RawDigitCorrelatedCorrectionAlg.h

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#ifndef RAWDIGITCORRELATEDCORRECTIONALG_H
#define RAWDIGITCORRELATEDCORRECTIONALG_H
////////////////////////////////////////////////////////////////////////
//
// Class:       RawDigitCorrelatedCorrectionAlg
// Module Type: algorithm
// File:        RawDigitCorrelatedCorrectionAlg.cxx
//
//              The intent of this algorithm is to perform "correlated noise"
//              correction across the input waveforms
//
// Configuration parameters:
//
// TheChoseWire          - Wire chosen for "example" hists
// MaxPedestalDiff       - Baseline difference to pedestal to flag
// SmoothCorrelatedNoise - Turns on the correlated noise suppression
// NumWiresToGroup       - When removing correlated noise, # wires to group
// FillHistograms        - Turn on histogram filling for diagnostics
// RunFFTInputWires      - FFT analyze the input RawDigits if true - diagnostics
// RunFFTCorrectedWires  - FFT analyze the output RawDigits if true - diagnostics
// TruncateTicks:        - Provide mechanism to truncate a readout window to a smaller size
// WindowSize:           - The desired size of the output window
// NumTicksToDropFront:  - The number ticks dropped off the front of the original window
//
//
// Created by Tracy Usher (usher@slac.stanford.edu) on January 6, 2016
// Based on work done by Brian Kirby, Mike Mooney and Jyoti Joshi
//
////////////////////////////////////////////////////////////////////////

#include "RawDigitNoiseFilterDefs.h"
#include "fhiclcpp/ParameterSet.h"
#include "art/Framework/Services/Registry/ServiceHandle.h"
#include "art_root_io/TFileService.h"
#include "larcore/Geometry/Geometry.h"

#include "TH1.h"
#include "TH2.h"
#include "TProfile.h"
#include "TProfile2D.h"

#include <set>

namespace caldata
{
class RawDigitCorrelatedCorrectionAlg
{
public:

    // Copnstructors, destructor.
    RawDigitCorrelatedCorrectionAlg(fhicl::ParameterSet const & pset);
    ~RawDigitCorrelatedCorrectionAlg();

    // Provide for initialization
    void reconfigure(fhicl::ParameterSet const & pset);
    void initializeHists(art::ServiceHandle<art::TFileService>&);

    void removeCorrelatedNoise(RawDigitAdcIdxPair& digitIdxPair,
                               unsigned int        viewIdx,
                               std::vector<float>& truncMeanWireVec,
                               std::vector<float>& truncRmsWireVec,
                               std::vector<short>& minMaxWireVec,
                               std::vector<short>& meanWireVec,
                               std::vector<float>& skewnessWireVec,
                               std::vector<float>& neighborRatioWireVec,
                               std::vector<float>& pedCorWireVec,
                               unsigned int& fftSize, unsigned int& halfFFTSize,
                               void* fplan, void* rplan) const;

private:

    void smoothCorrectionVec(std::vector<float>&, unsigned int&) const;

    template<class T> T getMedian(std::vector<T>&, T) const;

    template <typename T> void findPeaks(typename std::vector<T>::iterator startItr,
                                         typename std::vector<T>::iterator stopItr,
                                         std::vector<std::tuple<size_t,size_t,size_t>>& peakTupleVec,
                                         T                                 threshold,
                                         size_t                            firstTick) const;

    // Fcl parameters.
    float                fTruncMeanFraction;     ///< Fraction for truncated mean
//    bool                 fSmoothCorrelatedNoise; ///< Should we smooth the noise?
    bool                 fApplyCorSmoothing;     ///< Attempt to smooth the correlated noise correction?
    bool                 fApplyFFTCorrection;    ///< Use an FFT to get the correlated noise correction
    bool                 fFillFFTHistograms;     ///< Fill associated FFT histograms
    std::vector<size_t>  fFFTHistsWireGroup;     ///< Wire Group to pick on
    std::vector<size_t>  fFFTNumHists;           ///< Number of hists total per view
    std::vector<double>  fFFTHistsStartTick;     ///< Starting tick for histograms
    std::vector<double>  fFFTMinPowerThreshold;  ///< Threshold for trimming FFT power spectrum
    std::vector<size_t>  fNumWiresToGroup;       ///< If smoothing, the number of wires to look at
    bool                 fFillHistograms;        ///< if true then will fill diagnostic hists
    bool                 fRunFFTCorrected;       ///< Should we run FFT's on corrected wires?
    std::vector<float>   fNumRmsToSmoothVec;     ///< # "sigma" to smooth correlated correction vec

    std::vector<std::set<size_t>> fBadWiresbyViewAndWire;

    // Useful services, keep copies for now (we can update during begin run periods)
    art::ServiceHandle<geo::Geometry>            fGeometry;             ///< pointer to Geometry service
};

} // end caldata namespace

#endif