DBscorerV02032023_exported.m

classdef DBscorerV02032023_exported < matlab.apps.AppBase

    % Properties that correspond to app components
    properties (Access = public)
        Tool                 matlab.ui.Figure
        LoadVideo            matlab.ui.control.Button
        MarkROI              matlab.ui.control.Button
        StartsLabel          matlab.ui.control.Label
        ProcessVideoStart    matlab.ui.control.Spinner
        EndsLabel            matlab.ui.control.Label
        ProcessVideoEnd      matlab.ui.control.Spinner
        TimeEditFieldLabel   matlab.ui.control.Label
        Time                 matlab.ui.control.NumericEditField
        ProcessVideo         matlab.ui.control.Button
        FixBackground        matlab.ui.control.Button
        EnterInfo            matlab.ui.control.EditField
        CreateBackground     matlab.ui.control.Button
        ManualScoring        matlab.ui.control.Button
        Play                 matlab.ui.control.StateButton
        StateButton          matlab.ui.control.StateButton
        Cancel               matlab.ui.control.StateButton
        GetThresh            matlab.ui.control.Button
        AreaThresholdLabel   matlab.ui.control.Label
        AreaThreshold        matlab.ui.control.NumericEditField
        TimeThresholdsLabel  matlab.ui.control.Label
        TimeThresh           matlab.ui.control.NumericEditField
        CompileAuto          matlab.ui.control.Button
        CompileManual        matlab.ui.control.Button
        StartTimesLabel      matlab.ui.control.Label
        StartTime            matlab.ui.control.NumericEditField
        EndTimesLabel        matlab.ui.control.Label
        EndTime              matlab.ui.control.NumericEditField
        ClipLabel            matlab.ui.control.Label
        Clip                 matlab.ui.control.NumericEditField
        TimeBinsLabel        matlab.ui.control.Label
        TimeBin              matlab.ui.control.NumericEditField
        FigWindow            matlab.ui.control.Button
        DBscorerV2Label      matlab.ui.control.Label
    end


    properties (Access = public)
        v % Video
        changingValue1 % Video analysis start time
        changingValue2 % Video analysis end time
        show1 % Video analysis first frame
        show2 % Video analysis end frame
        path3 % Video Path
        filename
        filename_3
        Background
        cr
        crop
        ClearOutsideMask
        hImage
        T
        video
        ar
        cord
    end


    % Callbacks that handle component events
    methods (Access = private)

        % Button pushed function: LoadVideo
        function LoadVideoPushed(app, event)
            % Close all the figures first
            %exportapp(app.Tool,'V2.pdf')
            figure
            close all
            % Imports selected video
            [filename_2, pathname_2] = uigetfile('*.mov;*.wmv;*.mp4;*.avi','Open Video File');
            if filename_2 == 0
                % If user clicked the Cancel button.
                return;
            end
            app.filename_3 = cellstr(filename_2);
            pathname_3 = cellstr(pathname_2);
            app.video = fullfile(pathname_3{1},app.filename_3{1});
            % Get the name video and create folder with video name
            [folder, baseFileNameNoExt, ~] = fileparts(app.video);
            fileName = fullfile(pathname_3{1});
            dotLocations = find(fileName == '.');
            if isempty(dotLocations)
                nameBeforeFirstDot = fileName;
            else
                nameBeforeFirstDot = fileName(1:dotLocations(1)-1);
            end
            cd(folder)
            app.path3=nameBeforeFirstDot;
            app.filename=baseFileNameNoExt;
            % creates video reader and shows firstframe from the video
            app.v = VideoReader(app.video);
            frame = read(app.v, 1);
            app.hImage=imshow(frame);
            xlabel(baseFileNameNoExt)
            app.changingValue1=0;
            app.changingValue2=floor(app.v.Duration);
            app.ProcessVideoStart.Value=1;
            app.ProcessVideoEnd.Value=round(app.v.Duration-1);
            app.Time.Value =floor(app.v.Duration);
            app.LoadVideo.BackgroundColor='g';
            app.CreateBackground.BackgroundColor='w';
            app.CreateBackground.Text='Create Background';
            app.FixBackground.Text='Fix Background';
            app.FixBackground.BackgroundColor='w';
            app.MarkROI.Text='Mark ROI';
            app.MarkROI.BackgroundColor='w';
        end

        % Button pushed function: MarkROI
        function MarkROIPushed(app, event)
            numrois=2;
            map=hsv(numrois);
            custommap = map;
            app.show1 = read(app.v,floor(app.changingValue1*app.v.FrameRate)+1);
            imshow(app.show1)
            set(gcf, 'Position', get(0,'Screensize'));
            roi = drawpolygon('FaceAlpha',0,'Color',custommap(1,:));
            app.ClearOutsideMask=createMask(roi);
            croproi=roi.Position;
            app.cord=roi.Position;
            thisROI=[app.cord];
            close
            app.crop=[min(croproi(:,1)),min(croproi(:,2)),max(croproi(:,1))-min(croproi(:,1)),max(croproi(:,2))-min(croproi(:,2))];
            Ic=imcrop(app.show1,app.crop);
            app.hImage=imshow(Ic);
            [~,~,o]=size(Ic);
            medfilt=3;
            BackgroundCropped=imcrop(app.Background,app.crop);
            ClearOutsideMaskCropped=imcrop(app.ClearOutsideMask,app.crop);
            [~,n,~]=size(BackgroundCropped);
            rescale=(300/n);
            % Average
            fps=app.v.FrameRate;
            wanted_frames=floor(5*fps);
            a = app.changingValue1*app.v.FrameRate;
            b = app.changingValue2*app.v.FrameRate;
            x= floor((b-a).*rand(wanted_frames,1) + a);
            indices = sort(x);
            binarythresh=[];
            app.MarkROI.Text='Getting Binary Threshold';
            app.MarkROI.BackgroundColor='y';
            % if rgb then convert to grayscale
            if o==3
                for k=1:length(x)
                    frame=read(app.v,indices(k));
                    gray =rgb2gray(frame);
                    gray=imcrop(gray,app.crop);
                    MaskedImage = imgaussfilt(medfilt2(imabsdiff(BackgroundCropped,(gray)),[medfilt,medfilt]),3);
                    MaskedImage = adapthisteq(MaskedImage,'clipLimit',0.005,'Distribution','rayleigh');
                    MaskedImage=imresize(MaskedImage,rescale);
                    level = graythresh(MaskedImage);
                    binarythresh=[binarythresh,level];
                end
            else
                for k=1:length(x)
                    gray=read(app.v,indices(k));
                    gray=imcrop(gray,app.crop);
                    MaskedImage = imgaussfilt(medfilt2(imabsdiff(BackgroundCropped,(gray)),[medfilt,medfilt]),3);
                    MaskedImage = adapthisteq(MaskedImage,'clipLimit',0.005,'Distribution','rayleigh');
                    MaskedImage=imresize(MaskedImage,rescale);
                    level = graythresh(MaskedImage);
                    binarythresh=[binarythresh,level];
                end
            end
            MaskedImage = imgaussfilt(medfilt2(imabsdiff(BackgroundCropped,(gray)),[medfilt,medfilt]),3);
            MaskedImage = adapthisteq(MaskedImage,'clipLimit',0.005,'Distribution','rayleigh');
            MaskedImage=imresize(MaskedImage,rescale);
            gray=imresize(gray,rescale);
            bint = mean(binarythresh);
            app.T=round(bint*100);
            MaskedBinary=imbinarize(MaskedImage,(app.T/100));
            imshow(app.show1)
            Animal=drawpolygon('Position',thisROI,'LineWidth',.1,'FaceAlpha',.10,'Color','r','MarkerSize',.1);
            fig=gcf;
            exportgraphics(fig,[[app.EnterInfo.Value],' ',[app.filename],'.tif'],'Resolution',300)
            close
            app.hImage=imshow(gray);
            B = labeloverlay(gray,MaskedBinary,'Colormap','hsv','Transparency',0.75);
            set(app.hImage, 'CData',B)
            axis on
            app.MarkROI.Text='Mark ROI';
            app.MarkROI.BackgroundColor='g';
            app.ProcessVideo.BackgroundColor='w';
        end

        % Value changing function: ProcessVideoStart
        function ProcessVideoStartValueChanging(app, event)
            app.changingValue1 = event.Value;
            if  app.changingValue1<app.v.Duration
                app.show1 = read(app.v,floor(app.changingValue1*app.v.FrameRate)+1);
                set(app.hImage, 'CData', app.show1)
            end
            app.Time.Value =0;
            app.MarkROI.BackgroundColor='w';
            app.ProcessVideo.BackgroundColor='w';
            app.Play.BackgroundColor='w';
            app.StateButton.BackgroundColor='w';
        end

        % Value changing function: ProcessVideoEnd
        function ProcessVideoEndValueChanging(app, event)
            app.changingValue2 = event.Value;
            if  app.changingValue2<app.v.Duration
                app.show2 = read(app.v,floor(app.changingValue2*app.v.FrameRate));
                set(app.hImage, 'CData', app.show2)
            end
            app.Time.Value =app.changingValue2-app.changingValue1;
            app.MarkROI.BackgroundColor='w';
            app.ProcessVideo.BackgroundColor='w';
            app.Play.BackgroundColor='w';
            app.StateButton.BackgroundColor='w';
        end

        % Button pushed function: ProcessVideo
        function ProcessVideoButtonPushed(app, event)
            close
            app.Cancel.Value=0;
            medfilt=3;
            app.ProcessVideo.BackgroundColor='Yellow';
            app.Play.BackgroundColor='w';
            app.StateButton.BackgroundColor='w';
            BackgroundCropped=imcrop(app.Background,app.crop);
            clear cr
            A=size(BackgroundCropped);
            app.cr = struct('cdata',zeros(A(1),A(2),1,'uint8'),...
                'colormap',[]);
            StartFrame=floor(app.changingValue1*app.v.FrameRate)+1;
            EndFrame=floor(app.changingValue2*app.v.FrameRate);
            totaltime=(EndFrame-StartFrame);
            [~,n,~]=size(BackgroundCropped);
            rescale=(300/n);
            app.ar=[];
            cf=-2;
            for k=StartFrame:1:EndFrame+1
                cf=cf+1;
                app.Time.Value=floor(k/app.v.FrameRate);
                %app.Time.Value=(cf/totaltime)*100;
                pause(.0001)
                if app.Cancel.Value==1
                    break
                end
                frame=rgb2gray(read(app.v,k));
                RandomFrame = imcrop(frame,app.crop);
                MaskedImage = imgaussfilt(medfilt2(imabsdiff(BackgroundCropped,RandomFrame),[medfilt,medfilt]),3);
                MaskedImage = adapthisteq(MaskedImage,'clipLimit',0.005,'Distribution','rayleigh');
                MaskedImage=imresize(MaskedImage,rescale);
                MaskedBinary=imbinarize(MaskedImage,(app.T/100));
                All=sum(MaskedBinary,'all');%
                app.ar=[app.ar,All];%
            end
            BINTHRES=app.T;
            ar_score=app.ar;
            roicord=app.cord;
            fps=app.v.FrameRate;
            save([[app.EnterInfo.Value],' ',[app.filename]])
            app.ProcessVideo.BackgroundColor='g';
            app.hImage=imshow(app.Background);
        end

        % Button pushed function: FixBackground
        function FixBackgroundPushed(app, event)
            numrois=2;
            map=hsv(numrois);
            custommap = map;
            figure;
            imshow(app.Background);
            set(gcf, 'Position', get(0,'Screensize'));
            xlabel('Fill')
            RegionFill = drawpolygon('FaceAlpha',0,'Color',custommap(1,:));
            RegionFillMask = createMask(RegionFill);
            app.Background= regionfill(app.Background,RegionFillMask);
            delete(RegionFill);
            close
            app.hImage=imshow(app.Background);
            app.FixBackground.Text='Fix More Background';
            app.FixBackground.BackgroundColor='g';

        end

        % Button pushed function: CreateBackground
        function CreateBackgroundButtonPushed(app, event)
            app.v = VideoReader(app.video);
            fps=app.v.FrameRate;
            wanted_frames=floor(1*fps);
            a = app.changingValue1*app.v.FrameRate;
            b = app.changingValue2*app.v.FrameRate;
            x= floor((b-a).*rand(wanted_frames,1) + a);
            indices = sort(x);
            frame = read(app.v, wanted_frames(1));
            A=size(frame);
            app.cr= struct('cdata',zeros(A(1),A(2),1,'uint8'),...
                'colormap',[]);
            [m,n,o]=size(frame);
            Abkg = zeros(m,n,1,'uint8');
            % if rgb then convert to grayscale
            if o==3
                for k=1:length(x)
                    frame=read(app.v,indices(k));
                    frame =rgb2gray(frame);
                    Abkg(:,:,k) =uint8(app.cr(1).cdata);
                    app.cr(1).cdata = frame;
                end
            else
                for k=1:length(x)
                    frame=read(app.v,indices(k));
                    Abkg(:,:,k) =uint8(app.cr(1).cdata);
                    app.cr(1).cdata = frame;
                end
            end
            app.Background = uint8(median(double(Abkg),3));
            medfilt=3;
            app.Background=medfilt2(app.Background,[medfilt,medfilt]);
            app.hImage=imshow(app.Background);
            app.CreateBackground.BackgroundColor='g';
            app.CreateBackground.Text='Recreate Background';
            app.FixBackground.Text='Fix Background';
            app.FixBackground.BackgroundColor='w';
        end

        % Button pushed function: ManualScoring
        function ManualScoringButtonPushed(app, event)
            figure
            close all
            app.Play.Value=1;
            app.Cancel.Value=0;
            is=0;
            frame_by_frame_time_original = 1/app.v.FrameRate;
            StartFrame=floor(app.changingValue1*app.v.FrameRate)+1;
            EndFrame=floor(app.changingValue2*app.v.FrameRate);
            Full=EndFrame-StartFrame+2;
            im2 = zeros(Full,1);
            BackgroundCropped=imcrop(app.Background,app.crop);
            [~,n,~]=size(BackgroundCropped);
            width=round(300*0.05);
            rescale=(300/n);
            I=imcrop(app.show1,app.crop);
            I=imresize(I,rescale);
            figure
            app.hImage=imshow(I);
            app.StateButton.Value=0;
            app.StateButton.Text='Immobile';
            tic
            for k=StartFrame:1:EndFrame+1
                if app.Cancel.Value==1
                    break
                end
                while app.Play.Value==1
                    app.Play.Text='Play';
                    app.Play.BackgroundColor='y';
                    app.StateButton.BackgroundColor='y';
                    pause(.0001)
                    if app.Cancel.Value==1
                        break
                    end
                end
                app.Play.Text='Pause';
                app.Play.BackgroundColor='g';
                if app.StateButton.Value==1
                    app.StateButton.BackgroundColor='G';
                    app.StateButton.Text='Mobile';
                    c1=yline(width,'-g','LineWidth',width);
                    is=is+1;
                    im2(k+1-StartFrame)=1;
                else
                    app.StateButton.BackgroundColor='M';
                    app.StateButton.Text='Immobile';
                    c1=yline(width,'-m','LineWidth',width);
                    is=is+0;
                    im2(k+1-StartFrame)=0;
                end
                app.Time.Value=floor(k/app.v.FrameRate);
                frame=read(app.v,k);
                I=imcrop(frame,app.crop);
                I=imresize(I,rescale);
                set(app.hImage, 'CData', I)
                frame_normalization = toc;
                if frame_normalization < frame_by_frame_time_original
                    pause(frame_by_frame_time_original - frame_normalization);
                end
                tic
                delete(c1)
            end
            hold off
            app.StateButton.Text='State';
            app.StateButton.BackgroundColor='w';
            app.Play.Value=1;
            app.Time.Value=floor(sum(im2,'all')/app.v.FrameRate);
            fps=app.v.FrameRate;
            save([[app.EnterInfo.Value],' ',[app.filename],' ','Manual'])
            app.Cancel.Value=0;
            close all
            app.hImage=imshow(app.Background);
        end

        % Button pushed function: GetThresh
        function GetThreshButtonPushed(app, event)
            [filenames, pathname] = uigetfile('*.mat',...
                'Select One or More Files', ...
                'MultiSelect', 'on');
            if pathname == 0
                % If user clicked the Cancel button.
                return;
            end
            filenames=filenames';
            cd(pathname)
            %% Variables
            FileNames=[];
            AllData=[];
            clip=app.Clip.Value;
            kfold=7;
            fps=15
            %% Batch Processing
            FileNames=[];
            AllData=[];
            for name=1:length(filenames)
                file=filenames{name}(1:end-4);
                tf = strcmp(filenames{name}(end-9:end-4),'Manual');
                if tf==1
                    manual=filenames{name}(1:end-4)
                    load(manual)
                    auto=[file(1:end-7),'.mat'];
                    %auto=filenames{name}(1:end-11);
                    load(auto)
                    %im2=im2==0; %only for old data remove it before uploading to git
                    rc =length(im2)- rem(length(im2),fps);
                    Rc=im2(1:rc);
                    binc = reshape(Rc,fps,[]);
                    meanbinpercentage1c = mean(binc,1);
                    meanbinpercentage2c=meanbinpercentage1c<0.5;
                    GT=meanbinpercentage2c;
                    % area change %
                    AreaChange=abs(diff(ar_score(1:end-1)));
                    AreaPrevious=ar_score(1:end-2);
                    AreaChangePercent=(AreaChange./AreaPrevious)*100;
                    AreaChangePercent(AreaChangePercent>10)=10;
                    r_ar =length(AreaChangePercent)- rem(length(AreaChangePercent),fps);
                    R_ar=AreaChangePercent(1:r_ar);
                    bin_ar = reshape(R_ar,fps,[]);
                    Area_Change=mean(bin_ar,1);
                    FileNames=[FileNames;{file(1:end)}];
                    T1=table(GT(2:end)',Area_Change');
                    AllData=[AllData;T1];
                    %close all
                else
                    continue
                end
            end
            %% Clip data
            GT=AllData.Var1';
            Area_Change=AllData.Var2;
            Tillc=length(GT);
            transitionsc = diff([0,GT,0]); % find where the array goes from non-zero to zero and vice versa
            runstartsc = find(transitionsc == 1);
            runendsc = (find(transitionsc == -1)); %one past the end
            runlengthsc = abs(runendsc - runstartsc);
            GT=zeros(length(GT),1);
            for i=1:length(runstartsc)
                GT(runstartsc(i):runendsc(i))=1;
            end
            rasterc=sort([0,runstartsc,runendsc,Tillc]);
            clipped_Manual_score=GT;
            clipped_area_change=Area_Change;
            if clip>0
                for i=clip+1:length(rasterc)
                    if rasterc(i)-clip<=0
                        rasterc(i)=1;
                    else
                        clipped_Manual_score(rasterc(i)-clip:rasterc(i)+clip)=50;
                        clipped_area_change(rasterc(i)-clip:rasterc(i)+clip)=50;
                    end
                end
            end
            clipped_Manual_score(clipped_Manual_score==50)=[];
            clipped_area_change(clipped_area_change==50)=[];
            s=min(length(clipped_Manual_score),length(clipped_area_change));
            TrainData=[clipped_Manual_score(1:s),clipped_area_change(1:s)];
            % shuffle the data
            AveragedThreshold=[];
            AveragedAUC=[];
            AveragedAccuracy=[];
            AveragedPrecision=[];
            AveragedRecall=[];
            %AveragedMCC=[];
            Thresholds=[];
            Precisions=[];
            Recalls=[];
            dp=s;
            for sfl=1:100
                idx= floor((s-1).*rand(dp,1) + 1);
                % k divide
                if  mod(s,kfold)>0
                    blocksize=floor(s/kfold);
                else
                    blocksize=floor(s/kfold)-1;
                end
                % create valset testset
                TrainSet=[];
                ValSet=[];
                for i=1: kfold-2
                    MCCs=[];
                    ValSet=TrainData(idx(blocksize*i:blocksize*i+blocksize),:);
                    TrainSet=TrainData;
                    TrainSet(idx(blocksize*i:blocksize*i+blocksize),:)=[];
                    % ROC based threshold determination
                    AreaChange=TrainSet(:,2);
                    IM=AreaChange(TrainSet(:,1)==1);
                    M=AreaChange(TrainSet(:,1)==0);
                    [~,edges] = histcounts(AreaChange',100);
                    Nim = histcounts(IM,edges);
                    Nm = histcounts(M,edges);
                    NmPa=[]; % tpr
                    for i=1:length(Nm)
                        Pm=(sum(Nm(i:length(Nm)))/sum(Nm));
                        NmPa=[NmPa,Pm];
                    end
                    NimPa=[]; % fpr
                    for i=1:length(Nim)
                        Pim=sum(Nim(i:length(Nim)))/sum(Nim);
                        NimPa=[NimPa,Pim];
                    end
                    %CZ
                    gmeansa=(NmPa.*(1-NimPa));
                    ThresholdPa=(edges(gmeansa==max(gmeansa)));
                    CalibratedThresholdMin=min(ThresholdPa);
                    CalibratedThresholdMax=max(ThresholdPa);
                    AUCa=abs(trapz(NimPa,NmPa));
                    CalibratedThresholdValue = max(ThresholdPa);
                    AveragedThreshold=[AveragedThreshold,CalibratedThresholdValue];
                    AveragedAUC=[AveragedAUC,AUCa];
                    % here calculate true positive, false positive, true negative, false
                    % negative
                    trueval=ValSet(:,1);
                    predicted=ValSet(:,2)<CalibratedThresholdValue;
                    TP=sum(trueval==1 & predicted==1);
                    FP=sum(trueval==0 & predicted==1);
                    TN=sum(trueval==0 & predicted==0);
                    FN=sum(trueval==1 & predicted==0);
                    Precision=TP/(TP+FP);
                    Recall=TP/(TP+FN);
                    AveragedPrecision=[AveragedPrecision,Precision];
                    AveragedRecall=[AveragedRecall,Recall];
                    % MCC based threshold determination
                    for i=1:length(edges)
                        th=edges(i);
                        trueval=TrainSet(:,1);
                        predicted=TrainSet(:,2)<th;
                        TP=sum(trueval==1 & predicted==1);
                        FP=sum(trueval==0 & predicted==1);
                        TN=sum(trueval==0 & predicted==0);
                        FN=sum(trueval==1 & predicted==0);
                        MCC=((TP*TN)-(FP*FN))/sqrt((TP+FP)*(TP+FN)*(TN+FP)*(TN+FN));
                        MCCs=[MCCs,MCC];
                    end
                    ThresholdMCC=(edges(MCCs==max(MCCs)));
                    ThresholdValue=max(ThresholdMCC);
                    %true positive, false positive, true negative, false negative
                    trueval=ValSet(:,1);
                    predicted=ValSet(:,2)<ThresholdValue;
                    TP=sum(trueval==1 & predicted==1);
                    FP=sum(trueval==0 & predicted==1);
                    TN=sum(trueval==0 & predicted==0);
                    FN=sum(trueval==1 & predicted==0);
                    Precision=TP/(TP+FP);
                    Recall=TP/(TP+FN);
                    Precisions=[Precisions,Precision];
                    Recalls=[Recalls,Recall];
                    Thresholds=[Thresholds,ThresholdValue];
                end
                if sfl==100
                        %p4=plot(NimPa,NmPa,'-k','LineWidth',2);
                        p4=area(NimPa,NmPa,'LineWidth',2,'LineStyle','-',"FaceColor", '#87cefa');
                        hold on
                        %p5=plot((NimPa(gmeansa==max(gmeansa))),(NmPa(gmeansa==max(gmeansa))),'g*','LineWidth',1);
                        hold off
                        pbaspect([1 1 1]);
                        ax = gca;
                        ax.Color = 'none';
                        ax.FontWeight='bold';
                        ax.FontSize = 12;
                        %ax.TickLength = [.005 0.035];
                        ax.LineWidth=1;
                        xlabel('1-Specificity')
                        ylabel('Sensitivity')
                        title('ROC Curve')
                        saveas(gcf,['ROC curve generated from Manual Quantification','.png'])
                 end
            end
            ThresholdG=mean(AveragedThreshold,'all');
            PrecisionG=mean(AveragedPrecision);
            RecallG=mean(AveragedRecall);
            AUC=mean(AUCa);
            Threshold=mean(Thresholds);
            Precision=mean(Precisions);
            Recall=mean(Recalls);
            % MCC based threshold
            Immobility=(sum(GT)/length(GT))*100;
%             if 20<Immobility || Immobility>80
%                 Precision=mean(Precisions)
%                 Recall=mean(Recalls)
%                 Threshold=mean(Thresholds)
%             end
            T2=table(AUC,Threshold,Precision,Recall,Immobility);
            writetable(T2,'Threshold.csv');
            %str = {['Optimum Threshold-',num2str(Threshold)]};
            %text(.25,.5,str)
            close all
        end

        % Button pushed function: CompileAuto
        function CompileAutoButtonPushed(app, event)
            [filenames, pathname] = uigetfile('*.mat',...
                'Select One or More Files', ...
                'MultiSelect', 'on');
            if pathname == 0
                % If user clicked the Cancel button.
                return;
            end
            cd(pathname)
            filenames=filenames';
            %% Variables
            FileNames=[];
            AllData=[];
            if isempty(app.StartTime.Value)
                startsec=0;
            else
                startsec=app.StartTime.Value;
            end

            if isempty(app.EndTime.Value)
                endsec=0;
            else
                endsec=app.EndTime.Value;
            end
            Threshold=app.AreaThreshold.Value;
            Minimumchange=app.TimeThresh.Value;
            Ylimit=5;
            Binsize=app.TimeBin.Value;
            %% Batch Processing
            FileNames=[];
            AllData=[];
            fps=15;
            figure
            for name=1:length(filenames)
                file=filenames{name}(1:end-4);
                tf = strcmp(filenames{name}(end-9:end-4),'Manual');
                if tf==0
                    load([file,'.mat'])
                    startframe=( startsec*fps)+1;
                    endframe=(endsec*fps)+1;
                    if endframe<length(ar_score)
                        Area=ar_score(startframe:endframe);
                    else
                        Area=ar_score(startframe:length(ar_score));
                        endsec=(length(ar_score)-1)/fps;
                    end
                    AreaChange=abs(diff(Area));
                    AreaPrevious=Area(1:end-1);
                    AreaChangePercent=(AreaChange./AreaPrevious)*100;
                    AreaChangePercent(AreaChangePercent>10)=10;
                    r_ar =length(AreaChangePercent)- rem(length(AreaChangePercent),fps);
                    R_ar=AreaChangePercent(1:r_ar);
                    bin_ar = reshape(R_ar,fps,[]);
                    Area_Change=mean(bin_ar,1);
                    im=Area_Change<Threshold;
                    A=im;
                    Till=length(A);
                    transitions = diff([0,A,0]); % find where the array goes from non-zero to zero and vice versa
                    runstarts = find(transitions == 1);
                    runends = (find(transitions == -1)-1); %one past the end
                    runlengths = abs(runends - runstarts);
                    runstarts(runlengths<= Minimumchange) = [];
                    runends(runlengths<= Minimumchange) = [];
                    Y=zeros(length(A),1);
                    for i=1:length(runstarts)
                        Y(runstarts(i):runends(i))=1;
                    end
                    Immobility_Percentage=(sum(Y(1:Till))/Till)*100;
                    Number_of_bouts=length(runends);
                    if sum(runlengths,'all')==0
                        Longest_bout=0;
                    else
                        Longest_bout=max(runlengths)+1;
                    end
                    if sum(runstarts,'all')==0
                        Immobility_latency=NaN;
                    else
                        Immobility_latency=runstarts(1)-1;
                    end
                    % binned immobility
                    if Binsize<length(Y)
                        bin =length(Y)- rem(length(Y),Binsize);
                        Rim=Y(1:bin);
                        if length(Y)>bin
                            Rim2=Y(bin+1:end);
                            Rimbin = reshape(Rim,Binsize,[]);
                            Bins = [sum(Rimbin,1)/Binsize,sum(Rim2)/length(Rim2)]*100;
                        else
                            Rimbin = reshape(Rim,Binsize,[]);
                            Bins = (sum(Rimbin,1)/Binsize)*100;
                        end
                    else
                        Bins=sum(Y)/length(Y)*100;
                    end
                    % plot graphs
                    subplot(length(filenames),1,name,'align');
                    bar(Y*Ylimit,1,'FaceColor','#000000','EdgeColor','none')
                    hold on
                    bar(double(Y==0)*Ylimit,1,'FaceColor','#FFFAFA','EdgeColor','none')
                    %alpha(.4) % sets transparency
                    xticks(0:Binsize:Till)
                    yticklabels({})
                    if length(filenames)>name
                    xticklabels({})
                    end
                    %pbaspect([Till Till/10 1])
                    xlim([0 Till])
                    ylim([0 Ylimit])
                    ax = gca;
                    ax.Color ='none';
                    ax.FontWeight='bold';
                    ax.FontSize = 5;
                    ax.TickLength = [.01 0.01];
                    ax.LineWidth=.1;
                    box on
                    hold on
                    yticks([])
%                     subplot(length(filenames),2,name+1,'align');
%                     image(abs(100-Bins))
%                     colormap(gray(100))
%                     yticks([])
%                     ax = gca;
%                     ax.Color ='none';
%                     ax.FontWeight='bold';
%                     ax.FontSize = 5;
%                     ax.TickLength = [.01 0.01];
%                     ax.LineWidth=.1;
%                     box on
%                     if length(filenames)>name
%                     xticklabels({})
%                     end
                    T1=table(Immobility_Percentage,Immobility_latency,Longest_bout,Number_of_bouts,...
                        startsec,endsec,Minimumchange,Threshold,Binsize,Bins);
                    %writetable(T1,[file,' Results Auto.csv']);
                    writematrix(Y,[file,' Auto .txt'])
                    FileNames=[FileNames;{file(1:end)}];
                    AllData=[AllData;T1];
                    
                else
                    continue
                end
            end
            set(gcf, 'Position', get(0,'Screensize'));
            saveas(gcf,'Raster Auto.png')
            saveas(gcf,'Raster Auto.pdf')
            hold off
            close all
            T2=table(FileNames);
            CombinedData=[T2,AllData];
            writetable(CombinedData,' Results Auto Compiled.csv');

        end

        % Button pushed function: CompileManual
        function CompileManualButtonPushed(app, event)
            [filenames, pathname] = uigetfile('*.mat',...
                'Select One or More Files', ...
                'MultiSelect', 'on');
            if pathname == 0
                % If user clicked the Cancel button.
                return;
            end
            cd(pathname)
            filenames=filenames';
            %% Variables
            FileNames=[];
            AllData=[];
            fps=15;
            %fps=app.FPS.Value;
            if isempty(app.StartTime.Value)
                startsec=0;
            else
                startsec=app.StartTime.Value;
            end

            if isempty(app.EndTime.Value)
                endsec=0;
            else
                endsec=app.EndTime.Value;
            end
            Threshold=app.AreaThreshold.Value;
            Minimumchange=app.TimeThresh.Value;
            Ylimit=5;
            Binsize=app.TimeBin.Value;
            %% Batch Processing
            FileNames=[];
            AllData=[];
            figure
            set(gcf, 'Position', get(0,'Screensize'));
            for name=1:length(filenames)
                file=filenames{name}(1:end-4);
                tf = strcmp(filenames{name}(end-9:end-4),'Manual');
                if tf==1
                    load([file,'.mat'])
                    %im2=im2==0; %only for old data remove it before uploading to git
                    startframe=( startsec*fps)+1;
                    endframe=(endsec*fps)+1;
                    if endframe<length(im2)
                        im2=im2(startframe:endframe);
                    else
                        im2=im2(startframe:length(im2));
                    end
                    rc =length(im2)- rem(length(im2),fps);
                    Rc=im2(1:rc);
                    binc = reshape(Rc,fps,[]);
                    meanbinpercentage1c = mean(binc,1);
                    meanbinpercentage2c=meanbinpercentage1c<0.5;
                    A=meanbinpercentage2c;
                    Till=length(A);
                    transitions = diff([0,A,0]); % find where the array goes from non-zero to zero and vice versa
                    runstarts = find(transitions == 1);
                    runends = (find(transitions == -1)-1); %one past the end
                    runlengths = abs(runends - runstarts);
                    runstarts(runlengths<= Minimumchange) = [];
                    runends(runlengths<= Minimumchange) = [];
                    Y=zeros(length(A),1);
                    for i=1:length(runstarts)
                        Y(runstarts(i):runends(i))=1;
                    end
                    Immobility_Percentage=(sum(Y(1:Till))/Till)*100;
                    Number_of_bouts=length(runends);
                    if sum(runlengths,'all')==0
                        Longest_bout=0;
                    else
                        Longest_bout=max(runlengths)+1;
                    end
                    if sum(runstarts,'all')==0
                        Immobility_latency=Till;
                    else
                        Immobility_latency=runstarts(1)-1;
                    end

                    % binned immobility

                    if Binsize<length(Y)
                        bin =length(Y)- rem(length(Y),Binsize);
                        Rim=Y(1:bin);
                        if length(Y)>bin
                            Rim2=Y(bin+1:end);
                            Rimbin = reshape(Rim,Binsize,[]);
                            Bins = [sum(Rimbin,1)/Binsize,sum(Rim2)/length(Rim2)]*100;
                        else
                            Rimbin = reshape(Rim,Binsize,[]);
                            Bins = (sum(Rimbin,1)/Binsize)*100;
                        end
                    else
                        Bins=sum(Y)/length(Y)*100;
                    end
                    % plot graphs
                    subplot(length(filenames),1,name,'align');
                    bar(Y*Ylimit,1,'FaceColor','#000000','EdgeColor','none')
                    hold on
                    bar(double(Y==0)*Ylimit,1,'FaceColor','#FFFAFA','EdgeColor','none')
                    xticks(0:Binsize:Till)
                    yticklabels({})
                    if length(filenames)>name
                    xticklabels({})
                    end
                    %pbaspect([Till Till/10 1])
                    xlim([0 Till])
                    ylim([0 Ylimit])
                    ax = gca;
                    ax.Color ='none';
                    ax.FontWeight='bold';
                    ax.FontSize = 5;
                    ax.TickLength = [.01 0.01];
                    ax.LineWidth=.1;
                    if length(filenames)==name
                    xlabel('Time (Second)')
                    end
                    yticks([])
                    T1=table(Immobility_Percentage,Immobility_latency,Longest_bout,Number_of_bouts,...
                        startsec,endsec,Minimumchange,Threshold,Binsize,Bins);
                    FileNames=[FileNames;{file(1:end)}];
                    %writetable(T1,[file,' Results Manual.csv']);
                    writematrix(Y,[file,' Manual.txt'])
                    AllData=[AllData;T1];
                else
                    continue
                end
            end
            saveas(gcf,'Raster Manual.png')
            saveas(gcf,'Raster Manual.pdf')
            hold off
            close all
            T2=table(FileNames);
            CombinedData=[T2,AllData];
            writetable(CombinedData,' Results Manual Compiled.csv');

        end

        % Button pushed function: FigWindow
        function FigWindowButtonPushed(app, event)
            app.hImage=imshow(app.Background);
        end
    end

    % Component initialization
    methods (Access = private)

        % Create UIFigure and components
        function createComponents(app)

            % Create Tool and hide until all components are created
            app.Tool = uifigure('Visible', 'off');
            app.Tool.AutoResizeChildren = 'off';
            app.Tool.Color = [1 1 1];
            app.Tool.Position = [100 100 358 407];
            app.Tool.Name = 'DBscorerV2';
            app.Tool.Resize = 'off';

            % Create LoadVideo
            app.LoadVideo = uibutton(app.Tool, 'push');
            app.LoadVideo.ButtonPushedFcn = createCallbackFcn(app, @LoadVideoPushed, true);
            app.LoadVideo.Interruptible = 'off';
            app.LoadVideo.FontName = 'Arial';
            app.LoadVideo.Position = [14 377 159 25];
            app.LoadVideo.Text = 'Load Video';

            % Create MarkROI
            app.MarkROI = uibutton(app.Tool, 'push');
            app.MarkROI.ButtonPushedFcn = createCallbackFcn(app, @MarkROIPushed, true);
            app.MarkROI.Interruptible = 'off';
            app.MarkROI.Tooltip = {''};
            app.MarkROI.Position = [14 181 159 25];
            app.MarkROI.Text = 'Mark ROI';

            % Create StartsLabel
            app.StartsLabel = uilabel(app.Tool);
            app.StartsLabel.HorizontalAlignment = 'right';
            app.StartsLabel.Position = [12 311 58 22];
            app.StartsLabel.Text = 'Start (s)';

            % Create ProcessVideoStart
            app.ProcessVideoStart = uispinner(app.Tool);
            app.ProcessVideoStart.ValueChangingFcn = createCallbackFcn(app, @ProcessVideoStartValueChanging, true);
            app.ProcessVideoStart.Limits = [0 Inf];
            app.ProcessVideoStart.Interruptible = 'off';
            app.ProcessVideoStart.Position = [97 311 76 22];

            % Create EndsLabel
            app.EndsLabel = uilabel(app.Tool);
            app.EndsLabel.HorizontalAlignment = 'right';
            app.EndsLabel.Position = [14 280 56 22];
            app.EndsLabel.Text = 'End (s)';

            % Create ProcessVideoEnd
            app.ProcessVideoEnd = uispinner(app.Tool);
            app.ProcessVideoEnd.ValueChangingFcn = createCallbackFcn(app, @ProcessVideoEndValueChanging, true);
            app.ProcessVideoEnd.Limits = [1 Inf];
            app.ProcessVideoEnd.Interruptible = 'off';
            app.ProcessVideoEnd.Position = [97 280 76 22];
            app.ProcessVideoEnd.Value = 1;

            % Create TimeEditFieldLabel
            app.TimeEditFieldLabel = uilabel(app.Tool);
            app.TimeEditFieldLabel.HorizontalAlignment = 'right';
            app.TimeEditFieldLabel.Position = [39 249 31 22];
            app.TimeEditFieldLabel.Text = 'Time';

            % Create Time
            app.Time = uieditfield(app.Tool, 'numeric');
            app.Time.Interruptible = 'off';
            app.Time.Editable = 'off';
            app.Time.Position = [97 249 76 22];

            % Create ProcessVideo
            app.ProcessVideo = uibutton(app.Tool, 'push');
            app.ProcessVideo.ButtonPushedFcn = createCallbackFcn(app, @ProcessVideoButtonPushed, true);
            app.ProcessVideo.Interruptible = 'off';
            app.ProcessVideo.Position = [14 147 159 25];
            app.ProcessVideo.Text = 'Process Video';

            % Create FixBackground
            app.FixBackground = uibutton(app.Tool, 'push');
            app.FixBackground.ButtonPushedFcn = createCallbackFcn(app, @FixBackgroundPushed, true);
            app.FixBackground.Interruptible = 'off';
            app.FixBackground.Tooltip = {''};
            app.FixBackground.Position = [186 246 159 25];
            app.FixBackground.Text = 'Fix Background';

            % Create EnterInfo
            app.EnterInfo = uieditfield(app.Tool, 'text');
            app.EnterInfo.Position = [14 215 159 25];

            % Create CreateBackground
            app.CreateBackground = uibutton(app.Tool, 'push');
            app.CreateBackground.ButtonPushedFcn = createCallbackFcn(app, @CreateBackgroundButtonPushed, true);
            app.CreateBackground.Interruptible = 'off';
            app.CreateBackground.Tooltip = {''};
            app.CreateBackground.Position = [186 277 159 25];
            app.CreateBackground.Text = 'Create Background';

            % Create ManualScoring
            app.ManualScoring = uibutton(app.Tool, 'push');
            app.ManualScoring.ButtonPushedFcn = createCallbackFcn(app, @ManualScoringButtonPushed, true);
            app.ManualScoring.Tooltip = {''};
            app.ManualScoring.Position = [14 113 159 25];
            app.ManualScoring.Text = 'Manual Scoring';

            % Create Play
            app.Play = uibutton(app.Tool, 'state');
            app.Play.Tooltip = {''};
            app.Play.Text = 'Play';
            app.Play.Position = [14 79 159 25];

            % Create StateButton
            app.StateButton = uibutton(app.Tool, 'state');
            app.StateButton.Tooltip = {''};
            app.StateButton.Text = 'State';
            app.StateButton.Position = [14 47 159 25];

            % Create Cancel
            app.Cancel = uibutton(app.Tool, 'state');
            app.Cancel.Tooltip = {''};
            app.Cancel.Text = 'Cancel';
            app.Cancel.Position = [14 13 159 25];

            % Create GetThresh
            app.GetThresh = uibutton(app.Tool, 'push');
            app.GetThresh.ButtonPushedFcn = createCallbackFcn(app, @GetThreshButtonPushed, true);
            app.GetThresh.Interruptible = 'off';
            app.GetThresh.Tooltip = {''};
            app.GetThresh.Position = [186 308 159 25];
            app.GetThresh.Text = 'Get Threshold';

            % Create AreaThresholdLabel
            app.AreaThresholdLabel = uilabel(app.Tool);
            app.AreaThresholdLabel.HorizontalAlignment = 'right';
            app.AreaThresholdLabel.Position = [184 81 96 22];
            app.AreaThresholdLabel.Text = 'Δ Area Threshold';

            % Create AreaThreshold
            app.AreaThreshold = uieditfield(app.Tool, 'numeric');
            app.AreaThreshold.Limits = [0 Inf];
            app.AreaThreshold.Tooltip = {'Optional'};
            app.AreaThreshold.Position = [293 81 52 23];
            app.AreaThreshold.Value = 0.6;

            % Create TimeThresholdsLabel
            app.TimeThresholdsLabel = uilabel(app.Tool);
            app.TimeThresholdsLabel.HorizontalAlignment = 'right';
            app.TimeThresholdsLabel.Position = [184 115 101 22];
            app.TimeThresholdsLabel.Text = 'Time Threshold (s)';

            % Create TimeThresh
            app.TimeThresh = uieditfield(app.Tool, 'numeric');
            app.TimeThresh.Limits = [0 Inf];
            app.TimeThresh.RoundFractionalValues = 'on';
            app.TimeThresh.Tooltip = {'Optional'};
            app.TimeThresh.Position = [293 115 52 23];

            % Create CompileAuto
            app.CompileAuto = uibutton(app.Tool, 'push');
            app.CompileAuto.ButtonPushedFcn = createCallbackFcn(app, @CompileAutoButtonPushed, true);
            app.CompileAuto.Interruptible = 'off';
            app.CompileAuto.Tooltip = {''};
            app.CompileAuto.Position = [186 13 159 25];
            app.CompileAuto.Text = 'Compile ';

            % Create CompileManual
            app.CompileManual = uibutton(app.Tool, 'push');
            app.CompileManual.ButtonPushedFcn = createCallbackFcn(app, @CompileManualButtonPushed, true);
            app.CompileManual.Interruptible = 'off';
            app.CompileManual.Tooltip = {''};
            app.CompileManual.Position = [186 47 159 25];
            app.CompileManual.Text = 'Compile Manual';

            % Create StartTimesLabel
            app.StartTimesLabel = uilabel(app.Tool);
            app.StartTimesLabel.HorizontalAlignment = 'right';
            app.StartTimesLabel.Position = [204 217 81 22];
            app.StartTimesLabel.Text = 'Start Time (s)';

            % Create StartTime
            app.StartTime = uieditfield(app.Tool, 'numeric');
            app.StartTime.Limits = [0 Inf];
            app.StartTime.RoundFractionalValues = 'on';
            app.StartTime.Tooltip = {'Optional'};
            app.StartTime.Position = [293 217 52 23];

            % Create EndTimesLabel
            app.EndTimesLabel = uilabel(app.Tool);
            app.EndTimesLabel.HorizontalAlignment = 'right';
            app.EndTimesLabel.Position = [208 183 77 22];
            app.EndTimesLabel.Text = 'End Time (s)';

            % Create EndTime
            app.EndTime = uieditfield(app.Tool, 'numeric');
            app.EndTime.Limits = [0 Inf];
            app.EndTime.RoundFractionalValues = 'on';
            app.EndTime.Tooltip = {'Optional'};
            app.EndTime.Position = [293 183 52 23];
            app.EndTime.Value = 300;

            % Create ClipLabel
            app.ClipLabel = uilabel(app.Tool);
            app.ClipLabel.HorizontalAlignment = 'right';
            app.ClipLabel.Position = [187 344 96 22];
            app.ClipLabel.Text = 'Clip for threshold';

            % Create Clip
            app.Clip = uieditfield(app.Tool, 'numeric');
            app.Clip.Limits = [0 Inf];
            app.Clip.RoundFractionalValues = 'on';
            app.Clip.Tooltip = {'Optional'};
            app.Clip.Position = [293 344 52 23];
            app.Clip.Value = 1;

            % Create TimeBinsLabel
            app.TimeBinsLabel = uilabel(app.Tool);
            app.TimeBinsLabel.HorizontalAlignment = 'right';
            app.TimeBinsLabel.Position = [190 149 95 22];
            app.TimeBinsLabel.Text = 'Time Bin (s)';

            % Create TimeBin
            app.TimeBin = uieditfield(app.Tool, 'numeric');
            app.TimeBin.Limits = [0 Inf];
            app.TimeBin.RoundFractionalValues = 'on';
            app.TimeBin.Tooltip = {'Optional'};
            app.TimeBin.Position = [293 149 52 23];
            app.TimeBin.Value = 60;

            % Create FigWindow
            app.FigWindow = uibutton(app.Tool, 'push');
            app.FigWindow.ButtonPushedFcn = createCallbackFcn(app, @FigWindowButtonPushed, true);
            app.FigWindow.Interruptible = 'off';
            app.FigWindow.Tooltip = {''};
            app.FigWindow.Position = [14 342 159 25];
            app.FigWindow.Text = 'Figure Window';

            % Create DBscorerV2Label
            app.DBscorerV2Label = uilabel(app.Tool);
            app.DBscorerV2Label.HorizontalAlignment = 'center';
            app.DBscorerV2Label.FontName = 'Lucida Calligraphy';
            app.DBscorerV2Label.FontSize = 20;
            app.DBscorerV2Label.FontWeight = 'bold';
            app.DBscorerV2Label.FontColor = [1 0.4118 0.1608];
            app.DBscorerV2Label.Position = [185 376 160 27];
            app.DBscorerV2Label.Text = 'DBscorerV2';

            % Show the figure after all components are created
            app.Tool.Visible = 'on';
        end
    end

    % App creation and deletion
    methods (Access = public)

        % Construct app
        function app = DBscorerV02032023_exported

            % Create UIFigure and components
            createComponents(app)

            % Register the app with App Designer
            registerApp(app, app.Tool)

            if nargout == 0
                clear app
            end
        end

        % Code that executes before app deletion
        function delete(app)

            % Delete UIFigure when app is deleted
            delete(app.Tool)
        end
    end
end