text:
function varargout = matRadGUI(varargin)
% matRad GUI
%
% call
%      MATRADGUI, by itself, creates a new MATRADGUI or raises the existing
%      singleton*.
%
%      H = MATRADGUI returns the handle to a new MATRADGUI or the handle to
%      the existing singleton*.
%
%      MATRADGUI('CALLBACK',hObject,eventData,handles,...) calls the local
%      function named CALLBACK in MATRADGUI.M with the given input arguments.
%
%      MATRADGUI('Property','Value',...) creates a new MATRADGUI or raises the
%      existing singleton*.  Starting from the left, property value pairs are
%      applied to the GUI before matRadGUI_OpeningFcn gets called.  An
%      unrecognized property name or invalid value makes property application
%      stop.  All inputs are passed to matRadGUI_OpeningFcn via varargin.
%
%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
%      instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES
%
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Copyright 2015 the matRad development team.
%
% This file is part of the matRad project. It is subject to the license
% terms in the LICENSE file found in the top-level directory of this
% distribution and at https://github.com/e0404/matRad/LICENSES.txt. No part
% of the matRad project, including this file, may be copied, modified,
% propagated, or distributed except according to the terms contained in the
% LICENSE file.
%
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

matRad_cfg = MatRad_Config.instance();

if matRad_cfg.disableGUI
    matRad_cfg.dispInfo('matRad GUI disabled in matRad_cfg!\n');
    return;
end

if ~isdeployed
    matRadRootDir = fileparts(mfilename('fullpath'));
    addpath(genpath(matRadRootDir));
end

[env, versionString] = matRad_getEnvironment();

% abort for octave
switch env
     case 'MATLAB'

     case 'OCTAVE'
         matRad_cfg.dispInfo(['matRad GUI not available for ' env ' ' versionString ' \n']);
         return;
     otherwise
         matRad_cfg.dispInfo('not yet tested');
 end

% Begin initialization code - DO NOT EDIT
% set platform specific look and feel
if ispc
    lf = 'com.sun.java.swing.plaf.windows.WindowsLookAndFeel';
elseif isunix
    lf = 'com.jgoodies.looks.plastic.Plastic3DLookAndFeel';
elseif ismac
    lf = 'com.apple.laf.AquaLookAndFeel';
end
javax.swing.UIManager.setLookAndFeel(lf);

gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @matRadGUI_OpeningFcn, ...
                   'gui_OutputFcn',  @matRadGUI_OutputFcn, ...
                   'gui_LayoutFcn',  [] , ...
                   'gui_Callback',   []);
if nargin && ischar(varargin{1})
    gui_State.gui_Callback = str2func(varargin{1});
end

if nargout
    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
    gui_mainfcn(gui_State, varargin{:});
end

% End initialization code - DO NOT EDIT

function handles = resetGUI(hObject, handles, varargin)
% enable opengl software rendering to visualize linewidths properly
if ispc
  opengl software
elseif ismac
  % opengl is not supported
end

% Choose default command line output for matRadGUI
handles.output = hObject;
%show matrad logo
axes(handles.axesLogo)
[im, ~, alpha] = imread('matrad_logo.png');
f = image(im);
axis equal off
set(f, 'AlphaData', alpha);
% show dkfz logo
axes(handles.axesDKFZ)
[im, ~, alpha] = imread('DKFZ_Logo.png');
f = image(im);
axis equal off;
set(f, 'AlphaData', alpha);

% turn off the datacursormode (since it does not allow to set scrolling
% callbacks
handles.dcm_obj = datacursormode(handles.figure1);
set(handles.dcm_obj,'DisplayStyle','window');
if strcmpi(get(handles.dcm_obj,'Enable'),'on')
  set(handles.dcm_obj,'Enable','off');
end
%Add the callback for the datacursor display
set(handles.dcm_obj,'UpdateFcn',@dataCursorUpdateFunction);

% set callback for scroll wheel function
set(gcf,'WindowScrollWheelFcn',@matRadScrollWheelFcn);

% change color of toobar but only the first time GUI is started
if handles.initialGuiStart
  hToolbar = findall(hObject,'tag','uitoolbar1');
  jToolbar = get(get(hToolbar,'JavaContainer'),'ComponentPeer');
  jToolbar.setBorderPainted(false);
  color = java.awt.Color.gray;
  % Remove the toolbar border, to blend into figure contents
  jToolbar.setBackground(color);
  % Remove the separator line between toolbar and contents
  warning('off','MATLAB:HandleGraphics:ObsoletedProperty:JavaFrame');
  jFrame = get(handle(hObject),'JavaFrame');
  jFrame.showTopSeparator(false);
  jtbc = jToolbar.getComponents;
  for idx=1:length(jtbc)
      jtbc(idx).setOpaque(false);
      jtbc(idx).setBackground(color);
      for childIdx = 1 : length(jtbc(idx).getComponents)
          jtbc(idx).getComponent(childIdx-1).setBackground(color);
      end
  end
end

set(handles.legendTable,'String',{'no data loaded'});
% clear  VOIPlotFlag
if isfield(handles,'VOIPlotFlag')
  handles = rmfield(handles,'VOIPlotFlag');
end

%seach for availabes machines
handles.Modalities = {'photons','protons','carbon'};
for i = 1:length(handles.Modalities)
  pattern = [handles.Modalities{1,i} '_*'];
  if isdeployed
      baseroot = [ctfroot filesep 'matRad'];
  else
      baseroot = fileparts(mfilename('fullpath'));
  end
  Files = dir([baseroot filesep 'basedata' filesep pattern]);

  for j = 1:length(Files)
      if ~isempty(Files)
          MachineName = Files(j).name(numel(handles.Modalities{1,i})+2:end-4);
          if isfield(handles,'Machines')
              if sum(strcmp(handles.Machines,MachineName)) == 0
                handles.Machines{size(handles.Machines,2)+1} = MachineName;
              end
          else
              handles.Machines = cell(1);
              handles.Machines{1} = MachineName;
          end
      end
  end
end
set(handles.popUpMachine,'String',handles.Machines);

vChar = get(handles.editGantryAngle,'String');
if strcmp(vChar(1,1),'0') && length(vChar)==6
  set(handles.editGantryAngle,'String','0');
end
vChar = get(handles.editCouchAngle,'String');
if strcmp(vChar(1,1),'0') && length(vChar)==3
  set(handles.editCouchAngle,'String','0')
end
%%
% handles.State=0   no data available
% handles.State=1   ct cst and pln available; ready for dose calculation
% handles.State=2   ct cst and pln available and dij matric(s) are calculated;
%                   ready for optimization
% handles.State=3   plan is optimized

% if plan is changed go back to state 1
% if table VOI Type or Priorities changed go to state 1
% if objective parameters changed go back to state 2
handles.CutOffLevel            = 0.01; % relative cut off level for dose vis
handles.IsoDose.NewIsoDoseFlag = false;
handles.TableChanged           = false;
handles.State                  = 0;
handles.doseOpacity            = 0.6;
handles.IsoDose.Levels         = 0;
handles.dispWindow             = cell(3,2); % first dimension refers to the selected

% do not calculate / suggest isoCenter new by default
set(handles.checkIsoCenter, 'Value', 0);
set(handles.editIsoCenter,'Enable','on')

% suppose no ct cube in HU is available (because no ct could be available)
handles.cubeHUavailable = false;
% initial startup finished
handles.initialGuiStart = false;
guidata(hObject, handles);
% eof resetGUI

% --- Initializes the slice slider for the current ct & isocenter (or sets
% it to default)
function initViewSliceSlider(handles)
% handles    structure with handles and user data (see GUIDATA)

if handles.State > 0
    ct = evalin('base', 'ct');

    %Helpers for managing the resolution and Matlab xy permutation
    planePermute = [2 1 3];
    ctRes = [ct.resolution.x ct.resolution.y ct.resolution.z];
    planePermIx = planePermute(handles.plane);
    planeDim = ct.cubeDim(handles.plane);

    %Try to select the slice from defined isocenter
    try
        if evalin('base','exist(''pln'',''var'')')
            currPln = evalin('base','pln');

            if sum(currPln.propStf.isoCenter(:)) ~= 0
                %currSlice = round((currPln.propStf.isoCenter(1,planePermIx)+ctRes(planePermix)/2)/ctRes(planePermIx))-1;
                currSlice = round(currPln.propStf.isoCenter(1,planePermIx) / ctRes(planePermIx));
            else
                currSlice = 0;
            end
        end
    catch
        currSlice = 0; %Set to zero for next if
    end

    %If no isocenter or wrong value, choose central slice
    if currSlice < 1 || currSlice > planeDim
        currSlice = ceil(planeDim/2);
    end

    set(handles.sliderSlice,'Min',1,'Max',planeDim,...
        'Value',currSlice,...
        'SliderStep',[1/(planeDim-1) 1/(planeDim-1)]);
else
    % reset slider when nothing is loaded
    set(handles.sliderSlice,'Min',0,'Max',1,'Value',0,'SliderStep',[1 1]);
end

function handles = reloadGUI(hObject, handles, ct, cst)
AllVarNames = handles.AllVarNames;

if nargin >=3 && ismember('ct',AllVarNames)
    % compute HU values
    if ~isfield(ct, 'cubeHU')
        ct = matRad_electronDensitiesToHU(ct);
        assignin('base','ct',ct);
    end
    if ~isfield(ct, 'cubeHU')
        handles.cubeHUavailable = false;
    else
        handles.cubeHUavailable = true;
    end
end

%set plan if available - if not create one
try
    if ismember('pln',AllVarNames) && handles.State > 0
        % check if you are working with a valid pln
        pln = evalin('base','pln');
        if ~isfield(pln,'propStf')
            handles = showWarning(handles,'GUI OpeningFunc: Overwriting outdated pln format with default GUI pln');
            evalin('base','clear pln');
            getPlnFromGUI(handles);
        end
        setPln(handles);
    elseif handles.State > 0
         getPlnFromGUI(handles);
         setPln(handles);
    end

catch
       handles.State = 0;
       handles = showError(handles,'GUI OpeningFunc: Could not set or get pln');
end

% check for dij structure
if ismember('dij',AllVarNames)
    handles.State = 2;
end

% check for optimized results
if ismember('resultGUI',AllVarNames)
    handles.State = 3;
end

% set some default values
if handles.State == 2 || handles.State == 3
    set(handles.popupDisplayOption,'String','physicalDose');
    handles.SelectedDisplayOption ='physicalDose';
    handles.SelectedDisplayOptionIdx=1;
else
    handles.resultGUI = [];
    set(handles.popupDisplayOption,'String','no option available');
    handles.SelectedDisplayOption='';
    handles.SelectedDisplayOptionIdx=1;
end

% precompute iso dose lines
if handles.State == 3
    handles = updateIsoDoseLineCache(handles);
end

%per default the first beam is selected for the profile plot
handles.selectedBeam = 1;
handles.plane = get(handles.popupPlane,'Value');
handles.DijCalcWarning = false;

% set slice slider
initViewSliceSlider(handles);

% define context menu for structures
if handles.State > 0
    for i = 1:size(cst,1)
        if cst{i,5}.Visible
            handles.VOIPlotFlag(i) = true;
        else
            handles.VOIPlotFlag(i) = false;
        end
    end
end

%Initialize colormaps and windows
handles.doseColorMap = 'jet';
handles.ctColorMap   = 'bone';
handles.cMapSize     = 64;
handles.cBarChanged  = true;

%Set up the colormap selection box
availableColormaps = matRad_getColormap();
set(handles.popupmenu_chooseColormap,'String',availableColormaps);

currentCtMapIndex   = find(strcmp(availableColormaps,handles.ctColorMap));
currentDoseMapIndex = find(strcmp(availableColormaps,handles.doseColorMap));

if handles.State >= 1
   set(handles.popupmenu_chooseColormap,'Value',currentCtMapIndex);
end

if handles.State >= 3
    set(handles.popupmenu_chooseColormap,'Value',currentDoseMapIndex);
end

% Update handles structure
handles.profileOffset = 0;
UpdateState(handles)

axes(handles.axesFig)

handles.rememberCurrAxes = false;
UpdatePlot(handles)
handles.rememberCurrAxes = true;
guidata(hObject, handles);
% eof reloadGUI

% --- Executes just before matRadGUI is made visible.
function matRadGUI_OpeningFcn(hObject, ~, handles, varargin)
%#ok<*DEFNU>
%#ok<*AGROW>
% This function has no output args, see OutputFcn.
% hObject    handle to figure
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
% varargin   command line arguments to matRadGUI (see VARARGIN)

% variable to check whether GUI is opened or just refreshed / new data
% loaded, since resetGUI needs to distinguish at one point

handles.initialGuiStart = true;

p = inputParser;
addParameter(p,'devMode',false,@validateModeValue);
addParameter(p,'eduMode',false,@validateModeValue);
p.KeepUnmatched = true; %No error with incorrect parameters

parse(p,varargin{:});
parsedInput = p.Results;

if ischar(parsedInput.devMode) || isstring(parsedInput.devMode)
    parsedInput.devMode = str2double(parsedInput.devMode);
end

if ischar(parsedInput.eduMode) || isstring(parsedInput.eduMode)
    parsedInput.eduMode = str2double(parsedInput.eduMode);
end

%If devMode is true, error dialogs will include the full stack trace of the error
%If false, only the basic error message is shown (works for errors that
%handle the MException object)
handles.devMode = logical(parsedInput.devMode);
if handles.devMode
    disp('matRadGUI starting in developer mode!');
end

%Enables simple educational mode which removes certain functionality from
%the GUI
handles.eduMode = logical(parsedInput.eduMode);
if handles.eduMode
    disp('matRadGUI starting in educational mode!');
end

set(handles.radiobtnPlan,'value',0);

if handles.eduMode
    %Visisbility in Educational Mode
    eduHideHandles =   {handles.radiobutton3Dconf,...
        handles.btnRunDAO,...
        handles.pushbutton_importFromBinary,...
        handles.btnLoadDicom,...
        handles.btn_export,...
        handles.importDoseButton};
    eduDisableHandles = {handles.editCouchAngle,handles.popUpMachine};
    cellfun(@(h) set(h,'Visible','Off'),eduHideHandles);
    cellfun(@(h) set(h,'Enable','Off'),eduDisableHandles);
end

%Alter matRad Version string positioning
vString = matRad_version();
vPos = get(handles.text15,'Position');
urlPos = get(handles.text31,'Position');
btnPos = get(handles.btnAbout,'Position');

%vPos([1 3]) = urlPos([1 3]);
vPos([1 3]) = [0 1];
vPos(4) = vPos(4)*1.25;
btnPos(2) = 0.05;
urlPos(2) = btnPos(2)+btnPos(4)+0.05;
vPos(2) = urlPos(2) + urlPos(4) + 0.05;
vPos(4) = 0.98 - vPos(2);

set(handles.btnAbout,'Position',btnPos);
set(handles.text31,'String','www.matRad.org','Position',urlPos,'Enable','inactive','ButtonDownFcn', @(~,~) web('www.matrad.org','-browser'));
set(handles.text15,'String',vString,'Position',vPos);

handles = resetGUI(hObject, handles);

%% parse variables from base workspace
AllVarNames = evalin('base','who');
handles.AllVarNames = AllVarNames;
try
    if  ismember('ct',AllVarNames) &&  ismember('cst',AllVarNames)
        ct  = evalin('base','ct');
        cst = evalin('base','cst');
        %cst = setCstTable(handles,cst);
        cst = generateCstTable(handles,cst);
        handles.State = 1;
        cst = matRad_computeVoiContoursWrapper(cst,ct);
        assignin('base','cst',cst);

    elseif ismember('ct',AllVarNames) &&  ~ismember('cst',AllVarNames)
         handles = showError(handles,'GUI OpeningFunc: could not find cst file');
    elseif ~ismember('ct',AllVarNames) &&  ismember('cst',AllVarNames)
         handles = showError(handles,'GUI OpeningFunc: could not find ct file');
    end
catch
   handles = showError(handles,'GUI OpeningFunc: Could not load ct and cst file');
end

if ismember('ct',AllVarNames) &&  ismember('cst',AllVarNames)
    handles = reloadGUI(hObject, handles, ct, cst);
else
    handles = reloadGUI(hObject, handles);
end

guidata(hObject, handles);

%Validates the attributes for the command line Modes
function validateModeValue(x)
%When passed from OS terminal (or inline in Command Window) everything is a string
if isdeployed || ischar(x) || isstring(x)
    x=str2double(x);
end
validateattributes(x,{'logical','numeric'},{'scalar','binary'});

function Callback_StructVisibilty(source,~)

handles = guidata(findobj('Name','matRadGUI'));

contextUiChildren = get(get(handles.figure1,'UIContextMenu'),'Children');

Idx = find(strcmp(get(contextUiChildren,'Label'),get(source,'Label')));
if strcmp(get(source,'Checked'),'on')
    set(contextUiChildren(Idx),'Checked','off');
else
    set(contextUiChildren(Idx),'Checked','on');
end
%guidata(findobj('Name','matRadGUI'), handles);
UpdatePlot(handles);

% --- Outputs from this function are returned to the command line.
function varargout = matRadGUI_OutputFcn(~, ~, handles)
% varargout  cell array for returning output args (see VARARGOUT);
% hObject    handle to figure
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Get default command line output from handles structure
varargout{1} = handles.output;

% set focus on error dialog
if isfield(handles,'ErrorDlg')
    figure(handles.ErrorDlg)
end

% --- Executes on button press in btnLoadMat.
function btnLoadMat_Callback(hObject, ~, handles)
% hObject    handle to btnLoadMat (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

[FileName, FilePath] = uigetfile('*.mat');
if FileName == 0 % user pressed cancel --> do nothing.
    return;
end

handles = resetGUI(hObject, handles);

try

    % delete existing workspace - parse variables from base workspace
    AllVarNames = evalin('base','who');
    RefVarNames = {'ct','cst','pln','stf','dij','resultGUI'};

    for i = 1:length(RefVarNames)
        if sum(ismember(AllVarNames,RefVarNames{i}))>0
            evalin('base',['clear ', RefVarNames{i}]);
        end
    end

    % read new data
    load([FilePath FileName]);
    set(handles.legendTable,'String',{'no data loaded'});
    set(handles.popupDisplayOption,'String','no option available');

catch ME
    handles = showError(handles,'LoadMatFileFnc: Could not load *.mat file',ME);

    guidata(hObject,handles);
    UpdateState(handles);
    UpdatePlot(handles);
    return
end

try
    generateCstTable(handles,cst);
    handles.TableChanged = false;
    set(handles.popupTypeOfPlot,'Value',1);
    cst = matRad_computeVoiContoursWrapper(cst,ct);

    assignin('base','ct',ct);
    assignin('base','cst',cst);
    handles.State = 1;
catch ME
    handles = showError(handles,'LoadMatFileFnc: Could not load *.mat file',ME);
end

% check if a optimized plan was loaded
if exist('stf','var')
    assignin('base','stf',stf);
end
if exist('pln','var')
    assignin('base','pln',pln);
end
if exist('dij','var')
    assignin('base','dij',dij);
end
% if exist('stf','var') && exist('dij','var')
%     handles.State = 2;
% end

if exist('resultGUI','var')
    assignin('base','resultGUI',resultGUI);
    % handles.State = 3;
    % handles.SelectedDisplayOption ='physicalDose';
end

% recheck current workspace variables
AllVarNames = evalin('base','who');
handles.AllVarNames = AllVarNames;

if ismember('ct',AllVarNames) &&  ismember('cst',AllVarNames)
    handles = reloadGUI(hObject, handles, ct, cst);
else
    handles = reloadGUI(hObject, handles);
end

guidata(hObject,handles);

% --- Executes on button press in btnLoadDicom.
function btnLoadDicom_Callback(hObject, ~, handles)
% hObject    handle to btnLoadDicom (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
try
    % delete existing workspace - parse variables from base workspace
    set(handles.popupDisplayOption,'String','no option available');
    AllVarNames = evalin('base','who');
    RefVarNames = {'ct','cst','pln','stf','dij','resultGUI'};
    for i = 1:length(RefVarNames)
        if sum(ismember(AllVarNames,RefVarNames{i}))>0
            evalin('base',['clear ', RefVarNames{i}]);
        end
    end
    handles.State = 0;
    matRad_importDicomGUI;

catch
   handles = showError(handles,'DicomImport: Could not import data');
end
UpdateState(handles);
guidata(hObject,handles);

% --- Executes on button press in btn_export.
function btn_export_Callback(hObject, eventdata, handles)
% hObject    handle to btn_export (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

try
    matRad_exportGUI;
catch
    handles = showError(handles,'Could not export data');
end
UpdateState(handles);
guidata(hObject,handles);

function editBixelWidth_Callback(hObject, ~, handles)
% hObject    handle to editBixelWidth (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of editBixelWidth as text
%        str2double(get(hObject,'String')) returns contents of editBixelWidth as a double
getPlnFromGUI(handles);
if handles.State > 0
    handles.State = 1;
    UpdateState(handles);
    guidata(hObject,handles);
end

function editGantryAngle_Callback(hObject, ~, handles)
% hObject    handle to editGantryAngle (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of editGantryAngle as text
%        str2double(get(hObject,'String')) returns contents of editGantryAngle as a double
getPlnFromGUI(handles);
if handles.State > 0
    handles.State = 1;
    UpdateState(handles);
    UpdatePlot(handles);
    guidata(hObject,handles);
end

function editCouchAngle_Callback(hObject, ~, handles)
% hObject    handle to editCouchAngle (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of editCouchAngle as text
%        str2double(get(hObject,'String')) returns contents of editCouchAngle as a double
getPlnFromGUI(handles);
if handles.State > 0
    handles.State = 1;
    UpdateState(handles);
    guidata(hObject,handles);
end

% --- Executes on selection change in popupRadMode.
function popupRadMode_Callback(hObject, eventdata, handles)
% hObject    handle to popupRadMode (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
checkRadiationComposition(handles);
contents      = cellstr(get(hObject,'String'));
RadIdentifier = contents{get(hObject,'Value')};
contentPopUp  = get(handles.popMenuBioOpt,'String');
switch RadIdentifier
    case 'photons'

        set(handles.popMenuBioOpt,'Enable','off');
        ix = find(strcmp(contentPopUp,'none'));
        set(handles.popMenuBioOpt,'Value',ix);
        set(handles.btnSetTissue,'Enable','off');

        set(handles.btnRunSequencing,'Enable','on');
        set(handles.btnRunDAO,'Enable','on');
        set(handles.radiobutton3Dconf,'Enable','on');
        set(handles.txtSequencing,'Enable','on');
        set(handles.editSequencingLevel,'Enable','on');

    case 'protons'

        set(handles.popMenuBioOpt,'Enable','on');
        ix = find(strcmp(contentPopUp,'const_RBExD'));
        set(handles.popMenuBioOpt,'Value',ix);
        set(handles.btnSetTissue,'Enable','on');

        set(handles.btnSetTissue,'Enable','off');
        set(handles.btnRunSequencing,'Enable','off');
        set(handles.btnRunDAO,'Enable','off');
        set(handles.radiobutton3Dconf,'Enable','off');
        set(handles.txtSequencing,'Enable','off');
        set(handles.editSequencingLevel,'Enable','off');

    case 'carbon'

        set(handles.popMenuBioOpt,'Enable','on');
        ix = find(strcmp(contentPopUp,'LEMIV_RBExD'));
        set(handles.popMenuBioOpt,'Value',ix);
        set(handles.btnSetTissue,'Enable','on');

        set(handles.btnRunSequencing,'Enable','off');
        set(handles.btnRunDAO,'Enable','off');
        set(handles.radiobutton3Dconf,'Enable','off');
        set(handles.txtSequencing,'Enable','off');
        set(handles.editSequencingLevel,'Enable','off');
end

if handles.State > 0
    pln = evalin('base','pln');
    if handles.State > 0 && ~strcmp(contents(get(hObject,'Value')),pln.radiationMode)

        % new radiation modality is photons -> just keep physicalDose
        if strcmp(contents(get(hObject,'Value')),'photons')
            try
            AllVarNames = evalin('base','who');
               if  ismember('resultGUI',AllVarNames)
                   resultGUI = evalin('base','resultGUI');
                   if isfield(resultGUI,'alpha');    resultGUI = rmfield(resultGUI,'alpha');   end
                   if isfield(resultGUI,'beta');     resultGUI = rmfield(resultGUI,'beta');    end
                   if isfield(resultGUI,'RBExDose'); resultGUI = rmfield(resultGUI,'RBExDose');end
                   if isfield(resultGUI,'RBE');      resultGUI = rmfield(resultGUI,'RBE');     end
                   assignin('base','resultGUI',resultGUI);
                   handles = updateIsoDoseLineCache(handles);
               end
            catch
            end
        elseif strcmp(contents(get(hObject,'Value')),'protons')
            try
            AllVarNames = evalin('base','who');
               if  ismember('resultGUI',AllVarNames)
                   resultGUI = evalin('base','resultGUI');
                   if isfield(resultGUI,'alpha'); resultGUI = rmfield(resultGUI,'alpha');end
                   if isfield(resultGUI,'beta');  resultGUI = rmfield(resultGUI,'beta'); end
                   if isfield(resultGUI,'RBE');   resultGUI = rmfield(resultGUI,'RBE');  end
                   assignin('base','resultGUI',resultGUI);
                   handles = updateIsoDoseLineCache(handles);
               end
            catch
            end
        end

        guidata(hObject,handles);
        UpdatePlot(handles);

        getPlnFromGUI(handles);
        handles.State = 1;
        UpdateState(handles);

    end

guidata(hObject,handles);

end

% --- Executes on button press in btnCalcDose.
function btnCalcDose_Callback(hObject, ~, handles)
% hObject    handle to btnCalcDose (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% http://stackoverflow.com/questions/24703962/trigger-celleditcallback-before-button-callback
% http://www.mathworks.com/matlabcentral/newsreader/view_thread/332613
% wait some time until the CallEditCallback is finished
% Callback triggers the cst saving mechanism from GUI
try
    % indicate that matRad is busy
    % change mouse pointer to hour glass
    Figures = gcf;%findobj('type','figure');
    set(Figures, 'pointer', 'watch');
    drawnow;
    % disable all active objects
    InterfaceObj = findobj(Figures,'Enable','on');
    set(InterfaceObj,'Enable','off');

    % read plan from gui and save it to workspace
    % gets also IsoCenter from GUI if checkbox is not checked
    getPlnFromGUI(handles);

    % get default iso center as center of gravity of all targets if not
    % already defined
    pln = evalin('base','pln');

    if length(pln.propStf.gantryAngles) ~= length(pln.propStf.couchAngles)
        handles = showWarning(handles,'number of gantryAngles != number of couchAngles');
    end
    %%
    if ~checkRadiationComposition(handles)
        fileName = [pln.radiationMode '_' pln.machine];
        handles = showError(handles,errordlg(['Could not find the following machine file: ' fileName ]));
        guidata(hObject,handles);
        return;
    end

    %% check if isocenter is already set
    if ~isfield(pln.propStf,'isoCenter')
        handles = showWarning(handles,'no iso center set - using center of gravity based on structures defined as TARGET');
        pln.propStf.isoCenter = ones(pln.propStf.numOfBeams,1) * matRad_getIsoCenter(evalin('base','cst'),evalin('base','ct'));
        assignin('base','pln',pln);
    elseif ~get(handles.checkIsoCenter,'Value')
        if ~strcmp(get(handles.editIsoCenter,'String'),'multiple isoCenter')
            pln.propStf.isoCenter = ones(pln.propStf.numOfBeams,1)*str2num(get(handles.editIsoCenter,'String'));
        end
    end

catch ME
    handles = showError(handles,'CalcDoseCallback: Error in preprocessing!',ME);
    % change state from busy to normal
    set(Figures, 'pointer', 'arrow');
    set(InterfaceObj,'Enable','on');
    guidata(hObject,handles);
    return;
end

% generate steering file
try
    currPln = evalin('base','pln');
    % if we run 3d conf opt -> hijack runDao to trigger computation of
    % connected bixels
    if strcmp(pln.radiationMode,'photons') && get(handles.radiobutton3Dconf,'Value')
       currpln.propOpt.runDAO = true;
    end
    stf = matRad_generateStf(evalin('base','ct'),...
                                     evalin('base','cst'),...
                                     currPln);
    assignin('base','stf',stf);
catch ME
    handles = showError(handles,'CalcDoseCallback: Error in steering file generation!',ME);
    % change state from busy to normal
    set(Figures, 'pointer', 'arrow');
    set(InterfaceObj,'Enable','on');
    guidata(hObject,handles);
    return;
end

% carry out dose calculation
try
    if strcmp(pln.radiationMode,'photons')
        dij = matRad_calcPhotonDose(evalin('base','ct'),stf,pln,evalin('base','cst'));
    elseif strcmp(pln.radiationMode,'protons') || strcmp(pln.radiationMode,'carbon')
        dij = matRad_calcParticleDose(evalin('base','ct'),stf,pln,evalin('base','cst'));
    end

    % assign results to base worksapce
    assignin('base','dij',dij);
    handles.State = 2;
    handles.TableChanged = false;
    UpdateState(handles);
    UpdatePlot(handles);
    guidata(hObject,handles);
catch ME
    handles = showError(handles,'CalcDoseCallback: Error in dose calculation!',ME);
    % change state from busy to normal
    set(Figures, 'pointer', 'arrow');
    set(InterfaceObj,'Enable','on');
    guidata(hObject,handles);
    return;
end

% change state from busy to normal
set(Figures, 'pointer', 'arrow');
set(InterfaceObj,'Enable','on');

guidata(hObject,handles);

%% plots ct and distributions
function UpdatePlot(handles)

%profile on;

axes(handles.axesFig);

% this is necessary to prevent multiple callbacks of update plot drawing on
% top of each other in matlab <2014
drawnow;

defaultFontSize = 8;
currAxes            = axis(handles.axesFig);
AxesHandlesCT_Dose  = gobjects(0);
AxesHandlesVOI      = cell(0);
AxesHandlesIsoDose  = gobjects(0);

if handles.State == 0
    cla reset
    return
elseif handles.State > 0
     ct  = evalin('base','ct');
     cst = evalin('base','cst');
     pln = evalin('base','pln');
end

%% state 3 indicates that a optimization has been performed
 AllVarNames = evalin('base','who');
if  ismember('resultGUI',AllVarNames)
    Result = evalin('base','resultGUI');
end

if exist('Result','var')
    if ~isempty(Result) && ~isempty(ct.cubeHU) && ~isfield(handles,'DispInfo')

        DispInfo = fieldnames(Result);

        for i = 1:size(DispInfo,1)

            % delete weight vectors in Result struct for plotting
            if isstruct(Result.(DispInfo{i,1})) || isvector(Result.(DispInfo{i,1}))
                 Result = rmfield(Result,DispInfo{i,1});
                 DispInfo{i,2}=false;
            else
                %second dimension indicates if it should be plotted
                DispInfo{i,2} = true;
                % determine units
                if strfind(DispInfo{i,1},'physicalDose')
                    DispInfo{i,3} = '[Gy]';
                elseif strfind(DispInfo{i,1},'alpha')
                    DispInfo{i,3} = '[Gy^{-1}]';
                elseif strfind(DispInfo{i,1},'beta')
                    DispInfo{i,3} = '[Gy^{-2}]';
                elseif strfind(DispInfo{i,1},'RBExD')
                    DispInfo{i,3} = '[Gy(RBE)]';
                elseif strfind(DispInfo{i,1},'LET')
                    DispInfo{i,3} = '[keV/um]';
                else
                    DispInfo{i,3} = '[a.u.]';
                end
                DispInfo{i,4} = [];    % optional for the future: color range for plotting
                DispInfo{i,5} = [];    % optional for the future: min max values
            end
        end

        set(handles.popupDisplayOption,'String',fieldnames(Result));
        if sum(strcmp(handles.SelectedDisplayOption,fieldnames(Result))) == 0
            handles.SelectedDisplayOption = DispInfo{find([DispInfo{:,2}],1,'first'),1};
        end
        set(handles.popupDisplayOption,'Value',find(strcmp(handles.SelectedDisplayOption,fieldnames(Result))));

    end
end

%% set and get required variables
plane = get(handles.popupPlane,'Value');
slice = round(get(handles.sliderSlice,'Value'));
hold(handles.axesFig,'on');
if get(handles.popupTypeOfPlot,'Value')==1
    set(handles.axesFig,'YDir','Reverse');
end

%% Remove colorbar?
plotColorbarSelection = get(handles.popupmenu_chooseColorData,'Value');

if get(handles.popupTypeOfPlot,'Value')==2 || plotColorbarSelection == 1
    if isfield(handles,'cBarHandel')
        delete(handles.cBarHandel);
    end
    %The following seems to be necessary as MATLAB messes up some stuff
    %with the handle storage
    ch = findall(gcf,'tag','Colorbar');
    if ~isempty(ch)
        delete(ch);
    end
end

selectIx = get(handles.popupmenu_chooseColorData,'Value');

cla(handles.axesFig);
%% plot ct - if a ct cube is available and type of plot is set to 1 and not 2; 1 indicate cube plotting and 2 profile plotting
if ~isempty(ct) && get(handles.popupTypeOfPlot,'Value')==1

    if selectIx == 3
        ctIx = 2;
    else
        ctIx = selectIx;
    end

    if handles.cubeHUavailable
        plotCtCube = ct.cubeHU;
        ctLabel = 'Hounsfield Units';
    else
        plotCtCube = ct.cube;
        ctLabel = 'Electron Density / WEQ';
    end

    ctMap = matRad_getColormap(handles.ctColorMap,handles.cMapSize);

    if isempty(handles.dispWindow{ctIx,2})
        handles.dispWindow{ctIx,2} = [min(reshape([ct.cubeHU{:}],[],1)) max(reshape([ct.cubeHU{:}],[],1))];
    end

    if get(handles.radiobtnCT,'Value')
        [AxesHandlesCT_Dose(end+1),~,handles.dispWindow{ctIx,1}] = matRad_plotCtSlice(handles.axesFig,plotCtCube,1,plane,slice,ctMap,handles.dispWindow{ctIx,1});

        % plot colorbar? If 1 the user asked for the CT
        if plotColorbarSelection == 2 && handles.cBarChanged
            %Plot the colorbar
            handles.cBarHandel = matRad_plotColorbar(handles.axesFig,ctMap,handles.dispWindow{ctIx,1},'fontsize',defaultFontSize);
            %adjust lables
            set(get(handles.cBarHandel,'ylabel'),'String', ctLabel,'fontsize',defaultFontSize);
            % do not interprete as tex syntax
            set(get(handles.cBarHandel,'ylabel'),'interpreter','none');
        end
    end
end

%% plot dose cube
if handles.State >= 1 &&  get(handles.popupTypeOfPlot,'Value')== 1  && exist('Result','var')
        doseMap = matRad_getColormap(handles.doseColorMap,handles.cMapSize);
        doseIx  = 3;
        % if the selected display option doesn't exist then simply display
        % the first cube of the Result struct
        if ~isfield(Result,handles.SelectedDisplayOption)
            CubeNames = fieldnames(Result);
            handles.SelectedDisplayOption = CubeNames{1,1};
        end

        dose = Result.(handles.SelectedDisplayOption);

        % dose colorwash
        if ~isempty(dose) && ~isvector(dose)

            if isempty(handles.dispWindow{doseIx,2})
                handles.dispWindow{doseIx,2} = [min(dose(:)) max(dose(:))];   % set min and max dose values
            end

            if get(handles.radiobtnDose,'Value')
                [doseHandle,~,handles.dispWindow{doseIx,1}] = matRad_plotDoseSlice(handles.axesFig,dose,plane,slice,handles.CutOffLevel,handles.doseOpacity,doseMap,handles.dispWindow{doseIx,1});
                AxesHandlesCT_Dose(end+1)         = doseHandle;
            end

            % plot colorbar?
            if plotColorbarSelection > 2 && handles.cBarChanged
                %Plot the colorbar
                handles.cBarHandel = matRad_plotColorbar(handles.axesFig,doseMap,handles.dispWindow{selectIx,1},'fontsize',defaultFontSize);
                %adjust lables
                Idx = find(strcmp(handles.SelectedDisplayOption,DispInfo(:,1)));
                set(get(handles.cBarHandel,'ylabel'),'String', [DispInfo{Idx,1} ' ' DispInfo{Idx,3} ],'fontsize',defaultFontSize);
                % do not interprete as tex syntax
                set(get(handles.cBarHandel,'ylabel'),'interpreter','none');
            end
        end

        %% plot iso dose lines
        if get(handles.radiobtnIsoDoseLines,'Value')
            plotLabels = get(handles.radiobtnIsoDoseLinesLabels,'Value') == 1;

            %Sanity Check for Contours, which actually should have been
            %computed before calling UpdatePlot
            if ~isfield(handles.IsoDose,'Contours')
                try
                    handles.IsoDose.Contours = matRad_computeIsoDoseContours(dose,handles.IsoDose.Levels);
                catch
                    %If the computation didn't work, we set the field to
                    %empty, which will force matRad_plotIsoDoseLines to use
                    %matlabs contour function instead of repeating the
                    %failing computation every time
                    handles.IsoDose.Contours = [];
                    warning('Could not compute isodose lines! Will try slower contour function!');
                end
            end
            AxesHandlesIsoDose = matRad_plotIsoDoseLines(handles.axesFig,dose,handles.IsoDose.Contours,handles.IsoDose.Levels,plotLabels,plane,slice,doseMap,handles.dispWindow{doseIx,1},'LineWidth',1.5);
        end
end

selectIx = get(handles.popupmenu_chooseColorData,'Value');
set(handles.txtMinVal,'String',num2str(handles.dispWindow{selectIx,2}(1,1)));
set(handles.txtMaxVal,'String',num2str(handles.dispWindow{selectIx,2}(1,2)));

%% plot VOIs
if get(handles.radiobtnContour,'Value') && get(handles.popupTypeOfPlot,'Value')==1 && handles.State>0
    AxesHandlesVOI = [AxesHandlesVOI matRad_plotVoiContourSlice(handles.axesFig,cst,ct,1,handles.VOIPlotFlag,plane,slice,[],'LineWidth',2)];
end

%% Set axis labels and plot iso center
matRad_plotAxisLabels(handles.axesFig,ct,plane,slice,defaultFontSize);

if get(handles.radioBtnIsoCenter,'Value') == 1 && get(handles.popupTypeOfPlot,'Value') == 1 && ~isempty(pln)
    hIsoCenterCross = matRad_plotIsoCenterMarker(handles.axesFig,pln,ct,plane,slice);
end

if get(handles.radiobtnPlan,'value') == 1 && ~isempty(pln)
    matRad_plotProjectedGantryAngles(handles.axesFig,pln,ct,plane);
end

% the following line ensures the plotting order (optional)
% set(gca,'Children',[AxesHandlesCT_Dose hIsoCenterCross AxesHandlesIsoDose  AxesHandlesVOI ]);

%set axis ratio
ratios = [1/ct.resolution.x 1/ct.resolution.y 1/ct.resolution.z];
set(handles.axesFig,'DataAspectRatioMode','manual');
if plane == 1
      res = [ratios(3) ratios(1)]./max([ratios(3) ratios(1)]);
      set(handles.axesFig,'DataAspectRatio',[res 1])
elseif plane == 2 % sagittal plane
      res = [ratios(3) ratios(2)]./max([ratios(3) ratios(2)]);
      set(handles.axesFig,'DataAspectRatio',[res 1])
elseif  plane == 3 % Axial plane
      res = [ratios(1) ratios(2)]./max([ratios(1) ratios(2)]);
      set(handles.axesFig,'DataAspectRatio',[res 1])
end

%% profile plot
if get(handles.popupTypeOfPlot,'Value') == 2 && exist('Result','var')
    % set SAD
    fileName = [pln.radiationMode '_' pln.machine];
    try
        load(['basedata' filesep fileName]);
        SAD = machine.meta.SAD;
    catch
        error(['Could not find the following machine file: ' fileName ]);
    end

    % clear view and initialize some values
    cla(handles.axesFig,'reset')
    set(gca,'YDir','normal');
    ylabel('{\color{black}dose [Gy]}')
    cColor={'black','green','magenta','cyan','yellow','red','blue'};

    % Rotate the system into the beam.
    % passive rotation & row vector multiplication & inverted rotation requires triple matrix transpose
    rotMat_system_T = transpose(matRad_getRotationMatrix(pln.propStf.gantryAngles(handles.selectedBeam),pln.propStf.couchAngles(handles.selectedBeam)));

    if strcmp(handles.ProfileType,'longitudinal')
        sourcePointBEV = [handles.profileOffset -SAD   0];
        targetPointBEV = [handles.profileOffset  SAD   0];
    elseif strcmp(handles.ProfileType,'lateral')
        sourcePointBEV = [-SAD handles.profileOffset   0];
        targetPointBEV = [ SAD handles.profileOffset   0];
    end

    rotSourcePointBEV = sourcePointBEV * rotMat_system_T;
    rotTargetPointBEV = targetPointBEV * rotMat_system_T;

    % perform raytracing on the central axis of the selected beam, use unit
    % electron density for plotting against the geometrical depth
    [~,l,rho,~,ix] = matRad_siddonRayTracer(pln.propStf.isoCenter(handles.selectedBeam,:),ct.resolution,rotSourcePointBEV,rotTargetPointBEV,{0*ct.cubeHU{1}+1});
    d = [0 l .* rho{1}];
    % Calculate accumulated d sum.
    vX = cumsum(d(1:end-1));

    % this step is necessary if visualization is set to profile plot
    % and another optimization is carried out - set focus on GUI
    figHandles = get(0,'Children');
    idxHandle = [];
    if ~isempty(figHandles)
        v=version;
        if str2double(v(1:3))>= 8.5
            idxHandle = strcmp({figHandles(:).Name},'matRadGUI');
        else
            idxHandle = strcmp(get(figHandles,'Name'),'matRadGUI');
        end
    end
    figure(figHandles(idxHandle));

    % plot physical dose
    Content = get(handles.popupDisplayOption,'String');
    SelectedCube = Content{get(handles.popupDisplayOption,'Value')};
    if sum(strcmp(SelectedCube,{'physicalDose','effect','RBExDose','alpha','beta','RBE'})) > 0
         Suffix = '';
    else
        Idx    = find(SelectedCube == '_');
        Suffix = SelectedCube(Idx:end);
    end

    mPhysDose = Result.(['physicalDose' Suffix]);
    PlotHandles{1} = plot(handles.axesFig,vX,mPhysDose(ix),'color',cColor{1,1},'LineWidth',3); hold on;
    PlotHandles{1,2} ='physicalDose';
    ylabel(handles.axesFig,'dose in [Gy]');
    set(handles.axesFig,'FontSize',defaultFontSize);

    % plot counter
    Cnt=2;

    if isfield(Result,['RBE' Suffix])

        %disbale specific plots
        %DispInfo{6,2}=0;
        %DispInfo{5,2}=0;
        %DispInfo{2,2}=0;

        % generate two lines for ylabel
        StringYLabel1 = '\fontsize{8}{\color{red}RBE x dose [Gy(RBE)] \color{black}dose [Gy] ';
        StringYLabel2 = '';
        for i=1:1:size(DispInfo,1)
            if DispInfo{i,2} && sum(strcmp(DispInfo{i,1},{['effect' Suffix],['alpha' Suffix],['beta' Suffix]})) > 0
                %physicalDose is already plotted and RBExD vs RBE is plotted later with plotyy
                if ~strcmp(DispInfo{i,1},['RBExDose' Suffix]) &&...
                   ~strcmp(DispInfo{i,1},['RBE' Suffix]) && ...
                   ~strcmp(DispInfo{i,1},['physicalDose' Suffix])

                        mCube = Result.([DispInfo{i,1}]);
                        PlotHandles{Cnt,1} = plot(handles.axesFig,vX,mCube(ix),'color',cColor{1,Cnt},'LineWidth',3);hold on;
                        PlotHandles{Cnt,2} = DispInfo{i,1};
                        StringYLabel2 = [StringYLabel2  ' \color{'  cColor{1,Cnt} '}' DispInfo{i,1} ' ['  DispInfo{i,3} ']'];
                        Cnt = Cnt+1;
                end
            end
        end
        StringYLabel2 = [StringYLabel2 '}'];
        % always plot RBExD against RBE
        mRBExDose = Result.(['RBExDose' Suffix]);
        vBED = mRBExDose(ix);
        mRBE = Result.(['RBE' Suffix]);
        vRBE = mRBE(ix);

        % plot biological dose against RBE
        [ax, PlotHandles{Cnt,1}, PlotHandles{Cnt+1,1}]=plotyy(handles.axesFig,vX,vBED,vX,vRBE,'plot');hold on;
        PlotHandles{Cnt,2}='RBExDose';
        PlotHandles{Cnt+1,2}='RBE';

        % set plotyy properties
        set(get(ax(2),'Ylabel'),'String','RBE [a.u.]','FontSize',8);
        ylabel({StringYLabel1;StringYLabel2})
        set(PlotHandles{Cnt,1},'Linewidth',4,'color','r');
        set(PlotHandles{Cnt+1,1},'Linewidth',3,'color','b');
        set(ax(1),'ycolor','r')
        set(ax(2),'ycolor','b')
        set(ax,'FontSize',8);
        Cnt=Cnt+2;
    end

    % asses target coordinates
    tmpPrior = intmax;
    tmpSize = 0;
    for i=1:size(cst,1)
        if strcmp(cst{i,3},'TARGET') && tmpPrior >= cst{i,5}.Priority && tmpSize<numel(cst{i,4}{1})
           linIdxTarget = unique(cst{i,4}{1});
           tmpPrior=cst{i,5}.Priority;
           tmpSize=numel(cst{i,4}{1});
           VOI = cst{i,2};
        end
    end

    str = sprintf('profile plot - central axis of %d beam gantry angle %d? couch angle %d?',...
        handles.selectedBeam ,pln.propStf.gantryAngles(handles.selectedBeam),pln.propStf.couchAngles(handles.selectedBeam));
    h_title = title(handles.axesFig,str,'FontSize',defaultFontSize);
    pos = get(h_title,'Position');
    set(h_title,'Position',[pos(1)-40 pos(2) pos(3)])

    % plot target boundaries
    mTargetCube = zeros(ct.cubeDim);
    mTargetCube(linIdxTarget) = 1;
    vProfile = mTargetCube(ix);
    WEPL_Target_Entry = vX(find(vProfile,1,'first'));
    WEPL_Target_Exit  = vX(find(vProfile,1,'last'));
    PlotHandles{Cnt,2} =[VOI ' boundary'];

    if ~isempty(WEPL_Target_Entry) && ~isempty(WEPL_Target_Exit)
        hold on
        PlotHandles{Cnt,1} = ...
        plot([WEPL_Target_Entry WEPL_Target_Entry],get(handles.axesFig,'YLim'),'--','Linewidth',3,'color','k');hold on
        plot([WEPL_Target_Exit WEPL_Target_Exit],get(handles.axesFig,'YLim'),'--','Linewidth',3,'color','k');hold on

    else
        PlotHandles{Cnt,1} =[];
    end

   Lines  = PlotHandles(~cellfun(@isempty,PlotHandles(:,1)),1);
   Labels = PlotHandles(~cellfun(@isempty,PlotHandles(:,1)),2);
   h=legend(handles.axesFig,[Lines{:}],Labels{:});
   set(h,'FontSize',defaultFontSize);
   xlabel('radiological depth [mm]','FontSize',8);
   grid on, grid minor

end

zoom(handles.figure1,'reset');
axis(handles.axesFig,'tight');

if isfield(handles,'rememberCurrAxes') && handles.rememberCurrAxes
    axis(currAxes);
end

hold(handles.axesFig,'off');

handles.cBarChanged = false;
guidata(handles.axesFig,handles);
%guidata(gcf,handles);
if get(handles.popupTypeOfPlot,'Value')==1
    UpdateColormapOptions(handles);
end

Update3DView(handles);

%profile off;
%profile viewer;

function Update3DView(handles)

if isfield(handles,'axesFig3D') && isfield(handles,'fig3D') && isgraphics(handles.axesFig3D) && isgraphics(handles.fig3D)
    axesFig3D = handles.axesFig3D;
    fig3D = handles.fig3D;
else
    return
end

if handles.State == 0
    return
elseif handles.State > 0
    AllVarNames = evalin('base','who');
    if  ismember('resultGUI',AllVarNames)
        Result = evalin('base','resultGUI');
    end

    ct  = evalin('base','ct');
    cst = evalin('base','cst');
    pln = evalin('base','pln');

    if  ismember('stf',AllVarNames)
        stf = evalin('base','stf');

        %validate stf with current pln settings
        validStf = true;
        gantryAngles = [stf.gantryAngle];
        validStf = isequal(gantryAngles,pln.propStf.gantryAngles) & validStf;
        couchAngles = [stf.couchAngle];
        validStf = isequal(couchAngles,pln.propStf.couchAngles) & validStf;
        isoCenter = vertcat(stf.isoCenter);
        validStf = isequal(isoCenter,pln.propStf.isoCenter) & validStf;

        if ~validStf
            matRad_cfg = MatRad_Config.instance();
            matRad_cfg.dispWarning('stf and pln are not consistent, using pln for geometry display!');
            stf = [];
        end

    else
        stf = [];
    end

end

oldView = get(axesFig3D,'View');

cla(axesFig3D);
%delete(allchild(axesFig3D));

%test = allchild(axesFig3D);

plane = get(handles.popupPlane,'Value');
slice = round(get(handles.sliderSlice,'Value'));
defaultFontSize = 8;

%Check if we need to precompute the surface data
if size(cst,2) < 8
    cst = matRad_computeAllVoiSurfaces(ct,cst);
    assignin('base','cst',cst);
end

set(fig3D,'Color',0.5*[1 1 1]);
set(axesFig3D,'Color',1*[0 0 0]);

%% Plot 3D structures
hold(axesFig3D,'on');
if get(handles.radiobtnContour,'Value') && handles.State>0
    voiPatches = matRad_plotVois3D(axesFig3D,ct,cst,handles.VOIPlotFlag,colorcube);
end

%% plot the CT slice
if get(handles.radiobtnCT,'Value')
    window = handles.dispWindow{2,1}; %(2 for ct)
    ctMap = matRad_getColormap(handles.ctColorMap,handles.cMapSize);
    ctHandle = matRad_plotCtSlice3D(axesFig3D,ct,1,plane,slice,ctMap,window);
end

%% plot the dose slice
if handles.State >= 1 && exist('Result','var')
    doseMap = matRad_getColormap(handles.doseColorMap,handles.cMapSize);
    doseIx  = 3;
    % if the selected display option doesn't exist then simply display
    % the first cube of the Result struct
    if ~isfield(Result,handles.SelectedDisplayOption)
        CubeNames = fieldnames(Result);
        handles.SelectedDisplayOption = CubeNames{1,1};
    end

    dose = Result.(handles.SelectedDisplayOption);

    % dose colorwash
    if ~isempty(dose) && ~isvector(dose)

        if isempty(handles.dispWindow{doseIx,2})
            handles.dispWindow{doseIx,2} = [min(dose(:)) max(dose(:))];   % set min and max dose values
        end

        if get(handles.radiobtnDose,'Value')
            [doseHandle,~,handles.dispWindow{doseIx,1}] = matRad_plotDoseSlice3D(axesFig3D,ct,dose,plane,slice,handles.CutOffLevel,handles.doseOpacity,doseMap,handles.dispWindow{doseIx,1});
        end
        if get(handles.radiobtnIsoDoseLines,'Value')
            matRad_plotIsoDoseLines3D(axesFig3D,ct,dose,handles.IsoDose.Contours,handles.IsoDose.Levels,plane,slice,doseMap,handles.dispWindow{doseIx,1},'LineWidth',1.5);
        end
    end
end

if get(handles.radiobtnPlan,'Value')
    matRad_plotPlan3D(axesFig3D,pln,stf);
end

%hLight = light('Parent',axesFig3D);
%camlight(hLight,'left');
%lighting('gouraud');

xlabel(axesFig3D,'x [voxels]','FontSize',defaultFontSize)
ylabel(axesFig3D,'y [voxels]','FontSize',defaultFontSize)
zlabel(axesFig3D,'z [voxels]','FontSize',defaultFontSize)
title(axesFig3D,'matRad 3D view');

% set axis ratio
ratios = [1 1 1]; %[1/ct.resolution.x 1/ct.resolution.y 1/ct.resolution.z];
ratios = ratios([2 1 3]);
set(axesFig3D,'DataAspectRatioMode','manual');
set(axesFig3D,'DataAspectRatio',ratios./max(ratios));

set(axesFig3D,'Ydir','reverse');

set(axesFig3D,'view',oldView);

% --- Executes on selection change in popupPlane.
function popupPlane_Callback(hObject, ~, handles)
% hObject    handle to popupPlane (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: contents = cellstr(get(hObject,'String')) returns popupPlane contents as cell array
%        contents{get(hObject,'Value')} returns selected item from popupPlane

% set slice slider
handles.plane = get(hObject,'value');
initViewSliceSlider(handles);

handles.rememberCurrAxes = false;
UpdatePlot(handles);
handles.rememberCurrAxes = true;
guidata(hObject,handles);

% --- Executes on slider movement.
function sliderSlice_Callback(~, ~, handles)
% hObject    handle to sliderSlice (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'Value') returns position of slider
%        get(hObject,'Min') and get(hObject,'Max') to determine range of slider
UpdatePlot(handles)

% --- Executes on button press in radiobtnContour.
function radiobtnContour_Callback(~, ~, handles)
% hObject    handle to radiobtnContour (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of radiobtnContour
UpdatePlot(handles)

% --- Executes on button press in radiobtnDose.
function radiobtnDose_Callback(~, ~, handles)
% hObject    handle to radiobtnDose (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of radiobtnDose
UpdatePlot(handles)

% --- Executes on button press in radiobtnIsoDoseLines.
function radiobtnIsoDoseLines_Callback(~, ~, handles)
% hObject    handle to radiobtnIsoDoseLines (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of radiobtnIsoDoseLines
UpdatePlot(handles)

% --- Executes on button press in btnOptimize.
function btnOptimize_Callback(hObject, eventdata, handles)
% hObject    handle to btnOptimize (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

try
    % indicate that matRad is busy
    % change mouse pointer to hour glass
    Figures = gcf;%findobj('type','figure');
    set(Figures, 'pointer', 'watch');
    drawnow;
    % disable all active objects
    InterfaceObj = findobj(Figures,'Enable','on');
    set(InterfaceObj,'Enable','off');
    % wait until the table is updated
    btnTableSave_Callback([],[],handles); %We don't need it?

    % if a critical change to the cst has been made which affects the dij matrix
    if handles.DijCalcWarning == true

        choice = questdlg('Overlap priorites of OAR constraints have been edited, a new OAR VOI was added or a critical row constraint was deleted. A new Dij calculation might be necessary.', ...
        'Title','Cancel','Calculate Dij then Optimize','Optimze directly','Optimze directly');

        switch choice
            case 'Cancel'
                set(Figures, 'pointer', 'arrow');
                set(InterfaceObj,'Enable','on');
                guidata(hObject,handles);
                return;
            case 'Calculate dij again and optimize'
                handles.DijCalcWarning = false;
                btnCalcDose_Callback(hObject, eventdata, handles)
            case 'Optimze directly'
                handles.DijCalcWarning = false;
        end
    end

    pln = evalin('base','pln');
    ct  = evalin('base','ct');

    % optimize
    if get(handles.radiobutton3Dconf,'Value') && strcmp(handles.Modalities{get(handles.popupRadMode,'Value')},'photons')
        % conformal plan if photons and 3d conformal
        if ~matRad_checkForConnectedBixelRows(evalin('base','stf'))
            error('disconnetced dose influence data in BEV - run dose calculation again with consistent settings');
        end
        [resultGUIcurrentRun,usedOptimizer] = matRad_fluenceOptimization(matRad_collapseDij(evalin('base','dij')),evalin('base','cst'),pln);
        resultGUIcurrentRun.w = resultGUIcurrentRun.w * ones(evalin('base','dij.totalNumOfBixels'),1);
        resultGUIcurrentRun.wUnsequenced = resultGUIcurrentRun.w;
    else
        if pln.propOpt.runDAO
        if ~matRad_checkForConnectedBixelRows(evalin('base','stf'))
            error('disconnetced dose influence data in BEV - run dose calculation again with consistent settings');
        end
        end

        [resultGUIcurrentRun,usedOptimizer] = matRad_fluenceOptimization(evalin('base','dij'),evalin('base','cst'),pln);
    end

    %if resultGUI already exists then overwrite the "standard" fields
    AllVarNames = evalin('base','who');
    if  ismember('resultGUI',AllVarNames)
        resultGUI = evalin('base','resultGUI');
        sNames = fieldnames(resultGUIcurrentRun);
        oldNames = fieldnames(resultGUI);
        if(length(oldNames) > length(sNames))
            for j = 1:length(oldNames)
            if strfind(oldNames{j}, 'beam')
                resultGUI = rmfield(resultGUI, oldNames{j});
            end
            end
        end
        for j = 1:length(sNames)
            resultGUI.(sNames{j}) = resultGUIcurrentRun.(sNames{j});
        end
    else
        resultGUI = resultGUIcurrentRun;
    end
    assignin('base','resultGUI',resultGUI);

    % set some values
    if handles.plane == 1
        set(handles.sliderSlice,'Value',ceil(pln.propStf.isoCenter(1,2)/ct.resolution.x));
    elseif handles.plane == 2
        set(handles.sliderSlice,'Value',ceil(pln.propStf.isoCenter(1,1)/ct.resolution.y));
    elseif handles.plane == 3
        set(handles.sliderSlice,'Value',ceil(pln.propStf.isoCenter(1,3)/ct.resolution.z));
    end

    handles.State = 3;
    handles.SelectedDisplayOptionIdx = 1;
    if strcmp(pln.radiationMode,'carbon') || (strcmp(pln.radiationMode,'protons') && strcmp(pln.propOpt.bioOptimization,'const_RBExD'))
        handles.SelectedDisplayOption = 'RBExDose';
    else
        handles.SelectedDisplayOption = 'physicalDose';
    end
    handles.selectedBeam = 1;
    % check IPOPT status and return message for GUI user if no DAO or
    % particles
    if ~pln.propOpt.runDAO || ~strcmp(pln.radiationMode,'photons')
        CheckOptimizerStatus(usedOptimizer,'Fluence')
    end

catch ME
    handles = showError(handles,'OptimizeCallback: Could not optimize!',ME);
    % change state from busy to normal
    set(Figures, 'pointer', 'arrow');
    set(InterfaceObj,'Enable','on');
    guidata(hObject,handles);
    return;
end

% perform sequencing and DAO
try

    %% sequencing
    if strcmp(pln.radiationMode,'photons') && (pln.propOpt.runSequencing || pln.propOpt.runDAO)
    %   resultGUI = matRad_xiaLeafSequencing(resultGUI,evalin('base','stf'),evalin('base','dij')...
    %       ,get(handles.editSequencingLevel,'Value'));
    %   resultGUI = matRad_engelLeafSequencing(resultGUI,evalin('base','stf'),evalin('base','dij')...
    %       ,str2double(get(handles.editSequencingLevel,'String')));
        resultGUI = matRad_siochiLeafSequencing(resultGUI,evalin('base','stf'),evalin('base','dij')...
            ,str2double(get(handles.editSequencingLevel,'String')));

        assignin('base','resultGUI',resultGUI);
    end

catch ME
    handles = showError(handles,'OptimizeCallback: Could not perform sequencing',ME);
    % change state from busy to normal
    set(Figures, 'pointer', 'arrow');
    set(InterfaceObj,'Enable','on');
    guidata(hObject,handles);
    return;
end

try
    %% DAO
    if strcmp(pln.radiationMode,'photons') && pln.propOpt.runDAO
        handles = showWarning(handles,['Observe: You are running direct aperture optimization' filesep 'This is experimental code that has not been thoroughly debugged - especially in combination with constrained optimization.']);
       [resultGUI,usedOptimizer] = matRad_directApertureOptimization(evalin('base','dij'),evalin('base','cst'),...
           resultGUI.apertureInfo,resultGUI,pln);
       assignin('base','resultGUI',resultGUI);
       % check IPOPT status and return message for GUI user
       CheckOptimizerStatus(usedOptimizer,'DAO');
    end

    if strcmp(pln.radiationMode,'photons') && (pln.propOpt.runSequencing || pln.propOpt.runDAO)
        matRad_visApertureInfo(resultGUI.apertureInfo);
    end

catch ME
    handles = showError(handles,'OptimizeCallback: Could not perform direct aperture optimization',ME);
    % change state from busy to normal
    set(Figures, 'pointer', 'arrow');
    set(InterfaceObj,'Enable','on');
    guidata(hObject,handles);
    return;
end

% change state from busy to normal
set(Figures, 'pointer', 'arrow');
set(InterfaceObj,'Enable','on');
handles.dispWindow{3,1}  = [];   % reset dose ranges
handles.dispWindow{3,2}  = [];   % reset min max dose values
handles.rememberCurrAxes = false;
handles.IsoDose.Levels   = 0;  % ensure to use default iso dose line spacing
handles.cBarChanged      = true;

guidata(hObject,handles);
handles = updateIsoDoseLineCache(handles);
UpdateState(handles);
UpdatePlot(handles);
handles.rememberCurrAxes = true;
guidata(hObject,handles);

% the function CheckValidityPln checks if the provided plan is valid so
% that it can be used further on for optimization
function FlagValid = CheckValidityPln(cst)

FlagValid = true;
%check if mean constraint is always used in combination
for i = 1:size(cst,1)
   if ~isempty(cst{i,6})
        if ~isempty(strfind([cst{i,6}.type],'mean')) && isempty(strfind([cst{i,6}.type],'square'))
             FlagValid = false;
             warndlg('mean constraint needs to be defined in addition to a second constraint (e.g. squared deviation)');
             break
        end
   end
end

% --- Executes on selection change in popupTypeOfPlot
function popupTypeOfPlot_Callback(hObject, ~, handles)

 % intensity plot
if get(hObject,'Value') == 1

    set(handles.sliderBeamSelection,'Enable','off')
    set(handles.sliderOffset,'Enable','off')
    set(handles.popupDisplayOption,'Enable','on')
    set(handles.btnProfileType,'Enable','off');
    set(handles.popupPlane,'Enable','on');
    set(handles.radiobtnCT,'Enable','on');
    set(handles.radiobtnContour,'Enable','on');
    set(handles.radiobtnDose,'Enable','on');
    set(handles.radiobtnIsoDoseLines,'Enable','on');
    set(handles.radiobtnIsoDoseLinesLabels,'Enable','on');
    set(handles.sliderSlice,'Enable','on');

% profile plot
elseif get(hObject,'Value') == 2

    if handles.State > 0
        if length(parseStringAsNum(get(handles.editGantryAngle,'String'),true)) > 1

            set(handles.sliderBeamSelection,'Enable','on');
            handles.selectedBeam = 1;
            pln = evalin('base','pln');
            set(handles.sliderBeamSelection,'Min',handles.selectedBeam,'Max',pln.propStf.numOfBeams,...
                'Value',handles.selectedBeam,...
                'SliderStep',[1/(pln.propStf.numOfBeams-1) 1/(pln.propStf.numOfBeams-1)],...
                'Enable','on');

        else
            handles.selectedBeam = 1;
        end

        handles.profileOffset = get(handles.sliderOffset,'Value');

        vMinMax = [-100 100];
        vRange = sum(abs(vMinMax));

        ct = evalin('base','ct');
        if strcmp(get(handles.btnProfileType,'String'),'lateral')
            SliderStep = vRange/ct.resolution.x;
        else
            SliderStep = vRange/ct.resolution.y;
        end

        set(handles.sliderOffset,'Min',vMinMax(1),'Max',vMinMax(2),...
                    'Value',handles.profileOffset,...
                    'SliderStep',[1/SliderStep 1/SliderStep],...
                    'Enable','on');
    end

    set(handles.popupDisplayOption,'Enable','on');
    set(handles.btnProfileType,'Enable','on');
    set(handles.popupPlane,'Enable','off');
    set(handles.radiobtnCT,'Enable','off');
    set(handles.radiobtnContour,'Enable','off');
    set(handles.radiobtnDose,'Enable','off');
    set(handles.radiobtnIsoDoseLines,'Enable','off');
    set(handles.sliderSlice,'Enable','off');
    set(handles.radiobtnIsoDoseLinesLabels,'Enable','off');

    set(handles.btnProfileType,'Enable','on')

    if strcmp(get(handles.btnProfileType,'String'),'lateral')
        handles.ProfileType = 'longitudinal';
    else
        handles.ProfileType = 'lateral';
    end

end

handles.cBarChanged = true;

handles.rememberCurrAxes = false;
cla(handles.axesFig,'reset');
UpdatePlot(handles);
handles.rememberCurrAxes = true;
guidata(hObject, handles);

% --- Executes on selection change in popupDisplayOption.
function popupDisplayOption_Callback(hObject, ~, handles)
content = get(hObject,'String');
handles.SelectedDisplayOption = content{get(hObject,'Value'),1};
handles.SelectedDisplayOptionIdx = get(hObject,'Value');
%handles.dispWindow{3,1} = []; handles.dispWindow{3,2} = [];

if ~isfield(handles,'colormapLocked') || ~handles.colormapLocked
    handles.dispWindow{3,1} = []; handles.dispWindow{3,2} = [];
end

handles = updateIsoDoseLineCache(handles);
handles.cBarChanged = true;
guidata(hObject, handles);
UpdatePlot(handles);
guidata(hObject, handles);

% --- Executes on slider movement.
function sliderBeamSelection_Callback(hObject, ~, handles)
% hObject    handle to sliderBeamSelection (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'Value') returns position of slider
%        get(hObject,'Min') and get(hObject,'Max') to determine range of slider

handles.selectedBeam = round(get(hObject,'Value'));
set(hObject, 'Value', handles.selectedBeam);
handles.rememberCurrAxes = false;
UpdatePlot(handles);
handles.rememberCurrAxes = true;
guidata(hObject,handles);

% --- Executes on button press in btnProfileType.
function btnProfileType_Callback(hObject, ~, handles)
% hObject    handle to btnProfileType (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
if strcmp(get(hObject,'Enable') ,'on')
    if strcmp(handles.ProfileType,'lateral')
            handles.ProfileType = 'longitudinal';
             set(hObject,'String','lateral');
        else
            handles.ProfileType = 'lateral';
            set(hObject,'String','longitudinal');
    end

    handles.rememberCurrAxes = false;
    UpdatePlot(handles);
    handles.rememberCurrAxes = true;

    guidata(hObject, handles);

end

% enables/ disables buttons according to the current state
function UpdateState(handles)

if handles.State > 0
    pln = evalin('base','pln');

    if strcmp(pln.radiationMode,'carbon')
        set(handles.popMenuBioOpt,'Enable','on');
        set(handles.btnSetTissue,'Enable','on');
    elseif strcmp(pln.radiationMode,'protons')
        set(handles.popMenuBioOpt,'Enable','on');
        set(handles.btnSetTissue,'Enable','off');
    else
        set(handles.popMenuBioOpt,'Enable','off');
        set(handles.btnSetTissue,'Enable','off');
    end

    cMapControls = allchild(handles.uipanel_colormapOptions);
    for runHandles = cMapControls
        set(runHandles,'Enable','on');
    end
end

if handles.cubeHUavailable
    cMapOptionsSelectList = {'None','CT (HU)','Result (i.e. dose)'};
    set(handles.popupmenu_windowPreset,'Visible','on');
    set(handles.text_windowPreset,'String','Window Preset');
else
    cMapOptionsSelectList = {'None','CT (ED)','Result (i.e. dose)'};
    set(handles.popupmenu_windowPreset,'Visible','off');
    set(handles.text_windowPreset,'String','No available Window Presets');
end
handles.cBarChanged = true;

 switch handles.State

     case 0

      set(handles.txtInfo,'String','no data loaded');
      set(handles.btnCalcDose,'Enable','off');
      set(handles.btnOptimize ,'Enable','off');
      set(handles.pushbutton_recalc,'Enable','off');
      set(handles.btnSaveToGUI,'Enable','off');
      set(handles.btnDVH,'Enable','off');
      set(handles.importDoseButton,'Enable','off');
      set(handles.btn_export,'Enable','off');
      set(handles.btn3Dview,'Enable','off');

      cMapControls = allchild(handles.uipanel_colormapOptions);
      for runHandles = cMapControls
          set(runHandles,'Enable','off');
      end

      set(handles.popupmenu_chooseColorData,'String',cMapOptionsSelectList{1})
      set(handles.popupmenu_chooseColorData,'Value',1);

     case 1

      set(handles.txtInfo,'String','ready for dose calculation');
      set(handles.btnCalcDose,'Enable','on');
      set(handles.btnOptimize ,'Enable','off');
      set(handles.pushbutton_recalc,'Enable','off');
      set(handles.btnSaveToGUI,'Enable','off');
      set(handles.btnDVH,'Enable','off');
      set(handles.importDoseButton,'Enable','off');
      set(handles.btn_export,'Enable','on');
      set(handles.btn3Dview,'Enable','on');

      set(handles.popupmenu_chooseColorData,'String',cMapOptionsSelectList(1:2))
      set(handles.popupmenu_chooseColorData,'Value',2);
      AllVarNames = evalin('base','who');
      if ~isempty(AllVarNames)
            if  ismember('resultGUI',AllVarNames)
              set(handles.pushbutton_recalc,'Enable','on');
              set(handles.btnSaveToGUI,'Enable','on');
              set(handles.btnDVH,'Enable','on');
              set(handles.popupmenu_chooseColorData,'String',cMapOptionsSelectList(1:3))
              set(handles.popupmenu_chooseColorData,'Value',3);
            end
      end

     case 2

      set(handles.txtInfo,'String','ready for optimization');
      set(handles.btnCalcDose,'Enable','on');
      set(handles.btnOptimize ,'Enable','on');
      set(handles.pushbutton_recalc,'Enable','off');
      set(handles.btnSaveToGUI,'Enable','off');
      set(handles.btnDVH,'Enable','off');
      set(handles.importDoseButton,'Enable','off');
      set(handles.btn_export,'Enable','on');
      set(handles.btn3Dview,'Enable','on');
      set(handles.popupmenu_chooseColorData,'String',cMapOptionsSelectList(1:2))
      set(handles.popupmenu_chooseColorData,'Value',2);
      AllVarNames = evalin('base','who');

      if ~isempty(AllVarNames)
            if  ismember('resultGUI',AllVarNames)
              set(handles.pushbutton_recalc,'Enable','on');
              set(handles.btnSaveToGUI,'Enable','on');
              set(handles.btnDVH,'Enable','on');
              set(handles.popupmenu_chooseColorData,'String',cMapOptionsSelectList(1:3))
              set(handles.popupmenu_chooseColorData,'Value',3);
            end
      end

     case 3
      set(handles.txtInfo,'String','plan is optimized');
      set(handles.btnCalcDose,'Enable','on');
      set(handles.btnOptimize ,'Enable','on');
      set(handles.pushbutton_recalc,'Enable','on');
      set(handles.btnSaveToGUI,'Enable','on');
      set(handles.btnDVH,'Enable','on');
      set(handles.btn_export,'Enable','on');
      set(handles.btn3Dview,'Enable','on');
      % resultGUI struct needs to be available to import dose
      % otherwise inconsistent states can be achieved
      set(handles.importDoseButton,'Enable','on');
      set(handles.popupmenu_chooseColorData,'String',cMapOptionsSelectList(1:3))
      set(handles.popupmenu_chooseColorData,'Value',3);
 end

guidata(handles.figure1,handles);

% fill GUI elements with plan information
function setPln(handles)

matRad_cfg = MatRad_Config.instance();

pln = evalin('base','pln');
% sanity check of isoCenter
if size(pln.propStf.isoCenter,1) ~= pln.propStf.numOfBeams && size(pln.propStf.isoCenter,1) == 1
  pln.propStf.isoCenter = ones(pln.propStf.numOfBeams,1) * pln.propStf.isoCenter(1,:);
elseif size(pln.propStf.isoCenter,1) ~= pln.propStf.numOfBeams && size(pln.propStf.isoCenter,1) ~= 1
  matRad_cfg.dispError('Isocenter in plan file are incosistent.');
end

%Sanity check for the bixelWidth field
bixelWidth = pln.propStf.bixelWidth;

if isnumeric(bixelWidth) && isscalar(bixelWidth)
    bixelWidth = num2str(pln.propStf.bixelWidth);
elseif ~isnumeric(bixelWidth) && ~strcmp(bixelWidth,'field')
    matRad_cfg.dispError('Invalid bixel width! Must be a scalar number or ''field'' for field-based dose calculation with shapes stored in stf!');
end

set(handles.editBixelWidth,'String',bixelWidth);
set(handles.editFraction,'String',num2str(pln.numOfFractions));

if isfield(pln.propStf,'isoCenter')
    if size(unique(pln.propStf.isoCenter,'rows'),1) == 1
        set(handles.editIsoCenter,'String',regexprep(num2str((round(pln.propStf.isoCenter(1,:)*10))./10), '\s+', ' '));
        set(handles.editIsoCenter,'Enable','on');
        set(handles.checkIsoCenter,'Enable','on');
    else
        set(handles.editIsoCenter,'String','multiple isoCenter');
        set(handles.editIsoCenter,'Enable','off');
        set(handles.checkIsoCenter,'Value',0);
        set(handles.checkIsoCenter,'Enable','off');
    end
end
set(handles.editGantryAngle,'String',num2str((pln.propStf.gantryAngles)));
set(handles.editCouchAngle,'String',num2str((pln.propStf.couchAngles)));
set(handles.popupRadMode,'Value',find(strcmp(get(handles.popupRadMode,'String'),pln.radiationMode)));
set(handles.popUpMachine,'Value',find(strcmp(get(handles.popUpMachine,'String'),pln.machine)));

if ~strcmp(pln.propOpt.bioOptimization,'none')
    set(handles.popMenuBioOpt,'Enable','on');
    contentPopUp = get(handles.popMenuBioOpt,'String');
    ix = find(strcmp(pln.propOpt.bioOptimization,contentPopUp));
    set(handles.popMenuBioOpt,'Value',ix);
    set(handles.btnSetTissue,'Enable','on');
else
    set(handles.popMenuBioOpt,'Enable','off');
    set(handles.btnSetTissue,'Enable','off');
end
%% enable sequencing and DAO button if radiation mode is set to photons
if strcmp(pln.radiationMode,'photons') && pln.propOpt.runSequencing
    set(handles.btnRunSequencing,'Enable','on');
    set(handles.btnRunSequencing,'Value',1);
elseif strcmp(pln.radiationMode,'photons') && ~pln.propOpt.runSequencing
    set(handles.btnRunSequencing,'Enable','on');
    set(handles.btnRunSequencing,'Value',0);
else
    set(handles.btnRunSequencing,'Enable','off');
end
%% enable DAO button if radiation mode is set to photons
if strcmp(pln.radiationMode,'photons') && pln.propOpt.runDAO
    set(handles.btnRunDAO,'Enable','on');
    set(handles.btnRunDAO,'Value',1);
elseif strcmp(pln.radiationMode,'photons') && ~pln.propOpt.runDAO
    set(handles.btnRunDAO,'Enable','on');
    set(handles.btnRunDAO,'Value',0);
else
    set(handles.btnRunDAO,'Enable','off');
end
%% enable stratification level input if radiation mode is set to photons
if strcmp(pln.radiationMode,'photons')
    set(handles.txtSequencing,'Enable','on');
    set(handles.radiobutton3Dconf,'Enable','on');
    set(handles.editSequencingLevel,'Enable','on');
else
    set(handles.txtSequencing,'Enable','off');
    set(handles.radiobutton3Dconf,'Enable','off');
    set(handles.editSequencingLevel,'Enable','off');
end

% --- Executes on button press in btnTableSave.
function btnTableSave_Callback(~, ~, handles)
% hObject    handle to btnTableSave (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

if get(handles.checkIsoCenter,'Value')
    pln = evalin('base','pln');
    pln.propStf.isoCenter = ones(pln.propStf.numOfBeams,1) * matRad_getIsoCenter(evalin('base','cst'),evalin('base','ct'));
    set(handles.editIsoCenter,'String',regexprep(num2str((round(pln.propStf.isoCenter(1,:) * 10))./10), '\s+', ' '));
    assignin('base','pln',pln);
end
getPlnFromGUI(handles);

% --- Executes on selection change in listBoxCmd.
function listBoxCmd_Callback(hObject, ~, ~)
numLines = size(get(hObject,'String'),1);
set(hObject, 'ListboxTop', numLines);

% --- Executes on slider movement.
function sliderOffset_Callback(hObject, ~, handles)
handles.profileOffset = get(hObject,'Value');
UpdatePlot(handles);

%% HELPER FUNCTIONS
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% check validity of input for cst
function flagValidity = CheckValidity(Val)

flagValidity = true;

if ischar(Val)
    Val = str2num(Val);
end

if length(Val) > 2
    warndlg('invalid input!');
end

if isempty(Val)
   warndlg('Input not a number!');
   flagValidity = false;
end

if any(Val < 0)
   warndlg('Input not a positive number!');
   flagValidity = false;
end

% return IPOPT status as message box
function CheckOptimizerStatus(usedOptimizer,OptCase)

[statusmsg,statusflag] = usedOptimizer.GetStatus();

if statusflag == 0 || statusflag == 1
    status = 'none';
else
    status = 'warn';
end

msgbox(['Optimizer finished with status ' num2str(statusflag) ' (' statusmsg ')'],'Optimizer',status,'modal');

% get pln file form GUI
function getPlnFromGUI(handles)

% evalin pln (if existant) in order to decide whether isoCenter should be calculated
% automatically
if evalin('base','exist(''pln'',''var'')')
    pln = evalin('base','pln');
end

% Special parsing of bixelWidth (since it can also be "field") for imported
% shapes
bixelWidth = get(handles.editBixelWidth,'String'); % [mm] / also corresponds to lateral spot spacing for particles
if strcmp(bixelWidth,'field')
    pln.propStf.bixelWidth = bixelWidth;
else
    pln.propStf.bixelWidth = parseStringAsNum(bixelWidth,false);
    if isnan(pln.propStf.bixelWidth)
        warndlg('Invalid bixel width! Use standard bixel width of 5mm!');
        pln.propStf.bixelWidth = 5;
        set(handles.editBixelWidth,'String','5');
    end
end

pln.propStf.gantryAngles    = parseStringAsNum(get(handles.editGantryAngle,'String'),true); % [???]

if handles.eduMode
    set(handles.editCouchAngle,'String',num2str(zeros(size(pln.propStf.gantryAngles))));
end

pln.propStf.couchAngles     = parseStringAsNum(get(handles.editCouchAngle,'String'),true); % [???]
pln.propStf.numOfBeams      = numel(pln.propStf.gantryAngles);
try
    ct = evalin('base','ct');
    pln.numOfVoxels     = prod(ct.cubeDim);
    pln.voxelDimensions = ct.cubeDim;
catch
end
pln.numOfFractions  = parseStringAsNum(get(handles.editFraction,'String'),false);
contents            = get(handles.popupRadMode,'String');
pln.radiationMode   = contents{get(handles.popupRadMode,'Value')}; % either photons / protons / carbon
contents            = get(handles.popUpMachine,'String');
pln.machine         = contents{get(handles.popUpMachine,'Value')};

if (~strcmp(pln.radiationMode,'photons'))
    contentBioOpt = get(handles.popMenuBioOpt,'String');
    pln.propOpt.bioOptimization = contentBioOpt{get(handles.popMenuBioOpt,'Value'),:};
else
    pln.propOpt.bioOptimization = 'none';
end

pln.propOpt.runSequencing = logical(get(handles.btnRunSequencing,'Value'));
pln.propOpt.runDAO = logical(get(handles.btnRunDAO,'Value'));

try
    cst = evalin('base','cst');
    if (sum(strcmp('TARGET',cst(:,3))) > 0 && get(handles.checkIsoCenter,'Value')) || ...
            (sum(strcmp('TARGET',cst(:,3))) > 0 && ~isfield(pln.propStf,'isoCenter'))
       pln.propStf.isoCenter = ones(pln.propStf.numOfBeams,1) * matRad_getIsoCenter(cst,ct);
       set(handles.checkIsoCenter,'Value',1);
    else
        if ~strcmp(get(handles.editIsoCenter,'String'),'multiple isoCenter')
            pln.propStf.isoCenter = ones(pln.propStf.numOfBeams,1) * str2num(get(handles.editIsoCenter,'String'));
        end
    end
catch
    warning('couldnt set isocenter in getPln function')
end

handles.pln = pln;
assignin('base','pln',pln);

% parsing a string as number array
function number = parseStringAsNum(stringIn,isVector)
if isnumeric(stringIn)
    number = stringIn;
else
    number = str2num(stringIn);
    if isempty(number) || length(number) > 1 && ~isVector
        warndlg(['could not parse all parameters (pln, optimization parameter)']);
        number = NaN;
    elseif isVector && iscolumn(number)
        number = number';
    end
end

% show error
function handles = showError(handles,Message,ME)

if nargin == 3
    %Add exception message
    if isfield(handles,'devMode') && handles.devMode
        meType = 'extended';
    else
        meType = 'basic';
    end
    Message = {Message,ME.getReport(meType,'hyperlinks','off')};
end

if isfield(handles,'ErrorDlg')
    if ishandle(handles.ErrorDlg)
        close(handles.ErrorDlg);
    end
end
handles.ErrorDlg = errordlg(Message);

% show warning
function handles = showWarning(handles,Message,ME)

if nargin == 3
    %Add exception message
    if isfield(handles,'devMode') && handles.devMode
        meType = 'extended';
    else
        meType = 'basic';
    end
    Message = {Message,ME.getReport(meType,'hyperlinks','off')};
end

if isfield(handles,'WarnDlg')
    if ishandle(handles.WarnDlg)
        close(handles.WarnDlg);
    end
end
handles.WarnDlg = warndlg(Message);

% check for valid machine data input file
function flag = checkRadiationComposition(handles)
flag = true;
contents = cellstr(get(handles.popUpMachine,'String'));
Machine = contents{get(handles.popUpMachine,'Value')};
contents = cellstr(get(handles.popupRadMode,'String'));
radMod = contents{get(handles.popupRadMode,'Value')};

if isdeployed
    baseroot = [ctfroot filesep 'matRad'];
else
    baseroot = fileparts(mfilename('fullpath'));
end
FoundFile = dir([baseroot filesep 'basedata' filesep radMod '_' Machine '.mat']);

if isempty(FoundFile)
    warndlg(['No base data available for machine: ' Machine]);
    flag = false;
end

function matRadScrollWheelFcn(src,event)

% get handles
handles = guidata(src);

% compute new slice
currSlice = round(get(handles.sliderSlice,'Value'));
newSlice  = currSlice - event.VerticalScrollCount;

% project to allowed set
newSlice = min(newSlice,get(handles.sliderSlice,'Max'));
newSlice = max(newSlice,get(handles.sliderSlice,'Min'));

% update slider
set(handles.sliderSlice,'Value',newSlice);

% update handles object
guidata(src,handles);

% update plot
UpdatePlot(handles);

%% CALLBACKS
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% button: show DVH
function btnDVH_Callback(~, ~, handles)

resultGUI = evalin('base','resultGUI');
Content = get(handles.popupDisplayOption,'String');
SelectedCube = Content{get(handles.popupDisplayOption,'Value')};

pln = evalin('base','pln');
resultGUI_SelectedCube.physicalDose = resultGUI.(SelectedCube);

if ~strcmp(pln.propOpt.bioOptimization,'none')

    %check if one of the default fields is selected
    if sum(strcmp(SelectedCube,{'physicalDose','effect','RBE,','RBExDose','alpha','beta'})) > 0
        resultGUI_SelectedCube.physicalDose = resultGUI.physicalDose;
        resultGUI_SelectedCube.RBExDose     = resultGUI.RBExDose;
    else
        Idx    = find(SelectedCube == '_');
        SelectedSuffix = SelectedCube(Idx(1):end);
        resultGUI_SelectedCube.physicalDose = resultGUI.(['physicalDose' SelectedSuffix]);
        resultGUI_SelectedCube.RBExDose     = resultGUI.(['RBExDose' SelectedSuffix]);
    end
end

%adapt visibilty
cst = evalin('base','cst');
for i = 1:size(cst,1)
    cst{i,5}.Visible = handles.VOIPlotFlag(i);
end

matRad_indicatorWrapper(cst,pln,resultGUI_SelectedCube);

assignin('base','cst',cst);

% radio button: plot isolines labels
function radiobtnIsoDoseLinesLabels_Callback(~, ~, handles)
UpdatePlot(handles);

% button: refresh
function btnRefresh_Callback(hObject, ~, handles)

handles = resetGUI(hObject, handles);

%% parse variables from base workspace
AllVarNames = evalin('base','who');
handles.AllVarNames = AllVarNames;
try
    if  ismember('ct',AllVarNames) &&  ismember('cst',AllVarNames)
        ct  = evalin('base','ct');
        cst = evalin('base','cst');
        %cst = setCstTable(handles,cst);
        cst = generateCstTable(handles,cst);
        handles.State = 1;
        cst = matRad_computeVoiContoursWrapper(cst,ct);
        assignin('base','cst',cst);
        handles = reloadGUI(hObject, handles, ct, cst);
    elseif ismember('ct',AllVarNames) &&  ~ismember('cst',AllVarNames)
        handles = showError(handles,'GUI OpeningFunc: could not find cst file');
        ct  = evalin('base','ct');
        handles = reloadGUI(hObject,handles,ct);
    elseif ~ismember('ct',AllVarNames) &&  ismember('cst',AllVarNames)
        handles = showError(handles,'GUI OpeningFunc: could not find ct file');
        handles = reloadGUI(hObject, handles);
    else
        handles = reloadGUI(hObject, handles);
    end
catch
    handles = showError(handles,'GUI OpeningFunc: Could not load ct and cst file');
    handles = reloadGUI(hObject, handles);
end

guidata(hObject, handles);

% text box: # fractions
function editFraction_Callback(hObject, ~, handles)
getPlnFromGUI(handles);
guidata(hObject,handles);

% text box: stratification levels
function editSequencingLevel_Callback(~, ~, ~)

% text box: isoCenter in [mm]
function editIsoCenter_Callback(hObject, ~, handles)

pln = evalin('base','pln');
tmpIsoCenter = str2num(get(hObject,'String'));

if length(tmpIsoCenter) == 3
    if sum(any(unique(pln.propStf.isoCenter,'rows')~=tmpIsoCenter))
        pln.propStf.isoCenter = ones(pln.propStf.numOfBeams,1)*tmpIsoCenter;
        handles.State = 1;
        UpdateState(handles);
    end
else
    handles = showError(handles,'EditIsoCenterCallback: Could not set iso center');
end

assignin('base','pln',pln);
guidata(hObject,handles);

% check box: iso center auto
function checkIsoCenter_Callback(hObject, ~, handles)

W = evalin('base','whos');
doesPlnExist = ismember('pln',{W(:).name});

if get(hObject,'Value') && doesPlnExist
    pln = evalin('base','pln');
    if ~isfield(pln.propStf,'isoCenter')
        pln.propStf.isoCenter = NaN;
    end
    tmpIsoCenter = matRad_getIsoCenter(evalin('base','cst'),evalin('base','ct'));
    if ~isequal(tmpIsoCenter,pln.propStf.isoCenter)
        pln.propStf.isoCenter = ones(pln.propStf.numOfBeams,1)*tmpIsoCenter;
        handles.State = 1;
        UpdateState(handles);
    end
    set(handles.editIsoCenter,'String',regexprep(num2str((round(tmpIsoCenter*10))./10), '\s+', ' '));
    set(handles.editIsoCenter,'Enable','off')
    assignin('base','pln',pln);
else
    set(handles.editIsoCenter,'Enable','on')
end

% radio button: run sequencing
function btnRunSequencing_Callback(~, ~, handles)
getPlnFromGUI(handles);

% radio button: run direct aperture optimization
function btnRunDAO_Callback(~, ~, handles)
getPlnFromGUI(handles);

% button: set iso dose levels
function btnSetIsoDoseLevels_Callback(hObject, ~, handles)
prompt = {['Enter iso dose levels in [Gy]. Enter space-separated numbers, e.g. 1.5 2 3 4.98. Enter 0 to use default values']};
if isequal(handles.IsoDose.Levels,0) || ~isvector(handles.IsoDose.Levels) || any(~isnumeric(handles.IsoDose.Levels)) || any(isnan(handles.IsoDose.Levels))
    defaultLine = {'1 2 3 '};
else
    if isrow(handles.IsoDose.Levels)
        defaultLine = cellstr(num2str(handles.IsoDose.Levels,'%.2g '));
    else
        defaultLine = cellstr(num2str(handles.IsoDose.Levels','%.2g '));
    end
end

try
    Input = inputdlg(prompt,'Set iso dose levels ', [1 70],defaultLine);
    if ~isempty(Input)
        handles.IsoDose.Levels = (sort(str2num(Input{1})));
        if length(handles.IsoDose.Levels) == 1 && (handles.IsoDose.Levels(1) ~= 0)
            handles.IsoDose.Levels = [handles.IsoDose.Levels handles.IsoDose.Levels];
        end
        handles.IsoDose.NewIsoDoseFlag = true;
    end
catch
    warning('Couldnt parse iso dose levels - using default values');
    handles.IsoDose.Levels = 0;
end
handles = updateIsoDoseLineCache(handles);
handles.IsoDose.NewIsoDoseFlag = false;
UpdatePlot(handles);
guidata(hObject,handles);

% popup menu: machine
function popUpMachine_Callback(hObject, ~, handles)
contents = cellstr(get(hObject,'String'));
checkRadiationComposition(handles);
if handles.State > 0
    pln = evalin('base','pln');
    if handles.State > 0 && ~strcmp(contents(get(hObject,'Value')),pln.machine)
        handles.State = 1;
        UpdateState(handles);
        guidata(hObject,handles);
    end
   getPlnFromGUI(handles);
end

% toolbar load button
function toolbarLoad_ClickedCallback(hObject, eventdata, handles)
btnLoadMat_Callback(hObject, eventdata, handles);

% toolbar save button
function toolbarSave_ClickedCallback(hObject, eventdata, handles)

btnTableSave_Callback(hObject, eventdata, handles);

try

    if handles.State > 0
        ct  = evalin('base','ct');
        cst = evalin('base','cst');
        pln = evalin('base','pln');
    end

    if handles.State > 1
       stf = evalin('base','stf');
       dij = evalin('base','dij');
    end

    if handles.State > 2
       resultGUI = evalin('base','resultGUI');
    end

    switch handles.State
        case 1
            uisave({'cst','ct','pln'});
        case 2
            uisave({'cst','ct','pln','stf','dij'});
        case 3
            uisave({'cst','ct','pln','stf','dij','resultGUI'});
    end

catch
     handles = showWarning(handles,'Could not save files');
end
guidata(hObject,handles);

% button: about
function btnAbout_Callback(hObject, eventdata, handles)

[~,matRadVer] = matRad_version;

msg{1} = ['matRad ''' matRadVer.name '''']; %Name
if handles.eduMode
    msg{1} = [msg{1} ' Educational'];
end
msg{end+1} = sprintf('v%d.%d.%d',matRadVer.major,matRadVer.minor,matRadVer.patch); %Version Number
if isdeployed
   msg{end+1} = 'Standalone Version';
elseif ~isempty(matRadVer.branch) && ~isempty(matRadVer.commitID)
    msg{end+1} = sprintf('Git: Branch %s, commit %s',matRadVer.branch,matRadVer.commitID(1:8));
end

[env,envver]  = matRad_getEnvironment();
msg{end+1} = sprintf('Environment: %s v%s %s',env,envver,version('-release'));

msg{end+1} = 'Web: www.matrad.org';
msg{end+1} = 'E-Mail: contact@matrad.org';

msgbox(msg,'About matRad');

% button: close
function figure1_CloseRequestFcn(hObject, ~, ~)
set(0,'DefaultUicontrolBackgroundColor',[0.5 0.5 0.5]);
selection = questdlg('Do you really want to close matRad?',...
                     'Close matRad',...
                     'Yes','No','Yes');

%BackgroundColor',[0.5 0.5 0.5]
 switch selection
   case 'Yes'
     delete(hObject);
   case 'No'
     return
 end

% --- Executes on button press in pushbutton_recalc.
function pushbutton_recalc_Callback(hObject, ~, handles)

% recalculation only makes sense if ...
if evalin('base','exist(''pln'',''var'')') && ...
   evalin('base','exist(''stf'',''var'')') && ...
   evalin('base','exist(''ct'',''var'')') && ...
   evalin('base','exist(''cst'',''var'')') && ...
   evalin('base','exist(''resultGUI'',''var'')')

try

    % indicate that matRad is busy
    % change mouse pointer to hour glass
    Figures = gcf;%findobj('type','figure');
    set(Figures, 'pointer', 'watch');
    drawnow;
    % disable all active objects
    InterfaceObj = findobj(Figures,'Enable','on');
    set(InterfaceObj,'Enable','off');

    % get all data from workspace
    pln       = evalin('base','pln');
    stf       = evalin('base','stf');
    ct        = evalin('base','ct');
    cst       = evalin('base','cst');
    resultGUI = evalin('base','resultGUI');

    % get weights of the selected cube
    Content = get(handles.popupDisplayOption,'String');
    SelectedCube = Content{get(handles.popupDisplayOption,'Value')};
    Suffix = strsplit(SelectedCube,'_');
    if length(Suffix)>1
        Suffix = ['_' Suffix{2}];
    else
        Suffix = '';
    end

    wField = ['w' Suffix];

    if ~isfield(resultGUI,wField)
        warndlg(['No exact match found for weight vector ''' wField ''' with selected dose insance. Trying common weight vector ''w'' instead!']);
        wField = 'w';
    end

    %Second sanity check to exclude case with no 'w' present
    if ~isfield(resultGUI,wField)
        errordlg('No weight vector found for forward dose recalculation!');
        return;
    end

    if sum([stf.totalNumOfBixels]) ~= length(resultGUI.(wField))
        errordlg('Selected weight vector does not correspond to current steering file (wrong number of entries/bixels!)!');
        return;
    end

    % change isocenter if that was changed and do _not_ recreate steering
    % information
    for i = 1:numel(pln.propStf.gantryAngles)
        stf(i).isoCenter = pln.propStf.isoCenter(i,:);
    end

    % recalculate influence matrix
    if strcmp(pln.radiationMode,'photons')
        dij = matRad_calcPhotonDose(ct,stf,pln,cst);
    elseif strcmp(pln.radiationMode,'protons') || strcmp(pln.radiationMode,'carbon')
        dij = matRad_calcParticleDose(ct,stf,pln,cst);
    end

    % recalculate cubes in resultGUI
    resultGUIreCalc = matRad_calcCubes(resultGUI.(wField),dij);

    % delete old variables to avoid confusion
    if isfield(resultGUI,'effect')
        resultGUI = rmfield(resultGUI,'effect');
        resultGUI = rmfield(resultGUI,'RBExDose');
        resultGUI = rmfield(resultGUI,'RBE');
        resultGUI = rmfield(resultGUI,'alpha');
        resultGUI = rmfield(resultGUI,'beta');
    end

    % overwrite the "standard" fields
    sNames = fieldnames(resultGUIreCalc);
    for j = 1:length(sNames)
        resultGUI.(sNames{j}) = resultGUIreCalc.(sNames{j});
    end

    % assign results to base worksapce
    assignin('base','dij',dij);
    assignin('base','resultGUI',resultGUI);

    handles.State = 3;

    % show physicalDose of newly computed state
    handles.SelectedDisplayOption = 'physicalDose';
    set(handles.popupDisplayOption,'Value',find(strcmp('physicalDose',Content)));

    % change state from busy to normal
    set(Figures, 'pointer', 'arrow');
    set(InterfaceObj,'Enable','on');

    handles.cBarChanged = true;

    handles = updateIsoDoseLineCache(handles);

    UpdateState(handles);

    handles.rememberCurrAxes = false;
    UpdatePlot(handles);
    handles.rememberCurrAxes = true;

    guidata(hObject,handles);

catch ME
    handles = showError(handles,'CalcDoseCallback: Error in dose recalculation!',ME);

    % change state from busy to normal
    set(Figures, 'pointer', 'arrow');
    set(InterfaceObj,'Enable','on');

    guidata(hObject,handles);
    return;

end

end

% --- Executes on button press in btnSetTissue.
function btnSetTissue_Callback(hObject, ~, handles)

%check if patient is loaded
if handles.State == 0
    return
end

%parse variables from base-workspace
cst = evalin('base','cst');
pln = evalin('base','pln');

fileName = [pln.radiationMode '_' pln.machine];
load(['basedata' filesep fileName]);

% check for available cell types characterized by alphaX and betaX
for i = 1:size(machine.data(1).alphaX,2)
    CellType{i} = [num2str(machine.data(1).alphaX(i)) ' ' num2str(machine.data(1).betaX(i))];
end

%fill table data array
for i = 1:size(cst,1)
    data{i,1} = cst{i,2};
    data{i,2} = [num2str(cst{i,5}.alphaX) ' ' num2str(cst{i,5}.betaX)];
    data{i,3} = (cst{i,5}.alphaX / cst{i,5}.betaX );
end

Width  = 400;
Height = 200 + 20*size(data,1);
ScreenSize = get(0,'ScreenSize');
% show "set tissue parameter" window
figHandles = get(0,'Children');
if ~isempty(figHandles)
    IdxHandle = strcmp(get(figHandles,'Name'),'Set Tissue Parameters');
else
    IdxHandle = [];
end

%check if window is already exists
if any(IdxHandle)
    IdxTable = find(strcmp({figHandles(IdxHandle).Children.Type},'uitable'));
    set(figHandles(IdxHandle).Children(IdxTable), 'Data', []);
    figTissue = figHandles(IdxHandle);
    %set focus
    figure(figTissue);
else
    figTissue = figure('Name','Set Tissue Parameters','Color',[.5 .5 .5],'NumberTitle','off','Position',...
        [ceil(ScreenSize(3)/2) ceil(ScreenSize(4)/2) Width Height]);
end

% define the tissue parameter table
cNames = {'VOI','alphaX betaX','alpha beta ratio'};
columnformat = {'char',CellType,'numeric'};

tissueTable = uitable('Parent', figTissue,'Data', data,'ColumnEditable',[false true false],...
                      'ColumnName',cNames, 'ColumnFormat',columnformat,'Position',[50 150 10 10]);
set(tissueTable,'CellEditCallback',@tissueTable_CellEditCallback);
% set width and height
currTablePos = get(tissueTable,'Position');
currTableExt = get(tissueTable,'Extent');
currTablePos(3) = currTableExt(3);
currTablePos(4) = currTableExt(4);
set(tissueTable,'Position',currTablePos);

% define two buttons with callbacks
uicontrol('Parent', figTissue,'Style', 'pushbutton', 'String', 'Save&Close',...
        'Position', [Width-(0.25*Width) 0.1 * Height 70 30],...
        'Callback', @(hpb,eventdata)SaveTissueParameters(hpb,eventdata,handles,tissueTable));

uicontrol('Parent', figTissue,'Style', 'pushbutton', 'String', 'Cancel&Close',...
        'Position', [Width-(0.5*Width) 0.1 * Height 80 30],...
        'Callback', 'close');

guidata(hObject,handles);
UpdateState(handles);

function SaveTissueParameters(~, ~, handles,tissueTable)
cst = evalin('base','cst');
% get handle to uiTable

% retrieve data from uitable
data       = get(tissueTable,'data');

for i = 1:size(cst,1)
   for j = 1:size(data,1)
       if strcmp(cst{i,2},data{j,1})
         alphaXBetaX = str2num(data{j,2});
         cst{i,5}.alphaX = alphaXBetaX(1);
         cst{i,5}.betaX  = alphaXBetaX(2);
       end
   end
end
assignin('base','cst',cst);
close(get(tissueTable,'Parent'));
handles.State = 2;
UpdateState(handles);

function tissueTable_CellEditCallback(hObject, eventdata, ~)
if eventdata.Indices(2) == 2
   alphaXBetaX = str2num(eventdata.NewData);
   data = get(hObject,'Data');
   data{eventdata.Indices(1),3} = alphaXBetaX(1)/alphaXBetaX(2);
   set(hObject,'Data',data);
end

% --- Executes on button press in btnSaveToGUI.
function btnSaveToGUI_Callback(hObject, ~, handles)

Width  = 400;
Height = 200;
ScreenSize = get(0,'ScreenSize');

% show "Provide result name" window
figHandles = get(0,'Children');
if ~isempty(figHandles)
    IdxHandle = strcmp(get(figHandles,'Name'),'Provide result name');
else
    IdxHandle = [];
end

%check if window is already exists
if any(IdxHandle)
    figDialog = figHandles(IdxHandle);
    %set focus
    figure(figDialog);
else
    figDialog = dialog('Position',[ceil(ScreenSize(3)/2) ceil(ScreenSize(4)/2) Width Height],'Name','Provide result name','Color',[0.5 0.5 0.5]);

    uicontrol('Parent',figDialog,...
              'Style','text',...
              'Position',[20 Height - (0.35*Height) 350 60],...
              'String','Please provide a decriptive name for your optimization result:','FontSize',10,'BackgroundColor',[0.5 0.5 0.5]);

    uicontrol('Parent',figDialog,...
              'Style','edit',...
              'Position',[30 60 350 60],...
              'String','Please enter name here...','FontSize',10,'BackgroundColor',[0.55 0.55 0.55]);

    uicontrol('Parent', figDialog,'Style', 'pushbutton', 'String', 'Save','FontSize',10,...
              'Position', [0.42*Width 0.1 * Height 70 30],...
              'Callback', @(hpb,eventdata)SaveResultToGUI(hpb,eventdata,guidata(hpb)));
end

uiwait(figDialog);
guidata(hObject, handles);
UpdateState(handles)
UpdatePlot(handles)

function SaveResultToGUI(~, ~, ~)
AllFigHandles = get(0,'Children');
ixHandle      = strcmp(get(AllFigHandles,'Name'),'Provide result name');
uiEdit        = get(AllFigHandles(ixHandle),'Children');

if strcmp(get(uiEdit(2),'String'),'Please enter name here...')

    formatOut = 'mmddyyHHMM';
    Suffix = ['_' datestr(now,formatOut)];
else
    % delete special characters
    Suffix = get(uiEdit(2),'String');
    logIx = isstrprop(Suffix,'alphanum');
    Suffix = ['_' Suffix(logIx)];
end

pln       = evalin('base','pln');
resultGUI = evalin('base','resultGUI');

if isfield(resultGUI,'physicalDose')
    resultGUI.(['physicalDose' Suffix])  = resultGUI.physicalDose;
end
if isfield(resultGUI,'w')
    resultGUI.(['w' Suffix])             = resultGUI.w;
end

if ~strcmp(pln.propOpt.bioOptimization,'none')

    if isfield(resultGUI,'RBExDose')
         resultGUI.(['RBExDose' Suffix]) = resultGUI.RBExDose;
    end

    if strcmp(pln.radiationMode,'carbon') == 1
        if isfield(resultGUI,'effect')
            resultGUI.(['effect' Suffix])= resultGUI.effect;
        end

        if isfield(resultGUI,'RBE')
            resultGUI.(['RBE' Suffix]) = resultGUI.RBE;
        end
        if isfield(resultGUI,'alpha')
            resultGUI.(['alpha' Suffix]) = resultGUI.alpha;
        end
        if isfield(resultGUI,'beta')
            resultGUI.(['beta' Suffix]) = resultGUI.beta;
        end
    end
end

close(AllFigHandles(ixHandle));
assignin('base','resultGUI',resultGUI);

% precompute contours of VOIs
function cst = precomputeContours(ct,cst)
mask = zeros(ct.cubeDim); % create zero cube with same dimeonsions like dose cube
for s = 1:size(cst,1)
    cst{s,7} = cell(max(ct.cubeDim(:)),3);
    mask(:) = 0;
    mask(cst{s,4}{1}) = 1;
    for slice = 1:ct.cubeDim(1)
        if sum(sum(mask(slice,:,:))) > 0
             cst{s,7}{slice,1} = contourc(squeeze(mask(slice,:,:)),.5*[1 1]);
        end
    end
    for slice = 1:ct.cubeDim(2)
        if sum(sum(mask(:,slice,:))) > 0
             cst{s,7}{slice,2} = contourc(squeeze(mask(:,slice,:)),.5*[1 1]);
        end
    end
    for slice = 1:ct.cubeDim(3)
        if sum(sum(mask(:,:,slice))) > 0
             cst{s,7}{slice,3} = contourc(squeeze(mask(:,:,slice)),.5*[1 1]);
        end
    end
end

%Update IsodoseLines
function handles = updateIsoDoseLineCache(handles)
resultGUI = evalin('base','resultGUI');
% select first cube if selected option does not exist
if ~isfield(resultGUI,handles.SelectedDisplayOption)
    CubeNames = fieldnames(resultGUI);
    dose = resultGUI.(CubeNames{1,1});
else
    dose = resultGUI.(handles.SelectedDisplayOption);
end

%if function is called for the first time then set display parameters
if isempty(handles.dispWindow{3,2})
    handles.dispWindow{3,1} = [min(dose(:)) max(dose(:))]; % set default dose range
    handles.dispWindow{3,2} = [min(dose(:)) max(dose(:))]; % set min max values
end

minMaxRange = handles.dispWindow{3,1};
% if upper colorrange is defined then use it otherwise 120% iso dose
 upperMargin = 1;
if abs((max(dose(:)) - handles.dispWindow{3,1}(1,2))) < 0.01  * max(dose(:))
    upperMargin = 1.2;
end

if (length(handles.IsoDose.Levels) == 1 && handles.IsoDose.Levels(1,1) == 0) || ~handles.IsoDose.NewIsoDoseFlag
    vLevels                  = [0.1:0.1:0.9 0.95:0.05:upperMargin];
    referenceDose            = (minMaxRange(1,2))/(upperMargin);
    handles.IsoDose.Levels   = minMaxRange(1,1) + (referenceDose-minMaxRange(1,1)) * vLevels;
end
handles.IsoDose.Contours = matRad_computeIsoDoseContours(dose,handles.IsoDose.Levels);

%% CREATE FUNCTIONS
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% popup menu: machine
function popUpMachine_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

% text box: max value
function txtMaxVal_CreateFcn(hObject, ~, ~)

if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

% text box: edit iso center
function editIsoCenter_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

% text box: stratification levels
function editSequencingLevel_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

function slicerPrecision_CreateFcn(hObject, ~, ~)
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor',[.9 .9 .9]);
end

function editBixelWidth_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

function editGantryAngle_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

function editCouchAngle_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

function popupRadMode_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

function editFraction_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

function popupPlane_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

function sliderSlice_CreateFcn(hObject, ~, ~)
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor',[.9 .9 .9]);
end

function popupTypeOfPlot_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

function popupDisplayOption_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

function sliderBeamSelection_CreateFcn(hObject, ~, ~)
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor',[.9 .9 .9]);
end

function listBoxCmd_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

function sliderOffset_CreateFcn(hObject, ~, ~)
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor',[.9 .9 .9]);
end

% --- Executes on selection change in legendTable.
function legendTable_Callback(hObject, eventdata, handles)
% hObject    handle to legendTable (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: contents = cellstr(get(hObject,'String')) returns legendTable contents as cell array
%        contents{get(hObject,'Value')} returns selected item from legendTable
cst = evalin('base','cst');

idx    = get(hObject,'Value');
clr    = dec2hex(round(cst{idx,5}.visibleColor(:)*255),2)';
clr    = ['#';clr(:)]';

%Get the string entries
tmpString = get(handles.legendTable,'String');

if handles.VOIPlotFlag(idx)
    handles.VOIPlotFlag(idx) = false;
    cst{idx,5}.Visible = false;
    tmpString{idx} = ['<html><table border=0 ><TR><TD bgcolor=',clr,' width="18"></TD><TD>',cst{idx,2},'</TD></TR> </table></html>'];
elseif ~handles.VOIPlotFlag(idx)
    handles.VOIPlotFlag(idx) = true;
    cst{idx,5}.Visible = true;
    tmpString{idx} = ['<html><table border=0 ><TR><TD bgcolor=',clr,' width="18"><center>✔</center></TD><TD>',cst{idx,2},'</TD></TR> </table></html>'];
end
set(handles.legendTable,'String',tmpString);

% update cst in workspace accordingly
assignin('base','cst',cst)

guidata(hObject, handles);
UpdatePlot(handles)

% --- Executes during object creation, after setting all properties.
function legendTable_CreateFcn(hObject, eventdata, handles)
% hObject    handle to legendTable (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: listbox controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

% --- Executes on button press in importDoseButton.
function importDoseButton_Callback(hObject,eventdata, handles)
% hObject    handle to importDoseButton (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
extensions{1} = '*.nrrd';
[filenames,filepath,~] = uigetfile(extensions,'MultiSelect','on');

if ~iscell(filenames)
    tmp = filenames;
    filenames = cell(1);
    filenames{1} = tmp;
end

ct = evalin('base','ct');
resultGUI = evalin('base','resultGUI');

for filename = filenames
    [~,name,~] = fileparts(filename{1});
    [cube,~] = matRad_readCube(fullfile(filepath,filename{1}));
    if ~isequal(ct.cubeDim, size(cube))
        errordlg('Dimensions of the imported cube do not match with ct','Import failed!','modal');
        continue;
    end

    fieldname = ['import_' matlab.lang.makeValidName(name, 'ReplacementStyle','delete')];
    resultGUI.(fieldname) = cube;
end

assignin('base','resultGUI',resultGUI);
btnRefresh_Callback(hObject, eventdata, handles)

% --- Executes on button press in pushbutton_importFromBinary.
function pushbutton_importFromBinary_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton_importFromBinary (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

try
    % delete existing workspace - parse variables from base workspace
    set(handles.popupDisplayOption,'String','no option available');
    AllVarNames = evalin('base','who');
    RefVarNames = {'ct','cst','pln','stf','dij','resultGUI'};
    for i = 1:length(RefVarNames)
        if sum(ismember(AllVarNames,RefVarNames{i}))>0
            evalin('base',['clear ', RefVarNames{i}]);
        end
    end
    handles.State = 0;

    %call the gui
    uiwait(matRad_importGUI);

    %Check if we have the variables in the workspace
    if evalin('base','exist(''cst'',''var'')') == 1 && evalin('base','exist(''ct'',''var'')') == 1
        cst = evalin('base','cst');
        ct = evalin('base','ct');
        %setCstTable(handles,cst);
        generateCstTable(handles,cst);
        handles.TableChanged = false;
        set(handles.popupTypeOfPlot,'Value',1);

        % compute HU values
        if ~isfield(ct, 'cubeHU')
            ct = matRad_electronDensitiesToHU(ct);
            assignin('base','ct',ct);
        end
        if ~isfield(ct, 'cubeHU')
            handles.cubeHUavailable = false;
        else
            handles.cubeHUavailable = true;
        end

        % precompute contours
        cst = precomputeContours(ct,cst);

        assignin('base','ct',ct);
        assignin('base','cst',cst);

        if evalin('base','exist(''pln'',''var'')')
            assignin('base','pln',pln);
            setPln(handles);
        else
            getPlnFromGUI(handles);
            setPln(handles);
        end
        handles.State = 1;
    end

    % set slice slider
    handles.plane = get(handles.popupPlane,'value');
    if handles.State >0
        set(handles.sliderSlice,'Min',1,'Max',ct.cubeDim(handles.plane),...
            'Value',round(ct.cubeDim(handles.plane)/2),...
            'SliderStep',[1/(ct.cubeDim(handles.plane)-1) 1/(ct.cubeDim(handles.plane)-1)]);
    end

    if handles.State > 0
        % define context menu for structures
        for i = 1:size(cst,1)
            if cst{i,5}.Visible
                handles.VOIPlotFlag(i) = true;
            else
                handles.VOIPlotFlag(i) = false;
            end
        end
    end

    handles.dispWindow = cell(3,2);
    handles.cBarChanged = true;

    UpdateState(handles);
    handles.rememberCurrAxes = false;
    UpdatePlot(handles);
    handles.rememberCurrAxes = true;
catch
   handles = showError(handles,'Binary Patient Import: Could not import data');
   UpdateState(handles);
end

guidata(hObject,handles);

% --- Executes on button press in radioBtnIsoCenter.
function radioBtnIsoCenter_Callback(hObject, eventdata, handles)
% hObject    handle to radioBtnIsoCenter (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
UpdatePlot(handles)
% Hint: get(hObject,'Value') returns toggle state of radioBtnIsoCenter

% --------------------------------------------------------------------
function uipushtool_screenshot_ClickedCallback(hObject, eventdata, handles)
% hObject    handle to uipushtool_screenshot (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

tmpFig = figure('position',[100 100 700 600],'Visible','off','name','Current View');
cBarHandle = findobj(handles.figure1,'Type','colorbar');
if ~isempty(cBarHandle)
    new_handle = copyobj([handles.axesFig cBarHandle],tmpFig);
else
    new_handle = copyobj(handles.axesFig,tmpFig);
end

oldPos = get(handles.axesFig,'Position');
set(new_handle(1),'units','normalized', 'Position',oldPos);

if ~isfield(handles,'lastStoragePath') || exist(handles.lastStoragePath,'dir') ~= 7
    lastStoragePath = [];
else
    lastStoragePath = handles.lastStoragePath;
end

[filename, pathname] = uiputfile({'*.jpg;*.tif;*.png;*.gif','All Image Files'; '*.fig','MATLAB figure file'},'Save current view',[lastStoragePath 'screenshot.png']);

if ~isequal(filename,0) && ~isequal(pathname,0)
    handles.lastStoragePath = pathname;
    set(gcf, 'pointer', 'watch');
    saveas(tmpFig,fullfile(pathname,filename));
    set(gcf, 'pointer', 'arrow');
    close(tmpFig);
    uiwait(msgbox('Current view has been succesfully saved!'));
else
    uiwait(msgbox('Aborted saving, showing figure instead!'));
    set(tmpFig,'Visible','on');
end

guidata(hObject,handles);

%% Callbacks & Functions for color setting
function UpdateColormapOptions(handles)

if isfield(handles,'colormapLocked') && handles.colormapLocked
    return;
end

selectionIndex = get(handles.popupmenu_chooseColorData,'Value');

cMapSelectionIndex = get(handles.popupmenu_chooseColormap,'Value');
cMapStrings = get(handles.popupmenu_chooseColormap,'String');

if selectionIndex > 1
    set(handles.uitoggletool8,'State','on');
else
    set(handles.uitoggletool8,'State','off');
end

try
    if selectionIndex == 2
        ct = evalin('base','ct');
        currentMap = handles.ctColorMap;
        window = handles.dispWindow{selectionIndex,1};
        if handles.cubeHUavailable
            minMax = [min(ct.cubeHU{1}(:)) max(ct.cubeHU{1}(:))];
        else
            minMax = [min(ct.cube{1}(:)) max(ct.cube{1}(:))];
        end
        % adjust value for custom window to current
        handles.windowPresets(1).width = max(window) - min(window);
        handles.windowPresets(1).center = mean(window);
        % update full window information
        handles.windowPresets(2).width = minMax(2) - minMax(1);
        handles.windowPresets(2).center = mean(minMax);
    elseif selectionIndex == 3
        result = evalin('base','resultGUI');
        dose = result.(handles.SelectedDisplayOption);
        currentMap = handles.doseColorMap;
        minMax = [min(dose(:)) max(dose(:))];
        window = handles.dispWindow{selectionIndex,1};
    else
        window = [0 1];
        minMax = window;
        currentMap = 'bone';
    end
catch
    window = [0 1];
    minMax = window;
    currentMap = 'bone';
end

valueRange = minMax(2) - minMax(1);

windowWidth = window(2) - window(1);
windowCenter = mean(window);

%This are some arbritrary settings to configure the sliders
sliderCenterMinMax = [minMax(1)-valueRange/2 minMax(2)+valueRange/2];
sliderWidthMinMax = [0 valueRange*2];

%if we have selected a value outside this range, we adapt the slider
%windows
if windowCenter < sliderCenterMinMax(1)
    sliderCenterMinMax(1) = windowCenter;
end
if windowCenter > sliderCenterMinMax(2)
    sliderCenterMinMax(2) = windowCenter;
end
if windowWidth < sliderWidthMinMax(1)
    sliderWidthMinMax(1) = windowWidth;
end
if windowCenter > sliderCenterMinMax(2)
    sliderWidthMinMax(2) = windowWidth;
end

set(handles.edit_windowCenter,'String',num2str(windowCenter,3));
set(handles.edit_windowWidth,'String',num2str(windowWidth,3));
set(handles.edit_windowRange,'String',num2str(window,4));
set(handles.slider_windowCenter,'Min',sliderCenterMinMax(1),'Max',sliderCenterMinMax(2),'Value',windowCenter);
set(handles.slider_windowWidth,'Min',sliderWidthMinMax(1),'Max',sliderWidthMinMax(2),'Value',windowWidth);

cMapPopupIndex = find(strcmp(currentMap,cMapStrings));
set(handles.popupmenu_chooseColormap,'Value',cMapPopupIndex);

guidata(gcf,handles);

% --- Executes on selection change in popupmenu_chooseColorData.
function popupmenu_chooseColorData_Callback(hObject, eventdata, handles)
% hObject    handle to popupmenu_chooseColorData (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: contents = cellstr(get(hObject,'String')) returns popupmenu_chooseColorData contents as cell array
%        contents{get(hObject,'Value')} returns selected item from popupmenu_chooseColorData

%index = get(hObject,'Value') - 1;

handles.cBarChanged = true;

guidata(hObject,handles);
UpdatePlot(handles);

% --- Executes during object creation, after setting all properties.
function popupmenu_chooseColorData_CreateFcn(hObject, eventdata, handles)
% hObject    handle to popupmenu_chooseColorData (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: popupmenu controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

% --- Executes on slider movement.
function slider_windowCenter_Callback(hObject, eventdata, handles)
% hObject    handle to slider_windowCenter (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'Value') returns position of slider
%        get(hObject,'Min') and get(hObject,'Max') to determine range of slider

newCenter      = get(hObject,'Value');
range          = get(handles.slider_windowWidth,'Value');
selectionIndex = get(handles.popupmenu_chooseColorData,'Value');

handles.dispWindow{selectionIndex,1}  = [newCenter-range/2 newCenter+range/2];
handles.cBarChanged = true;

guidata(hObject,handles);
UpdatePlot(handles);

% --- Executes during object creation, after setting all properties.
function slider_windowCenter_CreateFcn(hObject, eventdata, handles)
% hObject    handle to slider_windowCenter (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor',[.9 .9 .9]);
end

set(hObject,'Value',0.5);

% --- Executes on slider movement.
function slider_windowWidth_Callback(hObject, eventdata, handles)
% hObject    handle to slider_windowWidth (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'Value') returns position of slider
%        get(hObject,'Min') and get(hObject,'Max') to determine range of slider

newWidth = get(hObject,'Value');
center   = get(handles.slider_windowCenter,'Value');
selectionIndex                        = get(handles.popupmenu_chooseColorData,'Value');
handles.dispWindow{selectionIndex,1}  = [center-newWidth/2 center+newWidth/2];
handles.cBarChanged = true;

guidata(hObject,handles);
UpdatePlot(handles);

% --- Executes during object creation, after setting all properties.
function slider_windowWidth_CreateFcn(hObject, eventdata, handles)
% hObject    handle to slider_windowWidth (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor',[.9 .9 .9]);
end

set(hObject,'Value',1.0);

% --- Executes on selection change in popupmenu_chooseColormap.
function popupmenu_chooseColormap_Callback(hObject, eventdata, handles)
% hObject    handle to popupmenu_chooseColormap (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: contents = cellstr(get(hObject,'String')) returns popupmenu_chooseColormap contents as cell array
%        contents{get(hObject,'Value')} returns selected item from popupmenu_chooseColormap

index = get(hObject,'Value');
strings = get(hObject,'String');

selectionIndex = get(handles.popupmenu_chooseColorData,'Value');

switch selectionIndex
    case 2
        handles.ctColorMap = strings{index};
    case 3
        handles.doseColorMap = strings{index};
    otherwise
end

handles.cBarChanged = true;

guidata(hObject,handles);
UpdatePlot(handles);

% --- Executes during object creation, after setting all properties.
function popupmenu_chooseColormap_CreateFcn(hObject, eventdata, handles)
% hObject    handle to popupmenu_chooseColormap (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: popupmenu controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

function edit_windowRange_Callback(hObject, eventdata, handles)
% hObject    handle to edit_windowRange (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of edit_windowRange as text
%        str2double(get(hObject,'String')) returns contents of edit_windowRange as a double

selectionIndex = get(handles.popupmenu_chooseColorData,'Value');
vRange         = str2num(get(hObject,'String'));
% matlab adds a zero in the beginning when text field is changed
if numel(vRange) == 3
    vRange = vRange(vRange~=0);
end

handles.dispWindow{selectionIndex,1} = sort(vRange);

handles.cBarChanged = true;

    % compute new iso dose lines
if selectionIndex > 2
    guidata(hObject,handles);
    handles = updateIsoDoseLineCache(handles);
end

guidata(hObject,handles);
UpdatePlot(handles);

% --- Executes during object creation, after setting all properties.
function edit_windowRange_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit_windowRange (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

set(hObject,'String','0 1');

function edit_windowCenter_Callback(hObject, eventdata, handles)
% hObject    handle to edit_windowCenter (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of edit_windowCenter as text
%        str2double(get(hObject,'String')) returns contents of edit_windowCenter as a double

newCenter           = str2double(get(hObject,'String'));
width               = get(handles.slider_windowWidth,'Value');
selectionIndex      = get(handles.popupmenu_chooseColorData,'Value');
handles.dispWindow{selectionIndex,1}  = [newCenter-width/2 newCenter+width/2];
handles.cBarChanged = true;
guidata(hObject,handles);
UpdatePlot(handles);

% --- Executes during object creation, after setting all properties.
function edit_windowCenter_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit_windowCenter (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

function edit_windowWidth_Callback(hObject, eventdata, handles)
% hObject    handle to edit_windowWidth (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of edit_windowWidth as text
%        str2double(get(hObject,'String')) returns contents of edit_windowWidth as a double

newWidth            = str2double(get(hObject,'String'));
center              = get(handles.slider_windowCenter,'Value');
selectionIndex      = get(handles.popupmenu_chooseColorData,'Value');
handles.dispWindow{selectionIndex,1}  = [center-newWidth/2 center+newWidth/2];
handles.cBarChanged = true;
guidata(hObject,handles);
UpdatePlot(handles);

% --- Executes during object creation, after setting all properties.
function edit_windowWidth_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit_windowWidth (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

% --------------------------------------------------------------------
function uitoggletool8_ClickedCallback(hObject, eventdata, handles)
% hObject    handle to uitoggletool8 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

%Check if on or off
val = strcmp(get(hObject,'State'),'on');

%Now we have to apply the new selection to our colormap options panel
if ~val
    newSelection = 1;
else
    %Chooses the selection from the highest state
    selections = get(handles.popupmenu_chooseColorData,'String');
    newSelection = numel(selections);
end
set(handles.popupmenu_chooseColorData,'Value',newSelection);

handles.cBarChanged = true;
guidata(hObject,handles);
UpdatePlot(handles);

% --- Executes on slider movement.
function sliderOpacity_Callback(hObject, eventdata, handles)
% hObject    handle to sliderOpacity (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
handles.doseOpacity = get(hObject,'Value');
guidata(hObject,handles);
UpdatePlot(handles);

% --- Executes during object creation, after setting all properties.
function sliderOpacity_CreateFcn(hObject, eventdata, handles)
% hObject    handle to sliderOpacity (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor',[.9 .9 .9]);
end

%% Data Cursors
function cursorText = dataCursorUpdateFunction(obj,event_obj)
% Display the position of the data cursor
% obj          Currently not used (empty)
% event_obj    Handle to event object
% output_txt   Data cursor text string (string or cell array of strings).

target = findall(0,'Name','matRadGUI');

% Get GUI data (maybe there is another way?)
handles = guidata(target);

% position of the data point to label
pos = get(event_obj,'Position');

%Different behavior for image and profile plot
if get(handles.popupTypeOfPlot,'Value')==1 %Image view
    cursorText = cell(0,1);
    try
        if handles.State >= 1
            plane = get(handles.popupPlane,'Value');
            slice = round(get(handles.sliderSlice,'Value'));

            %Get the CT values
            ct  = evalin('base','ct');

            %We differentiate between pos and ix, since the user may put
            %the datatip on an isoline which returns a continous position
            cubePos = zeros(1,3);
            cubePos(plane) = slice;
            cubePos(1:end ~= plane) = fliplr(pos);
            cubeIx = round(cubePos);

            %Here comes the index permutation stuff
            %Cube Index
            cursorText{end+1,1} = ['Cube Index: ' mat2str(cubeIx)];
            %Space Coordinates
            coords = zeros(1,3);
            coords(1) = cubePos(2)*ct.resolution.y;
            coords(2) = cubePos(1)*ct.resolution.x;
            coords(3) = cubePos(3)*ct.resolution.z;
            cursorText{end+1,1} = ['Space Coordinates: ' mat2str(coords,5) ' mm'];

            ctVal = ct.cubeHU{1}(cubeIx(1),cubeIx(2),cubeIx(3));
            cursorText{end+1,1} = ['HU Value: ' num2str(ctVal,3)];
        end

        %Add dose information if available
        if handles.State == 3
            %get result structure
            result = evalin('base','resultGUI');

            %Get all result names from popup
            resultNames = get(handles.popupDisplayOption,'String');

            %Display all values of fields found in the resultGUI struct
            for runResult = 1:numel(resultNames)
                name = resultNames{runResult};
                if isfield(result,name)
                    field = result.(name);
                    val = field(cubeIx(1),cubeIx(2),cubeIx(3));
                    cursorText{end+1,1} = [name ': ' num2str(val,3)];
                end
            end
        end
    catch
        cursorText{end+1,1} = 'Error while retreiving Data!';
    end
else %Profile view
    cursorText = cell(2,1);
    cursorText{1} = ['Radiological Depth: ' num2str(pos(1),3) ' mm'];
    cursorText{2} = [get(target,'DisplayName') ': ' num2str(pos(2),3)];
end

% --- Executes on selection change in popMenuBioOpt.
function popMenuBioOpt_Callback(hObject, ~, handles)
pln = evalin('base','pln');
contentBioOpt = get(handles.popMenuBioOpt,'String');
NewBioOptimization = contentBioOpt(get(handles.popMenuBioOpt,'Value'),:);

if handles.State > 0
    if (strcmp(pln.propOpt.bioOptimization,'LEMIV_effect') && strcmp(NewBioOptimization,'LEMIV_RBExD')) ||...
       (strcmp(pln.propOpt.bioOptimization,'LEMIV_RBExD') && strcmp(NewBioOptimization,'LEMIV_effect'))
       % do nothing - re-optimization is still possible
    elseif ((strcmp(pln.propOpt.bioOptimization,'const_RBE') && strcmp(NewBioOptimization,'none')) ||...
           (strcmp(pln.propOpt.bioOptimization,'none') && strcmp(NewBioOptimization,'const_RBE'))) && isequal(pln.radiationMode,'protons')
       % do nothing - re-optimization is still possible
    else
        handles.State = 1;
    end
end
getPlnFromGUI(handles);

UpdateState(handles);
guidata(hObject,handles);

% --- Executes during object creation, after setting all properties.
function popMenuBioOpt_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

% --- Executes on button press in btn3Dview.
function btn3Dview_Callback(hObject, eventdata, handles)
% hObject    handle to btn3Dview (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

if ~isfield(handles,'axesFig3D') || ~isfield(handles,'axesFig3D') || ~isgraphics(handles.axesFig3D)
    handles.fig3D = figure('Name','matRad 3D View');
    handles.axesFig3D = axes('Parent',handles.fig3D);
    view(handles.axesFig3D,3);
    try
        ct = evalin('base','ct');

        xlim(handles.axesFig3D,[0 ct.resolution.x*ct.cubeDim(2)]);
        ylim(handles.axesFig3D,[0 ct.resolution.y*ct.cubeDim(1)]);
        zlim(handles.axesFig3D,[0 ct.resolution.z*ct.cubeDim(3)]);
    catch
    end
end
%end

UpdatePlot(handles);

guidata(hObject,handles);

% --- Executes on button press in radiobtnCT.
function radiobtnCT_Callback(hObject, eventdata, handles)
% hObject    handle to radiobtnCT (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of radiobtnCT
UpdatePlot(handles)

% --- Executes on button press in radiobtnPlan.
function radiobtnPlan_Callback(hObject, eventdata, handles)
% hObject    handle to radiobtnPlan (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of radiobtnPlan
UpdatePlot(handles)

% --- Executes on selection change in popupmenu_windowPreset.
function popupmenu_windowPreset_Callback(hObject, eventdata, handles)
% hObject    handle to popupmenu_windowPreset (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: contents = cellstr(get(hObject,'String')) returns popupmenu_windowPreset contents as cell array
%        contents{get(hObject,'Value')} returns selected item from popupmenu_windowPreset

selectionIndexCube      = 2; % working on ct only
selectionIndexWindow    = get(handles.popupmenu_windowPreset,'Value');
newCenter               = handles.windowPresets(selectionIndexWindow).center;
newWidth                = handles.windowPresets(selectionIndexWindow).width;

handles.dispWindow{selectionIndexCube,1}  = [newCenter - newWidth/2 newCenter + newWidth/2];
handles.cBarChanged = true;
guidata(hObject,handles);
UpdatePlot(handles);
UpdateColormapOptions(handles);

% --- Executes during object creation, after setting all properties.
function popupmenu_windowPreset_CreateFcn(hObject, eventdata, handles)
% hObject    handle to popupmenu_windowPreset (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: popupmenu controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

% setup ct window list
% data and values from CERR https://github.com/adityaapte/CERR
windowNames = {'Custom','Full','Abd/Med', 'Head', 'Liver', 'Lung', 'Spine', 'Vrt/Bone'};
windowCenter = {NaN, NaN, -10, 45, 80, -500, 30, 400};
windowWidth = {NaN, NaN, 330, 125, 305, 1500, 300, 1500};
windowPresets = cell2struct([windowNames', windowCenter', windowWidth'], {'name', 'center', 'width'},2);

handles.windowPresets = windowPresets;

selectionList = {windowPresets(:).name};
set(hObject,'String',selectionList(:));
set(hObject,'Value',1);

guidata(hObject,handles);

% --- Executes on button press in checkbox_lockColormap.
function checkbox_lockColormap_Callback(hObject, eventdata, handles)
% hObject    handle to checkbox_lockColormap (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of checkbox_lockColormap
handles.colormapLocked = get(hObject,'Value');

if handles.colormapLocked
    state = 'Off'; %'Inactive';
else
    state = 'On';
end

set(handles.popupmenu_chooseColorData,'Enable',state);
set(handles.popupmenu_windowPreset,'Enable',state);
set(handles.slider_windowWidth,'Enable',state);
set(handles.slider_windowCenter,'Enable',state);
set(handles.edit_windowWidth,'Enable',state);
set(handles.edit_windowCenter,'Enable',state);
set(handles.edit_windowRange,'Enable',state);
set(handles.popupmenu_chooseColormap,'Enable',state);

guidata(hObject,handles);

function cst = updateStructureTable(handles,cst)
colorAssigned = true;

% check whether all structures have an assigned color
for i = 1:size(cst,1)
    if ~isfield(cst{i,5},'visibleColor')
        colorAssigned = false;
        break;
    elseif isempty(cst{i,5}.visibleColor)
        colorAssigned = false;
        break;
    end
end

% assign color if color assignment is not already present or inconsistent
if colorAssigned == false
  m         = 64;
  colorStep = ceil(m/size(cst,1));
  colors    = colorcube(colorStep*size(cst,1));
  % spread individual VOI colors in the colorcube color palette
  colors    = colors(1:colorStep:end,:);

  for i = 1:size(cst,1)
    cst{i,5}.visibleColor = colors(i,:);
  end
end

for s = 1:size(cst,1)
    handles.VOIPlotFlag(s) = cst{s,5}.Visible;
    clr = dec2hex(round(cst{s,5}.visibleColor(:)*255),2)';
    clr = ['#';clr(:)]';
    if handles.VOIPlotFlag(s)
        tmpString{s} = ['<html><table border=0 ><TR><TD bgcolor=',clr,' width="18"><center>✔</center></TD><TD>',cst{s,2},'</TD></TR> </table></html>'];
    else
        tmpString{s} = ['<html><table border=0 ><TR><TD bgcolor=',clr,' width="18"></TD><TD>',cst{s,2},'</TD></TR> </table></html>'];
    end
end
set(handles.legendTable,'String',tmpString);

%-- generates the CST table
function cst = generateCstTable(handles,cst)

cst = updateStructureTable(handles,cst);

cstPanel = handles.uipanel3;

%Get units in pixels to to calculate aspect ratio
cstPanelPosUnit = get(cstPanel,'Units');
set(cstPanel,'Units','pixels');
cstPanelPosPix = get(cstPanel,'Position');
set(cstPanel,'Units',cstPanelPosUnit);

aspectRatio = cstPanelPosPix(3) / cstPanelPosPix(4);

%Parameters for line height
objHeight = 0.095;% 22;
lineHeight = 0.1; %25; %Height of a table line
yTopSep = 0.12;%40; %Separation of the first line from the top
tableViewHeight = 1 - yTopSep;

%Define the widths of the fields relatively
buttonW = objHeight / aspectRatio; % Make button squared
nameW = 3.5*buttonW;
typeW = 3*buttonW;
opW = buttonW;
functionW = 6*buttonW;
penaltyW = 2*buttonW;
paramTitleW = 4*buttonW;
paramW = 2*buttonW;
fieldSep = 0.25*buttonW; %Separation between fields horizontally

%Scrollbar
%Check if a scrollbar already exists to get possible position of slider
cstPanelChildren = get(cstPanel,'Children');
cstVertTableScroll = findobj(cstPanelChildren,'Style','slider');
if isempty(cstVertTableScroll)
    sliderPos = 0;
else
    sliderPos = get(cstVertTableScroll,'Max') - get(cstVertTableScroll,'Value');
end

ypos = @(c) tableViewHeight - c*lineHeight + sliderPos;

%Clean the whole panel for new setup
delete(cstPanelChildren);

%Creates a dummy axis to allow for the use of textboxes instead of uicontrol to be able to use the (la)tex interpreter
tmpAxes = axes('Parent',cstPanel,'units','normalized','position',[0 0 1 1],'visible','off');

organTypes = {'OAR', 'TARGET'};

%columnname = {'VOI name','VOI type','priority','obj. / const.'};%,'penalty','dose', 'EUD','volume','robustness'};

%Get all Classes & classNames
mpkgObjectives = meta.package.fromName('DoseObjectives');
mpkgConstraints = meta.package.fromName('DoseConstraints');
classList = [mpkgObjectives.ClassList; mpkgConstraints.ClassList];

classList = classList(not([classList.Abstract]));

%Now get the "internal" name from the properties
classNames = cell(2,numel(classList));
for clIx = 1:numel(classList)
    cl = classList(clIx);
    pList = cl.PropertyList; %Get List of all properties
    pNameIx = arrayfun(@(p) strcmp(p.Name,'name'),pList); %get index of the "name" property
    p = pList(pNameIx); %select name property
    pName = p.DefaultValue; % get value / name
    classNames(:,clIx) = {cl.Name; pName}; %Store class name and display name
end

numOfObjectives = sum(cellfun(@numel,cst(:,6)));

cnt = 0;

newline = '\n';

%Setup Headlines
xPos = 0.01; %5

h = uicontrol(cstPanel,'Style','text','String','+/-','Units','normalized','Position',[xPos ypos(cnt) buttonW objHeight],'TooltipString','Remove or add Constraint or Objective');
tmp_pos = get(h,'Position');
xPos = xPos + tmp_pos(3) + fieldSep;
h = uicontrol(cstPanel,'Style','text','String','VOI name','Units','normalized','Position',[xPos ypos(cnt) nameW objHeight],'TooltipString','Name of the structure with objective/constraint');
tmp_pos = get(h,'Position');
xPos = xPos + tmp_pos(3) + fieldSep;
h = uicontrol(cstPanel,'Style','text','String','VOI type','Units','normalized','Position',[xPos ypos(cnt) typeW objHeight],'TooltipString','Segmentation Classification');
tmp_pos = get(h,'Position');
xPos = xPos + tmp_pos(3) + fieldSep;
h = uicontrol(cstPanel,'Style','text','String','OP','Units','normalized','Position',[xPos ypos(cnt) opW objHeight],'TooltipString',['Overlap Priority' char(10) '(Smaller number overlaps higher number)']);
tmp_pos = get(h,'Position');
xPos = xPos + tmp_pos(3) + fieldSep;
h = uicontrol(cstPanel,'Style','text','String','Function','Units','normalized','Position',[xPos ypos(cnt) functionW objHeight],'TooltipString','Objective/Constraint function type');
tmp_pos = get(h,'Position');
xPos = xPos + tmp_pos(3) + fieldSep;
h = uicontrol(cstPanel,'Style','text','String','p','Units','normalized','Position',[xPos ypos(cnt) penaltyW objHeight],'TooltipString','Optimization penalty');
tmp_pos = get(h,'Position');
xPos = xPos + tmp_pos(3) + fieldSep;
h = uicontrol(cstPanel,'Style','text','String','| Parameters','Units','normalized','Position',[xPos ypos(cnt) paramTitleW objHeight],'TooltipString','List of parameters','HorizontalAlignment','left');
tmp_pos = get(h,'Position');
xPos = xPos + tmp_pos(3) + fieldSep;
cnt = cnt + 1;

%Create Objectives / Constraints controls
for i = 1:size(cst,1)
    if strcmp(cst(i,3),'IGNORED')~=1
        %Compatibility Layer for old objective format
        if isstruct(cst{i,6})
            cst{i,6} = arrayfun(@matRad_DoseOptimizationFunction.convertOldOptimizationStruct,cst{i,6},'UniformOutput',false);
        end
        for j=1:numel(cst{i,6})

           obj = cst{i,6}{j};

           %Convert to class if not
           if ~isa(obj,'matRad_DoseOptimizationFunction')
                try
                    obj = matRad_DoseOptimizationFunction.createInstanceFromStruct(obj);
                catch ME
                    warning('Objective/Constraint not valid!\n%s',ME.message)
                    continue;
                end
           end

           %VOI
           xPos = 0.01;%5;

           h = uicontrol(cstPanel,'Style','pushbutton','String','-','Units','normalized','Position',[xPos ypos(cnt) buttonW objHeight],'TooltipString','Remove Objective/Constraint','Callback',{@btObjRemove_Callback,handles},...
               'UserData',[i,j]);
           tmp_pos = get(h,'Position');
           xPos = xPos + tmp_pos(3) + fieldSep;
           h = uicontrol(cstPanel','Style','edit','String',cst{i,2},'Units','normalized','Position',[xPos ypos(cnt) nameW objHeight],'TooltipString','Name',...
               'Enable','inactive',... %Disable editing of name atm
               'UserData',[i,2],'Callback',{@editCstParams_Callback,handles}); %Callback added, however, editing is disabled atm
           tmp_pos = get(h,'Position');
           xPos = xPos + tmp_pos(3) + fieldSep;
           h = uicontrol(cstPanel,'Style','popupmenu','String',organTypes','Value',find(strcmp(cst{i,3},organTypes)),'Units','normalized','Position',[xPos ypos(cnt) typeW objHeight],'TooltipString','Segmentation Classification',...
               'UserData',[i,3],'Callback',{@editCstParams_Callback,handles});
           tmp_pos = get(h,'Position');
           xPos = xPos + tmp_pos(3) + fieldSep;
           h = uicontrol(cstPanel,'Style','edit','String',num2str(cst{i,5}.Priority),'Units','normalized','Position',[xPos ypos(cnt) opW objHeight],'TooltipString',['Overlap Priority' newline '(Smaller number overlaps higher number)'],...
               'UserData',[i,5],'Callback',{@editCstParams_Callback,handles});
           tmp_pos = get(h,'Position');
           xPos = xPos + tmp_pos(3) + fieldSep;

           h = uicontrol(cstPanel,'Style','popupmenu','String',classNames(2,:)','Value',find(strcmp(obj.name,classNames(2,:))),'Units','normalized','Position',[xPos ypos(cnt) functionW objHeight],'TooltipString','Select Objective/Constraint',...
               'UserData',{[i,j],classNames(1,:)},'Callback',{@changeObjFunction_Callback,handles});
           tmp_pos = get(h,'Position');
           xPos = xPos + tmp_pos(3) + fieldSep;

           %Check if we have an objective to display penalty
           if isa(obj,'DoseObjectives.matRad_DoseObjective')
               h = uicontrol(cstPanel,'Style','edit','String',num2str(obj.penalty),'Units','normalized','Position',[xPos ypos(cnt) penaltyW objHeight],'TooltipString','Objective Penalty','UserData',[i,j,0],'Callback',{@editObjParam_Callback,handles});
           else
               h = uicontrol(cstPanel,'Style','edit','String','----','Units','normalized','Position',[xPos ypos(cnt) penaltyW objHeight],'Enable','off');
           end
           tmp_pos = get(h,'Position');
           xPos = xPos + tmp_pos(3) + fieldSep;

           %Iterate through parameters
           for p = 1:numel(obj.parameterNames)
              h = text('Parent',tmpAxes,'String',['| ' obj.parameterNames{p} ':'],'VerticalAlignment','middle','Units','normalized','Position',[xPos ypos(cnt)+lineHeight/2],'Interpreter','tex','FontWeight','normal',...
                  'FontSize',get(cstPanel,'FontSize'),'FontName',get(cstPanel,'FontName'),'FontUnits',get(cstPanel,'FontUnits'),'FontWeight','normal');
              tmp_pos = get(h,'Extent');
              xPos = xPos + tmp_pos(3) + fieldSep;

              %Check if we have a cell and therefore a parameter list
              if iscell(obj.parameterTypes{p})
                  h = uicontrol(cstPanel,'Style','popupmenu','String',obj.parameterTypes{p}','Value',obj.parameters{p},'TooltipString',obj.parameterNames{p},'Units','normalized','Position',[xPos ypos(cnt) paramW*2 objHeight],'UserData',[i,j,p],'Callback',{@editObjParam_Callback,handles});
              else
                h = uicontrol(cstPanel,'Style','edit','String',num2str(obj.parameters{p}),'TooltipString',obj.parameterNames{p},'Units','normalized','Position',[xPos ypos(cnt) paramW objHeight],'UserData',[i,j,p],'Callback',{@editObjParam_Callback,handles});
              end

              tmp_pos = get(h,'Position');
              xPos = xPos + tmp_pos(3) + fieldSep;
           end

           cnt = cnt +1;
       end
   end
end
xPos = 0.01; %5
hAdd = uicontrol(cstPanel,'Style','pushbutton','String','+','Units','normalized','Position',[xPos ypos(cnt) buttonW objHeight],'TooltipString','Add Objective/Constraint','Callback',{@btObjAdd_Callback,handles});
tmp_pos = get(hAdd,'Position');
xPos = xPos + tmp_pos(3) + fieldSep;
h = uicontrol(cstPanel,'Style','popupmenu','String',cst(:,2)','Units','normalized','Position',[xPos ypos(cnt) nameW objHeight]);
set(hAdd,'UserData',h);

%Calculate Scrollbar / Slider Position
lastPos = ypos(cnt);
firstPos = ypos(0);
tableHeight = abs(firstPos - lastPos);

exceedFac = tableHeight / tableViewHeight; %How much the current umber of rows exceeds the window height capacity
if exceedFac > 1
    sliderFac = exceedFac - 1;
    uicontrol(cstPanel,'Style','slider','Units','normalized','Position',[0.975 0 0.025 1],'Min',0,'Max',ceil(sliderFac)*tableViewHeight,'SliderStep',[lineHeight tableViewHeight] ./ (ceil(sliderFac)*tableViewHeight),'Value',ceil(sliderFac)*tableViewHeight - sliderPos,'Callback',{@cstTableSlider_Callback,handles});
end

% --- Executes when uipanel3 is resized.
function uipanel3_SizeChangedFcn(hObject, eventdata, handles)
% hObject    handle to uipanel3 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

try
    generateCstTable(handles,evalin('base','cst'));
catch
end

function btObjAdd_Callback(hObject, ~, handles)
% hObject    handle to btObjAdd
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
popupHandle = hObject.UserData;
cstIndex = popupHandle.Value;

cst = evalin('base','cst');
%Add Standard Objective
if strcmp(cst{cstIndex,3},'TARGET')
    cst{cstIndex,6}{end+1} = struct(DoseObjectives.matRad_SquaredDeviation);
else
    cst{cstIndex,6}{end+1} = struct(DoseObjectives.matRad_SquaredOverdosing);
end

assignin('base','cst',cst);

generateCstTable(handles,cst);

function btObjRemove_Callback(hObject, ~, handles)
% hObject    handle to btObjRemove (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
ix = hObject.UserData;

cst = evalin('base','cst');
%Add Standard Objective

cst{ix(1),6}(ix(2)) = [];

assignin('base','cst',cst);

generateCstTable(handles,cst);

function editObjParam_Callback(hObject, ~, handles)
% hObject    handle to current objective parameter
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
ix = hObject.UserData;

cst = evalin('base','cst');
%Add Standard Objective

%if the third index is 0 we changed the penalty
%if we have a popupmenu selection we use value
%otherwise we use the edit string

if ix(3) == 0
    cst{ix(1),6}{ix(2)}.penalty = str2double(hObject.String);
elseif isequal(hObject.Style,'popupmenu')
    cst{ix(1),6}{ix(2)}.parameters{ix(3)} = hObject.Value;
else
    cst{ix(1),6}{ix(2)}.parameters{ix(3)} = str2double(hObject.String);
end

assignin('base','cst',cst);

generateCstTable(handles,cst);

function changeObjFunction_Callback(hObject, ~, handles)
% hObject    handle to objective popup
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
data = hObject.UserData;
ix = data{1};
classNames = data{2};
classToCreate = classNames{hObject.Value};

cst = evalin('base','cst');
%Add Standard Objective

%We just check if the user really wanted to change the objective to be
%user-friendly
currentObj = cst{ix(1),6}{ix(2)};
currentClass = class(currentObj);
if ~strcmp(currentClass,classToCreate)
    newObj = eval(classToCreate);

    % Only if we have a penalty value for optimization, apply the new one
    % Maybe this check should be more exact?
    if (isfield(currentObj,'penalty') || isprop(currentObj,'penalty')) && isprop(newObj,'penalty')
        newObj.penalty = currentObj.penalty;
    end

    cst{ix(1),6}{ix(2)} = struct(newObj);

    assignin('base','cst',cst);

    generateCstTable(handles,cst);
end

function editCstParams_Callback(hObject,~,handles)
data = hObject.UserData;
ix = data(1);
col = data(2);

cst = evalin('base','cst');

switch col
    case 2
        cst{ix,col} = hObject.String;
    case 3
        cst{ix,col} = hObject.String{hObject.Value};
    case 5
        cst{ix,col}.Priority = uint32(str2double(hObject.String));
    otherwise
        warning('Wrong column assignment in GUI based cst setting');
end

assignin('base','cst',cst);

generateCstTable(handles,cst);

% --- Executes on button press in radiobutton3Dconf.
function radiobutton3Dconf_Callback(hObject, eventdata, handles)
% hObject    handle to radiobutton3Dconf (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of radiobutton3Dconf

function x = matRad_checkForConnectedBixelRows(stf)

x = true;

for i = 1:size(stf,2)

    bixelPos = reshape([stf(i).ray.rayPos_bev],3,[]);

    rowCoords = unique(bixelPos(3,:));

    for j = 1:numel(rowCoords)

        increments = diff(bixelPos(1,rowCoords(j) == bixelPos(3,:)));

        % if we find one not connected row -> return false
        if numel(unique(increments)) > 1
            x = false;
            return;
        end
    end

end

% --- Executes on slider movement.
function cstTableSlider_Callback(hObject, eventdata, handles)
% hObject    handle to cstTableSlider (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'Value') returns position of slider
%        get(hObject,'Min') and get(hObject,'Max') to determine range of slider
generateCstTable(handles,evalin('base','cst'));

% --- Executes during object creation, after setting all properties.
function cstTableSlider_CreateFcn(hObject, eventdata, handles)
% hObject    handle to cstTableSlider (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor',[.9 .9 .9]);
end

repo: matRad