addpath('C:\Documents and Settings\Steve\My Documents\Research\matlab')
addpath('C:\Documents and Settings\Steve\My Documents\Research\optNew\linlsqUtil')

% petFileName = 'C:\Documents and Settings\Steve\My Documents\Research\optNew\linlsqOpt\input\PET004cuATSM\cu64prescInput.mat'

petFileName = 'C:\Documents and Settings\Steve\My Documents\Research\Human\HeadAndNeck\HN003\MatlabData\cuATSMoptFlipped.am';

% PET = load(petFileName);
% PETsparse = sparse3D(PET.data);

PET = am2geom(petFileName);
TDP = open_presc('C:\Documents and Settings\Steve\My Documents\Research\optNew\linlsqOpt\input\HN003uniPrescVolNew\PTV70dosePlus.bin');
TDPfull = full3D(TDP);
TDPbinary = single(~~TDPfull);
PETcorrected = PET.data.*TDPbinary;
PETsparse = sparse3D(PETcorrected);
PETnorm = PETsparse.non_zero_values./(max(PETsparse.non_zero_values));

Power = {};
Power = {PETnorm,PETnorm.^(1/2),PETnorm.^(1/4),PETnorm.^2,PETnorm.^4};

PETprescPower = {};

for i=1:5;
    mkdir(['normPower' num2str(i)]);
    cd(['normPower' num2str(i)]);
    PETprescPower{i}=PETsparse;
    PETprescPower{i}.non_zero_values = 60.+10*Power{i};
    write_presc(PETprescPower{i});
end

Gomp = {};
E=2.718281828;
k = [2*E,4*E,10*E];
x0 = [0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8];

PETprescGomp = {};

for i=1:3;
    for j=1:8;
        mkdir(['normGomp' num2str(i) '.' num2str(j)]);
        cd(['normGomp' num2str(i) '.' num2str(j)]);
        PETprescGomp{i,j}=PETsparse;
        PETprescGomp{i,j}.non_zero_values=exp(-exp(-k(i)*(PETnorm-x0(j))));
        PETprescGomp{i,j}.non_zero_values=60+10*PETprescGomp{i,j}.non_zero_values;
        write_presc(PETprescGomp{i,j});
    end
end