WiscPlan_v2/WiscPlanPhotonkV125/matlab_frontend/fullRO_mergeBeams.m

function fullRO_mergeBeams(Geometry)
% this function loops through a full RO folder and merges all the beamlets

    if isfield(Geometry, 'num_batches')
        str = num2str(obj.handles.hSVPS.Geometry.num_batches);
    else
        str = input('Enter num of beam batches: ','s');
    end
    
    % get the full RO folder
    beamlet_dir = uigetdir([Geometry.patient_dir ], 'Select full RO folder' );
    if beamlet_dir == 0
       disp('no file selected, aborting')
       return
    end
    
    % loop through all scenario folders
    files = dir(beamlet_dir);
    % Get a logical vector that tells which is a directory.
    dirFlags = [files.isdir];
    % Extract only those that are directories.
    scenarioList = files(dirFlags);

    
    idxList = [1:numel(scenarioList)];
    for i = 3:numel(idxList);
        scenario_i = idxList(i);
        scenario_path = [scenarioList(scenario_i).folder, '\', scenarioList(scenario_i).name];
        merge_beamlets(str2double(str), scenario_path);
        
        disp(['Scenario ' num2str(i)  ' merged!'])
    end
    
    disp('All scenario beamlets merged!')

end