rematchAtDistance.m

function MC2 = rematchAtDistance(rootFolder, tag1, tag2, MC, maxDist)
% rematchAtDistance  Rebuild a cell matching at a new distance cutoff, reusing
% the transform already in MC (same matching math as matchCells, but without
% re-loading images or re-picking points).
%
% Used by the Extended Activity Tracking add-on to recover cells when the
% default 5 px cutoff is too strict (e.g. higher-drift comparisons such as 24 h).
% Note: a larger cutoff recovers more pairs but raises the risk of pairing the
% wrong cells, and it can never match more cells than were detected at the
% sparser timepoint.
%
% INPUTS
%   rootFolder - sample root folder (with <tag>/center.mat and <tag>/radii.mat)
%   tag1, tag2 - timepoint tags (tag1 = column 1 of matchedCellNumbers)
%   MC         - existing MatchedCells struct (must contain transformMatrix)
%   maxDist    - new distance cutoff in pixels (timepoint-1 frame)
%
% OUTPUT
%   MC2 - MatchedCells struct with the re-matched pairs at the new cutoff
%         (keeps the original images/transform; updates the matched fields and
%         sets MC2.matchDist = maxDist).

    if ~isstruct(MC) || ~isfield(MC,'transformMatrix') || isempty(MC.transformMatrix)
        error('rematchAtDistance:noTransform', 'The existing matching has no transform to reuse.');
    end

    centroids1 = importdata(fullfile(rootFolder, tag1, 'center.mat'));
    radii1     = importdata(fullfile(rootFolder, tag1, 'radii.mat'));
    centroids2 = importdata(fullfile(rootFolder, tag2, 'center.mat'));
    radii2     = importdata(fullfile(rootFolder, tag2, 'radii.mat'));

    centroids2_aligned = transformPointsForward(MC.transformMatrix, centroids2);
    [idx, dist] = knnsearch(centroids2_aligned, centroids1, 'K', 1);
    valid = dist < maxDist;

    MC2 = MC;
    MC2.matchedCellNumbers = [find(valid), idx(valid)];              % [id_tag1, id_tag2]
    MC2.matchedCentroidCoordinates_0minus     = centroids1(valid,:);
    MC2.matchedRadii_0minus                   = radii1(valid);
    MC2.matchedCentroidCoordinates_timepoint2 = centroids2(idx(valid),:);
    MC2.matchedRadii_timepoint2               = radii2(idx(valid));
    MC2.validMatches_image1                   = valid;
    MC2.matchDist                             = maxDist;
end