%% script to apply non-uniform prescription in IMRT dose optimization
%  prescription matrix 'PTVDosePlus.bin' and 'PTVDoseMinus.bin'

% addpath('C:\Documents and Settings\Steve\Desktop\daveTPS\photonDoseCalc\scripts_m');
% addpath('C:\Documents and Settings\Steve\Desktop\daveTPS\opt\linlsqUtil');

% open prescription in sparse format matlab structure and create PTV mask
%
%  presc.x_count (int)
%  presc.y_count (int)
%  presc.z_count (int)
%  presc.Nind    (int)
%  presc.non_zero_indices  (int32)
%  presc.non_zero_values   (single)

% pet = am2geom('D:\FTP\Dose Painting\AAPM09\AV003f\Doses\AV003f_Continuous_cropped.am');
% pet = am2geom('D:\FTP\Dose Painting\AAPM09\AV003f\Doses\AV003f_PVC_Continuous_cropped.am');
% pet = am2geom('D:\FTP\Dose Painting\AAPM09\AV003f\Doses\AV003f_Threshold_cropped.am');
% pet = am2geom('D:\FTP\Dose Painting\AAPM09\AV003f\Doses\AV003f_PVC_Threshold_cropped.am');

% pet = am2geom('D:\FTP\Dose Painting\AAPM09\AV004c\Doses\AV004c_Continuous_cropped.am');
% pet = am2geom('D:\FTP\Dose Painting\AAPM09\AV004c\Doses\AV004c_PVC_Continuous_cropped.am');
% pet = am2geom('D:\FTP\Dose Painting\AAPM09\AV004c\Doses\AV004c_Threshold_cropped.am');
pet = am2geom('D:\FTP\Dose Painting\AAPM09\AV004c\Doses\AV004c_PVC_Threshold_cropped.am');

% pet = am2geom('D:\FTP\Dose Painting\AAPM09\HN002b\Doses\HN002b_Continuous_cropped.am');
% pet = am2geom('D:\FTP\Dose Painting\AAPM09\HN002b\Doses\HN002b_PVC_Continuous_cropped.am');
% pet = am2geom('D:\FTP\Dose Painting\AAPM09\HN002b\Doses\HN002b_Threshold_cropped.am');
% pet = am2geom('D:\FTP\Dose Painting\AAPM09\HN002b\Doses\HN002b_PVC_Threshold_cropped.am');

% pet = am2geom('D:\FTP\Dose Painting\AAPM09\AV001c\Doses\AV001c_Continuous_cropped.am');
% pet = am2geom('D:\FTP\Dose Painting\AAPM09\AV001c\Doses\AV001c_PVC_Continuous_cropped.am');
% pet = am2geom('D:\FTP\Dose Painting\AAPM09\AV001c\Doses\AV001c_Threshold_cropped.am');
% pet = am2geom('D:\FTP\Dose Painting\AAPM09\AV001c\Doses\AV001c_PVC_Threshold_cropped.am');

% pet = am2geom('D:\FTP\Dose Painting\AAPM09\AV001f\Doses\AV001f_Continuous_cropped.am');
% pet = am2geom('D:\FTP\Dose Painting\AAPM09\AV001f\Doses\AV001f_PVC_Continuous_cropped.am');
% pet = am2geom('D:\FTP\Dose Painting\AAPM09\AV001f\Doses\AV001f_Threshold_cropped.am');
% pet = am2geom('D:\FTP\Dose Painting\AAPM09\AV001f\Doses\AV001f_PVC_Threshold_cropped.am');

% pet = am2geom('D:\FTP\Dose Painting\AAPM09\HN003c\Doses\HN003c_Continuous_cropped.am');
% pet = am2geom('D:\FTP\Dose Painting\AAPM09\HN003c\Doses\HN003c_PVC_Continuous_cropped.am');
% pet = am2geom('D:\FTP\Dose Painting\AAPM09\HN003c\Doses\HN003c_Threshold_cropped.am');
% pet = am2geom('D:\FTP\Dose Painting\AAPM09\HN003c\Doses\HN003c_PVC_Threshold_cropped.am');

% pet = am2geom('D:\FTP\Dose Painting\AAPM09\AV004f\Doses\AV004f_Continuous_cropped.am');
% pet = am2geom('D:\FTP\Dose Painting\AAPM09\AV004f\Doses\AV004f_PVC_Continuous_cropped.am');
% pet = am2geom('D:\FTP\Dose Painting\AAPM09\AV004f\Doses\AV004f_Threshold_cropped.am');
% pet = am2geom('D:\FTP\Dose Painting\AAPM09\AV004f\Doses\AV004f_PVC_Threshold_cropped.am');

% pet = am2geom('D:\FTP\Dose Painting\AAPM09\AV002f\Doses\AV002f_Continuous_cropped.am');
% pet = am2geom('D:\FTP\Dose Painting\AAPM09\AV002f\Doses\AV002f_PVC_Continuous_cropped.am');
% pet = am2geom('D:\FTP\Dose Painting\AAPM09\AV002f\Doses\AV002f_Threshold_cropped.am');
% pet = am2geom('D:\FTP\Dose Painting\AAPM09\AV002f\Doses\AV002f_PVC_Threshold_cropped.am');

% pet = am2geom('D:\FTP\Dose Painting\AAPM09\AV005c\Doses\AV005c_Continuous_cropped.am');
% pet = am2geom('D:\FTP\Dose Painting\AAPM09\AV005c\Doses\AV005c_PVC_Continuous_cropped.am');
% pet = am2geom('D:\FTP\Dose Painting\AAPM09\AV005c\Doses\AV005c_Threshold_cropped.am');
% pet = am2geom('D:\FTP\Dose Painting\AAPM09\AV005c\Doses\AV005c_PVC_Threshold_cropped.am');

% load('D:\FTP\Dose Painting\AAPM09\HN003c\Doses\HN003c_U01_3MM_continuous.mat');
% load('D:\FTP\Dose Painting\AAPM09\HN003c\Doses\HN003c_U01_5MM_continuous.mat');
% load('D:\FTP\Dose Painting\AAPM09\HN003c\Doses\HN003c_U01_7MM_continuous.mat');
% 
% load('D:\FTP\Dose Painting\AAPM09\HN003c\Doses\HN003c_U01_3MM_SUV70_threshold.mat');
% load('D:\FTP\Dose Painting\AAPM09\HN003c\Doses\HN003c_U01_5MM_SUV70_threshold.mat');
% load('D:\FTP\Dose Painting\AAPM09\HN003c\Doses\HN003c_U01_7MM_SUV70_threshold.mat');
% 
% load('D:\FTP\Dose Painting\AAPM09\HN003c\Doses\HN003c_U01_3MM_SUV40_CTV54_GTV72.mat');
load('D:\FTP\Dose Painting\AAPM09\HN003c\Doses\HN003c_U01_5MM_SUV40_CTV54_GTV72.mat');
% load('D:\FTP\Dose Painting\AAPM09\HN003c\Doses\HN003c_U01_7MM_SUV40_CTV54_GTV72.mat');
% 
% load('D:\FTP\Dose Painting\AAPM09\HN003c\Doses\HN003c_U01_5MM_SUV40_CTV54_GTV94.mat');
% load('D:\FTP\Dose Painting\AAPM09\HN003c\Doses\HN003c_U01_5MM_SUV40_CTV54_GTV99.mat');

petSparse = sparse3D(presc);

% petSparse = sparse3D(pet.data);
petSparse.Nind = length(petSparse.non_zero_indices);

% write prescription to file
 
write_presc(petSparse,'GTV');

fprintf('Uniform prescription sucessfully replaced with non-uniform prescription.\n');