function B = merge_beamlets(num_batches, pat_dir)

% num_batches = 4;


B = [];
for k = 1:num_batches
    batch_doses = read_ryan_beamlets([pat_dir, '\batch_dose' num2str(k-1) '.bin']);
    B = [B batch_doses];
end
for k = 1:numel(B)
    B{k}.num = k-1;
end
write_ryan_beamlets([pat_dir '\batch_dose_unshifted.bin'],B);

% apply the shift (0.5 vox up and left) to make dose match geometry
if true 
    f = waitbar(0, 'Correcting beamlet shift');
    for beam_i = 1:numel(B)
        new_dose_list = B{beam_i};
        waitbar(beam_i/numel(B),f, ['Correcting beamlet shift: ' num2str(beam_i)])

        tabula = zeros(B{1, beam_i}.y_count, B{1, beam_i}.x_count, B{1, beam_i}.z_count);
        tabula(B{1, beam_i}.non_zero_indices) = B{1, beam_i}.non_zero_values;

        shifted_img = imtranslate(tabula, [-0.5,-0.5,-0.5]);
        nonzero_idx = find(shifted_img>0.005*max(shifted_img(:)));

        B{beam_i}.non_zero_indices = nonzero_idx;
        B{beam_i}.non_zero_values = shifted_img(nonzero_idx);
    end
    close(f)
end
write_ryan_beamlets([pat_dir '\batch_dose.bin'],B);
write_ryan_beamlets([pat_dir '\batch_dose_backup.bin'],B);