VP_RPE_2020/MatlabScripts/3_Figures/AdditionalFigures/opto/VideoAnalysis_Arch.m

clear all;
analyzedlcfiles=0;
%% get data from DeepLabCut files

if analyzedlcfiles
    %original videos needed, available upon request. otherwise, use
    %pre-generated struct below

    ffmpeg_path='C:\FFmpeg\bin';
    address=['']; %where are the running files located
    files=dir([address,'\\*_*']);

    videoaddress=[''];
    videofiles=dir([videoaddress,'\\*Op*']);

    for k=1:length(files)
        filename=fullfile(files(k).folder,files(k).name);
        rat=str2num(files(k).name(3:4)); %rat #
        videofile=[videofiles(k).folder '\' videofiles(k).name];

        %get timestamp data
        [timestamps,xcoordinates,ycoordinates]=AnalyzeDeepLabCutPP(filename,videofile,ffmpeg_path);

        VideoData{rat,1}=timestamps;
        VideoData{rat,2}=xcoordinates;
        VideoData{rat,3}=ycoordinates;

    end

    save('PPVideoData.mat','VideoData');

else
    load('PPVideoData.mat');

end
%%

spreadsheet=importdata('PPVideoKey.xlsx');
spreadsheetrat=spreadsheet.textdata(2:end,1);
for i=1:length(spreadsheetrat)
    sprat(i,1)=str2num(spreadsheetrat{i,1}(3:4));
end

lighton(sprat,1)=spreadsheet.data(:,1);
portcoord(sprat,1)=spreadsheet.data(:,2);
portcoord(sprat,2)=spreadsheet.data(:,3);
cutoff(sprat,1)=spreadsheet.data(:,5);

Colors = load_colors();
trlactivity={[];[];[]};
trldistance={[];[];[]};

address=['/Data/ArchBehavior']; %where are the running files located
files=dir([address,'//*!*']); %mac

for k=1:length(files)
    filename=fullfile(files(k).folder,files(k).name);
    file=fopen(filename);
    L=textscan(file,'%s','Delimiter',':');
    fclose('all');
    rat=str2num(files(k).name(end-1:end));

    %find start of A, start of C, and end of C
    Jstrt=find(strcmp('J',L{1,1})); %Cue
    Kstrt=find(strcmp('K',L{1,1})); %Sucrose Delivery
    Ostrt=find(strcmp('O',L{1,1})); %Port entry times
    Pstrt=find(strcmp('P',L{1,1})); %Port durations
    Qstrt=find(strcmp('Q',L{1,1})); %Laser stimulations
    Xstrt=find(strcmp('X',L{1,1})); %List (marks end of laser stims)

    %trial times
    choicet=(L{1,1}(Jstrt+2:2:Kstrt-1));
    choicetime=[];
    for i=1:length(choicet)
        medtext=textscan(char(choicet(i,1)),'%f','Delimiter',' ');
        ctime=medtext{1,1}(:,1);
        choicetime=(cat(1,choicetime,ctime(isnan(ctime)==0)));
    end
    choicetime(choicetime==0)=[]; %delete 0s


    %Sucrose delivery times
    sucrosedel=(L{1,1}(Kstrt+2:2:Ostrt-1));
    sucrosedeltime=[];
    for i=1:length(sucrosedel)
        medtext=textscan(char(sucrosedel(i,1)),'%f','Delimiter',' ');
        sdtime=medtext{1,1}(:,1);
        sucrosedeltime=(cat(1,sucrosedeltime,sdtime(isnan(sdtime)==0)));
    end
    sucrosedeltime(sucrosedeltime==0)=[]; %delete 0s

    %Port entry times
    pet=(L{1,1}(Ostrt+2:2:Pstrt-1));
    petime=[];
    for i=1:length(pet)
        medtext=textscan(char(pet(i,1)),'%f','Delimiter',' ');
        portentry=medtext{1,1}(:,1);
        petime=(cat(1,petime,portentry(isnan(portentry)==0)));
    end
    removes=petime==0;
    petime(petime==0)=[]; %delete 0s

    %Port entry durations
    durationt=(L{1,1}(Pstrt+2:2:Qstrt-1));
    durationtime=[];
    for i=1:length(durationt)
        medtext=textscan(char(durationt(i,1)),'%f','Delimiter',' ');
        duration=medtext{1,1}(:,1);
        durationtime=(cat(1,durationtime,duration(isnan(duration)==0)));
    end
    durationtime(removes)=[]; %delete 0s
    
    pexits=petime(1:length(durationtime))+durationtime;
    
    %Laser stims
    ST=(L{1,1}(Qstrt+2:2:Xstrt-1));
    STtime=[];
    for i=1:length(ST)
        medtext=textscan(char(ST(i,1)),'%f','Delimiter',' ');
        stime=medtext{1,1}(:,1);
        STtime=(cat(1,STtime,stime(isnan(stime)==0)));
    end

    STtime(STtime==0)=[]; %delete 0s    


    %Sucrose or water?
    latency=[];
    for i=1:length(choicetime)
        sucrose=find(sucrosedeltime(:,1) > choicetime(i,1),1);
        sucrosetime=sucrosedeltime(sucrose);
        if sucrosetime
            latency(i,1)=sucrosetime-choicetime(i,1)-0.5; %delay is 0.5s
        else
            latency(i,1)=NaN;
        end
    end
    latency(latency>10)=NaN;

    completed=latency>0;

    %stim trials
    post_stimmed=zeros(length(choicetime),1);
    for stim=1:length(STtime)
        trialtime=min(choicetime(choicetime>STtime(stim)));
        if ~isempty(trialtime)
            post_stimmed(choicetime==trialtime)=1;
        end
    end

    %no stim trials
    postsuc=zeros(length(choicetime),1);
    for suctrial=1:length(sucrosedeltime)
        trialtime=min(choicetime(choicetime>sucrosedeltime(suctrial)));
        if ~isempty(trialtime)
            postsuc(choicetime==trialtime)=1;
        end
    end
    nostim=postsuc==1 & post_stimmed==0;    
    
    
    rdtimes=sucrosedeltime;
    cuetimes=choicetime;
    petimes=petime;
    
    included_cue_trials=[];
    for trial=1:length(rdtimes)
        if sum(cuetimes>rdtimes(trial))>0
            included_cue_trials(trial,1)=find(cuetimes>rdtimes(trial),1,'first');
        end
    end
    post_stim=post_stimmed(included_cue_trials);
    
    %get coordinates from deeplabcut analysis
    timestamps=VideoData{rat,1}-lighton(rat,1); %adjust for when session started in video
    xcoordinates=VideoData{rat,2};
    ycoordinates=VideoData{rat,3};
    
    
    %for each cue onset
    xypoints={};
    xtrial=[];
    ytrial=[];
    ITI_distance=[];
    ITI_dfp=[];
    licks_trl=[];
    
   
    for trial=1:length(cuetimes)
        if sum(timestamps>(cuetimes(trial)-0.25) & timestamps<(cuetimes(trial)+0.25))>0
            xtrial(trial)=mean(xcoordinates((timestamps>cuetimes(trial)-0.25) & (timestamps<cuetimes(trial)+0.25)));
            ytrial(trial)=mean(ycoordinates((timestamps>cuetimes(trial)-0.25) & (timestamps<cuetimes(trial)+0.25)));            
          
           
           
        elseif sum(timestamps>(cuetimes(trial)-1) & timestamps<(cuetimes(trial)+0.3))>0
            xtrial(trial)=mean(xcoordinates((timestamps>cuetimes(trial)-1) & (timestamps<cuetimes(trial)+0.3)));
            ytrial(trial)=mean(ycoordinates((timestamps>cuetimes(trial)-1) & (timestamps<cuetimes(trial)+0.3)));

            
        else
            xtrial(trial)=NaN;
            ytrial(trial)=NaN;
        end
        
        %total distance traveled during ITI, and mean distance from port
        binsize=0.2; %seconds

        if sum(rdtimes<cuetimes(trial))>0 & postsuc(trial)==1
            
            rd_time=max(rdtimes(rdtimes<cuetimes(trial)));
            pe_time=max(petimes(petimes<(rd_time+10)));
            start_time=min([pexits(petimes==pe_time) rd_time+10]);
            %bins=start_time:binsize:cuetimes(trial);
            bins=start_time:binsize:cuetimes(trial)+binsize/2;
            bn=0;
            bin_t=[];
            bin_x=[];
            bin_y=[];
            bin_dfp=[];
            
            %location for each bin
            for bin=1:length(bins)-1
                if sum(timestamps>bins(bin) & timestamps<bins(bin+1))>0
                    bn=bn+1;
                    bin_t(bn,1)=bins(bin)+binsize/2;
                    bin_x(bn,1)=mean(xcoordinates(timestamps>bins(bin) & timestamps<bins(bin+1)));
                    bin_y(bn,1)=mean(ycoordinates(timestamps>bins(bin) & timestamps<bins(bin+1)));
                    bin_dfp(bn,1)=sqrt((bin_x(bn,1)-portcoord(rat,1))^2+(bin_y(bn,1)-portcoord(rat,2))^2);
                end
            end
            
            xypoints{trial,1}=cat(2,bin_x,bin_y);
            
%             subplot(5,5,rat);
%             hold on;
%             plot(bin_dfp);
%             xypoints{trial,1}=cat(2,bin_x,bin_y);
%             axis([0 25 0 500]);

            ITI_dfp(trial)=trapz(bin_t,bin_dfp)/(bin_t(end)-bin_t(1)); %dfp = distance from port
          
            
        else
            ITI_dfp(trial)=NaN;
            xypoints{trial,1}=NaN;
        end
    end
   
    
    %plot example traces
    if rat==18
        
        figure;

        %scatterplot of rat locations
        xypoints=xypoints(included_cue_trials,:);
        xtrial_inc=xtrial(included_cue_trials);
        ytrial_inc=ytrial(included_cue_trials);
        sucrosexy=cat(1,xypoints{post_stim==0});
        maltodextrinxy=cat(1,xypoints{post_stim==1});
        opacity=0.1;
        dotsize=24;

        sucrosetrls=xypoints(post_stim==0);
        maltodextrintrls=xypoints(post_stim==1);

        %sucrose traces
        subplot(1,4,1);
        hold on;
        s1=scatter(sucrosexy(:,1),sucrosexy(:,2),dotsize,[.4 .4 .4],'filled');
        s1.MarkerFaceAlpha = opacity;
        sc=scatter(xtrial_inc(post_stim==0),ytrial_inc(post_stim==0),'k','x');
        %plot individual trial traces
        %             for i=1:length(sucrosetrls)
        %                 if sucrosetrls{i,1}
        %                     plot(sucrosetrls{i,1}(:,1),sucrosetrls{i,1}(:,2),'color',Colors('sucrose'));
        %                 end
        %             end

        axis([0 950 75 750]);
        set(gca,'Ydir','reverse')
        set(gca,'xtick',[]);
        set(gca,'ytick',[]);
        plot([950 portcoord(rat,1)],[450 portcoord(rat,2)],'color','k');
        legend(sc,'Location at cue onset');
        text(955,450,'Reward Port');
        title('No laser');


        %maltodextrin traces
        subplot(1,4,2);
        hold on;
        s2=scatter(maltodextrinxy(:,1),maltodextrinxy(:,2),dotsize,[0 .6 .4],'filled');
        s2.MarkerFaceAlpha = opacity;
        scatter(xtrial_inc(post_stim==1),ytrial_inc(post_stim==1),[],'k','x')

        %plot individual trial traces
        %             for i=1:length(maltodextrintrls)
        %                 if maltodextrintrls{i,1}
        %                     plot(maltodextrintrls{i,1}(:,1),maltodextrintrls{i,1}(:,2),'color',Colors('maltodextrin'));
        %                 end
        %             end

        set(gca,'Ydir','reverse')
        set(gca,'xtick',[]);
        set(gca,'ytick',[]);
        axis([0 950 75 750]);
        plot([950 portcoord(rat,1)],[450 portcoord(rat,2)],'color','k');
        legend(sc,'Location at cue onset');
        text(955,450,'Reward Port');
        title('Laser');

    end   
  
    
    ITI_dfp_inc=ITI_dfp(included_cue_trials)';

    
    
    mean_distance(rat,1)=nanmean(ITI_dfp_inc(post_stim==0));
    mean_distance(rat,2)=nanmean(ITI_dfp_inc(post_stim==1));
    


    completed_trials(rat,1)=length(sucrosedeltime);

    disp(['File #' num2str(k)]);
end


%% plotting measures

%included rats
yfp=[1 2 6 9 10 15 23];
arc=[3 4 8 11 13 18 22];

colors{2}=[0 0.6 0.4];
colors{1}=[0.4 0.4 0.4];
groups{1,1}=yfp;
groups{2,1}=arc;
% a={};
% for group=1:2
%     subplot(1,4,3);
%     hold on
%     
%     a{group}=scatter(mean_distance(groups{group,1},1),mean_distance(groups{group,1},2),55,colors{group},'filled');
%     title('Distance from port during ITI (pixels)');
%     plot([0 500],[0 500],'color','k','linewidth',1);
%     xlabel('No stim');
%     ylabel('Stim');
% end
% legend([a{:}],'YFP','ARCH','location','southeast');
% axis([100 350 100 350]);

subplot(1,8,5);
hold on;
plot([1 2],mean_distance(yfp,:),'color',[0.4 0.4 0.4]);
errorbar(1,nanmean(mean_distance(yfp,1)),nanste(mean_distance(yfp,1),1),'color',[0.4 0.4 0.4],'marker','o','linewidth',1.5);
errorbar(2,nanmean(mean_distance(yfp,2)),nanste(mean_distance(yfp,2),1),'color',[0 0.6 0.4],'marker','o','linewidth',1.5);
ylabel('Distance from port during ITI (pixels)');
xticks([1 2]);
xticklabels({'No laser','Laser'});
xtickangle(45);
axis([0.5 2.5 0 400]);
title('YFP');

pval=signrank(mean_distance(yfp,1),mean_distance(yfp,2));
text(1.2,375,['p = ' num2str(round(pval,5))]);


subplot(1,8,6);
hold on;
plot([1 2],mean_distance(arc,:),'color',[0.4 0.4 0.4]);
errorbar(1,nanmean(mean_distance(arc,1)),nanste(mean_distance(arc,1),1),'color',[0.4 0.4 0.4],'marker','o','markerfacecolor',[0.4 0.4 0.4],'linewidth',1.5);
errorbar(2,nanmean(mean_distance(arc,2)),nanste(mean_distance(arc,2),1),'color',[0 0.6 0.4],'marker','o','markerfacecolor',[0 0.6 0.4],'linewidth',1.5);
ylabel('Distance from port during ITI (pixels)');
xticks([1 2]);
xticklabels({'No laser','Laser'});
xtickangle(45);
axis([0.5 2.5 0 400]);
title('Arch');

pval=signrank(mean_distance(arc,1),mean_distance(arc,2));
text(1.2,375,['p = ' num2str(round(pval,5))]);

included=zeros(24,1);
included(arc)=1;
included(yfp)=1;
arclog=zeros(24,1);
arclog(arc)=1;

subplot(1,4,4);
hold on;
difference=(mean_distance(:,2)-mean_distance(:,1))./mean_distance(:,1);


boxplot(difference(included==1),arclog(included==1),'colorgroup',[0 1],'colors',[colors{2};colors{2}],'boxstyle','filled');
scatter(rand([length(yfp) 1])/4+1.2,difference(yfp),55,colors{2});
scatter(rand([length(arc) 1])/4+2.2,difference(arc),55,colors{2},'filled');
axis([0.7 2.74 -0.5 0.5]);
plot([0 3],[0 0],'color','k');
pval=ranksum(difference(yfp),difference(arc));
text(1.2,0.4,['p = ' num2str(round(pval,5))]);
ylabel('Fold-change over no laser');
xticks([1.22 2.22]);
xticklabels({'YFP','Arch'});


dataforanova=[mean_distance(arc,1) mean_distance(arc,2);mean_distance(yfp,1) mean_distance(yfp,2)];