Mouse-threat-and-escape-CBRAIN/subfunc/clean_coordinates.m

function xy_clean = clean_coordinates(xy, sigma)
if nargin ==1, sigma = 2.56; end
xy_clean = xy;
speed = [0, mean([abs(diff(xy(1,:))); abs(diff(xy(2,:)))])];
speed_threshold = mean(speed, 'omitnan')+sigma*std(speed, 'omitnan');

% Speed-based outlier elimination
outliers = find(speed>speed_threshold);
xy_clean(:,outliers-1) = nan;
xy_clean(:,outliers) = nan;
xy_clean(:,outliers+1) = nan;

bad = find(speed==0); % Proc not moving frames
bad(1)=[];
xy_clean(:,bad) = nan;

% interpolate empty spots
xy_clean(1,:) = interp_nan(xy_clean(1,:));
xy_clean(2,:) = interp_nan(xy_clean(2,:));
end

%% subfunction
function y = interp_nan(x)
nanx = isnan(x); t = 1:numel(x); 
y = x; y(nanx) = interp1(t(~nanx), x(~nanx), t(nanx));
end