SignX.m

function [FreezingEpisodes] = SignX(InputFiles)
%%SignX - A GUI to perform freezing detection.
%
% Uses the motion output from the tracking GUI and the original movie
% to extract freezing episodes and display the results. Parameters can
% then be adjusted to give the best results. The same parameters are
% usually usable for different animals in the same conditions.
%
%       - Uses a motion threshold to detect freezing episodes
%       - Allows to merge episodes closer than a defined gap
%       - Defines a minimum freezing duration
%       - Allows manual editing/removal of single episodes
%        (e.g. sometimes to remove grooming detected as freezing)
%
%   Output: a new variable in the .mat tracking file with the start/end
%   times of each freezing episode
%
% The current version has not been tested for compatibility and
% dependencies; in particular, it might not run under MATLAB versions
% older than R2018a. Also, unlike the tracking GUI, it needs the frames
% timestamps, that are currently either retrieved from the tracking
% file or a file generated by our acquisition system. This will soon be
% expanded to accommodate different systems.
%
% Future implementations/changes:
%       - Expand the manual
%       - Switch from function to class for more robustness and ease of
%         use on successive files
%       - Make the overall code less dependent on the recording system
%       - Use the calibration option from the tracking GUI to get an even
%         more absolute freezing threshold (here it is influenced by the 
%         real pixel size, that depends on the camera distance)
%       - Take into account potential differences in screen
%         resolutions/sizes
%       - Add inputs checking
%       - Adjust some parameters to get a smooth browsing (some movies
%         have ridiculous FPS and resolution that are too heavy to handle
%         like this)
%       - Add the possibility to compute a "moving" background
%
%     Copyright (C) 2019 Jérémy Signoret-Genest, DefenseCircuitsLab
%
%     This program is free software: you can redistribute it and/or modify
%     it under the terms of the GNU General Public License as published by
%     the Free Software Foundation, either version 3 of the License, or
%     (at your option) any later version.
%
%     This program is distributed in the hope that it will be useful,
%     but WITHOUT ANY WARRANTY; without even the implied warranty of
%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
%     GNU General Public License for more details.
%
%     You should have received a copy of the GNU General Public License
%     along with this program.  If not, see <https://www.gnu.org/licenses/>.

    
if nargin == 0,
    [FileName,FilePath] = uigetfile({'*.avi;*.mp4;*.m4v;*.mpg;*.mkv;*.wmv;*.mov'}); % Precise path here for more convenience
    if isempty(FileName),
        return
    end
    InputFiles = fullfile(FilePath,FileName);
else
    % Check inputs
    
end
if ~iscell(InputFiles),
    InputFiles = {InputFiles};
end

for ir = 1 : numel(InputFiles),
    OnlineReading = true;
    MergeThreshold = 0.2;
    FreezingMinTime = 2;
    ThresholdMM = 1.5;
    SmoothMM = 3;
    [PathFile,FileName,~] = fileparts(InputFiles{ir});
    if contains(InputFiles{ir},'_IR'),
        MovieType = 'Thermal';
        FileName = FileName(1:end-3);
        AviName = [PathFile,'\',FileName,'_IR.avi'];
    else
        MovieType = 'RGB';
            AviName = [PathFile,'\',FileName,'.avi'];
    end
    
    %% Retrieve data
    disp(['Processing file ' num2str(ir) ' out of ' num2str(numel(InputFiles)) '...'])
    TrackingLog = [PathFile,'\',FileName,'_Tracking'];
    Tracking = load(TrackingLog);
    %     numFrames = Tracking.(MovieType).FramesNum;
    Contour = Tracking.(MovieType).Contour;
    Center_GF = Tracking.(MovieType).Center;
    if ~isfield(Tracking.(MovieType),'Times') 
        if strcmpi(MovieType,'RGB'),
            MM_File = [PathFile '\' FileName '.DVT'];
            DVTRead = csvread(MM_File);
            Times = DVTRead(:,2);        
        else
            error('No time information found.');
        end
    else
        Times = Tracking.(MovieType).Times;
    end
    if strcmpi(MovieType,'Thermal'),
        Times = (round(Times-Times(1))/10)/100;
    end
    Frame0 = VideoReader(AviName);
    FrameTimes = (1/Frame0.FrameRate : 1/Frame0.FrameRate : Frame0.Duration)-1/Frame0.FrameRate;
      
%     if ~OnlineReading,
%         disp(newline)
%         disp('Retrieving all frames...')
%         Frames = cell(numFrames,1);
%         parfor F = 1 : numFrames-1,
%             FrameF = Frame0;
%             FrameF.CurrentTime = FrameTimes(F);
%             Frames{F} = FrameF.readFrame;
%         end
%     end
      
    % Get freezing events
    MotionMeasure = Tracking.(MovieType).MotionMeasure;
    MotionMeasure(isnan(MotionMeasure)) = 0;
    Contour(isinf(MotionMeasure)) = {[NaN;NaN]};
    Contour(cellfun('isempty', Contour)) = {[NaN;NaN]};
    MotionMeasure(isinf(MotionMeasure)) = 100;

    LoadedFE = false;
    if isfield(Tracking.(MovieType),'Freezing'),
        if isfield(Tracking.(MovieType).Freezing,'Ranges'),
            if ~isempty(Tracking.(MovieType).Freezing.Ranges),
                FreezingEpisodes = Tracking.(MovieType).Freezing.Ranges;
                ThresholdMM = Tracking.(MovieType).Freezing.MotionMeasureThreshold;
                MergeThreshold = Tracking.(MovieType).Freezing.MergingThreshold;
                FreezingMinTime = Tracking.(MovieType).Freezing.Duration;
                SmoothMM = Tracking.(MovieType).Freezing.Smoothing;
                LoadedFE = true;
            end
        end
    end
    if ~LoadedFE
        FindIndex = find(Smooth(MotionMeasure,SmoothMM)<ThresholdMM);
        FreezingEpisodes = FindContinuousRange(FindIndex);
        FreezingEpisodes = FindIndex(FreezingEpisodes(:,[1 2]));
        FreezingEpisodes = Times(FreezingEpisodes);
        % Merging
        for KF = 2 : numel(FreezingEpisodes(:,1))
            if (FreezingEpisodes(KF,1)-FreezingEpisodes(KF-1,2))<MergeThreshold,
                FreezingEpisodes(KF-1,2) = FreezingEpisodes(KF,2);
                FreezingEpisodes(KF,1) = FreezingEpisodes(KF-1,1);
            end
        end
        FreezingEpisodesLength = (FreezingEpisodes(:,2)-FreezingEpisodes(:,1));
        FreezingEpisodes(FreezingEpisodesLength<=FreezingMinTime,:) = [];
        
        [~,FreezingEpisodesIndex] = unique(FreezingEpisodes(:,1));
        FreezingEpisodes = FreezingEpisodes(FreezingEpisodesIndex,:);
    end
    OriginalEpisodes = FreezingEpisodes;
    
    
    %% Prepare figure and UI
    Scrsz = get(0,'ScreenSize');
    Fig = figure('Position',[Scrsz(3)/10 50 4/5*Scrsz(3) Scrsz(4)-150]);
    SubMovie = subplot('Position',[0.075 0.4290 0.4167 0.5161]);
    SubMM = subplot('Position',[0.075 2*(1-0.9451) 1-0.0449-0.075 1-4*(1-0.9451)-0.5161]);
    SubFreezing = subplot('Position',[SubMM.Position(1) SubMM.Position(2)+SubMM.Position(4) SubMM.Position(3) 0.5*(1-0.9451)]);
    MouseID = uicontrol('Style','text','String',FileName,'FontSize',14,'FontName','Arial','FontWeight','bold',...
        'Units','Normalized','Position',[0.075 0.95 0.2 0.025],'HorizontalAlignment','left');
    LockedZoom = uicontrol('Style','checkbox','String',' Lock Y-Axis','Value',true,'FontSize',16,'FontName','Arial','FontWeight','bold',...
        'Callback',@YZoom,'Units','Normalized','Position',[0.8 0.6 0.15 0.025]);
    CancelAdjustment = uicontrol('Style','pushbutton','String','Cancel last adjustment','FontSize',16,'FontName','Arial','FontWeight','bold',...
        'Callback',@RevertLastAdjustment,'Units','Normalized','Position',[0.55 0.525 0.175 0.05]);
    CancelDeletion = uicontrol('Style','pushbutton','String','Cancel last deletion','FontSize',16,'FontName','Arial','FontWeight','bold',...
        'Callback',@CancelLastDeletion,'Units','Normalized','Position',[0.55 0.585 0.175 0.05]);
    Delete = uicontrol('Style','pushbutton','String','Delete selected episode','FontSize',16,'FontName','Arial','FontWeight','bold',...
        'Callback',@DeleteEpisode,'Units','Normalized','Position',[0.55 0.645 0.175 0.05]);
    PlayButton = uicontrol('Style','pushbutton','String','Play','FontSize',16,'FontName','Arial','FontWeight','bold',...
        'Callback',@SetPlay,'Units','Normalized','Position',[0.62 0.45 0.07 0.05]);
    PauseButton = uicontrol('Style','pushbutton','String','Pause','FontSize',16,'FontName','Arial','FontWeight','bold',...
        'Callback',@PauseMovie,'Units','Normalized','Position',[0.69 0.45 0.07 0.05]);
    DecreaseRateButton = uicontrol('Style','pushbutton','String','Slower','FontSize',16,'FontName','Arial','FontWeight','bold',...
        'Callback',@DecreaseFrameRate,'Units','Normalized','Position',[0.55 0.45 0.07 0.05]);
    IncreaseRateButton = uicontrol('Style','pushbutton','String','Faster','FontSize',16,'FontName','Arial','FontWeight','bold',...
        'Callback',@IncreaseFrameRate,'Units','Normalized','Position',[0.76 0.45 0.07 0.05]);
    ThresholdEdit = uicontrol('Style','edit','String',num2str(ThresholdMM),'FontSize',16,'FontName','Arial','FontWeight','bold',...
        'Callback',@EditThreshold,'Units','Normalized','Position',[0.55 0.80 0.05 0.04]);
    ThresholdLegend = uicontrol('Style','text','String','Freezing threshold','FontSize',14,'FontName','Arial','FontWeight','bold',...
        'Units','Normalized','Position',[0.55 0.85 0.15 0.03],'HorizontalAlignment','left');
    ThresholdDrag = uicontrol('Style','pushbutton','String','Drag','FontSize',16,'FontName','Arial','FontWeight','bold',...
        'Callback',@DragThreshold,'Units','Normalized','Position',[0.55 0.75 0.05 0.04],'HorizontalAlignment','left');
    ThresholdEditSet = uicontrol('Style','pushbutton','String','Set','FontSize',16,'FontName','Arial','FontWeight','bold',...
        'Callback',@EditThresholdSet,'Units','Normalized','Position',[0.6005 0.80 0.05 0.04],'HorizontalAlignment','left');
    MergeThresholdEdit = uicontrol('Style','edit','String',num2str(MergeThreshold),'FontSize',16,'FontName','Arial','FontWeight','bold',...
        'Callback',@MergeEditThreshold,'Units','Normalized','Position',[0.7 0.80 0.05 0.04]);
    MergeThresholdLegend = uicontrol('Style','text','String','Merging threshold (s)','FontSize',14,'FontName','Arial','FontWeight','bold',...
        'Units','Normalized','Position',[0.7 0.85 0.15 0.03],'HorizontalAlignment','left');
    MergeThresholdEditSet = uicontrol('Style','pushbutton','String','Set','FontSize',16,'FontName','Arial','FontWeight','bold',...
        'Callback',@MergeEditThresholdSet,'Units','Normalized','Position',[0.7505 0.80 0.05 0.04],'HorizontalAlignment','left');
    MinEpisodeLegend = uicontrol('Style','text','String','Minimum (s)','FontSize',14,'FontName','Arial','FontWeight','bold',...
        'Units','Normalized','Position',[0.85 0.85 0.15 0.03],'HorizontalAlignment','left');
    MinEpisodeEdit = uicontrol('Style','edit','String',num2str(FreezingMinTime),'FontSize',16,'FontName','Arial','FontWeight','bold',...
        'Callback',@EditMinEpisode,'Units','Normalized','Position',[0.85 0.80 0.05 0.04]);
    MinEpisodeEditSet = uicontrol('Style','pushbutton','String','Set','FontSize',16,'FontName','Arial','FontWeight','bold',...
        'Callback',@EditMinEpisodeSet,'Units','Normalized','Position',[0.9005 0.80 0.05 0.04],'HorizontalAlignment','left');
    
    ValidateButton = uicontrol('Style','pushbutton','String','Validate','FontSize',16,'FontName','Arial','FontWeight','bold',...
        'Callback',@Exit,'Units','Normalized','Position',[0.8850 0.01 0.0700 0.0500],'HorizontalAlignment','left');
    
    
    %% Initialize
%     if ~OnlineReading,
%         ImFrame = image(Frames{1},'Parent',SubMovie);
%     else
if strcmpi(MovieType,'Thermal'),
    ImFrame = imagesc(rgb2gray(Frame0.readFrame),'Parent',SubMovie);
    HW = load('HotWhite');
    SubMovie.Colormap = HW.HotWhite;
    SubMovie.CLim = [25 175];
else
    ImFrame = image(Frame0.readFrame,'Parent',SubMovie);
end
%     end
    hold(SubMovie,'on')
    drawnow
    ContourPlot = plot(Contour{1}(1,:),Contour{1}(2,:),'k','LineWidth',2.5,'Parent',SubMovie);
    uistack(ContourPlot,'top')
    CenterPlot = plot(Center_GF(1,1),Center_GF(1,2),'+k','LineWidth',2.5,'MarkerSize',5,'Parent',SubMovie);
    uistack(CenterPlot,'top')
    SpeedText = text(0.9*Frame0.Width,0.95*Frame0.Height,'x1','FontSize',22,'FontName','Arial','FontWeight','bold','Color','k','Parent',SubMovie);
    uistack(SpeedText,'top')
    if OnlineReading,
        TimeText = text(0.05*Frame0.Width,0.95*Frame0.Height,'0','FontSize',22,'FontName','Arial','FontWeight','bold','Color','k','Parent',SubMovie);
    end
    uistack(TimeText,'top')
    hold(SubMovie,'off')
    SubMovie.XColor = 'none';
    SubMovie.YColor = 'none';
    plot(Times(2:end),Smooth(MotionMeasure,SmoothMM),'LineWidth',1.5,'Parent',SubMM);
    hold(SubMM,'on')
    drawnow
    YlimMM = SubMM.YLim;
    % Prepare a hidden plot for the threshold
    ThresholdLine = plot(Times([2 end]),[1 1],'Color','none','LineWidth',1.5,'Parent',SubMM);
    PimpAxis(SubMM,'xlabel','Time(s)','ylabel','Motion Measure')
    SubMM.XLim = [-5 Times(end)];
    LineCurrentTime = plot([0 0],[0 500],'LineWidth',2.5,'Parent',SubMM,'ButtonDownFcn',@TimeLine);
    SubMM.YLim = YlimMM;
    linkaxes([SubMM SubFreezing],'x')
    hold(SubFreezing,'on');
    FreezingHandles = arrayfun(@(x) plot([FreezingEpisodes(x,1) FreezingEpisodes(x,2)],[0 0],'k','LineWidth',3,'Parent',SubFreezing,'Tag',num2str(x),'ButtonDownFcn',@FreezingEdit),1:numel(FreezingEpisodes(:,1)));
    SubFreezing.XColor = 'none';
    SubFreezing.YColor = 'none';
    SubFreezing.YLim = [-0.5 0.5];
    drawnow
    ZoomHandleSubFreezing = zoom(SubFreezing);
    ZoomHandleSubFreezing.Motion = 'horizontal';
    ZoomHandleSubFreezing.ActionPostCallback = @EvaluateWindow;
    ZoomHandleSubMM = zoom(SubMM);
    ZoomHandleSubMM.Motion = 'horizontal';
    ZoomHandleSubMM.ActionPostCallback = @EvaluateWindow;
    Edition = false;
    DeletionIndex = [];
    SelectedEpisode = [];
    LeftLimit = [];
    RightLimit = [];
    Dragging = false;
    AdjustedRanges = [];
    CurrentTime = 0;
    Play = false;
    PrePlayState = [];
    FrameRate = Frame0.FrameRate;
    ShiftTimeLine = 0.2;
    drawnow
    ReProcessFreezing;
    waitfor(Fig);
end


    function YZoom(src,~)
        if src.Value==0,
            ZoomHandleSubMM.Motion = 'both';
        else
            ZoomHandleSubMM.Motion = 'horizontal';
        end
    end

    function IncreaseFrameRate(~,~)
        FrameRate = FrameRate*2;
        SpeedText.String = ['x' num2str(round(FrameRate/Frame0.FrameRate*10)/10)];
        uistack(SpeedText,'top')
        drawnow
    end

    function SetPlay(~,~)
        Play = true;
        PlayMovie;
    end

    function DecreaseFrameRate(~,~)
        FrameRate = FrameRate/2;
        SpeedText.String = ['x' num2str(round(FrameRate/Frame0.FrameRate*10)/10)];
        uistack(SpeedText,'top')
        drawnow
    end

    function FreezingEdit(src,~)
        % Check if an episode is being edited
        if ~Edition
            % Make sure the playing has stopped
            PrePlayState = Play;
            Play = false;
            % Get episode index
            SelectedEpisode = str2double(src.Tag);
            % Change line appearence
            src.LineWidth = 2.5;
            src.Color = [0.85,0.33,0.10];
            % Change callback
            src.ButtonDownFcn = @FreezingEndEdit;
            % Draw bars on limits
            LeftLimit = plot([FreezingEpisodes(SelectedEpisode,1) FreezingEpisodes(SelectedEpisode,1)],[-0.25 0.25],'k','LineWidth',2,'ButtonDownFcn',@DragLimitLeft);
            RightLimit = plot([FreezingEpisodes(SelectedEpisode,2) FreezingEpisodes(SelectedEpisode,2)],[-0.25 0.25],'k','LineWidth',2,'ButtonDownFcn',@DragLimitRight);
            % Set status
            Edition = true;
        end
    end

    function DragLimitLeft(~,~)
        if ~Dragging,
            Dragging = true;
            Fig.WindowButtonMotionFcn = @MovingCursorLeft;
            Fig.WindowButtonUpFcn = @DragLimitLeft;
        else
            Dragging = false;
            Fig.WindowButtonMotionFcn = [];
            Fig.WindowButtonUpFcn = [];
            AdjustedRanges = [AdjustedRanges;SelectedEpisode];
            FreezingEpisodes(SelectedEpisode,1) = LeftLimit.XData(1);
        end
    end

    function MovingCursorLeft(~,~)
        CurrentCursor = SubFreezing.CurrentPoint;
        if CurrentCursor(1)<FreezingEpisodes(SelectedEpisode,2),
            LeftLimit.XData = [CurrentCursor(1) CurrentCursor(1)];
            FreezingHandles(SelectedEpisode).XData(1) = CurrentCursor(1);
        end
    end
    function DragLimitRight(~,~)
        if ~Dragging,
            Dragging = true;
            Fig.WindowButtonMotionFcn = @MovingCursorRight;
            Fig.WindowButtonUpFcn = @DragLimitRight;
        else
            Dragging = false;
            Fig.WindowButtonMotionFcn = [];
            Fig.WindowButtonUpFcn = [];
            FreezingEpisodes(SelectedEpisode,2) = RightLimit.XData(1);
        end
    end

    function MovingCursorRight(~,~)
        CurrentCursor = SubFreezing.CurrentPoint;
        if CurrentCursor(1)>FreezingEpisodes(SelectedEpisode,1),
            RightLimit.XData = [CurrentCursor(1) CurrentCursor(1)];
            FreezingHandles(SelectedEpisode).XData(2) = CurrentCursor(1);
        end
    end

    function RevertLastAdjustment(~,~)
        if ~isempty(AdjustedRanges),
            FreezingEpisodes(AdjustedRanges(end),:) = OriginalEpisodes(AdjustedRanges(end),:);
            FreezingHandles(AdjustedRanges(end)).XData = OriginalEpisodes(AdjustedRanges(end),:);
            AdjustedRanges(end) = [];
        end
    end

    function FreezingEndEdit(src,~)
        % Revert appearence
        src.LineWidth = 3;
        src.Color = 'k';
        % Set status
        Edition = false;
        AdjustedRanges = [AdjustedRanges;SelectedEpisode];
        FreezingEpisodes(SelectedEpisode,1) = LeftLimit.XData(1);
        FreezingEpisodes(SelectedEpisode,2) = RightLimit.XData(1);
        SelectedEpisode = [];
        % Remove bars on limits
        delete(LeftLimit)
        delete(RightLimit)
        % Change callback
        src.ButtonDownFcn = @FreezingEdit;
        % Restore playing state
        Play = PrePlayState;
    end

    function DeleteEpisode(~,~)
        if ~isempty(SelectedEpisode),
            % Remove bars on limits
            delete(LeftLimit)
            delete(RightLimit)
            FreezingHandles(SelectedEpisode).LineWidth = 3;
            FreezingHandles(SelectedEpisode).ButtonDownFcn = [];
            FreezingHandles(SelectedEpisode).Color = 'none';
            DeletionIndex = [DeletionIndex,SelectedEpisode];
            % Set status
            Edition = false;
            SelectedEpisode = [];
            % Restore playing state
            Play = PrePlayState;
        end
    end

    function CancelLastDeletion(~,~)
        if ~isempty(DeletionIndex),
            FreezingHandles(DeletionIndex(end)).Color = 'k';
            FreezingHandles(DeletionIndex(end)).ButtonDownFcn = @FreezingEdit;
            DeletionIndex(end) = [];
        end
    end

    function TimeLine(~,~)
        if ~Dragging,
            PrePlayState = Play;
            Play = false;
            Dragging = true;
            Fig.WindowButtonMotionFcn = @MovingTimeLine;
            Fig.WindowButtonUpFcn = @TimeLine;
        else
            Dragging = false;
            Fig.WindowButtonMotionFcn = [];
            Fig.WindowButtonUpFcn = [];
            Play = PrePlayState;
            PlayMovie;
        end
    end


    function MovingTimeLine(~,~)
        CurrentCursor = SubMM.CurrentPoint;
        if CurrentCursor(1)>=0 && CurrentCursor(1)<=Times(end),
            if CurrentCursor(1) >= SubMM.XLim(2),
                NewY = SubMM.XLim(2) + 0.025*diff(SubMM.XLim);
                if NewY<=Times(end),
                    SubMM.XLim = SubMM.XLim + 0.025*diff(SubMM.XLim);
                else
                    SubMM.XLim = SubMM.XLim+(Times(end)-SubMM.XLim(2));
                end
                CurrentTime = SubMM.XLim(2);
            elseif CurrentCursor(1) <= SubMM.XLim(1),
                NewY = SubMM.XLim(1) - 0.025*diff(SubMM.XLim);
                if NewY<=Times(end),
                    SubMM.XLim = SubMM.XLim - 0.025*diff(SubMM.XLim);
                else
                    SubMM.XLim = SubMM.XLim - (SubMM.XLim(1));
                end
                CurrentTime = SubMM.XLim(1);
            else
                CurrentTime = CurrentCursor(1);
            end
        end
        LineCurrentTime.XData = [CurrentTime CurrentTime];
        FrameUpdate;
    end

    function FrameUpdate(~,~)
        NewIndex = FindInInterval(Times,[CurrentTime CurrentTime]);
        %         if ~OnlineReading,
        %             ImFrame.CData = Frames{NewIndex(1)};
        %         else
        ContourPlot.XData = Contour{NewIndex(1)}(1,:);
        ContourPlot.YData = Contour{NewIndex(1)}(2,:);
        CenterPlot.XData = Center_GF(NewIndex(1),1);
        CenterPlot.YData = Center_GF(NewIndex(1),2);
        Frame0.CurrentTime = FrameTimes(NewIndex(1));
        if strcmpi(MovieType,'Thermal'),
            ImFrame.CData = rgb2gray(Frame0.readFrame);
        else
            ImFrame.CData = (Frame0.readFrame);
        end
        TimeText.String = num2str(Times(NewIndex(1)));
        %         end
        uistack(SpeedText,'top')
        drawnow
    end

    function EvaluateWindow(~,~)
        PrePlayState = Play;
        Play = false;
        if SubMM.XLim(1)<0,
            SubMM.XLim(1) = 0;
        elseif SubMM.XLim(2)>Times(end),
            SubMM.XLim(2) = Times(end);
        end
        if CurrentTime<SubMM.XLim(1) || CurrentTime>SubMM.XLim(2),
            CurrentTime = SubMM.XLim(1) + 0.5*diff(SubMM.XLim);
            LineCurrentTime.XData = [CurrentTime CurrentTime];
            FrameUpdate;
        end
        Play = PrePlayState;
        PlayMovie;
    end

    function PlayMovie(~,~)
        if Play
            % Only approximate framerate (for faster plotting)
            CurrentTime = CurrentTime+1/FrameRate;
            CurrentIndex = FindInInterval(Times,[CurrentTime CurrentTime]);
            % Plot once to get a starting value for the delay
            tic
%             if ~OnlineReading,
%                 ImFrame.CData = Frames{CurrentIndex(1)};
%             else
                CurrentIndex = FindInInterval(Times,[CurrentTime CurrentTime]);
                ContourPlot.XData = Contour{CurrentIndex(1)}(1,:);
                ContourPlot.YData = Contour{CurrentIndex(1)}(2,:);
                CenterPlot.XData = Center_GF(CurrentIndex(1),1);
                CenterPlot.YData = Center_GF(CurrentIndex(1),2);
                Frame0.CurrentTime = FrameTimes(CurrentIndex(1));
                if strcmpi(MovieType,'Thermal'),
                    ImFrame.CData = rgb2gray(Frame0.readFrame);
                else
                    ImFrame.CData = (Frame0.readFrame);
                end
                TimeText.String = num2str(Times(CurrentIndex(1)));
                %             end
                uistack(SpeedText,'top')
            LineCurrentTime.XData = [Times(CurrentIndex(1)) Times(CurrentIndex(1))];
            drawnow
        end
        while Play
            TocT = toc;
            EstimatedShift = TocT*FrameRate;
            if EstimatedShift>1
                tic;
                CurrentIndex = CurrentIndex + round(EstimatedShift);
                CurrentTime = Times(CurrentIndex(1));
                %                 if ~OnlineReading,
                %                     ImFrame.CData = Frames{CurrentIndex(1)};
                %                 else
                ContourPlot.XData = Contour{CurrentIndex(1)}(1,:);
                ContourPlot.YData = Contour{CurrentIndex(1)}(2,:);
                CenterPlot.XData = Center_GF(CurrentIndex(1),1);
                CenterPlot.YData = Center_GF(CurrentIndex(1),2);
                Frame0.CurrentTime = FrameTimes(CurrentIndex(1));
                if strcmpi(MovieType,'Thermal'),
                    ImFrame.CData = rgb2gray(Frame0.readFrame);
                else
                    ImFrame.CData = (Frame0.readFrame);
                end
                TimeText.String = num2str(Times(CurrentIndex(1)));
                %                 end
                uistack(SpeedText,'top')
                LineCurrentTime.XData = [CurrentTime CurrentTime];
                if CurrentTime>=(SubMM.XLim(2)-ShiftTimeLine*diff(SubMM.XLim)),
                    SubMM.XLim = SubMM.XLim + CurrentTime-SubMM.XLim(2)+ShiftTimeLine*diff(SubMM.XLim);
                end
                drawnow
            end
        end
    end

    function PauseMovie(~,~)
        Play = false;
    end

    function EditThreshold(src,~)
    end

    function EditThresholdSet(~,~)
        if str2double(ThresholdEdit.String)>0,
            ThresholdMM = str2double(ThresholdEdit.String);
            ThresholdLine.Color = 'none';
            ThresholdLine.ButtonDownFcn = [];
            ReProcessFreezing;
        end
    end

    function DragThreshold(~,~)
        ThresholdLine.Color = [0.85,0.33,0.10];
        ThresholdLine.ButtonDownFcn = @StartDragThreshold;
        uistack(ThresholdLine,'top')
        Play = false;
        Dragging = false;
    end

    function StartDragThreshold(~,~)
        if ~Dragging,
            Fig.WindowButtonMotionFcn = @MovingThresholdLine;
            Fig.WindowButtonUpFcn = @StartDragThreshold;
            Dragging = true;
        else
            Dragging = false;
            Fig.WindowButtonMotionFcn = [];
            Fig.WindowButtonUpFcn = [];
        end
    end

    function MovingThresholdLine(~,~)
        CurrentCursor = SubMM.CurrentPoint;
        if CurrentCursor(1,2)>=0 && CurrentCursor(1,2)<=SubMM.YLim(2),
            ThresholdLine.YData = [CurrentCursor(1,2) CurrentCursor(1,2)];
            ThresholdEdit.String = num2str(CurrentCursor(1,2));
            drawnow;
        end
    end

    function MergeEditThreshold(~,~)
    end

    function MergeEditThresholdSet(~,~)
        if str2double(MergeThresholdEdit.String)>=0,
            MergeThreshold = str2double(MergeThresholdEdit.String);
            ReProcessFreezing;
        end
    end

    function EditMinEpisode(~,~)
    end

    function EditMinEpisodeSet(~,~)
        if str2double(MinEpisodeEdit.String)>0,
            FreezingMinTime = str2double(MinEpisodeEdit.String);
            ReProcessFreezing;
        end
    end

    function ReProcessFreezing(~,~)
        FindIndex = find(Smooth(MotionMeasure,SmoothMM)<ThresholdMM);
        FreezingEpisodes = FindContinuousRange(FindIndex);
        FreezingEpisodes = FindIndex(FreezingEpisodes(:,[1 2]));
        FreezingEpisodes = Times(FreezingEpisodes);
        
        % Merging
        for KFS = 2 : numel(FreezingEpisodes(:,1))
            if (FreezingEpisodes(KFS,1)-FreezingEpisodes(KFS-1,2))<MergeThreshold,
                FreezingEpisodes(KFS,1) = FreezingEpisodes(KFS-1,1);
                FreezingEpisodes(KFS-1,:) = NaN(1,2);
            end
        end
        FreezingEpisodes = FreezingEpisodes(~isnan(FreezingEpisodes(:,1)),:);
        
        FreezingEpisodesLength = (FreezingEpisodes(:,2)-FreezingEpisodes(:,1));
        FreezingEpisodes(FreezingEpisodesLength<=FreezingMinTime,:) = [];
        
        OriginalEpisodes = FreezingEpisodes;
        delete(FreezingHandles(:));
        FreezingHandles = arrayfun(@(x) plot([FreezingEpisodes(x,1) FreezingEpisodes(x,2)],[0 0],'k','LineWidth',3,'Parent',SubFreezing,'Tag',num2str(x),'ButtonDownFcn',@FreezingEdit),1:numel(FreezingEpisodes(:,1)));
        SubFreezing.XColor = 'none';
        SubFreezing.YColor = 'none';
        SubFreezing.YLim = [-0.5 0.5];
    end



    function Exit(~,~)
        Play = false;
        FreezingEpisodes(DeletionIndex,:) = [];
        % Add to logfile
        Tracking.(MovieType).Freezing.MotionMeasureThreshold = ThresholdMM;
        Tracking.(MovieType).Freezing.MergingThreshold = MergeThreshold;
        Tracking.(MovieType).Freezing.Duration = FreezingMinTime;
        Tracking.(MovieType).Freezing.Smoothing = SmoothMM;
        Tracking.(MovieType).Freezing.Ranges = FreezingEpisodes;
        save(TrackingLog,'-struct','Tracking')
        close(Fig)
    end


end