function [ output_args ] = sloPhoBoPhotoPref( data,minY,maxY )
%sloPhoBoPhotoPref breaks down the output of the slow photo box LabView .vi
%program and returns a MATLAB struct with useful metrics
% function name = SLOw PHOto BOx PHOTOtactic PREFerence
%=========================================================================
% Usage:
% output_args = sloPhoBoPhotoPref( data,minY,maxY )
% Inputs:
%       * data = t x N matrix of tracking centroid position values, where t
%       is number of data points recorded in each experiment, normally 24
%       * minY = lowest value of the .vi ROI bounds (bottom of the tubes)
%       * maxY = highest value of the .vi ROI bounds (top of the tubes)
% Output structure contains these objects:
%           * .prefs = vector of the light choice probabilities of each fly.
%           * .count = number of trials completed by each fly.
%           * .raw = the original data, stripped of timestamps.
%           * .thresh = choices thresholded by the edge of the shade, but without missing value NaNs.
%           * .flyID = matrix with index row, prefs and count

%calculate shade boundary position
edgeShade=(maxY-minY)/2;

% discard first two rows (which are timekeeping and indexing), detect missing values
data=data(:,3:end);
data(data==32767)=NaN;

%convert positions into shade/light scores based on edgeShade cutoff, retain missing values
dataThresholded=data<edgeShade;
dataThresholded=double(dataThresholded);
dataThresholded(isnan(data))=NaN;

%calculate mean pref and number of turns completed per ROI
prefs=nanmean(dataThresholded);
count=sum(~isnan(dataThresholded));

%outputs photopreference and counts and raw Y-positions and shade boolean
%for slowphotobox
output_args.prefs=prefs;
output_args.count=count;
output_args.raw=data;
output_args.thresh=dataThresholded;
output_args.flyID=[1:size(data,2);prefs;count];

end