showCellMatching.m

function fig = showCellMatching(mc, tag1, tag2)
% showCellMatching  Draw the cell-matching alignment figure from a saved
% matching (no re-picking): the two aligned frames overlaid (imshowpair) with
% the matched somas and links between them.
%
% USAGE
%   showCellMatching('...\BaselineChange\MatchedCells_0minus_24minus.mat','0minus','24minus')
%   showCellMatching(MatchedCells)          % or pass the struct directly
%
% INPUTS
%   mc         - a MatchedCells struct, or a path to a .mat file containing one
%   tag1, tag2 - timepoint names for the labels (optional)

    if nargin < 2 || isempty(tag1), tag1 = 'timepoint 1'; end
    if nargin < 3 || isempty(tag2), tag2 = 'timepoint 2'; end
    tag1 = char(tag1); tag2 = char(tag2);

    if ischar(mc) || isstring(mc)
        S = load(mc);
        if isfield(S,'MatchedCells')
            mc = S.MatchedCells;
        else
            fn = fieldnames(S);
            hit = fn(contains(fn,'MatchedCells','IgnoreCase',true));
            if isempty(hit), error('No MatchedCells struct found in %s', mc); end
            mc = S.(hit{1});
        end
    end
    if ~isfield(mc,'GCaMP_Image1') || ~isfield(mc,'GCaMP_Image2') || ~isfield(mc,'transformMatrix')
        error('MatchedCells is missing GCaMP images or the transform needed to draw the overlay.');
    end

    im1  = im2double(mc.GCaMP_Image1);
    im2  = im2double(mc.GCaMP_Image2);
    T    = mc.transformMatrix;
    im2a = imwarp(im2, T, 'OutputView', imref2d(size(im1)));

    fig = figure('Color','w','Name','Cell matching','NumberTitle','off');
    imshowpair(im1, im2a, 'falsecolor'); hold on;   % im1 -> green, im2 -> magenta

    nMatched = 0;
    if isfield(mc,'matchedCentroidCoordinates_0minus') && ~isempty(mc.matchedCentroidCoordinates_0minus) ...
            && isfield(mc,'matchedCentroidCoordinates_timepoint2')
        c1  = mc.matchedCentroidCoordinates_0minus;                 % timepoint-1 frame
        c2a = transformPointsForward(T, mc.matchedCentroidCoordinates_timepoint2); % -> timepoint-1 frame
        nMatched = size(c1,1);
        h1 = plot(c1(:,1),  c1(:,2),  'ro', 'MarkerSize',10, 'LineWidth',1.5);
        h2 = plot(c2a(:,1), c2a(:,2), 'g+', 'MarkerSize',10, 'LineWidth',1.5);
        h3 = gobjects(1);
        for i = 1:nMatched
            h3 = plot([c1(i,1) c2a(i,1)], [c1(i,2) c2a(i,2)], 'b-', 'LineWidth',1);
        end
        legend([h1 h2 h3], {[tag1 ' somas'], [tag2 ' somas (aligned)'], 'matches'}, ...
            'Location','northeast');   % default (black) legend text so it is visible
    end
    hold off;

    title({sprintf('Aligned images and matched somas (%d cells matched)', nMatched), ...
           sprintf('overlay: green = %s, magenta = %s', tag1, tag2)});
end