FlySongClusterSegment/makeDefaultOptions.m at master · dstern/FlySongClusterSegment · GitHub

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function options = makeDefaultOptions(options)


    %smoothSigma -> standard dev. of gaussian with which to smooth data,
    %               use -1 to have no smoothing (default = 5)

    %sigmaThreshold -> # of standard deviations above zero required for
    %                  peaks (default = 2)

    %diffThreshold -> half-width of peak window (default = 150)

    %noiseLevel -> noise level (default = .005)

    %template_pca_dimension -> # of modes in clustering PCA (default = 50)

    %first_mode -> first mode in the PCA to uselikelihood model (default = 5)

    %k -> number of clusters in kmeans (default = 12)

    %maxNumPeaks -> maximum # of peaks to use in clustering (default = 10000);

    %kmean_replicates -> # of replicates in kmeans (default = 5)

    %kmeans_maxIter -> max # of iterations for kmeans (default = 1000)

    %fs = sampling frequency of original data

    %baseline_quantile = quantile of noise data to take as baseline value.
    %                    If set less than or equal to zero, there will be no
    %                    baseline (default = .9)

    %min_template_size = minimum # of peaks in a template (default = 50)

    %baseline_threshold = likelihood threshold for baseline (default = 0)

    %use_likelihood_threshold = logical to use baseline threshold or not (default = false)


    smoothSigma_default = 3;
    sigmaThreshold_default = 2;
    diffThreshold_default = 150;
    noiseLevel_default = -1;
    first_mode_default = 2;
    template_pca_dimension_default = 50;
    k_default = 12;
    maxNumPeaks_default = 10000;
    kmeans_replicates_default = 5;
    kmeans_maxIter_default = 1000;
    fs_default = 1e4;
    baseline_quantile_default = .9;
    min_template_size_default = 50;
    baseline_threshold_default = 0;
    use_likelihood_threshold_default = false;


    if options.setAll

        options.smoothSigma = smoothSigma_default;
        options.sigmaThreshold = sigmaThreshold_default;
        options.diffThreshold = diffThreshold_default;
        options.noiseLevel = noiseLevel_default;
        options.first_mode = first_mode_default;
        options.k = k_default;
        options.maxNumPeaks = maxNumPeaks_default;
        options.kmeans_replicates = kmeans_replicates_default;
        options.template_pca_dimension = template_pca_dimension_default;
        options.kmeans_maxIter = kmeans_maxIter_default;
        options.fs = fs_default;
        options.baseline_quantile = baseline_quantile_default;
        options.min_template_size = min_template_size_default;
        options.baseline_threshold = baseline_threshold_default;
        options.use_likelihood_threshold = use_likelihood_threshold_default;

    else

        if ~isfield(options,'smoothSigma') || isempty(options.smoothSigma)
            options.smoothSigma = smoothSigma_default;
        end


        if ~isfield(options,'sigmaThreshold') || isempty(options.sigmaThreshold)
            options.sigmaThreshold = sigmaThreshold_default;
        end


        if ~isfield(options,'diffThreshold') || isempty(options.diffThreshold)
            options.diffThreshold = diffThreshold_default;
        end


        if ~isfield(options,'noiseLevel') || isempty(options.noiseLevel)
            options.noiseLevel = noiseLevel_default;
        end


        if ~isfield(options,'first_mode') || isempty(options.first_mode)
            options.first_mode = first_mode_default;
        end


        if ~isfield(options,'k') || isempty(options.k)
            options.k = k_default;
        end


        if ~isfield(options,'maxNumPeaks') || isempty(options.maxNumPeaks)
            options.maxNumPeaks = maxNumPeaks_default;
        end


        if ~isfield(options,'kmeans_replicates') || isempty(options.kmeans_replicates)
            options.kmeans_replicates = kmeans_replicates_default;
        end


        if ~isfield(options,'template_pca_dimension') || isempty(options.template_pca_dimension)
            options.template_pca_dimension = template_pca_dimension_default;
        end


        if ~isfield(options,'kmeans_maxIter') || isempty(options.kmeans_maxIter)
            options.kmeans_maxIter = kmeans_maxIter_default;
        end


        if ~isfield(options,'fs') || isempty(options.fs)
            options.fs = fs_default;
        end


        if ~isfield(options,'baseline_quantile') || isempty(options.baseline_quantile)
            options.baseline_quantile = baseline_quantile_default;
        end


        if ~isfield(options,'min_template_size') || isempty(options.min_template_size)
            options.min_template_size = min_template_size_default;
        end

        if ~isfield(options,'baseline_threshold') || isempty(options.baseline_threshold)
            options.baseline_threshold = baseline_threshold_default;
        end


        if ~isfield(options,'use_likelihood_threshold') || isempty(options.use_likelihood_threshold)
            options.use_likelihood_threshold = use_likelihood_threshold_default;
        end

    end