Fleshed out project. Needs testing

src/CalDict/cal_dict.cxx_tmp_3535

@@ -0,0 +1,36 @@
+// Do NOT change. Changes will be lost next time file is generated
+
+#define R__DICTIONARY_FILENAME srcdICalDictdIcal_dict
+#define R__NO_DEPRECATION
+
+/*******************************************************************/
+#include <stddef.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <assert.h>
+#define G__DICTIONARY
+#include "RConfig.h"
+#include "TClass.h"
+#include "TDictAttributeMap.h"
+#include "TInterpreter.h"
+#include "TROOT.h"
+#include "TBuffer.h"
+#include "TMemberInspector.h"
+#include "TInterpreter.h"
+#include "TVirtualMutex.h"
+#include "TError.h"
+
+#ifndef G__ROOT
+#define G__ROOT
+#endif
+
+#include "RtypesImp.h"
+#include "TIsAProxy.h"
+#include "TFileMergeInfo.h"
+#include <algorithm>
+#include "TCollectionProxyInfo.h"
+/*******************************************************************/
+
+#include "TDataMember.h"
+

src/CalDict/cal_dict.cxx_tmp_3544

@@ -0,0 +1,36 @@
+// Do NOT change. Changes will be lost next time file is generated
+
+#define R__DICTIONARY_FILENAME srcdICalDictdIcal_dict
+#define R__NO_DEPRECATION
+
+/*******************************************************************/
+#include <stddef.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <assert.h>
+#define G__DICTIONARY
+#include "RConfig.h"
+#include "TClass.h"
+#include "TDictAttributeMap.h"
+#include "TInterpreter.h"
+#include "TROOT.h"
+#include "TBuffer.h"
+#include "TMemberInspector.h"
+#include "TInterpreter.h"
+#include "TVirtualMutex.h"
+#include "TError.h"
+
+#ifndef G__ROOT
+#define G__ROOT
+#endif
+
+#include "RtypesImp.h"
+#include "TIsAProxy.h"
+#include "TFileMergeInfo.h"
+#include <algorithm>
+#include "TCollectionProxyInfo.h"
+/*******************************************************************/
+
+#include "TDataMember.h"
+

src/CalDict/cal_dict.cxx_tmp_3665

@@ -0,0 +1,36 @@
+// Do NOT change. Changes will be lost next time file is generated
+
+#define R__DICTIONARY_FILENAME srcdICalDictdIcal_dict
+#define R__NO_DEPRECATION
+
+/*******************************************************************/
+#include <stddef.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <assert.h>
+#define G__DICTIONARY
+#include "RConfig.h"
+#include "TClass.h"
+#include "TDictAttributeMap.h"
+#include "TInterpreter.h"
+#include "TROOT.h"
+#include "TBuffer.h"
+#include "TMemberInspector.h"
+#include "TInterpreter.h"
+#include "TVirtualMutex.h"
+#include "TError.h"
+
+#ifndef G__ROOT
+#define G__ROOT
+#endif
+
+#include "RtypesImp.h"
+#include "TIsAProxy.h"
+#include "TFileMergeInfo.h"
+#include <algorithm>
+#include "TCollectionProxyInfo.h"
+/*******************************************************************/
+
+#include "TDataMember.h"
+

src/CalibrationMap.cpp

@@ -0,0 +1,52 @@
+#include "CalibrationMap.h"
+#include <fstream>
+
+namespace SabreCal {
+
+    CalibrationMap::CalibrationMap() :
+        m_isValid(false)
+    {
+    }
+
+    CalibrationMap::CalibrationMap(const std::string& filename) :
+        m_isValid(false)
+    {
+        Init(filename);
+    }
+
+    CalibrationMap::~CalibrationMap() {}
+
+    void CalibrationMap::Init(const std::string &filename)
+    {
+        std::ifstream input(filename);
+        if(!input.is_open())
+        {
+            m_isValid = false;
+            return;
+        }
+        
+        std::string junk;
+        int gchan;
+        Parameters params;
+        
+        std::getline(input, junk);
+        std::getline(input, junk);
+        
+        while(input>>gchan)
+        {
+            input>>params.slope>>params.offset;
+            m_map[gchan] = params;
+        }
+        
+        m_isValid = true;
+    }
+
+    const Parameters& CalibrationMap::GetParameters(int gchan) const
+    {
+        auto iter = m_map.find(gchan);
+        if(iter != m_map.end())
+            return iter->second;
+        else
+            return m_dummyParams;
+    }
+}

src/CalibrationMap.h

@@ -0,0 +1,29 @@
+#ifndef CALIBRATION_MAP_H
+#define CALIBRATION_MAP_H
+
+#include <string>
+#include <unordered_map>
+#include "CalibrationStructs.h"
+
+namespace SabreCal {
+
+    class CalibrationMap
+    {
+    public:
+        CalibrationMap();
+        CalibrationMap(const std::string& filename);
+        ~CalibrationMap();
+        
+        void Init(const std::string& filename);
+        
+        const Parameters& GetParameters(int gchan) const;
+        inline const bool IsValid() const { return m_isValid; }
+        
+    private:
+        bool m_isValid;
+        std::unordered_map<int, Parameters> m_map;
+        Parameters m_dummyParams; //for null result
+    };
+}
+
+#endif

src/Calibrator.cpp

@@ -0,0 +1,160 @@
+#include "Calibrator.h"
+#include "TFile.h"
+#include "TTree.h"
+#include "DataStructs.h"
+#include <iostream>
+#include <fstream>
+#include "TSpectrum.h"
+
+namespace SabreCal {
+
+    Calibrator::Calibrator(const std::string& gainfile) :
+        m_gainMap(gainfile)
+    {
+        TH1::AddDirectory(kFALSE);
+    }
+
+    Calibrator::~Calibrator() {}
+
+    void Calibrator::Run(const std::string& datafile, const std::string& outputfile, const std::string& plotfile)
+    {
+        if(!m_gainMap.IsValid())
+        {
+            std::cerr<<"ERR -- Bad gain map at Calibrator::Run!"<<std::endl;
+            return;
+        }
+        
+        TFile* input = TFile::Open(datafile.c_str(), "READ");
+        if(!input->IsOpen())
+        {
+            std::cerr<<"ERR -- Bad data file "<<datafile<<" at Calibrator::Run!"<<std::endl;
+            return;
+        }
+        
+        TTree* tree = (TTree*) input->Get("Data");
+        uint16_t energy, board, channel;
+        tree->SetBranchAddress("Energy", &energy);
+        tree->SetBranchAddress("Board", &board);
+        tree->SetBranchAddress("Channel", &channel);
+        
+        int gchan;
+        
+        uint64_t nentries = tree->GetEntries();
+        float flush_percent = 0.1f;
+        uint64_t count=0, flush_count=0, flush_val=nentries*flush_percent;
+        
+        std::vector<TH1F> histograms;
+        for(int i=0; i<s_totalChannels; i++)
+        {
+            std::string name = "channel"+std::to_string(i);
+            histograms.emplace_back(name.c_str(), name.c_str(), 16384, 0.0, 16384.0);
+        }
+        
+        for(uint64_t i=0; i<nentries; i++)
+        {
+            tree->GetEntry(i);
+            count++;
+            if(count == flush_val)
+            {
+                flush_count++;
+                count = 0;
+                std::cout<<"\rPercent of data processed: "<<flush_count*flush_percent*100.0<<"%"<<std::flush;
+            }
+            
+            gchan = board*16 + channel; //Global channel (16 channels per board)
+            auto& params = m_gainMap.GetParameters(gchan);
+            
+            if(energy > 100.0) //Reject electronic noise
+                histograms[i].Fill(params.slope*(energy*s_gainFactor) + params.offset);
+        }
+        std::cout<<std::endl;
+        input->Close();
+        
+        std::cout<<"Finding calibration parameters..."<<std::endl;
+        FindParameters(histograms);
+        std::cout<<"Writing to disk..."<<std::endl;
+        WriteHistograms(histograms, plotfile);
+        WriteParameters(outputfile);
+    }
+
+    void Calibrator::FindParameters(const std::vector<TH1F>& grams)
+    {
+        TSpectrum finder;
+        double threshold = 0.5;
+        double sigma = 5.0;
+        
+        Parameters these_params;
+        double peakMean;
+        
+        for(auto& histo : grams)
+        {
+            finder.Search(&histo, sigma, "nobackground", threshold);
+            if(finder.GetNPeaks() == 0)
+            {
+                std::cerr<<"No peaks found in histogram "<<histo.GetName()<<std::endl;
+                m_params.push_back(Parameters());
+            }
+            else if(finder.GetNPeaks() > 1)
+            {
+                peakMean = 0.0;
+                double peakAmp = 0.0;
+                std::cerr<<"Multiple peaks found in histogram "<<histo.GetName();
+                std::cerr<<"Keeping the largest peak."<<std::endl;
+                double mean, amp;
+                for(int i=0; i<finder.GetNPeaks(); i++)
+                {
+                    mean = finder.GetPositionX()[i];
+                    amp = finder.GetPositionY()[i];
+                    if(amp > peakAmp)
+                    {
+                        peakMean = mean;
+                        peakAmp = amp;
+                    }
+                }
+                these_params.slope = s_241Am_alphaKE/peakMean;
+                these_params.offset = 0.0;
+                m_params.push_back(these_params);
+            }
+            else
+            {
+                peakMean = finder.GetPositionX()[0];
+                these_params.slope = s_241Am_alphaKE/peakMean;
+                these_params.offset = 0.0;
+                m_params.push_back(these_params);
+            }
+        }
+    }
+
+    void Calibrator::WriteHistograms(const std::vector<TH1F> &grams, const std::string &plotfile)
+    {
+        TFile* output = TFile::Open(plotfile.c_str(), "RECREATE");
+        if(!output->IsOpen())
+        {
+            std::cerr<<"Unable to open file "<<plotfile<<" for saving histograms"<<std::endl;
+            return;
+        }
+        
+        for(auto& histo : grams)
+        {
+            histo.Write();
+        }
+        
+        output->Close();
+    }
+
+    void Calibrator::WriteParameters(const std::string &outputfile)
+    {
+        std::ofstream output(outputfile);
+        if(!output.is_open())
+        {
+            std::cerr<<"Unable to open file "<<outputfile<<" for saving parameters"<<std::endl;
+            return;
+        }
+        output<<"Channel  Slope  Offset"<<std::endl;
+        for(size_t i=0; i<m_params.size(); i++)
+        {
+            output<<i<<"  "<<m_params[i].slope<<"  "<<m_params[i].offset<<std::endl;
+        }
+        output.close();
+    }
+}

src/Calibrator.h

@@ -0,0 +1,36 @@
+#ifndef CALIBRATOR_H
+#define CALIBRATOR_H
+
+#include <string>
+#include <vector>
+#include "ChannelMap.h"
+#include "GainMap.h"
+#include "CalibrationStructs.h"
+
+#include "TH1.h"
+
+namespace SabreCal {
+
+    class Calibrator
+    {
+    public:
+        Calibrator(const std::string& gainfile);
+        ~Calibrator();
+        
+        void Run(const std::string& datafile, const std::string& outputfile, const std::string& plotfile="");
+        
+    private:
+        void FindParameters(const std::vector<TH1F>& grams);
+        void WriteHistograms(const std::vector<TH1F>& grams, const std::string& plotfile);
+        void WriteParameters(const std::string& outputfile);
+        
+        GainMap m_gainMap;
+        std::vector<Parameters> m_params;
+        
+        static constexpr int s_totalChannels = 127; //Total channels in SABRE
+        static constexpr double s_241Am_alphaKE = 5.468; //MeV
+        static constexpr double s_gainFactor = 1.5; //For if you're dumb and the electronics gain needs adjusted
+    };
+}
+
+#endif /* Calibrator_hpp */

src/DataOrganizer.cpp

@@ -0,0 +1,163 @@
+#include "DataOrganizer.h"
+#include "TFile.h"
+#include "TTree.h"
+
+#include <iostream>
+
+namespace SabreCal {
+
+    DataOrganizer::DataOrganizer(const std::string& channelfile, const std::string& gainfile,
+                                 const std::string& calfile) :
+        m_channelMap(channelfile), m_gainMap(gainfile), m_calMap(calfile)
+    {
+    }
+
+    DataOrganizer::~DataOrganizer() {}
+
+    void DataOrganizer::Run(const std::string& inputdata, const std::string& outputdata)
+    {
+        if(!(m_channelMap.IsValid() && m_gainMap.IsValid() && m_calMap.IsValid()))
+        {
+            std::cerr<<"ERR -- Invalid map files at DataOrganizer::Run()"<<std::endl;
+            return;
+        }
+        
+        TFile* input = TFile::Open(inputdata.c_str(), "READ");
+        if(!input->IsOpen())
+        {
+            std::cerr<<"ERR -- Unable to open input data file "<<inputdata<<" at DataOrganizer::Run()"<<std::endl;
+            return;
+        }
+        
+        TTree* intree = (TTree*) input->Get("SPSTree");
+        
+        TFile* output = TFile::Open(outputdata.c_str(), "RECREATE");
+        if(!output->IsOpen())
+        {
+            std::cerr<<"ERR -- Unable to open output data file "<<inputdata<<" at DataOrganizer::Run()"<<std::endl;
+            return;
+        }
+        
+        TTree* outtree = new TTree("CalTree", "CalTree");
+        
+        ProcessedEvent* inevent = new ProcessedEvent();
+        intree->SetBranchAddress("event", &inevent);
+        
+        CalEvent outevent;
+        outtree->Branch("event", &outevent);
+        
+        std::vector<SabreTemp> rings, wedges;
+        double eTemp;
+        double ratio;
+        SabrePair this_pair;
+        
+        uint64_t nevents = intree->GetEntries();
+        m_stats.totalEvents = nevents;
+        double flush_percent = 0.05;
+        uint64_t count=0, flush_count=0, flush_val=nevents*flush_percent;
+        
+        for(uint64_t i=0; i<nevents; i++)
+        {
+            intree->GetEvent(i);
+            count++;
+            if(count == flush_val)
+            {
+                flush_count++;
+                count = 0;
+                std::cout<<"\rPercent of data processed: "<<flush_count*flush_percent*100.0<<"%"<<std::flush;
+            }
+            
+            //copy FP crap
+            outevent.xavg = inevent->xavg;
+            outevent.scintE = inevent->scintLeft;
+            outevent.cathodeE = inevent->cathode;
+            outevent.anodeFrontE = inevent->anodeFront;
+            outevent.anodeBackE = inevent->anodeBack;
+            outevent.scintT = inevent->scintLeftTime;
+            
+            for(int j=0; j<5; j++)
+            {
+                rings.clear();
+                wedges.clear();
+                auto& this_sabre = inevent->sabreArray[j];
+                
+                int64_t diff = this_sabre.rings.size() - this_sabre.wedges.size();
+                m_stats.sabreRingFrags += diff > 0 ? diff : 0;
+                m_stats.sabreWedgeFrags += diff < 0 ? -1*diff : 0;
+                for(auto& ring : this_sabre.rings)
+                {
+                    m_stats.totalSabreHits++;
+                    auto& ringGains = m_gainMap.GetParameters(ring.Ch);
+                    auto& ringCals = m_calMap.GetParameters(ring.Ch);
+                    eTemp = ringCals.slope*(ringGains.slope*ring.Long + ringGains.offset) + ringCals.offset;
+                    if(eTemp > s_sabreThreshold)
+                    {
+                        m_stats.goodSabreHits++;
+                        rings.emplace_back(eTemp, ring.Time, ring.Ch, false);
+                    }
+                    else
+                        m_stats.sabreBelowThreshold++;
+                }
+                for(auto& wedge : this_sabre.wedges)
+                {
+                    m_stats.totalSabreHits++;
+                    auto& wedgeGains = m_gainMap.GetParameters(wedge.Ch);
+                    auto& wedgeCals = m_calMap.GetParameters(wedge.Ch);
+                    eTemp = wedgeCals.slope*(wedgeGains.slope*wedge.Long + wedgeGains.offset) + wedgeCals.offset;
+                    if(eTemp > s_sabreThreshold)
+                    {
+                        m_stats.goodSabreHits++;
+                        wedges.emplace_back(eTemp, wedge.Time, wedge.Ch, false);
+                    }
+                    else
+                        m_stats.sabreBelowThreshold++;
+                }
+                
+                //Now match rings and wedges
+                for(auto& ring : rings)
+                {
+                    for(auto& wedge : wedges)
+                    {
+                        if(wedge.used || ring.used)
+                            continue;
+                        ratio = std::abs(1.0 - ring.energy/wedge.energy);
+                        if(ratio < s_sabreMatchCond)
+                        {
+                            auto& ringdata = m_channelMap.GetChannel(ring.gchan);
+                            auto& wedgedata = m_channelMap.GetChannel(wedge.gchan);
+                            this_pair.ringch = ring.gchan;
+                            this_pair.wedgech = wedge.gchan;
+                            this_pair.local_ring = ringdata.localChannel;
+                            this_pair.local_wedge = wedgedata.localChannel;
+                            this_pair.detID = wedgedata.detID;
+                            this_pair.ringE = ring.energy;
+                            this_pair.wedgeE = wedge.energy;
+                            outevent.sabre.push_back(this_pair);
+                            m_stats.pairsMade++;
+                            break;
+                        }
+                    }
+                }
+            }
+            outtree->Fill();
+        }
+        std::cout<<std::endl;
+        
+        input->Close();
+        output->cd();
+        outtree->Write(outtree->GetName(), TObject::kOverwrite);
+        output->Close();
+    }
+
+    void DataOrganizer::ShowStats()
+    {
+        std::cout<<"Total number of events: "<<m_stats.totalEvents<<std::endl;
+        std::cout<<"Total number of SABRE hits: "<<m_stats.totalSabreHits<<std::endl;
+        std::cout<<"Total number of good SABRE hits: "<<m_stats.goodSabreHits<<std::endl;
+        std::cout<<"Number of ring/wedge pairs made: "<<m_stats.pairsMade<<std::endl;
+        std::cout<<"Matching efficiency percentage: "<<((double)m_stats.pairsMade)/m_stats.goodSabreHits<<std::endl;
+        std::cout<<"Number of hits below threshold: "<<m_stats.sabreBelowThreshold<<std::endl;
+        std::cout<<"Number of wedge fragments: "<<m_stats.sabreWedgeFrags<<std::endl;
+        std::cout<<"Number of ring fragments: "<<m_stats.sabreRingFrags<<std::endl;
+    }
+}

src/DataOrganizer.h

@@ -0,0 +1,58 @@
+#ifndef DATA_ORGANIZER_H
+#define DATA_ORGANIZER_H
+
+#include "ChannelMap.h"
+#include "GainMap.h"
+#include "CalibrationMap.h"
+
+#include "CalDict/DataStructs.h"
+
+#include <string>
+
+namespace SabreCal {
+    
+    struct AnalysisStats
+    {
+        uint64_t totalEvents = 0;
+        uint64_t totalSabreHits = 0;
+        uint64_t goodSabreHits = 0; //Above threshold, good number for matching
+        uint64_t pairsMade = 0;
+        uint64_t sabreRingFrags = 0;
+        uint64_t sabreWedgeFrags = 0;
+        uint64_t sabreBelowThreshold = 0;
+    };
+
+    struct SabreTemp
+    {
+        SabreTemp(double e, double t, int g, bool u) :
+            energy(e), time(t), gchan(g), used(u)
+        {}
+        double energy;
+        double time;
+        int gchan;
+        bool used = false;
+    };
+
+    class DataOrganizer
+    {
+    public:
+        DataOrganizer(const std::string& channelfile, const std::string& gainfile, const std::string& calfile);
+        ~DataOrganizer();
+        
+        void Run(const std::string& inputdata, const std::string& outputdata);
+        void ShowStats();
+        
+    private:
+        ChannelMap m_channelMap;
+        GainMap m_gainMap;
+        CalibrationMap m_calMap;
+        
+        AnalysisStats m_stats;
+        
+        static constexpr double s_sabreMatchCond = 0.2; //Ring/wedge %diff
+        static constexpr double s_sabreThreshold = 0.2; //MeV
+        static constexpr double s_sabreTimeCond = 100.0; //ns
+    };
+}
+
+#endif

src/GainMap.cpp

@@ -0,0 +1,51 @@
+#include "GainMap.h"
+#include <fstream>
+
+namespace SabreCal {
+
+    GainMap::GainMap() :
+        m_isValid(false)
+    {
+    }
+
+    GainMap::GainMap(const std::string& filename) :
+        m_isValid(false)
+    {
+        Init(filename);
+    }
+
+    GainMap::~GainMap() {}
+
+    void GainMap::Init(const std::string& filename)
+    {
+        std::ifstream input(filename);
+        if(!input.is_open())
+        {
+            m_isValid = false;
+            return;
+        }
+        std::string junk;
+        int gchan;
+        Parameters pars;
+        
+        std::getline(input, junk);
+        std::getline(input, junk);
+        
+        while(input>>gchan)
+        {
+            input>>pars.slope>>pars.offset;
+            m_map[gchan] = pars;
+        }
+        
+        m_isValid = true;
+    }
+
+    const Parameters& GainMap::GetParameters(int gchan) const
+    {
+        auto iter = m_map.find(gchan);
+        if(iter != m_map.end())
+            return iter->second;
+        else
+            return m_dummyParams;
+    }
+}

src/GainMap.h

@@ -0,0 +1,30 @@
+#ifndef GAIN_MAP_H
+#define GAIN_MAP_H
+
+#include <string>
+#include <unordered_map>
+#include "CalibrationStructs.h"
+
+namespace SabreCal {
+
+    class GainMap
+    {
+    public:
+        GainMap();
+        GainMap(const std::string& filename);
+        ~GainMap();
+        
+        void Init(const std::string& filename);
+        
+        const Parameters& GetParameters(int gchan) const;
+        inline const bool IsValid() const { return m_isValid; }
+        
+    private:
+        std::unordered_map<int, Parameters> m_map;
+        Parameters m_dummyParams; //for null results
+        
+        bool m_isValid;
+    };
+}
+
+#endif

src/GainMatcher.cpp

@@ -50,7 +50,7 @@ namespace SabreCal {
 			{
 				count = 0;
 				flushes++;
-				std::cout<<"\rPercent of data processed: "<<flush_percent*flushes*100.0f<<"%"<<std::endl;
+				std::cout<<"\rPercent of data processed: "<<flush_percent*flushes*100.0f<<"%"<<std::flush;
 			}
 
 			for(int j=0; j<5; j++)
@@ -104,7 +104,7 @@ namespace SabreCal {
 		graph_array.resize(m_totalChannels);
 
 		//Make all of the wedge graphs, and get the gain match parameters
-		for(size_t i=0; i<m_firstRing; i++)
+		for(int i=0; i<m_firstRing; i++)
 		{
 			if(m_data[i].x.size() != 0)
 			{
@@ -120,7 +120,7 @@ namespace SabreCal {
 		}
 
 		//Now do rings, after applying parameters from wedges
-		for(size_t i=m_firstRing; i<m_totalChannels; i++)
+		for(int i=m_firstRing; i<m_totalChannels; i++)
 		{
 			if(m_data[i].x.size() != 0)
 			{
@@ -179,4 +179,4 @@ namespace SabreCal {
 		output.close();
 	}
 
-}
+}

src/main.cpp

@@ -0,0 +1,136 @@
+#include "GainMatcher.h"
+#include "Calibrator.h"
+#include "DataOrganizer.h"
+
+#include <string>
+#include <fstream>
+#include <iostream>
+
+int main(int argc, const char** argv)
+{
+    std::string inputfile;
+    std::string option;
+    if(argc < 2)
+    {
+        std::cerr<<"ERR -- SabreCal requires an input configuration file."<<std::endl;
+        return 1;
+    }
+    else if (argc == 2)
+    {
+        if(std::string(argv[1]) == "--help")
+        {
+            std::cout<<"SABRE Calibration Help"<<std::endl;
+            std::cout<<"To run: ./bin/SabreCal <option> <input config>"<<std::endl;
+            std::cout<<"Available Options"<<std::endl;
+            std::cout<<"--gainmatch: Only run gain-matching"<<std::endl;
+            std::cout<<"--calibrate: Only run calibration (requires gain-matching parameters)"<<std::endl;
+            std::cout<<"--apply: Apply calibration and gain-matching parameters to a dataset (requires gain-matching and        calibration parameters)"<<std::endl;
+            std::cout<<"--all: Run gain-matching, calibration, and apply to data set"<<std::endl;
+            std::cout<<"Default behavior (no option) is the same as --all"<<std::endl;
+            return 0;
+        }
+        inputfile = argv[1];
+        option = "";
+    }
+    else
+    {
+        inputfile = argv[2];
+        option = argv[1];
+    }
+    
+    std::ifstream input(argv[1]);
+    std::string junk;
+    
+    std::string gaindata, caldata, inputdata, outputdata;
+    std::string gainplots, calplots;
+    std::string gainfile, calfile, channelfile;
+    int ring_to_match, wedge_to_match;
+    
+    input>>junk>>gaindata;
+    input>>junk>>gainplots;
+    input>>junk>>caldata;
+    input>>junk>>calplots;
+    input>>junk>>inputdata;
+    input>>junk>>outputdata;
+    input>>junk>>gainfile;
+    input>>junk>>calfile;
+    input>>junk>>channelfile;
+    input>>junk>>ring_to_match>>junk>>wedge_to_match;
+    
+    std::cout<<"----------SABRE Calibration----------"<<std::endl;
+    std::cout<<"Gain-Matching Data: "<<gaindata<<std::endl;
+    std::cout<<"Gain-Matching Plots: "<<gainplots<<std::endl;
+    std::cout<<"Gain-Match Parameter file: "<<gainfile<<std::endl;
+    std::cout<<"Ring-to-Match: "<<ring_to_match<<" Wedge-to-Match: "<<wedge_to_match<<std::endl;
+    std::cout<<"Calibration Data: "<<caldata<<std::endl;
+    std::cout<<"Calibration Plots: "<<calplots<<std::endl;
+    std::cout<<"Calibration Parameter file: "<<calfile<<std::endl;
+    std::cout<<"Data to Calibrate: "<<inputdata<<std::endl;
+    std::cout<<"Calibration Output: "<<outputdata<<std::endl;
+    std::cout<<"Channel Map: "<<channelfile<<std::endl;
+    
+    if(option == "--gainmatch")
+    {
+        std::cout<<"Calculating SABRE gain-matching parameters..."<<std::endl;
+        SabreCal::GainMatcher matcher(channelfile, ring_to_match, wedge_to_match);
+        if(gainplots == "None")
+            matcher.Run(gaindata, gainfile);
+        else
+            matcher.Run(gaindata, gainfile, gainplots);
+    }
+    else if (option == "--calibrate")
+    {
+        std::cout<<"Calculating SABRE calibration parameters..."<<std::endl;
+        SabreCal::Calibrator calib(gainfile);
+        if(calplots == "None")
+            calib.Run(caldata, calfile);
+        else
+            calib.Run(caldata, calfile, calplots);
+    }
+    else if (option == "--apply")
+    {
+        std::cout<<"Applying SABRE gain-matching and calibration parameters to dataset..."<<std::endl;
+        SabreCal::DataOrganizer organ(channelfile, gainfile, calfile);
+        organ.Run(inputdata, outputdata);
+        organ.ShowStats();
+    }
+    else if (option == "" || option == "--all")
+    {
+        std::cout<<"Calculating SABRE gain-matching parameters..."<<std::endl;
+        SabreCal::GainMatcher matcher(channelfile, ring_to_match, wedge_to_match);
+        if(gainplots == "None")
+            matcher.Run(gaindata, gainfile);
+        else
+            matcher.Run(gaindata, gainfile, gainplots);
+        std::cout<<"Calculating SABRE calibration parameters..."<<std::endl;
+        SabreCal::Calibrator calib(gainfile);
+        if(calplots == "None")
+            calib.Run(caldata, calfile);
+        else
+            calib.Run(caldata, calfile, calplots);
+        std::cout<<"Applying SABRE gain-matching and calibration parameters to dataset..."<<std::endl;
+        SabreCal::DataOrganizer organ(channelfile, gainfile, calfile);
+        organ.Run(inputdata, outputdata);
+        organ.ShowStats();
+    }
+    else if (option == "--help")
+    {
+        std::cout<<"SABRE Calibration Help"<<std::endl;
+        std::cout<<"To run: ./bin/SabreCal <option> <input config>"<<std::endl;
+        std::cout<<"Available Options"<<std::endl;
+        std::cout<<"--gainmatch: Only run gain-matching"<<std::endl;
+        std::cout<<"--calibrate: Only run calibration (requires gain-matching parameters)"<<std::endl;
+        std::cout<<"--apply: Apply calibration and gain-matching parameters to a dataset (requires gain-matching and        calibration parameters)"<<std::endl;
+        std::cout<<"--all: Run gain-matching, calibration, and apply to data set"<<std::endl;
+        std::cout<<"Default behavior (no option) is the same as --all"<<std::endl;
+        return 0;
+    }
+    else
+    {
+        std::cout<<"Unrecognized option passed to SabreCal. Use --help to see available options"<<std::endl;
+        return 1;
+    }
+    
+    std::cout<<"Finished."<<std::endl;
+    return 0;
+}