WiscPlan_v2/WiscPlanPhotonkV125/matlab_frontend/FullRO_NLP_optimizer_v3.m

% paths.patient_dir
% paths.Goal_dir (previously called DP_dir)
% paths.patient
% paths.goalsName

% colorwash(Geometry.data, D_full, [500, 1500], [0,70])
% orthoslice(D_full, [0,70])

function [D_full, w_fin, Geometry, optGoal] = FullRO_NLP_optimizer_v3(varargin)
% This function performs the beamlet optimization
% [D_full, w_fin, Geometry, optGoal] = NLP_beamlet_optimizer;
% 
% Inputs:
%       () OR
%       (Pat_path, path2goal) OR
%       (Pat_path, path2goal, beamlet_weights)
%   Pat_path, path2goal = strings to patient folder and optimal goals
%   beamlet_weights = initial beamlet weights
%   
% Outputs:
%       full dose image dose: [D_full, w_fin, Geometry, optGoal]
% 
% Made by Peter Ferjancic 1. May 2018
% Last updated: 1. April 2019

if nargin<2
    load('WiscPlan_preferences.mat')
    [Pat_path] = uigetdir([WiscPlan_preferences.patientDataPath ], 'Select Patient folder');
    [Goal_file,Goal_path,indx] = uigetfile([Pat_path '\matlab_files\*.mat'], 'Select OptGoal file');
    
    path2geometry = [Pat_path, '\matlab_files\Geometry.mat'];
    path2goal = [Goal_path, Goal_file];
    
    [path2scBeams] = uigetdir([WiscPlan_preferences.patientDataPath ], 'Select folder with scenario beamlets');
else
    Pat_path = varargin{1};
    path2geometry = [Pat_path, '\matlab_files\Geometry.mat'];
    path2goal = varargin{2};
    [Goal_path,Goal_file,ext] = fileparts(path2goal);
    path2scBeams = varargin{3};
end

dialogue_box = 'no'
switch dialogue_box
    case 'yes'
        str = inputdlg({'N of iterations for initial calc', 'N of iterations for full calc', ...
            'Use pre-existing NLP_result to initiate? (y/n)'}, 'input', [1,35], {'100000', '500000', 'n'});
        N_fcallback1 = str2double(str{1}); % 100000  is a good guesstimate
        N_fcallback2 = str2double(str{2}); % 500000 is a good guesstimate
        pre_beamWeights = str{3};
    case 'no'
        disp('dialogue box skipped')
        N_fcallback1 = 1e5;
        N_fcallback2 = 2e6; % 500000;
        pre_beamWeights = 'n';
end


switch pre_beamWeights
    case 'y'
        [NLP_file,NLP_path,indx] = uigetfile([Pat_path '\matlab_files\*.mat'], 'Select NLP_result file');
        load([NLP_path, NLP_file])
        w_beamlets = NLP_result.weights;
        
        load([path2scBeams '\scenario1\all_beams.mat'])
        if numel(all_beams) ~= numel(w_beamlets)
            error('Provided weight number does not match beamlet number!')
        end
    case 'n'
        disp('Initial beam weights will be calculated.')
end

%% PROGRAM STARTS HERE
% - no tocar lo que hay debajo -
fprintf('starting NLP optimization process... \n')

% % -- LOAD GEOMETRY, GOALS, BEAMLETS --
load(path2geometry)
load(path2goal)
%%%% FIGURE out this part for the full RO appraoch.
% [beamlets, numBeamlet] = get_beamlets(Geometry, Pat_path, OptGoals);
% [beamlets, beamlets_joined, numBeamlet, numBeam, beam_i_list] = get_beam_lets(Geometry, Pat_path);


%% -- OPTIMIZATION TARGETS --
% -- make the optimization optGoal structure --
for i_goal = 1:size(OptGoals.goals,1)
        
    if isfield(OptGoals.data{i_goal}, 'SupVox_num')
        SupVox_num = OptGoals.data{i_goal}.SupVox_num;
    else
        answer = inputdlg(['# of supervoxels for "' OptGoals.data{i_goal}.name '" with ' num2str(numel(OptGoals.data{i_goal}.ROI_idx)) ' vox: ("0" to skip)'])
        SupVox_num = str2double(answer{1})
    end
    optGoal{i_goal} = OptGoals.data{i_goal};
    optGoal{i_goal}.sss_scene_list = OptGoals.sss_scene_list;
    optGoal{i_goal}.maxModulation = OptGoals.maxModulation;
    optGoal{i_goal}.BeamSmoothMax = OptGoals.BeamSmoothMax;
    
    optGoal{i_goal}.optFuncNum = OptGoals.optFuncNum;
    
    % modulation
    
    if strcmp( '-||-' , optGoal{i_goal}.ROI_name)
%         optGoal{i_goal}.ROI_idx_old = optGoal{i_goal-1}.ROI_idx_old; % copy old index data
%         optGoal{i_goal}.opt_weight = optGoal{i_goal}.opt_weight * numel(optGoal{i_goal}.ROI_idx_old)/numel(optGoal{i_goal}.ROI_idx);
        optGoal{i_goal}.ROI_idx = optGoal{i_goal-1}.ROI_idx

        if isfield(OptGoals.data{i_goal}, 'wgt_map')
            optGoal{i_goal}.vox_wgt = optGoal{i_goal-1}.vox_wgt;
        end
        optGoal{i_goal}.beamlets_pruned = optGoal{i_goal-1}.beamlets_pruned;

    else
        switch SupVox_num
            case 0
                error('You should always specify supervoxels now')
            % if not supervoxel, just select provided ROI_idx
%             optGoal{i_goal}.beamlets_pruned = sparse(beamlets(optGoal{i_goal}.ROI_idx, :));

            otherwise
            % -- if supervoxel, merge given columns
            % - make supervoxel map
            switch OptGoals.goals{i_goal, 3}
                case 'Fixed dose'
                    mask = zeros(OptGoals.data{i_goal}.imgDim);
                    mask(OptGoals.data{i_goal}.ROI_idx) = 1;
                    
                case 'Dose map'
                    mask = zeros(OptGoals.data{i_goal}.imgDim);
                    mask(OptGoals.data{i_goal}.ROI_idx) = OptGoals.data{i_goal}.D_final;
                    mask2 = round(mask/3)*3;
            end
            % group superpixels
            superMask = superpix_group(mask, SupVox_num, 'no');
            optGoal{i_goal}.superMask = superMask;
%             orthoslice(superMask)
        end
    end
end

% -- make them robust --
RO_params=0;
[optGoal, numBeamlet] = make_fullRO_optGoal(optGoal, RO_params, path2scBeams);
% save([Goal_path, Goal_file '_robust.mat'], 'optGoal')

% -- get beamlet indeces --
load([path2scBeams '\scenario1\all_beams.mat'])
Nbeamlets = all_beams{1}.Mxp;   % number of beamlets in a beam - usually 64 or 32
weightTable = zeros(3,Nbeamlets);
for ind_bmlt = 1:numel(all_beams)
    bLet_idx.y(ind_bmlt) = floor(all_beams{1, ind_bmlt}.num/Nbeamlets)+1;
    bLet_idx.x(ind_bmlt) = rem(all_beams{1, ind_bmlt}.num, Nbeamlets)+1;
    weightTable(bLet_idx.y(ind_bmlt),bLet_idx.x(ind_bmlt)) = 1;
end
bLet_idx.idx = find(weightTable>0);
bLet_idx.Nbeamlets = Nbeamlets;
disp('.')

% -- CALLBACK OPTIMIZATION FUNCTION --
fun1 = @(x) get_penalty(x, optGoal_beam, bLet_idx);
fun2 = @(x) get_penalty(x, optGoal,     bLet_idx);

% -- OPTIMIZATION PARAMETERS --
% define optimization parameters
A = [];
b = [];
Aeq = [];
beq = [];
lb = zeros(1, numBeamlet);
% lb_beam = zeros(1, numBeam);
ub = [];
nonlcon = [];

% define opt limits, and make it fmincon progress
options = optimoptions('fmincon');
options.MaxFunctionEvaluations = N_fcallback1;
options.Display = 'iter';
options.PlotFcn = 'optimplotfval';
% options.UseParallel = true;
options.UseParallel = false;
% options.OptimalityTolerance = 1e-9;

%% -- INITIALIZE BEAMLET WEIGHTS --
switch pre_beamWeights
    case 'y'
        % should have been assigned previously.
        disp('Provided beamlet weights used for initial comparison')
    case 'n'
        % if initial beamlet weights are not provided, get quick estimate
%         fprintf('\n running initial optimizer:')
        % initialize beamlet weights, OR
        w0 = ones(numBeamlet,1);
%         w0 = mean(optGoal{1}.D_final(optGoal{1}.ROI_idx) ./ (optGoal{1}.beamlets_pruned*w0+0.1)) * w0; % old
        w0 = mean(optGoal{1}.D_final(:)) ./ mean(optGoal{1}.nrs{1}.sss{1}.rgs{1}.beamlets_pruned*w0+0.05) * w0;
        w_beamlets = double(w0);

        % -- GET BEAM WEIGHTS --
%         tic
%         w_beam = fmincon(fun1,w0_beams,A,b,Aeq,beq,lb,ub,nonlcon,options);
%         fprintf('  done!:')
%         t=toc;
%         disp(['Optimization time for beams = ',num2str(t)]);
% 
%         w_beamlets = ones(numBeamlet,1);
%         numBeam=numel(unique(beam_i_list));
%         for beam_i = 1:numBeam % assign weights to beamlets
%             % beamlets from same beam get same initial weights
%             w_beamlets(beam_i_list == beam_i) = w_beam(beam_i);
%         end
end

%% FULL OPTIMIZATION

% -- GET FULL BEAMLET WEIGHTS --
options.MaxFunctionEvaluations = N_fcallback2;
tic
fprintf('\n running full optimizer:')
w_fin = fmincon(fun2,w_beamlets,A,b,Aeq,beq,lb,ub,nonlcon,options);
fprintf('  done!:')
t=toc;
disp(['Optimization time for beamlets = ',num2str(t)]);

%% evaluate the results
[beamlets, numBeamlet] = get_beamlets_fullRO(optGoal{1}.imgDim, [path2scBeams '\scenario1'], optGoal);
D_full = reshape(beamlets * w_fin, size(Geometry.data));

%% save outputs
NLP_result.dose = D_full;
NLP_result.weights = w_fin;
NLP_result.sss_scene_list = optGoal{1}.sss_scene_list;
NLP_result.maxModulation = OptGoals.maxModulation;
NLP_result.BeamSmoothMax = OptGoals.BeamSmoothMax;
save([path2scBeams, '\FRO_result_' Goal_file '.mat'], 'NLP_result');



% plot_DVH(Geometry, D_full)
DQM_DVH(Geometry, D_full)
colorwash(Geometry.data, D_full, [500, 1500], [0, 90]);


end

%% support functions
% ---- PENALTY FUNCTION ----
function penalty = get_penalty(x, optGoal, bLet_idx)
    % this function gets called by the optimizer. It checks the penalty for
    % all the robust implementation and returns the worst result.
    
    NumScenarios = optGoal{1}.NbrRandScenarios * optGoal{1}.NbrSystSetUpScenarios * optGoal{1}.NbrRangeScenarios;
    fobj = zeros(NumScenarios,numel(optGoal)+2);  
    sc_i = 1;
    

    
    for nrs_i = 1:optGoal{1}.NbrRandScenarios 
        for sss_i = 1 :optGoal{1}.NbrSystSetUpScenarios % syst. setup scenarios = sss
            for rgs_i = 1:optGoal{1}.NbrRangeScenarios % range scenario = rs
%                 fobj(sc_i)=eval_f(x, optGoal, nrs_i, sss_i, rgs_i, bLet_idx);
                fobj(sc_i,:) = eval_f(x, optGoal, nrs_i, sss_i, rgs_i, bLet_idx);
                sc_i = sc_i + 1;
            end
        end
    end
    
        
    switch optGoal{1}.optFuncNum
        case 1 % "RO max"
            penalty=max(sum(fobj,2));
        case 2 % "RO mean"
            penalty=mean(sum(fobj,2));
        case 3 % "RO objective-based"
            penalty=sum(max(fobj,[],1));
        case 4 % "Classical"
            penalty=sum(fobj(1,:));
    end 
    % take the worst case penalty of evaluated scenarios
%     penalty=max(fobj);
    
    % take the median worst case (stochastic robust)
%     penalty=median(fobj);


    
end
% ------ supp: penalty for single scenario ------
function penArray = eval_f(x, optGoal, nrs_i, sss_i, rgs_i, bLet_idx)
%     penalty = 0;
    penArray = zeros(1,numel(optGoal)+2); % all the optGoals, plus modulation plus smoothing
    % for each condition
    for goal_i = 1:numel(optGoal)
        switch optGoal{goal_i}.function
            % min, max, min_sq, max_sq, LeastSquare, min_perc_Volume, max_perc_Volume
            case 'min'
                % penalize if achieved dose is lower than target dose
                d_penalty = 1.0e0 * sum(max(0, ...
                    (optGoal{goal_i}.nrs{nrs_i}.sss{sss_i}.rgs{rgs_i}.target) -...
                    (optGoal{goal_i}.nrs{nrs_i}.sss{sss_i}.rgs{rgs_i}.beamlets_pruned * x)));
            case 'max'
                % penalize if achieved dose is higher than target dose
                d_penalty = 1.0e0 * sum(max(0, ...
                    (optGoal{goal_i}.nrs{nrs_i}.sss{sss_i}.rgs{rgs_i}.beamlets_pruned * x)-...
                    (optGoal{goal_i}.nrs{nrs_i}.sss{sss_i}.rgs{rgs_i}.target)));
            case 'min_sq'
                % penalize if achieved dose is lower than target dose
                temp1=min(0, (optGoal{goal_i}.nrs{nrs_i}.sss{sss_i}.rgs{rgs_i}.beamlets_pruned * x)-...
                    (optGoal{goal_i}.nrs{nrs_i}.sss{sss_i}.rgs{rgs_i}.target));
                d_penalty = 1.0e0 * sum(temp1.*temp1);
            case 'max_sq'
                % penalize if achieved dose is higher than target dose
                temp1=max(0, (optGoal{goal_i}.nrs{nrs_i}.sss{sss_i}.rgs{rgs_i}.beamlets_pruned * x)-...
                    (optGoal{goal_i}.nrs{nrs_i}.sss{sss_i}.rgs{rgs_i}.target));
                d_penalty = 1.0e0 * sum(temp1.*temp1);
            case 'min_step'
                % penalize if achieved dose is lower than target dose
                temp1=-min(0, (optGoal{goal_i}.nrs{nrs_i}.sss{sss_i}.rgs{rgs_i}.beamlets_pruned * x)-...
                    (optGoal{goal_i}.nrs{nrs_i}.sss{sss_i}.rgs{rgs_i}.target));
                d_penalty = 1.0e1 * (sum(temp1.*temp1) + 1.0e3* sum(temp1>0)/numel(temp1));
            case 'max_step'
                % penalize if achieved dose is higher than target dose
                temp1=max(0, (optGoal{goal_i}.nrs{nrs_i}.sss{sss_i}.rgs{rgs_i}.beamlets_pruned * x)-...
                    (optGoal{goal_i}.nrs{nrs_i}.sss{sss_i}.rgs{rgs_i}.target));
                d_penalty = 1.0e1 * (sum(temp1.*temp1) + 1.0e3* sum(temp1>0)/numel(temp1));
            case 'LeastSquare'
                % penalize with sum of squares any deviation from target
                % dose
                temp1 = (optGoal{goal_i}.nrs{nrs_i}.sss{sss_i}.rgs{rgs_i}.beamlets_pruned * x) - ...
                    optGoal{goal_i}.nrs{nrs_i}.sss{sss_i}.rgs{rgs_i}.target;
                d_penalty = 1.0e0* sum(temp1.^2);
            case 'min_perc_Volume'
                % penalize by amount of volume under threshold
                perc_vox = numel(find((optGoal{goal_i}.nrs{nrs_i}.sss{sss_i}.rgs{rgs_i}.target) -...
                    (optGoal{goal_i}.nrs{nrs_i}.sss{sss_i}.rgs{rgs_i}.beamlets_pruned * x) > 0)) ...
                    / numel(optGoal{goal_i}.nrs{nrs_i}.sss{sss_i}.rgs{rgs_i}.target);
                d_penalty = 3.0e4 * min(perc_vox-0.05, 0)
                
            case 'max_perc_Volume'
                % penalize by amount of volume under threshold
                perc_vox = numel(find((optGoal{goal_i}.nrs{nrs_i}.sss{sss_i}.rgs{rgs_i}.target) -...
                    (optGoal{goal_i}.nrs{nrs_i}.sss{sss_i}.rgs{rgs_i}.beamlets_pruned * x) < 0)) ...
                    / numel(optGoal{goal_i}.nrs{nrs_i}.sss{sss_i}.rgs{rgs_i}.target);
                d_penalty = 3.0e4 * min(perc_vox-0.05, 0)
            case 'min_sq_voxwgt'
                % penalize if achieved dose is lower than target dose
                temp1=min(0, (optGoal{goal_i}.nrs{nrs_i}.sss{sss_i}.rgs{rgs_i}.beamlets_pruned * x)-...
                    (optGoal{goal_i}.nrs{nrs_i}.sss{sss_i}.rgs{rgs_i}.target));
                d_penalty = 1.0e0 * sum(temp1.*temp1.* optGoal{goal_i}.vox_wgt');
            case 'max_sq_voxwgt'
                % penalize if achieved dose is lower than target dose
                temp1=min(0, (optGoal{goal_i}.nrs{nrs_i}.sss{sss_i}.rgs{rgs_i}.beamlets_pruned * x)-...
                    (optGoal{goal_i}.nrs{nrs_i}.sss{sss_i}.rgs{rgs_i}.target));
                d_penalty = 1.0e0 * sum(temp1.*temp1.* optGoal{goal_i}.vox_wgt'); 
        end
%         penalty = penalty + d_penalty * optGoal{goal_i}.opt_weight;
        penArray(goal_i) = d_penalty * optGoal{goal_i}.opt_weight;
    end
    
    %% add modulation penalty
    if true
        if isfield(optGoal{goal_i}, 'maxModulation')
            max_modulation = optGoal{goal_i}.maxModulation;
        else
            error('no Max modulation parameter enterd!')
            max_modulation = 5;
        end
        
        mod_pen_weight = 1.0e10;
        % calc the penalty
        mod_excess = max(0, x-max_modulation*mean(x));
%         mod_excess = max(0, x-max_modulation*mean(x(x>1)));
        mod_pen1 = mod_pen_weight*(sum(mod_excess) + numel(mod_excess)* any(mod_excess));
%         penalty = penalty + mod_pen1;
        penArray(end-1) = mod_pen1;
    end
    
    %% add penlty for single off beamlets - version 2
    if false
        if isfield(optGoal{goal_i}, 'BeamSmoothMax')
            BeamSmoothMax = optGoal{goal_i}.BeamSmoothMax;
        else
            error('no Max beam smooth parameter enterd!')
            BeamSmoothMax = 1e6;
        end
        mod_pen_weight = BeamSmoothMax; %1.0e6
        x_down = zeros(size(x));
        x_down(2:end) = x(1:end-1);
        x_down2 = zeros(size(x));
        x_down2(3:end) = x(1:end-2);
        x_up = zeros(size(x));
        x_up(1:end-1) = x(2:end);
        x_up2 = zeros(size(x));
        x_up2(1:end-2) = x(3:end);
        mod_pen2 = mod_pen_weight*sum((x_down+x_up-2*x).^2 + 0.5*(x_down2+x_up2-2*x).^2)/(mean(x)^(2)*numel(x));
%         penalty = penalty + mod_pen2;
        penArray(end) = mod_pen2;
    end
    %% add penlty for single off beamlets - version 3
    if true
        if isfield(optGoal{goal_i}, 'BeamSmoothMax')
            BeamSmoothMax = optGoal{goal_i}.BeamSmoothMax;
        else
            error('no Max beam smooth parameter enterd!')
            BeamSmoothMax = 1e6;
        end
        mod_pen_weight = BeamSmoothMax; %1.0e6
        
        % make 2D beamletWeight map
        maxY = max(bLet_idx.y);
        tabula = zeros(maxY, bLet_idx.Nbeamlets);
        tabula(bLet_idx.idx) = x;
        % for each index calculate laplace
        myWeights = 1/12*[1,3,1; 1,-12,1; 1,3,1];
        i=2:maxY-1;
        j=2:bLet_idx.Nbeamlets-1;
        tabula2(i,j) = ...
             myWeights(1)*tabula(i-1,j-1) + myWeights(4)*tabula(i-1,j) + myWeights(7)*tabula(i-1,j+1)...
            +myWeights(2)*tabula(i,j-1)  + myWeights(8)*tabula(i,j+1) ...
            +myWeights(3)*tabula(i+1,j-1) + myWeights(6)*tabula(i+1,j) + myWeights(9)*tabula(i+1,j+1)...
            +myWeights(5)*tabula(i,j);
        tabula2(1,j) = ...
             myWeights(2)*tabula(1,j-1) + myWeights(8)*tabula(1,j+1)...
            +myWeights(3)*tabula(2,j-1) + myWeights(6)*tabula(2,j) + myWeights(9)*tabula(2,j+1)...
            +myWeights(5)*tabula(1,j);
        tabula2(maxY,j) =...
             myWeights(1)*tabula(maxY-1,j-1) + myWeights(4)*tabula(maxY-1,j) + myWeights(7)*tabula(maxY-1,j+1)...
            +myWeights(2)*tabula(maxY,j-1)  + myWeights(8)*tabula(maxY,j+1) ...
            +myWeights(5)*tabula(maxY,j);
        % make sum of squares
        mod_pen2 = mod_pen_weight*sum((tabula2(:)).^2)/(mean(x.^2)*numel(x));
%         penalty = penalty + mod_pen2;
        penArray(end) = mod_pen2;
    end
end



% ---- MAKE ROI ROBUST ----
function [optGoal, numBeamlet] = make_fullRO_optGoal(optGoal, RO_params, path2scBeams);
    % take regular optimal goal and translate it into several robust cases
    
    % RO_params - should have the information below
    % nrs - random scenarios
    % sss - system setup scenarios
    % rgs - random range scenarios
    
    % X - X>0 moves image right
    % Y - Y>0 moves image down
    % Z - in/out.
    
    shift_X = 2; % vox of shift
    shift_Y = 2; % vox of shift
    shift_Z = 1; % vox of shift
    nrs_scene_list={[0,0,0]};

    
    % ----====#### CHANGE ROBUSTNESS HERE ####====----
    if isfield(optGoal{1}, 'sss_scene_list')
        sss_scene_list = optGoal{1}.sss_scene_list;
    else
        error('New OptGoals should no longer reach this code!')
%         sss_scene_list={[0,0,0], [-shift_Y,0,0], [shift_Y,0,0], [0,-shift_X,0], [0,shift_X,0], [0,0,-shift_Z], [0,0,shift_Z]};
%         optGoal{1}.sss_scene_list = sss_scene_list;
    end
%     sss_scene_list={[0,0,0]};

    % ----====#### CHANGE ROBUSTNESS HERE ####====----
    rgs_scene_list={[0,0,0]};
    for i = 1:numel(optGoal)
        optGoal{i}.NbrRandScenarios     =numel(nrs_scene_list);
        optGoal{i}.NbrSystSetUpScenarios=numel(sss_scene_list);
        optGoal{i}.NbrRangeScenarios    =numel(rgs_scene_list);
    end
    
    % for each scenario
    for sss_i = 1 :optGoal{1}.NbrSystSetUpScenarios   % syst. setup scenarios = sss
    % load new beamlets
    
    
    patient_dir = [path2scBeams '\scenario' num2str(sss_i)];
    [beamlets, numBeamlet] = get_beamlets_fullRO(optGoal{1}.imgDim, patient_dir, optGoal);
    
    disp(['-  scenario ' num2str(sss_i) ' beamlets loaded.'])
        for goal_i = 1:numel(optGoal)
            % get target
            idx=optGoal{goal_i}.ROI_idx;
            targetImg1=zeros(optGoal{goal_i}.imgDim);
            targetImg1(idx)=1;
            % get beamlets
            for nrs_i = 1:optGoal{goal_i}.NbrRandScenarios          % num. of random scenarios
                % modify target and beamlets
%                 targetImg3=targetImg1;
                % beamlets stay the same
            
                for rgs_i = 1:optGoal{goal_i}.NbrRangeScenarios   % range scenario = rgs
                    % modify target and beamlets
                    targetImg4=targetImg1;
                    % beamlets stay the same
                    
                    % function to put in superMask and get out updated optGoal
                    [beamlets_pruned, targetD] = superVoxMerge(optGoal{goal_i}, beamlets);
                    % needs to return "beamlets_pruned" and "target" arrays

                    % save to optGoal output
%                     optGoal{goal_i}.nrs{nrs_i}.sss{sss_i}.rgs{rgs_i}.ROI_idx          = ROI_idx; % some old code, not used?
                    optGoal{goal_i}.nrs{nrs_i}.sss{sss_i}.rgs{rgs_i}.beamlets_pruned    = beamlets_pruned; % beamlets, only within target and supervoxeled
                    optGoal{goal_i}.nrs{nrs_i}.sss{sss_i}.rgs{rgs_i}.target             = targetD'; % target does that we try to achieve
                    
                end
            end
        end
    end
end

%% ---- Supervoxel merge optGoals ----
function [beamlets_pruned, targetD]  = superVoxMerge(optGoal, beamlets)
    superMask = optGoal.superMask;
    superVoxList = unique(superMask);
    superVoxList = superVoxList(superVoxList>0);

    optGoal.ROI_idx_full = optGoal.ROI_idx; % copy old index data
    % optGoal.ROI_idx = zeros(numel(superVoxList), 1);
    optGoal.opt_weight = optGoal.opt_weight * numel(optGoal.ROI_idx_full)/numel(optGoal.ROI_idx);


    if isfield(optGoal, 'wgt_map')
        tabula_wgtmap = zeros(size(superMask));
        tabula_wgtmap(optGoal.optGoal.ROI_idx_full) = optGoal.wgt_map;
    end

    h_w1 = waitbar(0, 'merging superboxels');
    
    dose_tabula = zeros(optGoal.imgDim);
    dose_tabula(optGoal.ROI_idx_full) = optGoal.D_final;
    
    for i_supVox = 1:numel(superVoxList)
        waitbar(i_supVox/numel(superVoxList), h_w1)
        supVox_idx = superVoxList(i_supVox);
        idxList = find(superMask == supVox_idx);
        % merge beamlet doses
        beamlets_pruned(i_supVox,:) = sparse(mean(beamlets(idxList, :),1));

        targetD(i_supVox) = mean(dose_tabula(idxList),1);
        
        if isfield(optGoal, 'vox_wgt')
            optGoal.vox_wgt(i_supVox) = sum(tabula_wgtmap(idxList));
        end

        % -- make new indeces
    %     optGoal.ROI_idx(i_supVox) = idxList(1);
    end
    close(h_w1)

end

%% ------ supp: RO case SSS ------
function [targetImg3 ia]=get_RO_sss(targetImg2, sss_scene_shift);
    % translate the target image 
    
    targetImg3 = imtranslate(targetImg2,sss_scene_shift);
    
    % now we need to figure out if any target voxels fell out during the
    % shift
    imgValid = imtranslate(targetImg3,-sss_scene_shift);
    imgInvalid = (targetImg2-imgValid);
    
    idx_1 = find(targetImg2);
    idx_2 = find(imgInvalid);
    
    [idxValid,ia] = setdiff(idx_1,idx_2);
    
    [C,ia, ib] = intersect(idx_1,idxValid);
    
end