Create hmrR_PreprocessIntensity_MedianFilter.m

% SYNTAX:

% intensity = hmrR_PreprocessIntensity_MedianFilter( intensity )

%

% UI NAME:

% hmrR_PreprocessIntensity_MedianFilter

%

% DESCRIPTION:

% Applies a median filter to data to remove huge spikes.

%

% INPUT:

% intensity - SNIRF data type where the d matrix is intensity

%

% OUTPUT:

% intensity - SNIRF data type where the d matrix is intensity

%

% USAGE OPTIONS:

% Intensity_to_Intensity: d = hmrR_PreprocessIntensity_MedianFilter(data)

function d = hmrR_PreprocessIntensity_MedianFilter( intensity)

for ii=1:length(intensity)

    d = intensity(ii).GetDataTimeSeries();

    for j = 1:size(d,2)

        foo = d(:,j);

        xdata = (1:length( foo))';

        d(:,j) = interp1(xdata(~isnan( foo)), foo(~isnan( foo)),xdata,'spline');

        new_signal = zeros(size(foo));

        new_signal(1) = foo(1);

        new_signal(end) = foo(end);

        for tp = 2:length(foo)-1

            values = foo([tp-1,tp,tp+1]);

            median_value = median(values);

            new_signal(tp) = median_value;

        end

        d(:,j) = new_signal;

    end

    intensity(ii).SetDataTimeSeries(d);

end