optimizeTrackingParameters.m

function [brThresh brFilt optTime] = optimizeTrackingParameters(vid, threshVals, filtVals, nframes, taglist)

%Inputs:
%vid: VideoReader object
%threshVals - range of bradley threshold values to test
%filtVals - range of bradley threshold values to test
%nframes - how many frames to sample over?


%Outputs:
%brThresh - optimal threshold value
%brFilt - optimal filter size value
%
%% Track across frames
frameIndex = round(linspace(1,vid.NumberOfFrames, nframes));
outData = nan(numel(threshVals), numel(filtVals), nframes,2);
h = waitbar(0, 'Optimizing tracking across frames...');
for i = 1:nframes
    %%
    %i
    im = rgb2gray(read(vid,frameIndex(i)));
    imshow(im);
    for j = 1:numel(threshVals)
        %j
        for k = 1:numel(filtVals)
            %k
            tic
            F = locateCodes(im,'threshMode', 1,'sizeThresh', [300 1500], 'bradleyFilterSize', [filtVals(k) filtVals(k)], 'bradleyThreshold', threshVals(j), 'vis', 0);
            timeS = toc;
            if ~isempty(F)
                outData(j,k,i,1) = sum(ismember([F.number], taglist));
                
            end
            outData(j,k,i,2) = timeS;
        end
    end
    waitbar(i/nframes,h)
end

%% Normalize and plot
outData(isnan(outData)) = 0; %Replace nans with zeros;

nbees = sum(outData(:,:,:,1),3);
nbeesNorm = nbees./max(max(nbees));
%Visualize performance surface

%% Identify maxima
[r,c] = find(nbeesNorm == 1);
brThresh = threshVals(r);
brFilt = filtVals(c);


%% track time spent 
timeSpent = outData(:,:,:,2);
timeSpent = mean(timeSpent,3);
optTime = timeSpent(find(nbeesNorm == 1));

%% break ties with time performance
if numel(brThresh) > 1 %If there's more than one optimum
    ind = find(optTime == min(optTime));
    ind = ind(1); %Tie breaker
    brThresh = brThresh(ind);
    brFilt = brFilt(ind);
    [r,c] = find(timeSpent == optTime(ind));
end

subplot(2,1,1);
imagesc(nbees);
colormap hot
set(gca, 'XTick', 1:numel(filtVals), 'XTickLabels', filtVals, 'YTick', 1:numel(threshVals), 'YTickLabels', threshVals);
colorbar
hold on
plot(c,r, 'go', 'MarkerSize', 30);
text(c,r,strcat('Optimum: thresh = ', num2str(brThresh), ',filter size = ', num2str(brFilt)));
hold off
subplot(2,1,2);
imagesc(timeSpent);
colormap hot
colorbar
hold on
plot(c,r, 'go', 'MarkerSize', 30);
hold off