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% Start CERR package
CERR

% Import DICOM RT studies
pb_dir = 'path/to/pencil-beam/study';
cc_dir = 'path/to/collapsed-cone/study';
importCERR(pb_dir);
importCERR(cc_dir);

% Load pencil-beam study into viewer
viewStructs(planC{end});

% Access dose distribution data
global planC
dose = zeros(size(planC{end}.dose));
for i = 1:numel(planC{end}.dose)
    dose = dose + planC{end}.dose{i};
end

% Extract dose distributions in three anatomical planes
slice = round(size(dose,3)/2); % choose middle slice
xy_plane = squeeze(dose(:,:,slice));
xz_plane = squeeze(dose(:,round(size(dose,2)/2),:))';
yz_plane = squeeze(dose(round(size(dose,1)/2),:,:))';

% Calculate and plot DVH for PTV and Rectum
ptv_roi_num = 5;
rectum_roi_num = 6;
ptv_dvh = calcDVH(dose,ptv_roi_num);
rectum_dvh = calcDVH(dose,rectum_roi_num);
figure; 
subplot(2,1,1); plot(ptv_dvh.doseBins,ptv_dvh.hist,'LineWidth',2); title('PTV DVH');
subplot(2,1,2); plot(rectum_dvh.doseBins,rectum_dvh.hist,'LineWidth',2); title('Rectum DVH');

% Extract ROI structures
ext_roi_num = 1;
ptv_roi_num = 5;
ext_polygon = planC{end}.structure(ext_roi_num).meshData{end}.polygonData;
ptv_polygon = planC{end}.structure(ptv_roi_num).meshData{end}.polygonData;

% Plot ROIs
figure;
fill3(ext_polygon(:,1),ext_polygon(:,2),ext_polygon(:,3),'k','EdgeColor','none','FaceAlpha',0.3); hold on;
fill3(ptv_polygon(:,1),ptv_polygon(:,2),ptv_polygon(:,3),'r','EdgeColor','none','FaceAlpha',0.5);

% Merge studies and calculate dose distribution
mergeStructs([1 2]); % merge pencil-beam and collapsed-cone studies
dose = zeros(size(planC{end}.dose));
for i = 1:numel(planC{end}.dose)
    dose = dose + planC{end}.dose{i};
end