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auto_resolve_problems.m
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auto_resolve_problems.m
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function success = auto_resolve_problems(folder_name)
% automatically resolve centerline problems
addpath(genpath(pwd))
parameters = load_parameters(folder_name); %load experiment parameters
if parameters.TrackOnly
success = true;
return
end
frames_around_problem_to_cut = parameters.TimeAroundProblemToCut * parameters.SampleRate;
min_track_length = parameters.MinTrackLength * parameters.SampleRate;
%% Load tracks
Tracks = load_single_folder(folder_name);
if isempty(Tracks)
error('Empty Tracks');
end
modifications_index = 1;
Modifications = [];
for track_index = 1:length(Tracks)
Track = Tracks(track_index);
potential_problems = Track.PotentialProblems;
if isempty(potential_problems)
% this track is marked for deletion in centerline_finding
Modifications(modifications_index).TrackIndex = track_index;
Modifications(modifications_index).Action = 1; %delete
modifications_index = modifications_index + 1;
elseif sum(potential_problems) > 0
%there is a potential problem in this track
frames_with_potential_problems = potential_problems > 0;
if sum(frames_with_potential_problems) / length(frames_with_potential_problems) > 0.10
%more than 10% of the frames have issues, lets throw the
%track out
Modifications(modifications_index).TrackIndex = track_index;
Modifications(modifications_index).Action = 1; %delete
modifications_index = modifications_index + 1;
else
%less than 3% of the frames have issues, resolve one by one
potential_problems(potential_problems == 1) = 0; %ignore H/T flips
frames_to_show = conv(single(potential_problems), ones(1, frames_around_problem_to_cut), 'same'); %show for 2 sec around the problem
frames_to_show = frames_to_show > 0;
worm_frame_start_index = 0;
while worm_frame_start_index <= length(potential_problems)
[worm_frame_start_index, worm_frame_end_index] = find_next_section(frames_to_show, worm_frame_start_index, 'f');
if isempty(worm_frame_start_index)
break
else
%determine what action to take
if abs(worm_frame_end_index-worm_frame_start_index) <= frames_around_problem_to_cut
%there is only one frame that is bad
action = 1;
else
%there are multiple frames that are bad. cut
%them
action = 5;
end
switch action
%depending on what the user selected,
case 1
%no action: repress the error
Track.PotentialProblems(worm_frame_start_index:worm_frame_end_index) = -1;
case 2
%flip head/tail before
Track.Centerlines(:,:,1:current_frame) = flip(Track.Centerlines(:,:,1:current_frame),1);
case 3
%flip head/tail after
Track.Centerlines(:,:,current_frame:end) = flip(Track.Centerlines(:,:,current_frame:end),1);
case 4
%delete track
Modifications(modifications_index).TrackIndex = track_index;
Modifications(modifications_index).Action = 1; %delete
modifications_index = modifications_index + 1;
break
case 5
%delete section and split track
Modifications(modifications_index).TrackIndex = track_index;
Modifications(modifications_index).Action = 2;
Modifications(modifications_index).StartFrame = Track.Frames(worm_frame_start_index);
Modifications(modifications_index).EndFrame = Track.Frames(worm_frame_end_index);
modifications_index = modifications_index + 1;
end
end
worm_frame_start_index = worm_frame_end_index + 1;
end
end
end
end
if ~isempty(Modifications)
% there are modifications to be done
newTracks = [];
deleted_tracks = [];
modification_track_indecies = [Modifications.TrackIndex];
current_track_index = 1;
current_end_index = length(Tracks);
for track_index = 1:length(Tracks)
Track = Tracks(track_index);
%get if there are modifications
if ismember(track_index, modification_track_indecies)
%there are modifications, get all the modifications
modifications_to_this_track = Modifications(modification_track_indecies == track_index);
%see if there is a single delete command
modifications_to_this_track_actions = [modifications_to_this_track.Action];
if ismember(1, modifications_to_this_track_actions)
%there is a delete command, delete the track
if current_track_index == current_end_index
delete([folder_name, filesep, 'individual_worm_imgs', filesep, 'worm_', num2str(current_track_index), '.mat'])
else
rename_individual_worm_images(folder_name,current_track_index+1,current_end_index,-1);
end
current_end_index = current_end_index - 1;
%remember deleted tracks
deleted_tracks = [deleted_tracks, Track];
else
%there are one or many split commands
split_tracks = [];
split_modifications = modifications_to_this_track(modifications_to_this_track_actions == 2);
loaded_file = load([folder_name, filesep, 'individual_worm_imgs', filesep, 'worm_', num2str(current_track_index), '.mat']);
Track.WormImages = loaded_file.worm_images;
for split_modification_index = 1:length(split_modifications)
current_split_modification_begin = split_modifications(split_modification_index).StartFrame;
current_split_modification_end = split_modifications(split_modification_index).EndFrame;
new_subtrack = FilterTracksByTime(Track, Track.Frames(1), current_split_modification_begin);
if length(new_subtrack.Frames) >= min_track_length
split_tracks = [split_tracks, new_subtrack];
end
Track = FilterTracksByTime(Track, current_split_modification_end, Track.Frames(end));
end
if length(Track.Frames) >= min_track_length
split_tracks = [split_tracks, Track];
end
%shift up by the number of new tracks added
rename_individual_worm_images(folder_name, current_track_index+1, current_end_index, length(split_tracks)-1);
current_end_index = current_end_index + length(split_tracks) - 1;
%split the worm frames exactly as before
for saveindex = 1:length(split_tracks)
worm_images = split_tracks(saveindex).WormImages;
save([folder_name, filesep, 'individual_worm_imgs', filesep, ...
'worm_', num2str(current_track_index+saveindex-1), '.mat'], 'worm_images');
end
if ~isempty(split_tracks)
split_tracks = rmfield(split_tracks, 'WormImages');
newTracks = [newTracks, split_tracks];
end
current_track_index = length(newTracks) + 1;
end
else
%no modifications, add the old track
newTracks = [newTracks, Track];
current_track_index = length(newTracks) + 1;
end
end
delete_extra_individual_worm_images(folder_name, length(newTracks))
% save the resolved tracks
savetracks(newTracks, folder_name, true);
% save the deleted tracks
if parameters.TrackingDebugMode && ~isempty(deleted_tracks)
fields_to_keep = {'Path','Size','Frames','WormIndex'};
track_field_names = fieldnames(deleted_tracks);
fields_for_removal = setdiff(track_field_names,fields_to_keep);
deleted_tracks = rmfield(deleted_tracks,fields_for_removal);
saveFileName = [folder_name, filesep, 'centerline_deleted_tracks.mat'];
save(saveFileName, 'deleted_tracks', '-v7.3');
end
end
success = true;
end