icarus_tool::ROIMorphological2D Class Reference

Inheritance diagram for icarus_tool::ROIMorphological2D:

Public Member Functions
	ROIMorphological2D (const fhicl::ParameterSet &pset)
	~ROIMorphological2D ()
void	configure (const fhicl::ParameterSet &pset) override
void	initializeHistograms (art::TFileDirectory &) override
void	FindROIs (const art::Event &, const ArrayFloat &, const std::vector< raw::ChannelID_t > &, const geo::PlaneID &, ArrayFloat &, ArrayBool &) override
Public Member Functions inherited from icarus_tool::IROILocator
virtual	~IROILocator () noexcept=default

Private Member Functions
float	getMedian (const icarus_signal_processing::VectorFloat, const unsigned int) const

Private Attributes
bool	fOutputHistograms
	Diagnostic histogram output. More...
std::vector< size_t >	fStructuringElement
	Structuring element for morphological filter. More...
std::vector< float >	fThreshold
	Threshold to apply for saving signal. More...
std::vector< float >	fMedianVec
std::vector< float >	fRMSVec
std::vector< float >	fMinValVec
std::vector< float >	fMaxValVec
std::vector< float >	fRangeVec
std::vector< bool >	fHasROIVec
TTree *	fTupleTree
	output analysis tree More...

Additional Inherited Members
Public Types inherited from icarus_tool::IROILocator
using	VectorBool = std::vector< bool >
using	VectorFloat = std::vector< float >
using	ArrayBool = std::vector< VectorBool >
using	ArrayFloat = std::vector< VectorFloat >
using	PlaneIDVec = std::vector< geo::PlaneID >

Detailed Description

Definition at line 30 of file ROIMorphological2D_tool.cc.

Constructor & Destructor Documentation

icarus_tool::ROIMorphological2D::ROIMorphological2D ( const fhicl::ParameterSet &  pset )

explicit

Definition at line 71 of file ROIMorphological2D_tool.cc.

                                                                    : fOutputHistograms(false)
{
    configure(pset);
}

icarus_tool::ROIMorphological2D::~ROIMorphological2D

(

)

Definition at line 76 of file ROIMorphological2D_tool.cc.

{
}

Member Function Documentation

void icarus_tool::ROIMorphological2D::configure ( const fhicl::ParameterSet &  pset )

overridevirtual

Implements icarus_tool::IROILocator.

Definition at line 80 of file ROIMorphological2D_tool.cc.

{
    // Start by recovering the parameters
    fStructuringElement   = pset.get<std::vector<size_t> >("StructuringElement", std::vector<size_t>()={8,16});
    fThreshold            = pset.get<std::vector<float>  >("Threshold",          std::vector<float>()={2.75,2.75,2.75});
     
//    fButterworthOrder     = pset.get<unsigned int        >("ButterworthOrder",     2);
//    fButterworthThreshold = pset.get<unsigned int        >("ButterworthThreshld", 30);

//    fButterworthFilter = std::make_unique<icarus_signal_processing::HighPassButterworthFilter>(fButterworthThreshold,fButterworthOrder,4096);

    return;
}

void icarus_tool::ROIMorphological2D::FindROIs ( const art::Event &  event, const ArrayFloat &  constInputImage, const std::vector< raw::ChannelID_t > &  channelVec, const geo::PlaneID &  planeID, ArrayFloat &  morphedWaveforms, ArrayBool &  outputROIs  )

overridevirtual

Implements icarus_tool::IROILocator.

Definition at line 94 of file ROIMorphological2D_tool.cc.

{
    if (morphedWaveforms.size() != constInputImage.size()) morphedWaveforms.resize(constInputImage.size(),icarus_signal_processing::VectorFloat(constInputImage[0].size()));

    for(auto& morph : morphedWaveforms) std::fill(morph.begin(),morph.end(),0.);  // explicit initialization

    // Make a local copy of the input image so we can do some smoothing
    ArrayFloat inputImage(constInputImage.size(),VectorFloat(constInputImage[0].size()));

    // get an instance of the waveform tools
    icarus_signal_processing::WaveformTools<float> waveformTools;

    for(size_t waveIdx = 0; waveIdx < inputImage.size(); waveIdx++) waveformTools.triangleSmooth(constInputImage[waveIdx],inputImage[waveIdx]);

//    ArrayFloat inputImage(constInputImage);

//    for(auto& waveform : inputImage) (*fButterworthFilter)(waveform);

    // Use this to get the 2D Dilation of each waveform
    icarus_signal_processing::Dilation2D(fStructuringElement[0],fStructuringElement[1])(inputImage.begin(),inputImage.size(),morphedWaveforms.begin());

    if (fOutputHistograms)
    {
        fMedianVec.clear();
        fRMSVec.clear();
        fMinValVec.clear();
        fMaxValVec.clear();
        fRangeVec.clear();
        fHasROIVec.clear();
    }

    // Now traverse each waveform and look for the ROIs
    for(size_t waveIdx = 0; waveIdx < morphedWaveforms.size(); waveIdx++)
    {
        // We start working with the morphed waveform
        VectorFloat& morphedWave = morphedWaveforms[waveIdx];

        // We need to zero suppress so we can find the rms
        float median = getMedian(morphedWave, morphedWave.size());

        for(auto& val : morphedWave) val -= median;

//        float threshold = rms * fThreshold[planeID.Plane];
        float threshold = fThreshold[planeID.Plane];

        // Right size the selected values array
        VectorBool& selVals = outputROIs[waveIdx];

        if (selVals.size() != morphedWave.size()) selVals.resize(morphedWave.size());

        std::fill(selVals.begin(),selVals.end(),false);

        bool hasROI(false);

        for(size_t idx = 0; idx < morphedWave.size(); idx++)
        {
            if (morphedWave[idx] > threshold) 
            {
                selVals[idx] = true;
                hasROI       = true;
            }
        }

        if (fOutputHistograms)
        {
            VectorFloat rmsVec = morphedWave;
            size_t      maxIdx = 0.75 * rmsVec.size();

            std::nth_element(rmsVec.begin(), rmsVec.begin() + maxIdx, rmsVec.end());

            float rms    = std::sqrt(std::inner_product(rmsVec.begin(), rmsVec.begin() + maxIdx, rmsVec.begin(), 0.) / float(maxIdx));
            float minVal = *std::min_element(morphedWave.begin(),morphedWave.end());
            float maxVal = *std::max_element(morphedWave.begin(),morphedWave.end());
            
            fMedianVec.emplace_back(median);
            fRMSVec.emplace_back(rms);
            fMinValVec.emplace_back(minVal);
            fMaxValVec.emplace_back(maxVal);
            fRangeVec.emplace_back(maxVal-minVal);
            fHasROIVec.emplace_back(hasROI);
        }
    }

    if (fOutputHistograms) fTupleTree->Fill();
     
    return;
}

float icarus_tool::ROIMorphological2D::getMedian ( const icarus_signal_processing::VectorFloat  vals, const unsigned int  nVals  ) const

private

Definition at line 182 of file ROIMorphological2D_tool.cc.

{
    float median(0.);

    if (nVals > 2) 
    {
        if (nVals % 2 == 0) 
        {
            const auto m1 = vals.begin() + nVals / 2 - 1;
            const auto m2 = vals.begin() + nVals / 2;
            std::nth_element(vals.begin(), m1, vals.begin() + nVals);
            const auto e1 = *m1;
            std::nth_element(vals.begin(), m2, vals.begin() + nVals);
            const auto e2 = *m2;
            median = (e1 + e2) / 2.0;
        } 
        else 
        {
            const auto m = vals.begin() + nVals / 2;
            std::nth_element(vals.begin(), m, vals.begin() + nVals);
            median = *m;
        }
    }

    return median;
}

void icarus_tool::ROIMorphological2D::initializeHistograms ( art::TFileDirectory &  histDir )

overridevirtual

Implements icarus_tool::IROILocator.

Definition at line 209 of file ROIMorphological2D_tool.cc.

{
    // It is assumed that the input TFileDirectory has been set up to group histograms into a common
    // folder at the calling routine's level. Here we create one more level of indirection to keep
    // histograms made by this tool separate.

    fTupleTree = histDir.make<TTree>("ROIFinder", "Tree by ROIMorphological2D_tool");

    fTupleTree->Branch("medians",  "std::vector<float>", &fMedianVec);
    fTupleTree->Branch("RMS",      "std::vector<float>", &fRMSVec);
    fTupleTree->Branch("minvals",  "std::vector<float>", &fMinValVec);
    fTupleTree->Branch("maxvals",  "std::vector<float>", &fMaxValVec);
    fTupleTree->Branch("range",    "std::vector<float>", &fRangeVec);
    fTupleTree->Branch("hasROI",   "std::vector<bool>",  &fHasROIVec);

    fOutputHistograms = true;
    
    return;
}

Member Data Documentation

std::vector<bool> icarus_tool::ROIMorphological2D::fHasROIVec

private

Definition at line 62 of file ROIMorphological2D_tool.cc.

std::vector<float> icarus_tool::ROIMorphological2D::fMaxValVec

private

Definition at line 60 of file ROIMorphological2D_tool.cc.

std::vector<float> icarus_tool::ROIMorphological2D::fMedianVec

private

Definition at line 57 of file ROIMorphological2D_tool.cc.

std::vector<float> icarus_tool::ROIMorphological2D::fMinValVec

private

Definition at line 59 of file ROIMorphological2D_tool.cc.

bool icarus_tool::ROIMorphological2D::fOutputHistograms

private

Diagnostic histogram output.

Definition at line 46 of file ROIMorphological2D_tool.cc.

std::vector<float> icarus_tool::ROIMorphological2D::fRangeVec

private

Definition at line 61 of file ROIMorphological2D_tool.cc.

std::vector<float> icarus_tool::ROIMorphological2D::fRMSVec

private

Definition at line 58 of file ROIMorphological2D_tool.cc.

std::vector<size_t> icarus_tool::ROIMorphological2D::fStructuringElement

private

Structuring element for morphological filter.

Definition at line 49 of file ROIMorphological2D_tool.cc.

std::vector<float> icarus_tool::ROIMorphological2D::fThreshold

private

Threshold to apply for saving signal.

Definition at line 50 of file ROIMorphological2D_tool.cc.

TTree* icarus_tool::ROIMorphological2D::fTupleTree

private

output analysis tree

Definition at line 64 of file ROIMorphological2D_tool.cc.

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The documentation for this class was generated from the following file:

• ROIMorphological2D_tool.cc