off-motion-receptive-fields/receptiveFields/getRFsAlignedWithFit.m

function [offX, offY, onX, onY] = getRFsAlignedWithFit(StimTableCell, rSqThresh, respIndThresh, varargin)

if nargin > 3
    alignAll = varargin{1};
    if nargin > 4
        alignOrientation = varargin{2};
    else
        alignOrientation = true;
    end
else
    alignAll = false;
    alignOrientation = true;
end


[tcArrayCell, responseIndArrayCell, rSquareArrayCell, fitParamsCell, ...
  flyIndsCell, tcExtCellArray, tcArgExtCellArray] = getStimArraysForSameRois(StimTableCell);                                          
% Align to fit
posCell = cellfun(@(x) arrayfun(@(y) y.b1, x, 'uni', 0), fitParamsCell, 'uni', 1);
widthCell = cellfun(@(x) arrayfun(@(y) 2 * (2 * sqrt(log(2))) * y.c1, x, 'uni', 0), ...
                    fitParamsCell, 'uni', 1); % The 2 factor is because of bar separation.

lagsCell = cellfun(@(x, y) round(x - size(y, 2) / 2), posCell, tcArrayCell, 'uni', 0);
barRFs = cellfun(@(x, y) alignRFsToAbsMax(x, 0, y'), tcArrayCell, lagsCell, 'uni', 0);
validIndsCell = cellfun(@(x, y) x(:) > rSqThresh & y(:) > respIndThresh, ...
                        rSquareArrayCell, responseIndArrayCell, 'uni', 0)';
%% Blank epoch was already deleted, now delete vertical bars on edges of screen.
barRFs{2}(:, end-1: end) = [];
barRFs{4}(:, end-1: end) = [];
barRFs{2}(:, 1: 2) = [];
barRFs{4}(:, 1: 2) = [];
%%
if alignAll
    validAll = validIndsCell{1} & validIndsCell{2} & ...
               validIndsCell{3} & validIndsCell{4};
    offX = barRFs{1}(validAll, :);
    offY = barRFs{2}(validAll, :);
    onX = barRFs{3}(validAll, :);
    onY = barRFs{4}(validAll, :);
elseif alignOrientation
    offX = barRFs{1}(validIndsCell{1}&validIndsCell{2}, :);
    offY = barRFs{2}(validIndsCell{2}&validIndsCell{1}, :);
    onX = barRFs{3}(validIndsCell{3}&validIndsCell{4}, :);
    onY = barRFs{4}(validIndsCell{4}&validIndsCell{3}, :);
else
    offX = barRFs{1}(validIndsCell{1}, :);
    offY = barRFs{2}(validIndsCell{2}, :);
    onX = barRFs{3}(validIndsCell{3}, :);
    onY = barRFs{4}(validIndsCell{4}, :);
end


end