function make_ROI_goals (Geometry, beamlets, beamlets_joined, patient)
% this is a support function for NLP_beamlet_optimizer. It creates the
% goals planned for specific patients.
    
switch patient
    case 'patient'
        ROI_goals.optGoal = make_ROI_goals_Pat(Geometry, beamlets);
        ROI_goals.optGoal_beam = make_ROI_goals_Pat(Geometry, beamlets_joined);
        
        ROI_goals.optGoal_idx=[1,2]; 
        ROI_goals.targetMinMax_idx=[1,3];
        
    case 'tomoPhantom'   
        ROI_goals.optGoal = make_ROI_goals_Pat2(Geometry, beamlets);
        ROI_goals.optGoal_beam = make_ROI_goals_Pat2(Geometry, beamlets_joined);
        
        ROI_goals.optGoal_idx=[1,3];
        ROI_goals.targetMinMax_idx=[1,2];
        
    case 'phantom_HD'
        ROI_goals.optGoal = make_ROI_goals(Geometry, beamlets);
        ROI_goals.optGoal_beam = make_ROI_goals(Geometry, beamlets_joined);
        
        ROI_goals.optGoal_idx=[1,3];
        ROI_goals.targetMinMax_idx=[1,2];
        
    case 'doggo'
%         optGoal = make_ROI_goals_DOG(Geometry, beamlets);
%         optGoal_beam = make_ROI_goals_DOG(Geometry, beamlets_joined);

        ROI_goals.optGoal = make_ROI_goals_DOG_2(Geometry, beamlets);
        ROI_goals.optGoal_beam = make_ROI_goals_DOG_2(Geometry, beamlets_joined);
        
        ROI_goals.optGoal_idx=[1,2];
        ROI_goals.targetMinMax_idx=[1,3];
    case 'gbm_005'
        ROI_goals.optGoal = make_ROI_goals_gbm_005(Geometry, beamlets);
        ROI_goals.optGoal_beam = make_ROI_goals_gbm_005(Geometry, beamlets_joined);
        
        ROI_goals.optGoal_idx=[1,3]; % indeces of volumes you want on histogram
        ROI_goals.targetMinMax_idx=[1,2]; % indeces of limits for min/max target volume
    otherwise
        error('invalid case')
    end
    
    save(['C:\010-work\003_localGit\WiscPlan_v2\optGoals\' patient, '.mat'], 'ROI_goals')
end

% ---- MAKE ROI GOALS ----
% min, max, min_sq, max_sq, LeastSquare, min_perc_Volume, max_perc_Volume
function optGoal = make_ROI_goals_Pat(Geometry, beamlets)
    optGoal={};
    
    % -- START DEFINITION OF GOAL --
    goal_1.name = 'Target_min';
    goal_1.ROI_name = Geometry.ROIS{1, 2}.name;
    ROI_idx = Geometry.ROIS{1, 2}.ind;
    goal_1.ROI_idx = ROI_idx;
    goal_1.imgDim = size(Geometry.data);
    goal_1.D_final = 60;
    goal_1.function = 'min';
    goal_1.beamlets_pruned = beamlets(ROI_idx, :);
    goal_1.target   = ones(numel(ROI_idx), 1) * goal_1.D_final;
    goal_1.opt_weight = 10 / numel(ROI_idx); % normalize to volume of target area
    goal_1.dvh_col = [0.9, 0.2, 0.2]; % color of the final DVH plot
    % assign target
    optGoal{end+1}=goal_1;
    % -- END DEFINITION OF GOAL --
    
    % -- START DEFINITION OF GOAL --
    goal_2.name = 'Target_max';
    goal_2.ROI_name = Geometry.ROIS{1, 2}.name;
    ROI_idx = Geometry.ROIS{1, 2}.ind;
    goal_2.ROI_idx = ROI_idx;
    goal_2.imgDim = size(Geometry.data);
    goal_2.D_final = 65;
    goal_2.function = 'max';
    goal_2.beamlets_pruned = beamlets(ROI_idx, :);
    goal_2.target   = ones(numel(ROI_idx), 1) * goal_2.D_final;
    goal_2.opt_weight = 0.8 / numel(ROI_idx); % normalize to volume of target area
    goal_2.dvh_col = [0.9, 0.2, 0.2]; % color of the final DVH plot
    % assign target
    optGoal{end+1}=goal_2;
    % -- END DEFINITION OF GOAL --
    
    % -- START DEFINITION OF GOAL --
    goal_3.name = 'ROI 1_max';
    goal_3.ROI_name = Geometry.ROIS{1, 3}.name;
    ROI_idx = Geometry.ROIS{1, 3}.ind;
    goal_3.ROI_idx = ROI_idx;
    goal_3.imgDim = size(Geometry.data);
    goal_3.D_final = 10;
    goal_3.function = 'max';
    goal_3.beamlets_pruned = beamlets(ROI_idx, :);
    goal_3.target   = ones(numel(ROI_idx), 1) * goal_3.D_final;
    goal_3.opt_weight = 2 / numel(ROI_idx); % normalize to volume of target area
    goal_3.dvh_col = [0.2, 0.9, 0.2]; % color of the final DVH plot
    % assign target
    optGoal{end+1}=goal_3;
    % -- END DEFINITION OF GOAL --
    
end
function optGoal = make_ROI_goals_Pat2(Geometry, beamlets)
    optGoal={};
    
    % -- START DEFINITION OF GOAL --
    goal_1.name = 'Target_min';
    goal_1.ROI_name = Geometry.ROIS{1, 2}.name;
    ROI_idx = Geometry.ROIS{1, 2}.ind;
    goal_1.ROI_idx = ROI_idx;
    goal_1.imgDim = size(Geometry.data);
    goal_1.D_final = 62;
    goal_1.function = 'min';
    goal_1.beamlets_pruned = beamlets(ROI_idx, :);
    goal_1.target_alpha = 1.00;
    goal_1.target   = ones(numel(ROI_idx), 1) * goal_1.D_final;
    goal_1.opt_weight = 10 / numel(ROI_idx); % normalize to volume of target area
    goal_1.dvh_col = [0.9, 0.2, 0.2]; % color of the final DVH plot
    % assign target
    optGoal{end+1}=goal_1;
    % -- END DEFINITION OF GOAL --
    
    % -- START DEFINITION OF GOAL --
    goal_2.name = 'Target_max';
    goal_2.ROI_name = Geometry.ROIS{1, 2}.name;
    ROI_idx = Geometry.ROIS{1, 2}.ind;
    goal_2.ROI_idx = ROI_idx;
    goal_2.imgDim = size(Geometry.data);
    goal_2.D_final = 63;
    goal_2.function = 'max';
    goal_2.beamlets_pruned = beamlets(ROI_idx, :);
    goal_1.target_alpha = 1.05;
    goal_2.target   = ones(numel(ROI_idx), 1) * goal_2.D_final;
    goal_2.opt_weight = 2 / numel(ROI_idx); % normalize to volume of target area
    goal_2.dvh_col = [0.9, 0.2, 0.2]; % color of the final DVH plot
    % assign target
    optGoal{end+1}=goal_2;
    % -- END DEFINITION OF GOAL --

    % -- START DEFINITION OF GOAL --
    goal_3.name = 'ROI 1_max';
    goal_3.ROI_name = Geometry.ROIS{1, 3}.name;
    ROI_idx = Geometry.ROIS{1, 3}.ind;
    goal_3.ROI_idx = ROI_idx;
    goal_3.imgDim = size(Geometry.data);
    goal_3.D_final = 10;
    goal_3.function = 'max';
    goal_3.beamlets_pruned = beamlets(ROI_idx, :);
    goal_3.target   = ones(numel(ROI_idx), 1) * goal_3.D_final;
    goal_3.opt_weight = 2 / numel(ROI_idx); % normalize to volume of target area
    goal_3.dvh_col = [0.2, 0.9, 0.2]; % color of the final DVH plot
    % assign target
    optGoal{end+1}=goal_3;
    % -- END DEFINITION OF GOAL --
    
    % -- START DEFINITION OF GOAL --
    goal_4.name = 'Ring_max';
    goal_4.ROI_name = Geometry.ROIS{1, 6}.name;
    ROI_idx = Geometry.ROIS{1, 6}.ind;
    goal_4.ROI_idx = ROI_idx;
    goal_4.imgDim = size(Geometry.data);
    goal_4.D_final = 56;
    goal_4.function = 'max_sq';
    goal_4.beamlets_pruned = beamlets(ROI_idx, :);
    goal_4.target   = ones(numel(ROI_idx), 1) * goal_4.D_final;
    goal_4.opt_weight = 1 / numel(ROI_idx); % normalize to volume of target area
    goal_4.dvh_col = [0.9, 0.2, 0.2]; % color of the final DVH plot
    % assign target
    optGoal{end+1}=goal_4;
    % -- END DEFINITION OF GOAL --
    
end
function optGoal = make_ROI_goals_DOG(Geometry, beamlets)
    optGoal={};
    
    % -- START DEFINITION OF GOAL --
    goal_1.name = 'Target_min';
    goal_1.ROI_name = Geometry.ROIS{1, 1}.name;
    ROI_idx = Geometry.ROIS{1, 1}.ind;
    goal_1.ROI_idx = ROI_idx;
    goal_1.imgDim = size(Geometry.data);
    goal_1.D_final = 62;
    goal_1.function = 'min_sq';
    goal_1.beamlets_pruned = beamlets(ROI_idx, :);
    goal_1.target   = ones(numel(ROI_idx), 1) * goal_1.D_final;
    goal_1.opt_weight = 10 / numel(ROI_idx); % normalize to volume of target area
    goal_1.dvh_col = [0.9, 0.2, 0.2]; % color of the final DVH plot
    % assign target
    optGoal{end+1}=goal_1;
    % -- END DEFINITION OF GOAL --
    
    % -- START DEFINITION OF GOAL --
    goal_2.name = 'Doggo_max';
    goal_2.ROI_name = Geometry.ROIS{1, 4}.name;
    ROI_idx = Geometry.ROIS{1, 4}.ind;
    goal_2.ROI_idx = ROI_idx;
    goal_2.imgDim = size(Geometry.data);
    goal_2.D_final = 20;
    goal_2.function = 'max_sq';
    goal_2.beamlets_pruned = beamlets(ROI_idx, :);
    goal_2.target   = ones(numel(ROI_idx), 1) * goal_2.D_final;
    goal_2.opt_weight = 0.2 / numel(ROI_idx); % normalize to volume of target area
    goal_2.dvh_col = [0.2, 0.9, 0.2]; % color of the final DVH plot
    % assign target
    optGoal{end+1}=goal_2;
    % -- END DEFINITION OF GOAL --
    
    % -- START DEFINITION OF GOAL --
    goal_3.name = 'Target_max';
    goal_3.ROI_name = Geometry.ROIS{1, 1}.name;
    ROI_idx = Geometry.ROIS{1, 1}.ind;
    goal_3.ROI_idx = ROI_idx;
    goal_3.imgDim = size(Geometry.data);
    goal_3.D_final = 63;
    goal_3.function = 'max_sq';
    goal_3.beamlets_pruned = beamlets(ROI_idx, :);
    goal_3.target   = ones(numel(ROI_idx), 1) * goal_3.D_final;
    goal_3.opt_weight = 2 / numel(ROI_idx); % normalize to volume of target area
    goal_3.dvh_col = [0.9, 0.2, 0.2]; % color of the final DVH plot
    % assign target
    optGoal{end+1}=goal_3;
    % -- END DEFINITION OF GOAL --
    
    % -- START DEFINITION OF GOAL --
    goal_3.name = 'Doggo_max2';
    goal_3.ROI_name = Geometry.ROIS{1, 4}.name;
    ROI_idx = Geometry.ROIS{1, 4}.ind;
    goal_3.ROI_idx = ROI_idx;
    goal_3.imgDim = size(Geometry.data);
    goal_3.D_final = 50;
    goal_3.function = 'max_sq';
    goal_3.beamlets_pruned = beamlets(ROI_idx, :);
    goal_3.target   = ones(numel(ROI_idx), 1) * goal_3.D_final;
    goal_3.opt_weight = 1 / numel(ROI_idx); % normalize to volume of target area
    goal_3.dvh_col = [0.2, 0.9, 0.2]; % color of the final DVH plot
    % assign target
    optGoal{end+1}=goal_3;
    % -- END DEFINITION OF GOAL --
    
end
function optGoal = make_ROI_goals_DOG_2(Geometry, beamlets)
    optGoal={};
    
    % -- START DEFINITION OF GOAL --
    goal_1.name = 'Target_min';
    goal_1.ROI_name = Geometry.ROIS{1, 1}.name;
    ROI_idx = Geometry.ROIS{1, 1}.ind;
    goal_1.ROI_idx = ROI_idx;
    goal_1.imgDim = size(Geometry.data);
    goal_1.D_final = 62;
    goal_1.function = 'min_sq';
    goal_1.beamlets_pruned = beamlets(ROI_idx, :);
    goal_1.target_alpha = 1.00;
    goal_1.target   = ones(numel(ROI_idx), 1) * goal_1.D_final;
    goal_1.opt_weight = 10 / numel(ROI_idx); % normalize to volume of target area
    goal_1.dvh_col = [0.9, 0.2, 0.2]; % color of the final DVH plot
    % assign target
    optGoal{end+1}=goal_1;
    % -- END DEFINITION OF GOAL --
    
    % -- START DEFINITION OF GOAL --
    goal_2.name = 'Doggo_max';
    goal_2.ROI_name = Geometry.ROIS{1, 4}.name;
    ROI_idx = Geometry.ROIS{1, 4}.ind;
    goal_2.ROI_idx = ROI_idx;
    goal_2.imgDim = size(Geometry.data);
    goal_2.D_final = 20;
    goal_2.function = 'max_sq';
    goal_2.beamlets_pruned = beamlets(ROI_idx, :);
    goal_2.target   = ones(numel(ROI_idx), 1) * goal_2.D_final;
    goal_2.opt_weight = 0.2 / numel(ROI_idx); % normalize to volume of target area
    goal_2.dvh_col = [0.2, 0.9, 0.2]; % color of the final DVH plot
    % assign target
    optGoal{end+1}=goal_2;
    % -- END DEFINITION OF GOAL --
    
    % -- START DEFINITION OF GOAL --
    goal_3.name = 'Target_max';
    goal_3.ROI_name = Geometry.ROIS{1, 1}.name;
    ROI_idx = Geometry.ROIS{1, 1}.ind;
    goal_3.ROI_idx = ROI_idx;
    goal_3.imgDim = size(Geometry.data);
    goal_3.D_final = 63;
    goal_3.function = 'max_sq';
    goal_3.beamlets_pruned = beamlets(ROI_idx, :);
    goal_3.target_alpha = 1.05;
    goal_3.target   = ones(numel(ROI_idx), 1) * goal_3.D_final;
    goal_3.opt_weight = 2 / numel(ROI_idx); % normalize to volume of target area
    goal_3.dvh_col = [0.9, 0.2, 0.2]; % color of the final DVH plot
    % assign target
    optGoal{end+1}=goal_3;
    % -- END DEFINITION OF GOAL --
    
    % -- START DEFINITION OF GOAL --
    goal_4.name = 'Doggo_max2';
    goal_4.ROI_name = Geometry.ROIS{1, 4}.name;
    ROI_idx = Geometry.ROIS{1, 4}.ind;
    goal_4.ROI_idx = ROI_idx;
    goal_4.imgDim = size(Geometry.data);
    goal_4.D_final = 50;
    goal_4.function = 'max_sq';
    goal_4.beamlets_pruned = beamlets(ROI_idx, :);
    goal_4.target   = ones(numel(ROI_idx), 1) * goal_4.D_final;
    goal_4.opt_weight = 1 / numel(ROI_idx); % normalize to volume of target area
    goal_4.dvh_col = [0.2, 0.9, 0.2]; % color of the final DVH plot
    % assign target
    optGoal{end+1}=goal_4;
    % -- END DEFINITION OF GOAL --
    
end
function optGoal = make_ROI_goals_DOG_3(Geometry, beamlets)
    optGoal={};
    
    % -- START DEFINITION OF GOAL --
    goal_1.name = 'Target_min';
    goal_1.ROI_name = Geometry.ROIS{1, 1}.name;
    ROI_idx = Geometry.ROIS{1, 1}.ind;
    goal_1.ROI_idx = ROI_idx;
    goal_1.imgDim = size(Geometry.data);
    goal_1.D_final = 62;
    goal_1.function = 'min_perc_Volume';
    goal_1.beamlets_pruned = beamlets(ROI_idx, :);
    goal_1.target_alpha = 1.00;
    goal_1.target   = ones(numel(ROI_idx), 1) * goal_1.D_final;
    goal_1.opt_weight = 10 / numel(ROI_idx); % normalize to volume of target area
    goal_1.dvh_col = [0.9, 0.2, 0.2]; % color of the final DVH plot
    % assign target
    optGoal{end+1}=goal_1;
    % -- END DEFINITION OF GOAL --
    
    % -- START DEFINITION OF GOAL --
    goal_2.name = 'Doggo_max';
    goal_2.ROI_name = Geometry.ROIS{1, 4}.name;
    ROI_idx = Geometry.ROIS{1, 4}.ind;
    goal_2.ROI_idx = ROI_idx;
    goal_2.imgDim = size(Geometry.data);
    goal_2.D_final = 20;
    goal_2.function = 'max_sq';
    goal_2.beamlets_pruned = beamlets(ROI_idx, :);
    goal_2.targetImg   = ones(numel(ROI_idx), 1) * goal_2.D_final;
    goal_2.target   = ones(numel(ROI_idx), 1) * goal_2.D_final;
    goal_2.opt_weight = 0.2 / numel(ROI_idx); % normalize to volume of target area
    goal_2.dvh_col = [0.2, 0.9, 0.2]; % color of the final DVH plot
    % assign target
    optGoal{end+1}=goal_2;
    % -- END DEFINITION OF GOAL --
    
    % -- START DEFINITION OF GOAL --
    goal_3.name = 'Target_max';
    goal_3.ROI_name = Geometry.ROIS{1, 1}.name;
    ROI_idx = Geometry.ROIS{1, 1}.ind;
    goal_3.ROI_idx = ROI_idx;
    goal_3.imgDim = size(Geometry.data);
    goal_3.D_final = 63;
    goal_3.function = 'max_perc_Volume';
    goal_3.beamlets_pruned = beamlets(ROI_idx, :);
    goal_3.target_alpha = 1.05;
    goal_3.target   = ones(numel(ROI_idx), 1) * goal_3.D_final;
    goal_3.opt_weight = 0.5 / numel(ROI_idx); % normalize to volume of target area
    goal_3.dvh_col = [0.9, 0.2, 0.2]; % color of the final DVH plot
    % assign target
    optGoal{end+1}=goal_3;
    % -- END DEFINITION OF GOAL --
    
    % -- START DEFINITION OF GOAL --
    goal_4.name = 'Doggo_max2';
    goal_4.ROI_name = Geometry.ROIS{1, 4}.name;
    ROI_idx = Geometry.ROIS{1, 4}.ind;
    goal_4.ROI_idx = ROI_idx;
    goal_4.imgDim = size(Geometry.data);
    goal_4.D_final = 50;
    goal_4.function = 'max_sq';
    goal_4.beamlets_pruned = beamlets(ROI_idx, :);
    goal_4.target   = ones(numel(ROI_idx), 1) * goal_4.D_final;
    goal_4.opt_weight = 1 / numel(ROI_idx); % normalize to volume of target area
    goal_4.dvh_col = [0.2, 0.9, 0.2]; % color of the final DVH plot
    % assign target
    optGoal{end+1}=goal_4;
    % -- END DEFINITION OF GOAL --
    
end
function optGoal = make_ROI_goals_gbm_005(Geometry, beamlets)
    optGoal={};
    
    pathIn = '\\Mpufs5\data_wnx1\_Data\Glioma_aus\FET_FGL005\B1\Processed\';
    [minDose, minDose_meta] = nrrdread([pathIn 'RODP_files\FET_FGL005_B1_DP_minDose.nrrd']);
    [maxDose, maxDose_meta] = nrrdread([pathIn 'RODP_files\FET_FGL005_B1_DP_maxDose.nrrd']);
    minDose = double(minDose);
    maxDose = double(maxDose);
    
    % -- START DEFINITION OF GOAL --
    goal_1.name = 'CTV_min';
    goal_1.ROI_name = Geometry.ROIS{1, 1}.name;
    ROI_idx = Geometry.ROIS{1, 1}.ind;
    goal_1.ROI_idx = ROI_idx;
    goal_1.imgDim = size(Geometry.data);
    goal_1.D_final = minDose(ROI_idx);
    goal_1.function = 'min';
    goal_1.beamlets_pruned = beamlets(ROI_idx, :);
%     goal_1.target_alpha = 1.00;
    goal_1.target   = 60 % minDose(ROI_idx);
    goal_1.opt_weight = 40 / numel(ROI_idx); % normalize to volume of target area
    goal_1.dvh_col = [0.9, 0.2, 0.2]; % color of the final DVH plot
    % assign target
    optGoal{end+1}=goal_1;
    % -- END DEFINITION OF GOAL --
    
    % -- START DEFINITION OF GOAL --
    goal_2.name = 'CTV_max';
    goal_2.ROI_name = Geometry.ROIS{1, 1}.name;
    ROI_idx = Geometry.ROIS{1, 1}.ind;
    goal_2.ROI_idx = ROI_idx;
    goal_2.imgDim = size(Geometry.data);
    goal_2.D_final = maxDose(ROI_idx);
    goal_2.function = 'max_sq';
    goal_2.beamlets_pruned = beamlets(ROI_idx, :);
%     goal_1.target_alpha = 1.00;
    goal_2.target   = 60 % maxDose(ROI_idx);
    goal_2.opt_weight = 2 / numel(ROI_idx); % normalize to volume of target area
    goal_2.dvh_col = [0.9, 0.2, 0.2]; % color of the final DVH plot
    % assign target
    optGoal{end+1}=goal_2;
    % -- END DEFINITION OF GOAL --
    
    % -- START DEFINITION OF GOAL --
    goal_3.name = 'head_max';
    goal_3.ROI_name = Geometry.ROIS{1, 2}.name;
    ROI_idx = Geometry.ROIS{1, 2}.ind;
    goal_3.ROI_idx = ROI_idx;
    goal_3.imgDim = size(Geometry.data);
    goal_3.D_final = 0.1;
    goal_3.function = 'max_sq';
    goal_3.beamlets_pruned = beamlets(ROI_idx, :);
    goal_3.target   = ones(numel(ROI_idx), 1) * goal_3.D_final;
    goal_3.opt_weight = 7 / numel(ROI_idx); % normalize to volume of target area
    goal_3.dvh_col = [0.2, 0.9, 0.2]; % color of the final DVH plot
    % assign target
    optGoal{end+1}=goal_3;
    % -- END DEFINITION OF GOAL --
   
end