compute_landmarks_for_patrick_pipeline.m

function compute_landmarks_for_patrick_pipeline(p_map_root_path, landmarks_root_path, tile_relative_path, ...
                                                do_force_computation, do_run_in_debug_mode)                                    
    % Deal with args
    if ~exist('do_force_computation', 'var') || isempty(do_force_computation) ,
        do_force_computation = false ;
    end
    if ~exist('do_run_in_debug_mode', 'var') || isempty(do_run_in_debug_mode) ,
        do_run_in_debug_mode = false ;
    end
    
    % Out all the args to console, for debugging
    p_map_root_path  %#ok<NOPRT>
    landmarks_root_path  %#ok<NOPRT>
    tile_relative_path  %#ok<NOPRT>
    do_force_computation  %#ok<NOPRT>
    do_run_in_debug_mode  %#ok<NOPRT>
    
    % Make sure the output folder exists
    landmark_folder_path = fullfile(landmarks_root_path, tile_relative_path) ;
    ensure_folder_exists(landmark_folder_path) ;
    
    % Run for all channels
    channel_count = 2 ;
    for channel_index = 1 : channel_count ,
        compute_landmarks_for_single_tile_channels(p_map_root_path, landmarks_root_path, tile_relative_path, ...
                                                   channel_index, ...
                                                   do_force_computation, do_run_in_debug_mode) ;
    end
end



function compute_landmarks_for_single_tile_channels(p_map_root_path, landmarks_root_path, tile_relative_path, ...
                                                    channel_index, ...
                                                    do_force_computation, do_run_in_debug_mode)
                                                
    % Compute the p-map file path    
    [~,day_tile_index_as_string] = fileparts2(tile_relative_path) ;
    channel_index0 = channel_index - 1 ; 
    channel_index0_as_string = num2str(channel_index0) ;
    p_map_file_name = sprintf('%s-prob.%s.h5', day_tile_index_as_string, channel_index0_as_string) ;
    p_map_tile_folder_path = fullfile(p_map_root_path, tile_relative_path) ;
    p_map_file_path = fullfile(p_map_tile_folder_path, p_map_file_name) ;
    
    % Generate the landmarks from the p-map
    landmark_file_name = sprintf('%s-desc.%s.txt', day_tile_index_as_string, channel_index0_as_string) ;
    landmark_folder_path = fullfile(landmarks_root_path, tile_relative_path) ;
    landmark_file_path = fullfile(landmark_folder_path, landmark_file_name) ;

%     % Make sure the output folder exists
%     ensure_folder_exists(landmark_folder_path) ;
    
    % Run the core code
    siz = '[11 11 11]' ;
    sig1 = '[3.405500 3.405500 3.405500]' ;
    sig2 = '[4.049845 4.049845 4.049845]' ;
    ROI = '[5 1019 5 1531 5 250]' ;
    rt = '4' ;    
    exitcode = dogDescriptor(p_map_file_path, landmark_file_path, siz, sig1, sig2, ROI, rt) ;
    if exitcode ~= 0 ,
        error('dogDescriptor() returned a nonzero exit code (%s) when trying to produce output file %s', exitcode, landmark_file_path) ;
    end
end