%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% This script runs the clean versions of the movie analysis functions.
% Input and output are described for each function separately for ease of use.
% Functions can be run individually from separate cells for parameter tuning/problem-solving
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


%%%%%%%%%% Instructions/Notes %%%%%%%%%%
% 1) Make sure that all movie files to consider are backed up separately, as most of the functions overwrite to save space.
% 2) Make sure that all files (the functions references here, as well as the movies) are in the same folder.
% 3) Run the functions below. The organization is currently such that one task (e.g. cropping) is
    % performed for all movies (can be set to specific movies by overriding defaults), then the next task is started.


    
%%%%%%%%%% WARNING %%%%%%%%%%
% MANY OF THE FUNCTIONS (SUCH AS CROPPING) OVERWRITE THE ORIGINAL MOVIE.
% THE SCRIPT BELOW IS SET BY DEFAULT TO LOOK FOR ALL MOVIE FILES IN THE PRESCRIBED FOLDER.
% PLEASE PUT ORIGINAL MOVIES IN A SEPARATE FOLDER.

%% 
%%%%%%%%%% Cropping By Time %%%%%%%%%%
%%% INPUT %%%
% movName
    % Full movie name or {'All'}
% numSecsToKeep
    % Number of seconds at the end of the movie to keep (the rest gets deleted)

%%% OUTPUT %%%
% Movie is overwritten with cropped movie.

% Function leaves last few seconds of the movie, the rest gets removed

%%% INPUT %%%
movieNames = {'All'}; % specific example: {'MovieName.avi'}; 
numSecondsToLeave = 4;


if isequal(movieNames{1},'All')
    movieNames = {};
    MovieFilesInOriginalFolder = dir([pwd,'/*.avi']);
    for movfile = MovieFilesInOriginalFolder'
        movieNames = [movieNames movfile.name]; %#ok<*AGROW>
    end
end

% Run Cropping By Time Function
for movNameCell = movieNames
    movName = movNameCell{1};
    RemoveBeginningFramesByTimeFunction(movName,numSecondsToLeave);
end


%%
%%%%%%%%%% Cropping By Frame %%%%%%%%%%
%%% INPUT %%%
% movName
    % Full movie name or {'All'}
% removeCornersFlag
    % 'y' = remove (black) corners from image (these may arise in zoomed out imaging)
% removeEdgesFlag
    % 'y' = remove (black) pixels from image connected to edge (these may arise in zoomed out imaging)

%%% OUTPUT %%%
% Movie is overwritten with cropped movie.


%%% INPUT %%%
movieNames = {'All'}; % {'MovieName.avi'}; 
removeCornersFlag = 'y';
removeEdgesFlag = 'y';

if isequal(movieNames{1},'All')
    movieNames = {};
    MovieFilesInOriginalFolder = dir([pwd,'/*.avi']);
    for movfile = MovieFilesInOriginalFolder'
        movieNames = [movieNames movfile.name]; 
    end
end

% Run Cropping Function
for movNameCell = movieNames
    movName = movNameCell{1};
    RemoveFramesFunction(movName,removeCornersFlag,removeEdgesFlag);
    close
end

%%
%%%%%%%%%% Automatic Tracking %%%%%%%%%%
%%% INPUT %%%
% MovieNamesOriginals
    % list of full names of movie files to consider. If "All" is selected, it will run for all
    % movie files in the folder
        % EXAMPLE: {'movie1,avi','movie2.avi','movie3.avi'}
        % EXAMPLE: {'All'}
% methodFlag
    % 1 = new method (constrained region based), 2 = old method (global distance based)
% NOTE: Most function inputs are defaults. See function help for detailed explanation of all inputs.
       
        
%%% OUTPUT %%%
% Leg Endpoints Array (.mat file)
    % pixels (i,j) for each frame representing leg endpoints
% Flags Array (.mat file)
    % vector of integer flags (one for each frame) which indicate "high confidence", "lower confidence", and
    % "human intervention required"
% Saves (not output of function): vector of frame flags, array of leg endpoints, matrix of centroid coordinates,
    % matrix of head direction coordinates

%%% INPUT %%%
movieNames = {'All'}; % {'MovieName.avi'}; 
methodFlag = 1; % 1 = primary method, 2 = alternate method (see code for more details)
removeCornersFlag = 'y'; % 'y' means ignore corners of frame

d = 'default'; % default is accepted into almost all function arguments (except first two)

thresholdingFactorForCentroid = d; % IF THERE IS AN ERROR, VIDEO IS PROBABLY TOO DARK! Set this parameter low (e.g. 0.3) and try again for that movie.
pixelAcceptanceModifierThresholding = d;
smallComponentSizeForCentroid = d;
minDistanceThresholdFactor = d;
thresholdingFactorForTracking = d;
lowConfidenceQuantile = d;
lowConfidenceCutoffDistance = d;
targetNumLegs = d;
showMovieFlag = d;
moviePauseTime = 0.1;
%%%%%%%%%%%%%



% Find All Original Movies To Consider
if isequal(movieNames{1},'All')
    movieNames = {};
    MovieFilesInOriginalFolder = dir([pwd,'/*.avi']);
    for movfile = MovieFilesInOriginalFolder'
        movieNames = [movieNames movfile.name]; 
    end
end

% Run Automatic Tracking
for movNameCell = movieNames
    movName = movNameCell{1};
    disp([movName,': AUTOMATIC TRACKING: STARTED'])
    AutomaticTrackingFunction(movName,methodFlag,...
        thresholdingFactorForCentroid, pixelAcceptanceModifierThresholding, smallComponentSizeForCentroid,...
        minDistanceThresholdFactor, thresholdingFactorForTracking, lowConfidenceQuantile,lowConfidenceCutoffDistance,targetNumLegs,...
        'y',moviePauseTime);
    close
    disp([movName,': AUTOMATIC TRACKING: DONE'])
end


%%
%%%%%%%%%% Error Correction %%%%%%%%%%%
%%% INPUT %%%
% MovieNamesAutoTracked
    % list of full names of movie files to consider. If "All" is selected, it will run for all
    % movie files in the folder
        % EXAMPLE: {'movie1,avi','movie2.avi','movie3.avi'}
        % EXAMPLE: {'All'}
% finalMoviePauseTime
    % pause time between frames for final movie (showing ordered legs tracked after user
    % correction). Default is .03.
    
%%% OUTPUT %%%
% Leg Endpoints Array (.mat file)
    % pixels (i,j) for each frame representing leg endpoints
    % NOTE: the array is returned ordered by (front left, middle left, bottom left, front right, middle right, botton right) 
    % if all frame flags are 10 (all frames accepted or fixed by user). Otherwise, it gives unordered ones.
% frameFlags
    % these flags overwrite the previous ones in the Automatically Tracked Movies folder. A
    % frame flag of 10 means the frame was accepted by user, while a frame flag of -10 means the
    % frame was rejected by user. 0,1,2 correspond to confidence levels in auto tracking
    % (frames not yet checked by user).
% NOTE: % Movie (.avi file)
	% final movie with leg endpoint positions corrected by humans. This is currently not explicitly 
    % returned by the function. The movie gets saved and is only placed in the
    % Final Tracked Videos folder if all frame flags are 10 (completely corrected by hand). 
    % The saved movie (when all frame flags at 10) includes the actual tracked leg positions, with
    % legs color-coded
% Saves (not output of function): movie with corrected leg tracking, vector of frame flags, array of leg endpoints (sorted 
    % (front left, middle left, bottom left, front right, middle right, bottom right) if
    % all frame flags = 10, otherwise overwriting old ones if function is
    % left prematurely). An entry of (-1,-1) means the leg is missing. Note that a FRONT leg is
    % presumed missing if there are only 5 target legs.
% NOTE: tight_subplot is a user-contributed functions from Matlab Central
    
%%% INPUT %%%
movieNames = {'All'};

d = 'default';

overWriteFlag = d;
targetNumLegs = d;
finalMoviePauseTime = 0.0001;
%%%%%%%%%%%%%









% Find All Original Movies To Consider
if isequal(movieNames{1},'All')
    movieNames = {};
    MovieFilesInOriginalFolder = dir([pwd,'/*.avi']);
    for movfile = MovieFilesInOriginalFolder'
        movieNames = [movieNames movfile.name]; 
    end
end


% Run Error Checking
for movNameCell = movieNames
    movName = movNameCell{1};
    disp([movName,': ERROR CORRECTION: STARTED'])
    movName = movNameCell{1}; % cell to string
    ErrorCorrectionFunction(movName,overWriteFlag,targetNumLegs,finalMoviePauseTime);
    disp([movName,': ERROR CORRECTION: DONE'])
end








%%
%%%%%%%%%% Motion Detection %%%%%%%%%% 
%%% INPUT %%%
% MovieNamesFinal
    % list of full names of movie files to consider. If "All" is selected, it will run for all
    % movie files in the folder
        % EXAMPLE: {'movie1,avi','movie2.avi','movie3.avi'}
        % EXAMPLE: {'All'}
% distanceThreshold
    % threshold between difference in leg position between subsequent frames that determines whether
    % a leg is in motion. The distance counted will be parallel to the body axis (so pixel movements
    % up and down the leg due to prior thresholding effects/user error will be ignored).

%%% OUTPUT %%%

% Leg Motion Array (.mat file)
    % Array which indicates which legs are "moving" and which are "stationary"
    % Note the ordering: (FL, ML, BL, FR, MR, BR) and that a missing leg has coordinate (-1,-1)
    % in the original legEndpointsStore array.
% Movie with legs "about to move" marked

    
%%% INPUT %%%
MovieNamesFinal = {'All'};
d = 'default';

distanceThreshold = 8;
%%%%%%%%%%%%%

if isequal(MovieNamesFinal{1},'All')
    MovieNamesFinal = {};
    MovieFilesInFinalMoviesFolder = dir([pwd,'/*.avi']);
    for movfile = MovieFilesInFinalMoviesFolder'
        MovieNamesFinal = [MovieNamesFinal, movfile.name]; 
    end
end



% Run Motion Detection
for movNameCell = MovieNamesFinal
    movName = movNameCell{1};
    disp([movName,': MOTION DETECTION: STARTED'])
    movName = movNameCell{1};
    [~,projectedDistMatrix] = MotionDetectionFunction(movName,distanceThreshold);
    hist(projectedDistMatrix,20)
    title(movName,'Interpreter','none')
    xlabel('Projected distance')
    ylabel('Number of times leg moved that far')
%    pause
    disp([movName,': MOTION DETECTION: DONE']) 
end


%%
%%%%%%%%%% Show Current Movie %%%%%%%%%% 
%%% INPUT %%%
% movName
    % Name of movie to show
% finalMoviePauseTime
    % pause length between frames OR "default". Default is 0.03.
% MovieNamesFinalToShow
    % List of names of final movies to show OR {"All"}. If {"All"} is selected, it will run for each movie file in
    % the final tracked movie folder.

%%% OUTPUT %%%
% Nothing is saved. Final movie with tracked and sorted legs is shown.


clear

%%% INPUT %%%
MovieNamesFinalToShow = {'All'};
finalMoviePauseTime = .3;

%%%%%%%%%%%%%

if isequal(MovieNamesFinalToShow{1},'All')
    MovieNamesFinalToShow = {};
    MovieFilesInFinalMoviesFolder = dir([pwd,'/*.avi']);
    for movfile = MovieFilesInFinalMoviesFolder'
        MovieNamesFinalToShow = [MovieNamesFinalToShow, movfile.name]; 
    end
end


% Show movie
for movNameCell = MovieNamesFinalToShow
    movName = movNameCell{1};
    disp(['Showing: ',movName])
    movName = movNameCell{1};
    ShowFinalMovieFunction(movName,finalMoviePauseTime);
    pause(.1)
    close
end