compute_point_match_stack.m

function result = compute_point_match_stack(sample_date, tile_index_from_ijk1, ijk1_from_tile_index, relative_path_from_tile_index)
    % Get dimensions
    tile_lattice_shape = size(tile_index_from_ijk1) ;
    tile_count = length(relative_path_from_tile_index) ;
    channel_count = 2 ;
    
    % Determine which pairs are valid
    central_tile_relative_path_from_pair_index = cell(tile_count,1) ;
    other_tile_relative_path_from_pair_index = cell(tile_count,1) ;
    central_tile_ijk1_from_pair_index = nan(tile_count, 3) ;
    pair_count_so_far = 0 ;
    for central_tile_index = 1 : tile_count ,
        center_ijk1 = ijk1_from_tile_index(central_tile_index, :) ;
        other_ijk1 = center_ijk1 + [0 0 1] ;
        if all(other_ijk1 <= tile_lattice_shape) ,
            other_tile_index = tile_index_from_ijk1(other_ijk1(1), other_ijk1(2), other_ijk1(3)) ;
            if ~isnan(other_tile_index) ,
                % Found a pair, so add the relative paths to the lists
                other_tile_relative_path = relative_path_from_tile_index{other_tile_index} ;
                center_tile_relative_path = relative_path_from_tile_index{central_tile_index} ;
                pair_count_so_far = pair_count_so_far + 1 ;
                pair_index = pair_count_so_far ;
                central_tile_relative_path_from_pair_index{pair_index} = center_tile_relative_path ;
                other_tile_relative_path_from_pair_index{pair_index} = other_tile_relative_path ;
                central_tile_ijk1_from_pair_index(pair_index, :) = center_ijk1 ;
            end
        end
    end
    pair_count = pair_count_so_far ;
    central_tile_relative_path_from_pair_index = central_tile_relative_path_from_pair_index(1:pair_count) ;  % trim
    other_tile_relative_path_from_pair_index = other_tile_relative_path_from_pair_index(1:pair_count) ;  %#ok<NASGU> % trim
    central_tile_ijk1_from_pair_index = central_tile_ijk1_from_pair_index(1:pair_count,:) ;  % trim
    
    z_point_match_path = fullfile('/nrs/mouselight/pipeline_output', sample_date, 'stage_4_point_match_output') ;   
    
    match_count_from_ijk1_and_channel_index = nan(tile_lattice_shape(1), tile_lattice_shape(2), tile_lattice_shape(3), channel_count) ;
    for pair_index = 1 : pair_count ,
        central_tile_relative_path = central_tile_relative_path_from_pair_index{pair_index} ;
        %other_tile_relative_path = other_tile_relative_path_from_pair_index{pair_index} ;
        central_tile_ijk1 = central_tile_ijk1_from_pair_index(pair_index,:) ;
        
        for channel_index = 1 : channel_count ,
            if isequal(sample_date, '2020-11-26') ,
                % Special handling older samples
                if channel_index == 0 ,
                    continue
                else
                    z_match_output_file_name = fullfile(z_point_match_path, central_tile_relative_path, 'match-Z.mat') ;  % this is for channel 1
                end
            else 
                % The general case
                z_match_output_file_name = fullfile(z_point_match_path, central_tile_relative_path, sprintf('channel-%d-match-Z.mat', channel_index-1)) ;
            end
            if exist(z_match_output_file_name, 'file') ,
                load(z_match_output_file_name, 'paireddescriptor') ;
                match_count = size(paireddescriptor.X, 1) ;
                match_count_from_ijk1_and_channel_index(central_tile_ijk1(1), central_tile_ijk1(2), central_tile_ijk1(3), channel_index) = match_count ;
            end
        end
    end        
    result = match_count_from_ijk1_and_channel_index ;
end