Investigate_Layer_Variance.m

%% Investigation of layer thickness variation
% Load patient information
Cirrus_OCT_pathlist;
nPatients = length(pathlist);
nSurfaces = 11; %number of surfaces generated by the segmentation algo
nLayers = 10; %number of layer thicknesses

%% Load the surface coordinates for all patients
surfaces=cell(nPatients);

for iPatient = 1:nPatients
    folder = fullfile(basepath,pathlist{iPatient});
    surfaces{iPatient} = loadPatientSurfaces(folder);
end

%% Convert surface coordinates into layer thickness

layers=cell(nPatients);

for iPatient = 1:nPatients
    layers{iPatient} = calcLayerThickness(surfaces{iPatient});
end

%% Calculate the thickness variance for each layer
% each column in layer variance is a patient, each row a layer
layerVariance = nan(10,nPatients);

for iPatient = 1:nPatients
    tmpPatient = layers{iPatient};
    for iLayer = 1:nLayers
        tmpLayer = tmpPatient(:,:,iLayer);
        layerVariance(iLayer,iPatient) = var(tmpLayer(:));
    end
end

%% Plot the data

layerLabs= {'NFL','GCL','IPL','INL','OPL','ONL','IS','OS','RPE','Choroid'};
            

figure;
for iLayer = 1:9
    subplot(3,3,iLayer);
    boxplot(layerVariance(iLayer,:),patGroups, ...
        'labels',{'Diabetic','Control'});
    %set(gca, 'OuterPosition', [0 0 0.5 .95]) % Shrink the plot a little
    title(layerLabs{iLayer});
end

%Add a main title
ha = axes('Position',[0 0 1 1],'Xlim',[0 1],'Ylim',[0
1],'Box','off','Visible','off','Units','normalized', 'clipping' , 'off');

text(0.5, 1,'\bf Variance of retinal layer thicknesses',...
    'HorizontalAlignment','center','VerticalAlignment', 'top')


figure;
iPlot=0;
for iLayer=[2,3,4]
    iPlot=iPlot+1;
    subplot(1,3,iPlot);
       boxplot(layerVariance(iLayer,:),patGroups, ...
        'labels',{'Diabetic','Control'});
    %set(gca, 'OuterPosition', [0 0 0.5 .95]) % Shrink the plot a little
    title(layerLabs{iLayer});
    ylabel('Variance');
end 

%Add a main title
ha = axes('Position',[0 0 1 1],'Xlim',[0 1],'Ylim',[0
1],'Box','off','Visible','off','Units','normalized', 'clipping' , 'off');

text(0.5, 1,'\bf Variance of retinal layer thicknesses',...
    'HorizontalAlignment','center','VerticalAlignment', 'top')