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'

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));

ind30 = {};
ind20 = {};
ind15 = {};
ind6 = {};
ind3 = {};

for i=1:30;
    ind30{i} = find(PETnorm.non_zero_values >= (i-1)./30 && PETnorm.non_zero_values < i./30));
    PETnorm.non_zero_values(ind30{i}) = i.;
end

PETpresc1 = 100.+PETnorm.non_zero_values;
PETnorm = PETsparse.non_zero_values./(max(PETsparse.non_zero_values));

for i=1:20;
    ind20{i} = find(PETnorm.non_zero_values >= (i-1)./20 && PETnorm.non_zero_values < i./20));
    PETnorm.non_zero_values(ind20{i}) = 1.5*i.;
end

PETpresc15 = 100.+PETnorm.non_zero_values;
PETnorm = PETsparse.non_zero_values./(max(PETsparse.non_zero_values));

for i=1:15;
    ind15{i} = find(PETnorm.non_zero_values >= (i-1)./15 && PETnorm.non_zero_values < i./15));
    PETnorm.non_zero_values(ind15{i}) = 2*i.;
end

PETpresc2 = 100.+PETnorm.non_zero_values;
PETnorm = PETsparse.non_zero_values./(max(PETsparse.non_zero_values));

for i=1:6;
    ind6{i} = find(PETnorm.non_zero_values >= (i-1)./6 && PETnorm.non_zero_values < i./6));
    PETnorm.non_zero_values(ind6{i}) = 5*i.;
end

PETpresc5 = 100.+PETnorm.non_zero_values;
PETnorm = PETsparse.non_zero_values./(max(PETsparse.non_zero_values));

for i=1:3;
    ind3{i} = find(PETnorm.non_zero_values >= (i-1)./3 && PETnorm.non_zero_values < i./3));
    PETnorm.non_zero_values(ind15{i}) = 10*i.;
end 

PETpresc10 = 100.+PETnorm.non_zero_values;


mkdir('linDiscrete1');
cd('linDiscrete1');
write_presc(PETpresc1);
cd(..);

mkdir('linDiscrete15');
cd('linDiscrete15');
write_presc(PETpresc15);
cd(..);

mkdir('linDiscrete2');
cd('linDiscrete2');
write_presc(PETpresc2);
cd(..);

mkdir('linDiscrete5');
cd('linDiscrete5');
write_presc(PETpresc5);
cd(..);

mkdir('linDiscrete10');
cd('linDiscrete10');
write_presc(PETpresc10);
cd(..);