WiscPlan_v2/WiscPlanPhotonkV125/matlab_frontend/lab/XTPS.m

classdef XTPS < handle
%XTPS Main GUI for RDXTPS front end.
%
% Default to contain three SliceViewerPanels for viewing.
%
% TODO:
%   Move Geometry and optResults into SliceViewerPanelSource completely so that
%   only one copy exist.
%   Move color stuff into Geometry so that can be saved.
%
% See also SliceViewerPanel
%
% Author Xiaohu Mo

    properties
        handles

        patient_dir
        dosecalcSetup
    end

    methods
%-------------------------------------------------------------------------------
        function obj = XTPS() % XTPS constructor
            hMainFigure = figure('MenuBar', 'none', 'Name', 'RDXTPS: No Patient', 'Position', [100 100 800 600], 'Renderer', 'painters');
            obj.handles = guihandles(hMainFigure);
            obj.handles.hMainFigure = hMainFigure;

            % Adding widgets
            obj.handles.hROIPanel = uipanel('Parent', obj.handles.hMainFigure, 'Title', 'ROI display');
            obj.handles.hROITable = uitable('Parent', obj.handles.hROIPanel);
            obj.handles.hDosePanel = uipanel('Parent', obj.handles.hMainFigure, 'Title', 'Dose display');
            obj.handles.hDoseTable = uitable('Parent', obj.handles.hDosePanel);
            obj.handles.hDoseModeDropdown = uicontrol('Parent', obj.handles.hDosePanel, 'Style', 'popupmenu');
            obj.handles.hDoseModeLabel = uicontrol('Parent', obj.handles.hDosePanel, 'Style', 'text');
            obj.handles.hMiscPanel = uipanel('Parent', obj.handles.hMainFigure, 'Title', 'Misc settings');
            obj.handles.hTCSShow = uicontrol('Parent', obj.handles.hMiscPanel, 'Style', 'checkbox');
            obj.handles.hWWLabel = uicontrol('Parent', obj.handles.hMiscPanel, 'Style', 'edit');
            obj.handles.hWWSlider = uicontrol('Parent', obj.handles.hMiscPanel, 'Style', 'slider');
            obj.handles.hWWEdit = uicontrol('Parent', obj.handles.hMiscPanel, 'Style', 'edit');
            obj.handles.hWLLabel = uicontrol('Parent', obj.handles.hMiscPanel, 'Style', 'edit');
            obj.handles.hWLSlider = uicontrol('Parent', obj.handles.hMiscPanel, 'Style', 'slider');
            obj.handles.hWLEdit = uicontrol('Parent', obj.handles.hMiscPanel, 'Style', 'edit');

            obj.handles.hSVPS = SliceViewerPanelSource();
            obj.handles.hSliceViewerPanel(1) = SliceViewerPanel(obj.handles.hSVPS, 3, obj.handles.hMainFigure);
            obj.handles.hSliceViewerPanel(2) = SliceViewerPanel(obj.handles.hSVPS, 2, obj.handles.hMainFigure);
            obj.handles.hSliceViewerPanel(3) = SliceViewerPanel(obj.handles.hSVPS, 1, obj.handles.hMainFigure);

            % File menu
            obj.handles.hFileMenu             = uimenu(obj.handles.hMainFigure, 'Label','File');
            obj.handles.hImportDicomRTMenu    = uimenu(obj.handles.hFileMenu, 'Label', '1. Import DicomRT Geometry');

            % ---- Grozomah: This part edited by Peter
            obj.handles.hNRRD1                = uimenu(obj.handles.hFileMenu, 'Label', '1a. Geometry wizard (am/nrrd)');
            obj.handles.hNRRD2                = uimenu(obj.handles.hFileMenu, 'Label', '1b. Add Geometry ROI');
            obj.handles.hImgPerturb           = uimenu(obj.handles.hFileMenu, 'Label', '1e. Implement image pertrubations');
            
            obj.handles.hDosecalcMenu         = uimenu(obj.handles.hFileMenu, 'Label', '2. Beamlet Dose Calculation');
            
            % ---- Grozomah: This part edited by Peter
            obj.handles.hMergeBeamlets                = uimenu(obj.handles.hFileMenu, 'Label', '2a. Merge Beamlets');
            obj.handles.hTest2                = uimenu(obj.handles.hFileMenu, 'Label', '2b. Test 2');
            
            obj.handles.hOptimMenu            = uimenu(obj.handles.hFileMenu, 'Label', '3. Plan Optimization');
            obj.handles.hSaveOptimResultsMenu = uimenu(obj.handles.hFileMenu, 'Label', '4.a Save Optimization Results');
            obj.handles.hGetFullDose          = uimenu(obj.handles.hFileMenu, 'Label', '4.b Get Full Dose');
            
            obj.handles.hLoadGeometryMenu     = uimenu(obj.handles.hFileMenu, 'Label', 'Load Geometry', 'Separator','on');
            obj.handles.hLoadOptresultsMenu   = uimenu(obj.handles.hFileMenu, 'Label', 'Load OptResults');
            
            obj.handles.hSaveAsGeometryMenu   = uimenu(obj.handles.hFileMenu, 'Label', 'Save Geometry As...', 'Separator','on');
            obj.handles.hSaveAsOptResultsMenu = uimenu(obj.handles.hFileMenu, 'Label', 'Save OptResults As...');
            
            obj.handles.hExportPinnacleMenu   = uimenu(obj.handles.hFileMenu, 'Label', 'Export Pinnacle Files', 'Separator','on');
            
            % Tools menu
            obj.handles.hToolsMenu   = uimenu(obj.handles.hMainFigure, 'Label', 'Tools');            
            obj.handles.hPlotDVHMenu = uimenu(obj.handles.hToolsMenu,  'Label', 'Plot DVH');
            

            % Associate callbacks
            set(obj.handles.hMainFigure, 'ResizeFcn',               @obj.set_layout);
            set(obj.handles.hROITable, 'CellSelectionCallback',     @obj.ROITable_CellSelectionCallback);
            set(obj.handles.hDoseTable, 'CellSelectionCallback',    @obj.DoseTable_CellSelectionCallback);
            set(obj.handles.hDoseTable, 'CellEditCallback',         @obj.DoseTable_CellEditCallback);
            set(obj.handles.hImportDicomRTMenu, 'Callback',         @obj.ImportDicomRTMenu_Callback);
            set(obj.handles.hDosecalcMenu, 'Callback',              @obj.DosecalcMenu_Callback);
            
            % Grozomah
            set(obj.handles.hNRRD1, 'Callback',         @obj.NRRD1_Callback);
            set(obj.handles.hNRRD2, 'Callback',         @obj.NRRD2_Callback);
            set(obj.handles.hImgPerturb, 'Callback',    @obj.ImgPerturb_Callback);
            
             
            % Grozomah
            set(obj.handles.hMergeBeamlets, 'Callback',      @obj.MergeBeamlets_Callback);
            set(obj.handles.hTest2, 'Callback',              @obj.Test2_Callback);
            set(obj.handles.hGetFullDose, 'Callback',        @obj.GetFullDose_Callback);
            
            set(obj.handles.hSaveOptimResultsMenu, 'Callback',      @obj.SaveOptimResultsMenu_Callback);
            set(obj.handles.hOptimMenu, 'Callback',                 @obj.OptimMenu_Callback);
            set(obj.handles.hLoadGeometryMenu, 'Callback',          @obj.LoadGeometryMenu_Callback);
            set(obj.handles.hLoadOptresultsMenu, 'Callback',        @obj.LoadOptresultsMenu_Callback);
            set(obj.handles.hSaveAsGeometryMenu, 'Callback',        @obj.SaveAsGeometryMenu_Callback);
            set(obj.handles.hSaveAsOptResultsMenu, 'Callback',      @obj.SaveAsOptResultsMenu_Callback);
            set(obj.handles.hExportPinnacleMenu, 'Callback',        @obj.ExportPinnacleMenu_Callback);
            set(obj.handles.hPlotDVHMenu, 'Callback',               @obj.PlotDVHMenu_Callback);
            set(obj.handles.hDoseModeDropdown, 'Callback',          @obj.DoseModeDropdown_Callback);
            set(obj.handles.hWWSlider, 'Callback',                  @obj.WWSlider_Callback);
            set(obj.handles.hWWEdit, 'Callback',                    @obj.WWEdit_Callback);
            set(obj.handles.hWLSlider, 'Callback',                  @obj.WLSlider_Callback);
            set(obj.handles.hWLEdit, 'Callback',                    @obj.WLEdit_Callback);            
            
            set(obj.handles.hTCSShow, 'Callback',                   @obj.TCSShow_Callback);

            obj.set_widget_properties();
            obj.set_layout();
            obj.updateROITable();
            obj.updateDoseTable();
            obj.updateCTWindowControls();
        end % XTPS constructor
%-------------------------------------------------------------------------------
        function set_widget_properties(obj)
        %% Set widget default properties, excluding those related to data
            h = obj.handles; % shortcut

            set(h.hROITable, 'ColumnEditable', logical([1 0 0]));
            set(h.hROITable, 'ColumnFormat', {'logical', 'char', 'char'});
            set(h.hROITable, 'ColumnName', {'V' 'C' 'ROI'});
            set(h.hROITable, 'ColumnWidth',{20 15 'auto'});
            set(h.hROITable, 'RowName', {'numbered'});
            set(h.hROITable, 'RowStriping', 'off');
            set(h.hROITable, 'ToolTipString', 'click to set color');

            set(h.hDoseTable, 'ColumnEditable', logical([0 1 1]));
            set(h.hDoseTable, 'ColumnFormat', {'char' 'numeric' 'numeric'});
            set(h.hDoseTable, 'ColumnName', {'C' 'Dose' 'Alpha'});
            set(h.hDoseTable, 'ColumnWidth',{15 'auto' 'auto'});
            set(h.hDoseTable, 'RowName', []);
            set(h.hDoseTable, 'RowStriping', 'off');
            set(h.hDoseTable, 'ToolTipString', 'click to set color');

            set(h.hDoseModeLabel, 'String', 'display mode');            
            set(h.hDoseModeDropdown, 'String', {'None' 'Isodose' 'IsodoseLine' 'Colorwash'});
            
            set(h.hWWLabel, 'String', 'Win. Width');
            set(h.hWWSlider, 'Min', 0, 'Max', 2048, 'SliderStep', [10/2048 100/2048]);
            set(h.hWLLabel, 'String', 'Win. Level');
            set(h.hWLSlider, 'Min', 0, 'Max', 2048, 'SliderStep', [10/2048 100/2048]);
            
            set(h.hTCSShow, 'String', 'Show TCS planes', 'Value', get(h.hTCSShow, 'Max'));

            % BackgroundColor (get all ui object handles except uitable)
            set(findobj(h.hMainFigure, '-property', 'BackgroundColor', '-not', 'Type', 'uitable'), ...
                'BackgroundColor', get(h.hMainFigure, 'Color'));
        end
%-------------------------------------------------------------------------------
        function set_layout(obj, src, evt)
        % Set widget positions and size. Also as ResizeFcn.
            h = obj.handles; % shortcut

            set(findobj(h.hMainFigure, '-property', 'Units'), 'Units', 'Normalized');

            padding = [0.005 0.01];
            setPositionXY(h.hDosePanel, [0 0.2], [0.2 0.5], padding);
            setPositionXY(h.hROIPanel, [0 0.2], [0.5 1], padding);
            setPositionXY(h.hMiscPanel, [0 0.2], [0 0.2], padding);
            setPositionXY(h.hSliceViewerPanel(1).hPanel, [0.2 0.7], [0 1], padding);
            setPositionXY(h.hSliceViewerPanel(2).hPanel, [0.7 1], [0.5 1], padding);
            setPositionXY(h.hSliceViewerPanel(3).hPanel, [0.7 1], [0 0.5], padding);

            setPositionXY(h.hROITable, [0 1], [0 1], padding);
            setPositionXY(h.hDoseModeDropdown, [0.5 1], [0.9 1], padding);
            setPositionXY(h.hDoseModeLabel, [0 0.5], [0.9 1], padding);
            setPositionXY(h.hDoseTable, [0 1], [0 0.9], padding);
            
            setPositionXY(h.hWWLabel, [0 0.3], [0.67 1], padding, 1.5, 'characters');
            setPositionXY(h.hWWSlider, [0.3 0.85], [0.67 1], padding, 1.5, 'characters');
            setPositionXY(h.hWWEdit, [0.85 1], [0.67 1], padding, 1.5, 'characters');
            setPositionXY(h.hWLLabel, [0 0.3], [0.33 0.67], padding, 1.5, 'characters');
            setPositionXY(h.hWLSlider, [0.3 0.85], [0.33 0.67], padding, 1.5, 'characters');
            setPositionXY(h.hWLEdit, [0.85 1], [0.33 0.67], padding, 1.5, 'characters');
            setPositionXY(h.hTCSShow, [0 1], [0.0 0.33], padding, 1.5, 'characters');
            
            table_width = getWidthPixel(obj.handles.hROITable);
            set(obj.handles.hROITable, 'ColumnWidth', {20 15 table_width-20-15-35});
            table_width = getWidthPixel(obj.handles.hDoseTable);
            set(obj.handles.hDoseTable, 'ColumnWidth', {15 (table_width-15)/2-2 (table_width-15)/2-2});
            
            % Panel ResizeFcn not executed after init. Has to manually call.
            for i = 1:numel(h.hSliceViewerPanel)
                h.hSliceViewerPanel(i).set_layout();
            end
        end
%-------------------------------------------------------------------------------
        function load_geometry(obj, geometry_filename)
        %% load geometry
            if nargin == 2 % load the geometry file if supplied
                load(geometry_filename);
            elseif nargin == 1 % Geometry should be loaded already
                Geometry = obj.handles.hSVPS.Geometry;
                if isempty(obj.handles.hSVPS.Geometry)
                    % TODO appropriate handling
                    return;
                end
            end

            % add x,y,z axis for plotting purposes
            Geometry.x = Geometry.start(1) + Geometry.voxel_size(1) * (0:size(Geometry.rhomw, 1)-1);
            Geometry.y = Geometry.start(2) + Geometry.voxel_size(2) * (0:size(Geometry.rhomw, 2)-1);
            Geometry.z = Geometry.start(3) + Geometry.voxel_size(3) * (0:size(Geometry.rhomw, 3)-1);
            for i = 1:numel(Geometry.ROIS)
                % TODO unify curves as N x 3 cell array so we don't need Xcurves & Ycurves,
                % but that way will break back-compatibility.
                if isfield(Geometry.ROIS{i}, 'Xcurves')
                    Xcurves_coordinate = cellfun(@(c)c(1,1), Geometry.ROIS{i}.Xcurves);
                    Geometry.ROIS{i}.Xcurves_slices = ...
                        round((Xcurves_coordinate - Geometry.start(1)) / Geometry.voxel_size(1)) + 1;
                else
                    % Old version doesn't have XYcurves. Create an empty index to skip plotting.
                    Geometry.ROIS{i}.Xcurves_slices = [];
                end
                
                if isfield(Geometry.ROIS{i}, 'Ycurves')
                    Ycurves_coordinate = cellfun(@(c)c(1,2), Geometry.ROIS{i}.Ycurves);
                    Geometry.ROIS{i}.Ycurves_slices = ...
                        round((Ycurves_coordinate - Geometry.start(2)) / Geometry.voxel_size(2)) + 1;
                else
                    % Old version doesn't have XYcurves. Create an empty index to skip plotting.
                    Geometry.ROIS{i}.Ycurves_slices = [];
                end
                
                if isfield(Geometry.ROIS{i}, 'curves')
                    Zcurves_coordinate = cellfun(@(c)c(1,3), Geometry.ROIS{i}.curves);
                    Geometry.ROIS{i}.Zcurves_slices = ...
                        round((Zcurves_coordinate - Geometry.start(3)) / Geometry.voxel_size(3)) + 1;
                else
                    Geometry.ROIS{i}.Zcurves_slices = [];
                end
            end
            
            % Convert data into float
            if isinteger(Geometry.data)
                Geometry.data = single(Geometry.data);
            end

            % Init/set display settings if absent
            num_ROI = numel(Geometry.ROIS);
            for i = 1:num_ROI
                if ~isfield(Geometry.ROIS{i}, 'visible')
                    Geometry.ROIS{i}.visible = false;
                end
                if ~isfield(Geometry.ROIS{i}, 'color')
                    Geometry.ROIS{i}.color = rand(1,3);
                end
            end

            % Set/save to SliceViewerPanelSource
            obj.handles.hSVPS.Geometry = Geometry;
            obj.handles.hSVPS.TCSVisible = ...
                (get(obj.handles.hTCSShow, 'Value') == get(obj.handles.hTCSShow, 'Max'));
            
            % updates
            obj.handles.hSliceViewerPanel(1).load_data();
            obj.handles.hSliceViewerPanel(2).load_data();
            obj.handles.hSliceViewerPanel(3).load_data();
            obj.updateROITable();
        end
%-------------------------------------------------------------------------------
        function load_optResults(obj, optresults_filename)
            if nargin == 2 % load the optResults file if supplied
                load(optresults_filename, 'optResults');
                obj.handles.hSVPS.optResults = optResults;
            elseif nargin == 1 % optResults should exist already
                % Do nothing for now
            end

            obj.updateDoseTable();
        end
%-------------------------------------------------------------------------------
        function updateROITable(obj)
        % Update ROITable using values in Geometry.ROIS
            if isempty(obj.handles.hSVPS.Geometry); return; end

            tdata = get(obj.handles.hROITable, 'Data');
            % Update table data according to display settings
            for i = 1:numel(obj.handles.hSVPS.Geometry.ROIS)
                tdata{i, 1} = obj.handles.hSVPS.Geometry.ROIS{i}.visible;
                c = obj.handles.hSVPS.Geometry.ROIS{i}.color;
                tdata{i, 2} = sprintf('<html><span style="color:%s">&#x25A0</span></html>', rgb2str(c));
                tdata{i, 3} = obj.handles.hSVPS.Geometry.ROIS{i}.name;
            end
            set(obj.handles.hROITable, 'Data', tdata);
            drawnow;

            obj.set_layout();
        end
%-------------------------------------------------------------------------------
        function updateDoseTable(obj)
        % Update DoseTable using data in SliceViewerPanelSource.dosedisp
%             if isempty(obj.handles.hSVPS.Geometry) && isempty(obj.handles.hSVPS.optResults); return; end

            tdata = cell(0);
            % Update table data according to display settings
            for i = 1:numel(obj.handles.hSVPS.dosedisp.level)
                tdata{i, 1} = sprintf('<html><span style="color:%s">&#x25A0</span></html>', rgb2str(obj.handles.hSVPS.dosedisp.color(i,:)));
                tdata{i, 2} = obj.handles.hSVPS.dosedisp.level(i);
                tdata{i, 3} = obj.handles.hSVPS.dosedisp.alpha(i);
            end
            % disable the callback to prevent recursion
            set(obj.handles.hDoseTable, 'CellSelectionCallback', []);
            set(obj.handles.hDoseTable, 'Data', tdata);
            drawnow; % Flush //IMPORTANT
            set(obj.handles.hDoseTable, 'CellSelectionCallback', @obj.DoseTable_CellSelectionCallback);
        end
%-------------------------------------------------------------------------------
        function updateCTWindowControls(obj)
            set(obj.handles.hWWSlider, 'Value', obj.handles.hSVPS.ctWindow.ww);
            set(obj.handles.hWWEdit, 'String', num2str(obj.handles.hSVPS.ctWindow.ww));
            set(obj.handles.hWLSlider, 'Value', obj.handles.hSVPS.ctWindow.wl);
            set(obj.handles.hWLEdit, 'String', num2str(obj.handles.hSVPS.ctWindow.wl));
        end
%-------------------------------------------------------------------------------
        function ROITable_CellSelectionCallback(obj, hObject, eventdata)
        % eventdata  structure with the following fields (see UITABLE)
        %	Indices: row and column indices of the cell(s) currently selecteds
            % Avoid "fake" event during initialization
            if ~isempty(eventdata.Indices)
                roi_idx = eventdata.Indices(1);
                if eventdata.Indices(2) == 1
                    % toggle ROI display in display settings
                    tdata = get(hObject, 'Data');
                    obj.handles.hSVPS.Geometry.ROIS{roi_idx}.visible = ~tdata{roi_idx, 1};
                else % eventdata.Indices(2) ~= 1
                    % pick and save color
                    c = uisetcolor;
                    if ~(isscalar(c) && c == 0)
                        obj.handles.hSVPS.Geometry.ROIS{roi_idx}.color = c;
                        % also make it visible
                        obj.handles.hSVPS.Geometry.ROIS{roi_idx}.visible = true;
                    end
                end
                obj.updateROITable();
            end
        end
%-------------------------------------------------------------------------------
        function DoseTable_CellSelectionCallback(obj, tilde, eventdata)
        % eventdata  structure with the following fields (see UITABLE)
        %	Indices: row and column indices of the cell(s) currently selecteds
            % Avoid fake event during initialization
            if ~isempty(eventdata.Indices)
                if eventdata.Indices(2) == 1
                    % pick and save color
                    c = uisetcolor;
                    if ~(isscalar(c) && c == 0)
                        obj.handles.hSVPS.dosedisp.color(eventdata.Indices(1), :) = c;
                        obj.updateDoseTable();
                    end
                end
            end
        end
%-------------------------------------------------------------------------------
        function DoseTable_CellEditCallback(obj, tilde, eventdata)
        % Update handles.hSVPS.dosedisp
            if eventdata.Indices(2) == 2
                obj.handles.hSVPS.dosedisp.level(eventdata.Indices(1)) = eventdata.NewData;
            elseif eventdata.Indices(2) == 3
                obj.handles.hSVPS.dosedisp.alpha(eventdata.Indices(1)) = eventdata.NewData;
            end
            obj.updateDoseTable();
        end
%-------------------------------------------------------------------------------
        function WWSlider_Callback(obj, src, evt)
            % set window width property of SliceViewerPancelSource
            value = round(get(src, 'Value'));
            
            obj.handles.hSVPS.ctWindow.ww = value;
            obj.updateCTWindowControls();
        end
%-------------------------------------------------------------------------------
        function WWEdit_Callback(obj, src, evt)
            % set window width property of SliceViewerPancelSource
            value = round(str2double(get(src, 'String')));
            % clipping to valid value
            value = max(value, get(obj.handles.hWWSlider, 'Min'));
            value = min(value, get(obj.handles.hWWSlider, 'Max'));
            
            obj.handles.hSVPS.ctWindow.ww = value;
            obj.updateCTWindowControls();
        end
%-------------------------------------------------------------------------------
        function WLSlider_Callback(obj, src, evt)
            % set window width property of SliceViewerPancelSource
            value = round(get(src, 'Value'));
            
            obj.handles.hSVPS.ctWindow.wl = value;
            obj.updateCTWindowControls();
        end
%-------------------------------------------------------------------------------
        function WLEdit_Callback(obj, src, evt)
            % set window width property of SliceViewerPancelSource
            value = round(str2double(get(src, 'String')));
            % clipping to valid value
            value = max(value, get(obj.handles.hWLSlider, 'Min'));
            value = min(value, get(obj.handles.hWLSlider, 'Max'));
            
            obj.handles.hSVPS.ctWindow.wl = value;
            obj.updateCTWindowControls();
        end
%-------------------------------------------------------------------------------
        function ImportDicomRTMenu_Callback(obj, src, evt)
            [obj.handles.hSVPS.Geometry obj.patient_dir] = RDXTPS_geometry_setup_wizard_ASP();
            obj.load_geometry();
            
            a=obj.handles.hSVPS.Geometry;
            disp(1)
        end
        
%-------------------------------------------------------------------------------
% Grozomah
        function NRRD1_Callback(obj, src, evt)
            [obj.handles.hSVPS.Geometry] = load2geometry();
            obj.load_geometry();
            
            [obj.handles.hSVPS.Geometry] = nrrd2ROI(obj.handles.hSVPS.Geometry);
            obj.load_geometry();

            disp('New ROI loaded!')
        end
%-------------------------------------------------------------------------------
% Grozomah
        function NRRD2_Callback(obj, src, evt)
            [obj.handles.hSVPS.Geometry] = nrrd2ROI(obj.handles.hSVPS.Geometry);
            obj.load_geometry();

            disp('New ROI loaded!')
        end
        
%-------------------------------------------------------------------------------
        % Grozomah
        function ImgPerturb_Callback(obj, src, evt)
            disp('Perturb callback implemented')
        end
        
        
%-------------------------------------------------------------------------------
        function DosecalcMenu_Callback(obj, src, evt)
            % TODO fix patient_dir system
%             [obj.dosecalcSetup obj.patient_dir] = RDXTPS_dosecalcSetup(obj.dosecalcSetup, obj.patient_dir, obj.handles.hSVPS.Geometry);
%             [obj.dosecalcSetup obj.patient_dir] = RDXTPS_dosecalcSetup(obj.dosecalcSetup, [], obj.handles.hSVPS.Geometry);
% 
%             % Temporary fix for Gustavo asking energy limit
%             answer = inputdlg('Machine energy limit: (MeV)', 'Energy limit', 1, {'250'});
%             maxMachineEnergyStr = answer{1};
% 
%             % run beamlet dose calculation 
%             cmdline = ['.' filesep 'RDXdosecalc.exe "' fullfile(obj.patient_dir, 'dosecalc_input.txt') '"' ' ' maxMachineEnergyStr];
%             % Grozomah ##
% %             cmdline = ['.' filesep 'RDXoptimizer.exe "' fullfile(obj.patient_dir, 'dosecalc_input.txt') '"'];
%             
%             if ispc
%                 execline = ['cmd /c ' cmdline ' &'];
%             elseif isunix
%                 % xterm -e "export LD_LIBRARY_PATH=. ; ./RDXdosecalc.exe '../patients/Knew/dosecalc_input.txt' ; read" &
%                 % TODO fix single quote
%                 cmdline = ['xterm -e "export LD_LIBRARY_PATH=. ; ./RDXdosecalc.exe ' fullfile(obj.patient_dir, 'dosecalc_input.txt') ' ; read" &'];
%             end
%             msgbox(sprintf('Start beamlet dose calculation.\nRun this if not started automatically:\n%s', cmdline));
%             system(execline);

            obj.handles.hSVPS.Geometry.num_batches = helicalDosecalcSetup7(obj.handles.hSVPS.Geometry.patient_dir)


        end
        %-------------------------------------------------------------------------------
        % Grozomah
        function MergeBeamlets_Callback(obj, src, evt)
            merge_beamlets(obj.handles.hSVPS.Geometry.num_batches, obj.handles.hSVPS.Geometry.patient_dir);
            disp('Beamlets merged!')
        end
        %-------------------------------------------------------------------------------
        % Grozomah
        function Test2_Callback(obj, src, evt)
            disp('Test 2 works!')
        end
%-------------------------------------------------------------------------------
        function OptimMenu_Callback(obj, src, evt)
            % TODO fix patient_dir system
%             if isempty(obj.patient_dir)
                obj.patient_dir = uifile('getdir', 'Select the patient directory');
%             end

            source_filename = fullfile(obj.patient_dir, 'batch_dose.bin');
            target_filename = fullfile(obj.patient_dir, 'beamlet_batch_files', 'beamletbatch0.bin');
            mkdir(fullfile(obj.patient_dir, 'beamlet_batch_files'));

            try
                if ispc % MATLAB movefile() super slow on windows
                    % TODO confirm overwrite
                    system(['move "' source_filename '" "' target_filename '"']);
                else
                    movefile(source_filename, target_filename);
                end
            catch
                msgbox('Error moving the beamlet file. Please do so manually.');
            end

            Nbeamlets = read_ryan_beamlets(target_filename, 'info');

            RDXTPS_optimSetup(Nbeamlets, obj.patient_dir, obj.handles.hSVPS.Geometry);

            % run optimizer
            %---
            cd('C:\010-work\003_localGit\WiscPlan_v2\WiscPlanPhotonkV125\WiscPlanEXE')
            
            cmdline = ['.' filesep 'RDXoptimizer.exe "' fullfile(obj.patient_dir, 'optInput.txt') '"'];
            msgbox(sprintf('Start optimization\nRun this if not started automatically:\n%s', cmdline));
            if ispc
                execline = ['cmd /c ' cmdline ' &'];
            elseif isunix
                % TODO fix single quote
                execline = [cmdline];
            end
            system(execline);
        end
%-------------------------------------------------------------------------------
        function SaveOptimResultsMenu_Callback(obj, src, evt)
            % TODO fix patient_dir system
%             if isempty(obj.patient_dir)
                obj.patient_dir = uifile('getdir', 'Select the patient directory');
%             end

            [tilde, obj.handles.hSVPS.optResults] = loadOptResults(obj.patient_dir, 'optInput.txt');
            obj.load_optResults();
        end
%-------------------------------------------------------------------------------
        % Grozomah
        function GetFullDose_Callback(obj, src, evt)
            get_full_dose([obj.patient_dir])
            disp('Full dose calculated.')
        end
        
%-------------------------------------------------------------------------------
        function LoadGeometryMenu_Callback(obj, src, evt)
            [filename pathname] = uifile('get', '*.mat', 'Choose Geometry file to load');
            % do nothing if cancelled
            if isscalar(filename) && filename == 0; return; end

            obj.load_geometry(fullfile(pathname, filename));
        end
%-------------------------------------------------------------------------------
        function LoadOptresultsMenu_Callback(obj, src, evt)
            [filename pathname] = uifile('get', '*.mat', 'Choose OptResults file to load');
            % do nothing if cancelled
            if isscalar(filename) && filename == 0; return; end

            obj.load_optResults(fullfile(pathname, filename));
            
%             % Extra dose scaling. Temporary code for comparison with Tomo plans
%             answer = inputdlg({'Dose', '% Volume'}, 'Scale final dose');
%             if ~isempty(answer)
%                 % choose target
%                 ROI_names = cellfun(@(c)c.name, obj.handles.hSVPS.Geometry.ROIS, 'UniformOutput', false);
%                 [target_idx] = listdlg('ListString', ROI_names, ...
%                 'SelectionMode', 'single', 'Name', 'Target Selection', ...
%                 'PromptString', 'Please select the target ROI.');
%                 opt_dose = prctile(obj.handles.hSVPS.optResults.dose{end}(obj.handles.hSVPS.Geometry.ROIS{target_idx}.ind), 100 - str2double(answer{2}));
%                 obj.handles.hSVPS.optResults.dose{end} = obj.handles.hSVPS.optResults.dose{end} * str2double(answer{1}) / opt_dose;
%             end
%             % END OF Extra dose scaling
            
            msgbox('Load optResults successfully.')
        end
%-------------------------------------------------------------------------------
        function ExportPinnacleMenu_Callback(obj, src, evt)
            if isempty(obj.handles.hSVPS.Geometry)
                obj.LoadGeometryMenu_Callback([], [], obj);
            end
            if isempty(obj.handles.hSVPS.optResults)
                obj.LoadOptresultsMenu_Callback([], [], obj);
            end
            RDXTPS_exportPinnGrid4Tomo(obj.handles.hSVPS.Geometry, obj.handles.hSVPS.optResults);
        end
%-------------------------------------------------------------------------------
        function PlotDVHMenu_Callback(obj, src, evt)
            answer = inputdlg({'Enter figure number:', 'Enter line style'}, 'Choose figure');
            if isempty(answer{1})
                return;
            else
                fig_idx = str2double(answer{1});
            end
            if isempty(answer{2})
                line_style = '-';
            else
                line_style = answer{2};
            end
            figure(fig_idx); hold on;
            
            % temp solution for karthik dosimetry data
            answer = inputdlg('number of fractions');
            nfrac = str2double(answer{1});
                    
            for roi_idx = 1:numel(obj.handles.hSVPS.Geometry.ROIS)
                if obj.handles.hSVPS.Geometry.ROIS{roi_idx}.visible == true % display == ON
                    fprintf('%s\n', obj.handles.hSVPS.Geometry.ROIS{roi_idx}.name);
%                     [dvh dosebins] = dvhist(obj.handles.hSVPS.optResults.dose{end}, obj.handles.hSVPS.Geometry.ROIS{roi_idx}.ind);
                    % temp solution for karthik dosimetry data
                    [dvh dosebins] = dvhist(obj.handles.hSVPS.optResults.dose{end}, ...
                        obj.handles.hSVPS.Geometry, ...
                        roi_idx, ...
                        nfrac);                    
                    plot(dosebins, dvh, ...
                        'Color', obj.handles.hSVPS.Geometry.ROIS{roi_idx}.color, ...
                        'LineStyle', line_style, ...
                        'DisplayName', obj.handles.hSVPS.Geometry.ROIS{roi_idx}.name);
                end
            end
            set(gca, 'XMinorTick', 'on', 'YMinorTick', 'on');
            grid(gca, 'on');
            box(gca, 'on');
            legend('show');
            xlabel('Dose (Gy)');
            ylabel('% volume');
            hold off;
        end
%-------------------------------------------------------------------------------
        function DoseModeDropdown_Callback(obj, src, evt)
            str = get(obj.handles.hDoseModeDropdown, 'String');
            obj.handles.hSVPS.dosedisp.mode = str{get(obj.handles.hDoseModeDropdown, 'Value')};
        end
%-------------------------------------------------------------------------------
        function TCSShow_Callback(obj, src, evt)
            obj.handles.hSVPS.TCSVisible = ...
                get(src, 'Value') == get(src, 'Max');
        end
%-------------------------------------------------------------------------------
        function SaveAsGeometryMenu_Callback(obj, src, evt)
            [filename pathname] = uifile('put', '*.mat', 'Save Geometry as...');
            % do nothing if cancelled
            if isscalar(filename) && filename == 0; return; end
            
            Geometry = obj.handles.hSVPS.Geometry;
            for i = 1:numel(Geometry.ROIS)
                if isfield(Geometry.ROIS{i}, 'BW')
                    Geometry.ROIS{i}.BW = [];
                end
            end
            save(fullfile(pathname, filename), 'Geometry');
        end
%-------------------------------------------------------------------------------
        function SaveAsOptResultsMenu_Callback(obj, src, evt)
            [filename pathname] = uifile('put', '*.mat', 'Save OptResults as...');
            % do nothing if cancelled
            if isscalar(filename) && filename == 0; return; end
            
            optResults = obj.handles.hSVPS.optResults;
            save(fullfile(pathname, filename), 'optResults');
        end
%-------------------------------------------------------------------------------
    end % methods
end