%% Example of main analysis of raw tracking data, which was slightly modified for each experimental round
% Outputs tracking performance and other metrics for each cockroach within
% the 

function out=roachPositionAnalysis(varargin)

kymFixBool=1;

% If there wasn't a filename input, manually get the file name for analysis
% from user
if isempty(varargin)
    [FileName,PathName,~] = uigetfile;
    fullPath=[PathName FileName];
    
    %Otherwise, if a filename is supplied, use that as path name
elseif isequal(class(varargin{1}),'char')
    fullPath=varargin{1};
    FileName=varargin{1};
    if length(varargin)>1
        oldData=varargin{2};
        kymFixBool=0;
    end
end
load(fullPath);

[firstFrame, cohort] = roachAnalyzeMovieR2(fullPath);

dateStart=strfind(FileName,'2015');
dateStr=FileName(dateStart:dateStart+9);

numRoaches=size(roachAngles,2);
numFrames=size(roachAngles,1);
pxConv=0.0132; %cm/px (approximate)
fps=7;
walkThresh=1;

roachAnglesNoNans=roachAngles;
roachRadiusNoNans=roachRadius;
roachOrientationNoNans=roachOrientation;

% heal NaNs by linear interpolation
for i=1:numRoaches
    for t=firstFrame:numFrames
        if isnan(roachAngles(t,i))
            tempVec=roachAnglesNoNans(t:end,i);
            tempVec=find(~isnan(tempVec));
            if numel(tempVec)>0
                endPt=tempVec(1);
                i1=roachAngles(t-1,i);
                i2=roachAngles(t+endPt-1,i);
                d1=abs(i2-i1);
                d2=abs(i2+2*pi()-i1);
                d3=abs(i2-(i1+2*pi()));
                dVec=[d1 d2 d3];
                if min(dVec)==d1
                    roachAnglesNoNans(t-1:t+endPt-1,i)=linspace(roachAngles(t-1,i),roachAngles(t+endPt-1,i),endPt+1)';
                    roachRadiusNoNans(t-1:t+endPt-1,i)=linspace(roachRadius(t-1,i),roachRadius(t+endPt-1,i),endPt+1)';
                    roachOrientationNoNans(t-1:t+endPt-1,i)=linspace(roachOrientation(t-1,i),roachOrientation(t+endPt-1,i),endPt+1)';
                elseif min(dVec)==d2
                else
                end
            end
        end
    end
end

if kymFixBool   %clean up kymograph as needed
    newKym=roachFixKymograph(kymograph);
else
    newKym=oldData.kymograph;
end


summary=cell(numRoaches,5);

frameSpeeds=zeros(numFrames,numRoaches)+NaN;
frameInShadeBool=zeros(numFrames,numRoaches)+NaN;
frameSpeedsNoNans=zeros(numFrames,numRoaches)+NaN;
frameInShadeBoolNoNans=zeros(numFrames,numRoaches)+NaN;

[roachX, roachY]=pol2cart(roachAngles,roachRadius);
[roachXNoNans, roachYNoNans]=pol2cart(roachAnglesNoNans,roachRadiusNoNans);

socialNetwork=zeros(numRoaches,numRoaches,numFrames);
socialNetworkNoNans=zeros(numRoaches,numRoaches,numFrames);

for i=1:numRoaches
    
    for t=firstFrame:numFrames-1
        speedTemp=sqrt( (roachXNoNans(t+1,i)-roachXNoNans(t,i)).^2 + (roachYNoNans(t+1,i)-roachYNoNans(t,i)).^2);
        frameSpeedsNoNans(t+1,i)=speedTemp*pxConv*fps;
        
        if ~isnan(roachAnglesNoNans(t,i))
            kymBin=ceil(( (roachAnglesNoNans(t,i)+pi()) * 360/(2*pi()) )/2);
            frameInShadeBoolNoNans(t,i)=newKym(t,kymBin);
            
            if ~isnan(roachAngles(t,i))
                frameInShadeBool(t,i)=newKym(t,kymBin);
                frameSpeeds(t,i)=speedTemp*pxConv*fps;
            end
        end
        
    end
    
    summary{i,1}=dateStr;
    summary{i,2}=cohort;
    summary{i,3}=codelist(i);
    
    
    fiveMins=firstFrame:min([firstFrame+fps*300-1 numFrames]);
    
    summary{i,4}=nanmean(frameSpeeds(fiveMins,i));
    summary{i,5}=nanmean(frameInShadeBool(fiveMins,i));
    summary{i,6}=nanmean(frameSpeedsNoNans(fiveMins,i));
    summary{i,7}=nanmean(frameInShadeBoolNoNans(fiveMins,i));
    summary{i,8}=nanmean(frameSpeeds(firstFrame:end,i));
    summary{i,9}=nanmean(frameInShadeBool(firstFrame:end,i));
    summary{i,10}=nanmean(frameSpeedsNoNans(firstFrame:end,i));
    summary{i,11}=nanmean(frameInShadeBoolNoNans(firstFrame:end,i));
    
    summary{i,12}=sum(isnan(roachAngles(fiveMins,i)))/2100;
    summary{i,13}=sum(isnan(roachAngles(firstFrame:end,i)))/size(roachAngles(firstFrame:end,i),1);
    
    summary{i,14}=nansum(frameSpeeds(firstFrame:end,i)>walkThresh)/sum(~isnan(frameSpeeds(firstFrame:end,i)));
    summary{i,15}=nansum(frameSpeedsNoNans(firstFrame:end,i)>walkThresh)/sum(~isnan(frameSpeedsNoNans(firstFrame:end,i)));
    
    temp=frameSpeeds(firstFrame:end,i);
     summary{i,16}=nanmean(temp(temp>walkThresh));
     temp=frameSpeedsNoNans(firstFrame:end,i);
     summary{i,17}=nanmean(temp(temp>walkThresh));
    
    for j=1:numRoaches
        socialNetworkNoNans(i,j,:)=pxConv*sqrt((roachXNoNans(:,i)-roachXNoNans(:,j)).^2+(roachYNoNans(:,i)-roachYNoNans(:,j)).^2);
        socialNetwork(i,j,:)=pxConv*sqrt((roachX(:,i)-roachX(:,j)).^2+(roachY(:,i)-roachY(:,j)).^2);
    end
    
end

out.summaryLegend={};
out.summaryLegend{1}='date';
out.summaryLegend{2}='cohort name';
out.summaryLegend{3}='roach ID#';
out.summaryLegend{4}='mean speed (cm/s), first 5 minutes, raw data';
out.summaryLegend{5}='fraction time in red, first 5 minutes, raw data';
out.summaryLegend{6}='mean speed (cm/s), first 5 minutes, NaNs filled';
out.summaryLegend{7}='fraction time in red, first 5 minutes, NaNs filled';
out.summaryLegend{8}='mean speed (cm/s), all time points, raw data';
out.summaryLegend{9}='fraction time in red, all time points, raw data';
out.summaryLegend{10}='mean speed (cm/s), all time points, NaNs filled';
out.summaryLegend{11}='fraction time in red, all time points, NaNs filled';
out.summaryLegend{12}='fraction NaNs, first 5 minutes';
out.summaryLegend{13}='fraction NaNs, all time points';
out.summaryLegend{14}='fraction of time moving, raw data';
out.summaryLegend{15}='fraction of time moving, NaNs filled';
out.summaryLegend{16}='speed when walking, raw data';
out.summaryLegend{17}='speed when walking, NaNs filled';

kymoCompare=zeros(numFrames,180,3);
kymoCompare(:,:,1)=kymograph;
kymoCompare(:,:,2)=newKym;

%Plot Kymograph
roachKymograph(newKym,roachAngles);

out.summary=summary;
out.firstFrame=firstFrame;
out.fileName=fullPath;
out.kymograph=kymograph;
out.cleanKymograph=newKym;
out.kymoCompare=kymoCompare;
out.frameSpeeds=frameSpeeds;
out.frameSpeedsNoNans=frameSpeedsNoNans;
out.frameInShadeBool=frameInShadeBool;
out.frameInShadeBoolNoNans=frameInShadeBoolNoNans;
out.roachAngles=roachAngles;
out.roachAnglesNoNans=roachAnglesNoNans;
out.roachRadius=roachRadius;
out.roachRadiusNoNans=roachRadiusNoNans;
out.roachOrientation=roachOrientation;
out.roachOrientationNoNans=roachOrientationNoNans;
out.socialNetwork=socialNetwork;
out.socialNetworkNoNans=socialNetworkNoNans;
out.meanSocialNetwork=nanmean(socialNetwork,3);
out.meanSocialNetworkNoNans=nanmean(socialNetworkNoNans,3);