VisualTraceCheck/threshEstimate_v2.m at main · NERD-CO/VisualTraceCheck · GitHub

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function [ outthresh , outKclu ] = threshEstimate_v2( sampData , spkData,  spkFS , posnegFlag )
%UNTITLED7 Summary of this function goes here
%   Detailed explanation goes here
% V2 - Added negative threshold 12/31/2017

startThresh = 4;
startKclu = 6;
crit = true;

knCount = 0;
thCount = 0;

while crit

    if posnegFlag
        thresh = (mean(double(sampData)) + round(std(double(sampData)) * startThresh));
        noise = (mean(double(sampData)) + round(std(double(sampData)) * 12));
    else
        thresh = (mean(double(sampData)) - round(std(double(sampData)) * startThresh));
        noise = (mean(double(sampData)) - round(std(double(sampData)) * 12));
    end

    minDist = round(spkFS/1000) * 2; % was 1.9

    [ waveData ] = extractWaveforms_Clz_v01(spkData, thresh, noise, minDist, spkFS);

    waveForms = waveData.allWaves.waves;

    % STEP 4 COMPILE FEATURES

    if size(waveForms,2) < 7
        outKclu = startKclu;
        outthresh = startThresh;
        return
    end

    [ xFeats ] = createSpkFeatures( waveForms, spkFS  );

    % STEP 5 OBTAIN INITIAL CLUSTERS

    [idxF, Cen] = kmeans(xFeats,startKclu,'Distance','cityblock',...
        'Replicates',6);

    if size(xFeats,1) < 30
        outKclu = startKclu;
        outthresh = startThresh;
        crit = false;
    else

        [ ~ , lmetrics , ~] = spkClusterQual( xFeats, idxF, Cen, 1 );

        if startThresh <= 6

            if all(lmetrics.IsDs < 20 | lmetrics.LRat > 0.4)
                startThresh = startThresh + 0.5;
            elseif any(lmetrics.IsDs > 20 | lmetrics.LRat < 0.4)
                if sum(lmetrics.IsDs > 20 & lmetrics.LRat < 0.4) >= 2
                    outKclu = startKclu;
                    outthresh = startThresh;
                    crit = false;
                else

                    if knCount == thCount

                        startThresh = startThresh + 0.5;
                        thCount = thCount + 1;
                        crit = true;

                    elseif knCount ~= thCount

                        startKclu = startKclu - 1;
                        knCount = knCount + 1;
                        crit = true;

                    end
                end
            end

        else
            outKclu = 5;
            outthresh = 5;
            crit = false;
        end
    end
end


end