, runCounter);
        runCounter++;
      }
    }
  }
 
  // nonMusr
  size = runList->GetNoOfNonMusr();
  if (size > 0) {
    for (unsigned int i=0; i<size; i++) {
      data = runList->GetNonMusr(i);
      if (data) {
        // dump data
        musrfit_write_root(f, fln, data, runCounter);
        runCounter++;
      }
    }
  }
 
  f.Close("R");
}
 
//--------------------------------------------------------------------------
int main(int argc, char *argv[])
{
 
  bool show_syntax = false;
 
    // check syntax (root unrelated)
  if (argc < 2) {
    musrfit_syntax();
    return PMUSR_WRONG_STARTUP_SYNTAX;
  }
 
  if (argc == 2) {
    if (!strcmp(argv[1], "--version")) {
#ifdef HAVE_CONFIG_H
#ifdef HAVE_GIT_REV_H
      std::cout << std::endl << "musrfit 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 << "musrfit version: " << PACKAGE_VERSION << " (" << BUILD_TYPE << "), ROOT version: " << ROOT_VERSION_USED << std::endl << std::endl;
#endif
#else
#ifdef HAVE_GIT_REV_H
      std::cout << std::endl << "musrfit git-branch: " << GIT_BRANCH << ", git-rev: " << GIT_CURRENT_SHA1 << std::endl << std::endl;
#else
      std::cout << std::endl << "musrfit version: unknown" << std::endl << std::endl;
#endif
#endif
      return PMUSR_SUCCESS;
    } else if (!strcmp(argv[1], "--nexus-support")) {
#ifdef PNEXUS_ENABLED
      std::cout << std::endl << ">> musrfit: NeXus support enabled. ";
      std::cout << " HDF5 ready. ";
#ifdef HAVE_HDF4
      std::cout << " HDF4 ready."  << std::endl << std::endl;
#else
      std::cout << " HDF4 not ready."  << std::endl << std::endl;
#endif
#else
      std::cout << std::endl << "musrfit: NeXus support NOT enabled." << std::endl << std::endl;
#endif
      return PMUSR_SUCCESS;
    } else if (!strcmp(argv[1], "--help")) {
        show_syntax = true;
    }
  }
 
  if (show_syntax) {
    musrfit_syntax();
    return PMUSR_WRONG_STARTUP_SYNTAX;
  }
 
  int  status;
  bool keep_mn2_output = false;
  bool chisq_only = false;
  bool yaml_out = false;
  bool title_from_data_file = false;
  bool timeout_enabled = true;
  bool reset_startup_file = false;
  PStartupOptions startup_options;
  startup_options.writeExpectedChisq = false;
  startup_options.estimateN0 = false;  
  int number_of_cores=1;
 
#ifdef HAVE_GOMP
  number_of_cores = omp_get_num_procs();
#endif
 
  TString dump("");
  char filename[1024];
 
  // add default shared library path /usr/local/lib if not already persent
  const char *dsp = gSystem->GetDynamicPath();
  if (strstr(dsp, "/usr/local/lib") == nullptr)
    gSystem->AddDynamicPath("/usr/local/lib");
 
  // check syntax (root related)
  if (argc == 2) {
    if (!strcmp(argv[1], "--show-dynamic-path")) {
      std::cout << std::endl << "musrfit: internal dynamic search paths for shared libraries/root dictionaries:";
      std::cout << std::endl << "  '" << gSystem->GetDynamicPath() << "'" << std::endl << std::endl;
      return PMUSR_SUCCESS;
    }
  }
 
  memset(filename, '\0', sizeof(filename));
  strcpy(filename, "");
  for (int i=1; i<argc; i++) {
    if (strstr(argv[i], ".msr")) {
      strncpy(filename, argv[i], sizeof(filename));
    } else if (!strcmp(argv[i], "-k") || !strcmp(argv[i], "--keep-mn2-output")) {
      keep_mn2_output = true;
    } else if (!strcmp(argv[i], "-c") || !strcmp(argv[i], "--chisq-only")) {
      chisq_only = true;
    } else if (!strcmp(argv[i], "-t") || !strcmp(argv[i], "--title-from-data-file")) {
      title_from_data_file = true;
    } else if (!strcmp(argv[i], "--dump")) {
      if (i<argc-1) {
        dump = TString(argv[i+1]);
        i++;
      } else {
        std::cerr << std::endl << ">> musrfit: **ERROR** found option --dump without <type>" << std::endl;
        show_syntax = true;
        break;
      }
    } else if (!strcmp(argv[i], "-e") || !strcmp(argv[i], "--estimateN0")) {
      startup_options.estimateN0 = true;
    } else if (!strcmp(argv[i], "-p") || !strcmp(argv[i], "--per-run-block-chisq")) {
      startup_options.writeExpectedChisq = true;
    } else if (!strcmp(argv[i], "-y") || !strcmp(argv[i], "--yaml")) {
      yaml_out = true;
    } else if (!strcmp(argv[i], "-n") || !strcmp(argv[i], "--no-of-cores-avail")) {
#ifdef HAVE_GOMP
        std::cout << std::endl;
        std::cout << "musrfit: maxmimal number of cores for OpenMP available: " << omp_get_num_procs() << std::endl;
        std::cout << std::endl;
#else
        std::cout << std::endl;
        std::cout << ">> musrfit: this option is only vaild if OpenMP is present. This seems not to be the case here. Sorry!" << std::endl;
        std::cout << std::endl;
#endif
      return PMUSR_SUCCESS;
    } else if (!strcmp(argv[i], "-u") || !strcmp(argv[i], "--use-no-of-threads")) {
      if (i<argc-1) {
        TString str(argv[i+1]);
        if (str.IsFloat()) {
          int ival = str.Atoi();
          if (ival <= 0) {
            std::cerr << std::endl << ">> musrfit: **ERROR** found option --use-no-of-threads with <number> <= 0" << std::endl;
            std::cerr << "                      This doesn't make any sense." << std::endl;
            show_syntax = true;
            break;
          } else if (ival > number_of_cores) {
#ifdef HAVE_GOMP
            std::cerr << std::endl << ">> musrfit: **WARNING** found option --use-no-of-threads with <number>=" << ival << " > max available cores=" << number_of_cores << "." << std::endl;
            std::cerr << "                        Will set <number> to max available cores." << std::endl;
#else
            std::cerr << std::endl << ">> musrfit: **WARNING** option --use-no-of-threads can only be used if OpenMP is available." << std::endl;
            std::cerr << "            Here it is not the case, and hence this option will be ignored." << std::endl;
#endif
          } else {
            number_of_cores = ival;
          }
        } else {
          std::cerr << std::endl << ">> musrfit: **ERROR** found option --use-no-of-threads where <number> it not a number: '" << argv[i+1] << "'" << std::endl;
          show_syntax = true;
          break;
        }
        i++;
      } else {
        std::cerr << std::endl << ">> musrfit: **ERROR** found option --use-no-of-threads without <number>" << std::endl;
        show_syntax = true;
        break;
      }
    } else if (!strcmp(argv[i], "-r") || !strcmp(argv[i], "--reset")) {
      reset_startup_file = true;
    } else if (!strcmp(argv[i], "--timeout")) {
      if (i<argc-1) {
        TString str(argv[i+1]);
        if (str.IsFloat()) {
          timeout = str.Atoi();
          if (timeout <= 0) {
            timeout_enabled = false;
            std::cout << std::endl << ">> musrfit: timeout disabled." << std::endl;
          }
        } else {
          std::cerr << std::endl << ">> musrfit: **ERROR** found option --timeout with unsupported <timeout_tag> = " << argv[i+1] << std::endl;
          show_syntax = true;
          break;
        }
        i++;
      } else {
        std::cerr << std::endl << ">> musrfit: **ERROR** found option --timeout without <timeout_tag>" << std::endl;
        show_syntax = true;
        break;
      }
    } else {
      show_syntax = true;
      break;
    }
  }
 
  // check if a filename is present
  if ((strlen(filename) == 0) && !reset_startup_file) {
    show_syntax = true;
    std::cout << std::endl << ">> musrfit **ERROR** no msr-file present!" << std::endl;
  }
 
  if (show_syntax) {
    musrfit_syntax();
    return PMUSR_WRONG_STARTUP_SYNTAX;
  }
 
  // check if dump string does make sense
  if (!dump.IsNull()) {
    dump.ToLower();
    if (!dump.Contains("ascii") && !dump.Contains("root")) {
      std::cerr << std::endl << ">> musrfit: **ERROR** found option --dump with unsupported <type> = " << dump << std::endl;
      musrfit_syntax();
      return PMUSR_WRONG_STARTUP_SYNTAX;
    }
  }
 
  // read startup file
  char startup_path_name[128];
  std::unique_ptr<TSAXParser> saxParser = std::make_unique<TSAXParser>();
  std::unique_ptr<PStartupHandler> startupHandler = std::make_unique<PStartupHandler>(reset_startup_file);
  if (reset_startup_file) // only rewrite musrfit_startup.xml has been requested
    return PMUSR_SUCCESS;
  if (!startupHandler->StartupFileFound()) {
    std::cerr << std::endl << ">> musrfit **WARNING** couldn't find " << startupHandler->GetStartupFilePath().Data();
    std::cerr << std::endl;
  } else {
    memset(startup_path_name, '\0', sizeof(startup_path_name));
    strncpy(startup_path_name, startupHandler->GetStartupFilePath().Data(), sizeof(startup_path_name));
    saxParser->ConnectToHandler("PStartupHandler", startupHandler.get());
    //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.get(), startup_path_name);
    // check for parse errors
    if (status) { // error
      std::cerr << std::endl << ">> musrfit **WARNING** Reading/parsing musrfit_startup.xml failed.";
      std::cerr << std::endl;
    }
  }
 
#ifdef HAVE_GOMP
  // set omp_set_num_threads
  omp_set_num_threads(number_of_cores);
#endif
 
  // read msr-file
  std::unique_ptr<PMsrHandler> msrHandler;
  if (startupHandler)
    msrHandler = std::make_unique<PMsrHandler>(filename, &startup_options);
  else
    msrHandler = std::make_unique<PMsrHandler>(filename);
  status = msrHandler->ReadMsrFile();
  if (status != PMUSR_SUCCESS) {
    switch (status) {
      case PMUSR_MSR_FILE_NOT_FOUND:
        std::cout << std::endl << ">> musrfit **ERROR** couldn't find " << filename << std::endl << std::endl;
        break;
      case PMUSR_MSR_SYNTAX_ERROR:
        std::cout << std::endl << ">> musrfit **SYNTAX ERROR** in file " << filename << ", full stop here." << std::endl << std::endl;
        break;
      default:
        std::cout << std::endl << ">> musrfit **UNKOWN ERROR** when trying to read the msr-file" << std::endl << std::endl;
        break;
    }
    return status;
  }
 
  // read all the necessary runs (raw data)
  std::unique_ptr<PRunDataHandler> dataHandler;
  if (startupHandler)
    dataHandler = std::make_unique<PRunDataHandler>(msrHandler.get(), startupHandler->GetDataPathList());
  else
    dataHandler = std::make_unique<PRunDataHandler>(msrHandler.get());
 
  dataHandler->ReadData();
 
  bool success = dataHandler->IsAllDataAvailable();
  if (!success) {
    std::cerr << std::endl << ">> musrfit **ERROR** Couldn't read all data files, will quit ..." << std::endl;
  }
 
  // if present, replace the run title of the <msr-file> with the run title of the FIRST run in the run block of the msr-file
  if (title_from_data_file && success) {
    PMsrRunList *rl  = msrHandler->GetMsrRunList();
    if (rl->empty()) {
      success = false;
      std::cerr << std::endl << ">> musrfit **ERROR** no run list present." << std::endl;
    }
    if (success) {
      TString *name = rl->at(0).GetRunName();
      if (name == nullptr) {
        std::cerr << std::endl << ">> musrfit **ERROR** to obtain run list name." << std::endl;
        success = false;
      }
      PRawRunData *rrd = nullptr;
      if (success) {
        rrd = dataHandler->GetRunData(*(rl->at(0).GetRunName()));
        if (rrd == nullptr) {
          std::cerr << std::endl << ">> musrfit **ERROR** no raw run data avaliable." << std::endl;
          success = false;
        }
      }
      if (success) {
        if (rrd->GetRunTitle()->Length() > 0)
          msrHandler->SetMsrTitle(*rrd->GetRunTitle());
      }
    }
  }
 
  // generate the necessary fit histogramms for the fit
  std::unique_ptr<PRunListCollection> runListCollection;
  if (success) {
    // feed all the necessary histogramms for the fit   
    runListCollection = std::make_unique<PRunListCollection>(msrHandler.get(), dataHandler.get());
    for (unsigned int i=0; i < msrHandler->GetMsrRunList()->size(); i++) {
      success = runListCollection->Add(i, kFit);
      if (!success) {
        std::cout << std::endl << ">> musrfit **ERROR** Couldn't handle run no " << i+1 << ": ";
        std::cout << (*msrHandler->GetMsrRunList())[i].GetRunName()->Data();
        break;
      }
    }
  }
 
  // start timeout thread
  std::unique_ptr<TThread> th;
  if (timeout_enabled) {
    static pid_t musrfit_pid = getpid();
    th = std::make_unique<TThread>(musrfit_timeout, (void*)&musrfit_pid);
    if (th) {
      th->Run();
    }
  }
 
  // do fitting
  std::unique_ptr<PFitter> fitter;
  if (success) {
    fitter = std::make_unique<PFitter>(msrHandler.get(), runListCollection.get(), chisq_only, yaml_out);
    if (fitter->IsValid()) {
      fitter->DoFit();
      if (!fitter->IsScanOnly())
        msrHandler->SetMsrStatisticConverged(fitter->HasConverged());
    }
  }
 
  // write log file
  if (success && !chisq_only) {
    if (!fitter->IsScanOnly()) {
      status = msrHandler->WriteMsrLogFile();
      if (status != PMUSR_SUCCESS) {
        switch (status) {
        case PMUSR_MSR_LOG_FILE_WRITE_ERROR:
          std::cout << std::endl << ">> musrfit **ERROR** couldn't write mlog-file" << std::endl << std::endl;
          break;
        case PMUSR_TOKENIZE_ERROR:
          std::cout << std::endl << ">> musrfit **ERROR** couldn't generate mlog-file name" << std::endl << std::endl;
          break;
        default:
          std::cout << std::endl << ">> musrfit **UNKOWN ERROR** when trying to write the mlog-file" << std::endl << std::endl;
          break;
        }
      }
    }
  }
 
  // check if dump is wanted
  if (success && !dump.IsNull()) {
    std::cout << std::endl << "will write dump file ..." << std::endl;
    dump.ToLower();
    if (dump.Contains("ascii"))
      musrfit_dump_ascii(filename, runListCollection.get());
    else if (dump.Contains("root"))
      musrfit_dump_root(filename, runListCollection.get());
    else
      std::cout << std::endl << "do not know format " << dump.Data() << ", sorry :-| " << std::endl;
  }
 
  // rename MINUIT2.OUTPUT and MINUIT2.root file if wanted
  if (success) {
    if (keep_mn2_output && !chisq_only && !fitter->IsScanOnly()) {
      // 1st rename MINUIT2.OUTPUT
      TString fln = TString(filename);
      char ext[32];
      strcpy(ext, "-mn2.output");
      fln.ReplaceAll(".msr", 4, ext, strlen(ext));
      gSystem->CopyFile("MINUIT2.OUTPUT", fln.Data(), kTRUE);
 
      // 2nd rename MINUIT2.ROOT
      fln = TString(filename);
      strcpy(ext, "-mn2.root");
      fln.ReplaceAll(".msr", 4, ext, strlen(ext));
      gSystem->CopyFile("MINUIT2.root", fln.Data(), kTRUE);
    }
  }
 
  if (success) {
    if (!chisq_only && !fitter->IsScanOnly()) {
      // swap msr- and mlog-file
      std::cout << std::endl << ">> swapping msr-, mlog-file ..." << std::endl;
      // copy msr-file -> __temp.msr
      gSystem->CopyFile(filename, "__temp.msr", kTRUE);
      // copy mlog-file -> msr-file
      TString fln = TString(filename);
      char ext[32];
      strcpy(ext, ".mlog");
      fln.ReplaceAll(".msr", 4, ext, strlen(ext));
      gSystem->CopyFile(fln.Data(), filename, kTRUE);
      // copy __temp.msr -> mlog-file
      gSystem->CopyFile("__temp.msr", fln.Data(), kTRUE);
      // delete __temp.msr
      TSystemFile tmp("__temp.msr", "./");
      tmp.Delete();
    }
  }
 
  if (th && timeout_enabled) {
    th->Kill();
  }
 
  std::cout << std::endl << "done ..." << std::endl;
 
  return PMUSR_SUCCESS;
}
 
// end ---------------------------------------------------------------------