// $Id$
 // Original author: Jarrett Egertson <jegertso .a.t>
 // Licensed under the Apache License, Version 2.0 (the "License"); 
 // you may not use this file except in compliance with the License. 
 // You may obtain a copy of the License at 
 // Unless required by applicable law or agreed to in writing, software 
 // distributed under the License is distributed on an "AS IS" BASIS, 
 // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 
 // See the License for the specific language governing permissions and 
 // limitations under the License.
 #include "pwiz/data/msdata/MSDataFile.hpp"
 #include "pwiz/data/msdata/Serializer_mzML.hpp"
 #include "pwiz/data/msdata/Diff.hpp"
 #include "pwiz/utility/misc/unit.hpp"
 #include "pwiz/utility/misc/Std.hpp"
 #include "pwiz_tools/common/FullReaderList.hpp"
 #include <boost/program_options/options_description.hpp>
 #include <boost/program_options/parsers.hpp>
 #include <boost/program_options/variables_map.hpp>
 #include <pwiz/analysis/demux/EnumConstantNotPresentException.hpp>
 #include <pwiz/analysis/spectrum_processing/SpectrumList_Demux.hpp>
 #include <pwiz/analysis/spectrum_processing/SpectrumList_PeakPicker.hpp>
 #include <pwiz/analysis/spectrum_processing/SpectrumListFactory.hpp>
 #include <boost/chrono/chrono.hpp>
 #include <src/Core/products/Parallelizer.h>
 #define PRISM_VERSION "0.3"
 using namespace pwiz::data;
 using namespace pwiz::msdata;
 using namespace pwiz::util;
 using namespace pwiz::analysis;
 namespace po = boost::program_options;
 struct Optimization
     Optimization(const string& s) : value(s) {}
     string value;
 // This overload is needed for using default_value when building a variable_map. The default_value function relies on boost::lexical_cast, which relies on this operator.
 ostream& operator <<(ostream& stream, const Optimization& opt) { return stream << opt.value; }
 /// Overload the 'validate' function for the user-defined Optimization option class.
 void validate(boost::any& v,
     const vector<string>& values,
     // Make sure no previous assignment to 'a' was made.
     // Extract the first string from 'values'. If there is more than
     // one string, it's an error, and exception will be thrown.
     const string& s = po::validators::get_single_string(values);
     // Try conversion to desired enum type
         v = boost::any(Optimization(s));
     catch (EnumConstantNotPresentException&)
         throw po::invalid_option_value(s);
 class IterationListenerStream : public IterationListener
     explicit IterationListenerStream(ostream &os = std::cerr) : os_(os), entfmt_("%5.1f"){}
     Status update(const UpdateMessage& updateMessage) override
         auto percentProgress = 100.0 * float(updateMessage.iterationIndex) / float(updateMessage.iterationCount);
         os_ << "\rDemultiplexing: " << entfmt_ % percentProgress << "% (Spectrum "
             << updateMessage.iterationIndex << " of " << updateMessage.iterationCount << ")       ";
         return Status_Ok;
     ostream &os_;
     boost::format entfmt_;
 po::variables_map parseCommandLine(int argc, char **argv);
 void run(int argc, char ** argv)
     // The Eigen library must be initialized to support multithreaded operations before creating the threads
     auto start = boost::chrono::system_clock::now();
     std::cerr << "Welcome to Prism v" << PRISM_VERSION << endl;
     auto vm = parseCommandLine(argc, argv);
     SpectrumList_Demux::Params demuxParams;
     demuxParams.massError = vm["massError"].as<pwiz::chemistry::MZTolerance>();
     demuxParams.nnlsMaxIter = vm["nnlsMaxIter"].as<unsigned int>();
     demuxParams.nnlsEps = vm["nnlsEps"].as<double>();
     demuxParams.applyWeighting = !vm["noWeighting"].as<bool>();
     demuxParams.demuxBlockExtra = vm["demuxBlockExtra"].as<double>();
     demuxParams.variableFill = vm["variableFill"].as<bool>();
     demuxParams.regularizeSums = !vm["noSumNormalize"].as<bool>();
     demuxParams.optimization = SpectrumList_Demux::Params::stringToOptimization(vm["optimization"].as<Optimization>().value);
     demuxParams.padScanTimes = vm["padScanTimes"].as<bool>();
     demuxParams.interpolateRetentionTime = vm["interpolateRT"].as<bool>();
     bool skipCentroiding = vm["skipCentroiding"].as<bool>();
     FullReaderList readers;
     MSDataFile msd(vm["inputfile"].as<string>(), &readers);
     IntegerSet levelsToCentroid(1,2);
     // Bypass centroiding
     SpectrumListPtr toDemuxPtr =;
     if (!skipCentroiding)
         SpectrumListPtr tempPtr = toDemuxPtr;
         toDemuxPtr.reset(new SpectrumList_PeakPicker(tempPtr,
     SpectrumListPtr demux_list(new SpectrumList_Demux(toDemuxPtr, demuxParams));
     msd.filterApplied(); = demux_list;
     // set up progress indicator
     IterationListenerPtr listenerPtr(new IterationListenerStream(std::cerr));
     IterationListenerRegistry listenerRegistry;
     listenerRegistry.addListener(listenerPtr, 10);
     MSDataFile::WriteConfig writeConfig;
     MSDataFile::write(msd, vm["outputfile"].as<string>(), writeConfig, &listenerRegistry);
     std::cerr << endl;
     boost::chrono::duration<double> sec = boost::chrono::system_clock::now() - start;
     std::cout << "Demultiplexing took " << sec.count() / 60.0 << " minutes." << std::endl;
 po::variables_map parseCommandLine(int argc, char **argv)
     po::options_description desc("PRISM arguments");
     // Get default values
     SpectrumList_Demux::Params demuxParams;
     Optimization defaultOptimization(SpectrumList_Demux::Params::optimizationToString(demuxParams.optimization));
     bool skipCentroiding = false;
         ("help,h", "Produce this help message.")
         ("massError", po::value<pwiz::chemistry::MZTolerance>()->default_value(demuxParams.massError),
         "MS/MS error between spectra. Can specify number and units of either ppm or da, e.g. 10ppm or 0.4da. Default 10ppm.")
         ("variableFill", po::bool_switch()->default_value(demuxParams.variableFill),
         "MSX data was acquired with variable fill times.")
         ("demuxBlockExtra", po::value<double>()->default_value(demuxParams.demuxBlockExtra),
         "Extra slop to include in the set of spectra used for demux. Number of spectra added is input * num spectra in one cycle")
         ("nnlsMaxIter", po::value<unsigned int>()->default_value(demuxParams.nnlsMaxIter),
         "Maximum number of iterations for demux solve.")
         ("nnlsEps", po::value<double>()->default_value(demuxParams.nnlsEps),
         "Epsilon value for testing for convergence of demux solve.")
         ("noSumNormalize", po::bool_switch()->default_value(!demuxParams.regularizeSums),
         "Do not normalize the raw demux output for a spectrum so it sums up to the multiplexed peak intensity")
         ("noWeighting", po::bool_switch()->default_value(!demuxParams.applyWeighting),
         "Use non-weighted non negative least squares")
         ("optimization", po::value<Optimization>()->default_value(defaultOptimization),
         "Use optimizations. Available optimizations are \"none\", and \"overlap_only\"" )
         ("padScanTimes", po::bool_switch()->default_value(demuxParams.padScanTimes),
         "Pad scan times with small increment to prevent simultaneous spectra (which some software cannot handle)")
         ("interpolateRT", po::bool_switch()->default_value(demuxParams.interpolateRetentionTime),
         "Interpolate retention times. This only applies when overlap demultiplexing with no MSX (overlap only)")
         ("skipCentroiding", po::bool_switch()->default_value(skipCentroiding),
         "Set to true to use profile data if available")
         ("inputfile", po::value<string>()->required(),
         "Input spectra file")
         ("outputfile", po::value<string>()->required(),
         "Output spectra file");
     po::positional_options_description p;
     p.add("inputfile", 1);
     p.add("outputfile", 1);
     po::variables_map vm;
     po::store(po::command_line_parser(argc, argv).options(desc).positional(p).run(), vm);
     if (vm.count("help"))
         std::cout << desc << endl;
     return vm;
 int main(int argc, char **argv)
         run(argc, argv);
         return 0;
     catch (std::exception& e)
         std::cerr << e.what() << endl;
     catch (...)
         std::cerr << "Caught unknown exception.\n";
     return 1;