Merge branch 'dev_classGUI' into dev_classGUI_a

HomolkaN · Jan 4, 2023 · ecc6e0c · ecc6e0c
2 parents 8c9f8ee + 671baea
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diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -1,5 +1,5 @@
 # This is a basic workflow to help you get started with Actions
-name: Testing
+name: Tests
 # Controls when the action will run. 
 on: [push, pull_request, workflow_dispatch]  
 jobs:

diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,123 @@
+cff-version: 1.2.0
+message: "If you use matRad, consider citing it and the corresponding research paper"
+authors:
+- family-names: "Ackermann"
+  given-names: "Benjamin"
+- family-names: "Bangert"
+  given-names: "Mark"
+- family-names: "Bennan"
+  given-names: "Amit Ben Antony"
+- family-names: "Burigo"
+  given-names: "Lucas"
+- family-names: "Cabal"
+  given-names: "Gonzalo"
+- family-names: "Cisternas"
+  given-names: "Eduardo"
+- family-names: "Charton"
+  given-names: "Louis"
+- family-names: "Christiansen"
+  given-names: "Eric"
+- family-names: "Ecker"
+  given-names: "Swantje"
+- family-names: "Ellerbrock"
+  given-names: "Malte"
+- family-names: "Gabryś"
+  given-names: "Hubert"
+- family-names: "Handrack"
+  given-names: "Josefine"
+- family-names: "Heath"
+  given-names: "Emily"
+- family-names: "Hermann"
+  given-names: "Cindy"
+- family-names: "Homolka"
+  given-names: "Noa"
+- family-names: "Jäkel"
+  given-names: "Oliver"
+- family-names: "Klinge"
+  given-names: "Thomas"
+- family-names: "Mairani"
+  given-names: "Andrea"
+- family-names: "Mescher"
+  given-names: "Hennig"
+- family-names: "Müller"
+  given-names: "Lucas-Raphael"
+- family-names: "Neishabouri"
+  given-names: "Ahmad"
+- family-names: "Palkowitsch"
+  given-names: "Martina"
+- family-names: "Parodi"
+  given-names: "Katia"
+- family-names: "Pezzano"
+  given-names: "Giuseppe"
+- family-names: "Ramirez"
+  given-names: "Daniel"
+- family-names: "Stadler"
+  given-names: "Alexander"
+- family-names: "Ulrich"
+  given-names: "Silke"
+- family-names: "Wahl"
+  given-names: "Niklas"
+  orcid: "https://orcid.org/0000-0002-1451-223X"
+- family-names: "Welsch"
+  given-names: "Jona"
+- family-names: "Wieser"
+  given-names: "Hans-Peter"
+- family-names: "Winter"
+  given-names: "Johanna"
+- family-names: "Xu"
+  given-names: "Tong" 
+
+title: "matRad"
+version: 2.10.1
+doi: 10.5281/zenodo.3879616
+date-released: 2020-06-05
+url: "http://www.matRad.org"
+location: "Heidelberg"
+organization: "Deutsches Krebsforschungszentrum"
+preferred-citation:
+  type: article
+  authors:
+  - family-names: "Wieser"
+    given-names: "Hans-Peter"
+  - family-names: "Cisternas"
+    given-names: "Eduardo"
+  - family-names: "Wahl"
+    given-names: "Niklas"
+    orcid: "https://orcid.org/0000-0002-1451-223X"
+  - family-names: "Ulrich"
+    given-names: "Silke"
+  - family-names: "Stadler"
+    given-names: "Alexander"
+  - family-names: "Mescher"
+    given-names: "Hennig"
+  - family-names: "Müller"
+    given-names: "Lucas-Raphael"
+  - family-names: "Klinge"
+    given-names: "Thomas"
+  - family-names: "Gabryś"
+    given-names: "Hubert"
+  - family-names: "Burigo"
+    given-names: "Lucas"
+  - family-names: "Mairani"
+    given-names: "Andrea"
+  - family-names: "Ecker"
+    given-names: "Swantje"
+  - family-names: "Ackermann"
+    given-names: "Benjamin"
+  - family-names: "Ellerbrock"
+    given-names: "Malte"
+  - family-names: "Parodi"
+    given-names: "Katia"
+  - family-names: "Jäkel"
+    given-names: "Oliver"
+  - family-names: "Bangert"
+    given-names: "Mark"
+
+  doi: 10.1002/mp.12251
+  journal: "Medical Physics"
+  start: 2556 
+  end: 2568
+  title: "Development of the open-source dose calculation and optimization toolkit matRad"
+  issue: 6
+  volume: 46
+  year: 2017
diff --git a/MatRad_Config.m b/MatRad_Config.m
@@ -63,12 +63,15 @@
             %  Therefore its constructor is private
             %  For instantiation, use the static MatRad_Config.instance();
 
-            obj.matRadRoot = fileparts(mfilename('fullpath'));
+            obj.matRadRoot = fileparts(mfilename('fullpath'))
             addpath(genpath(obj.matRadRoot));
 
             %Set Version
             obj.getEnvironment();
-            obj.matRad_version = matRad_version();            
+            obj.matRad_version = matRad_version();
+
+            %Configure Environment
+            obj.configureEnvironment();
 
             %Just to catch people messing with the properties in the file
             if ~isempty(obj.writeLog) && obj.writeLog
@@ -186,6 +189,9 @@ function setDefaultProperties(obj)
             obj.propMC.direct_defaultHistories = 2e4;
 
             obj.disableGUI = false;
+
+            obj.devMode = false;
+            obj.eduMode = false;
         end
 
         %%For testing
@@ -221,6 +227,7 @@ function setDefaultPropertiesForTesting(obj)
             obj.propMC.direct_defaultHistories = 100;
 
             obj.disableGUI = true;
+
             obj.devMode = true;
             obj.eduMode = false;
         end  
@@ -252,8 +259,9 @@ function setDefaultPropertiesForEduMode(obj)
 
             obj.devMode = false;
             obj.eduMode = true;
-        end
 
+        end
+
         function setDefaultGUIProperties(obj)
            obj.gui.backgroundColor = [0.5 0.5 0.5];
            obj.gui.elementColor = [0.75 0.75 0.75];
@@ -263,7 +271,7 @@ function setDefaultGUIProperties(obj)
            obj.gui.fontWeight = 'bold';
            obj.gui.fontName = 'Helvetica';
         end
-        
+
         function dispDebug(obj,formatSpec,varargin)
             %dispDebug print debug messages (log level >= 4)
             %  input
@@ -353,6 +361,13 @@ function getEnvironment(obj)
 
             end
         end
+
+        function configureEnvironment(obj)
+            if obj.isOctave
+                struct_levels_to_print(0);                  %Disables full printing of struct array fields
+                warning("off","Octave:data-file-in-path");  %Disables warning of loading patients from the data folder
+            end
+        end
     end
 
     methods(Static)

diff --git a/README.md b/README.md
@@ -3,8 +3,8 @@
 [![Contributors](https://img.shields.io/github/contributors/e0404/matRad)](https://github.com/e0404/matRad/graphs/contributors)
 [![GitPitch](https://gitpitch.com/assets/badge.svg)](https://gitpitch.com/e0404/matRad/master) 
 
-[![TravisCI Build Status](https://travis-ci.org/e0404/matRad.svg?branch=dev)](https://travis-ci.org/e0404/matRad)
-[![Azure Pipelines Build Status](https://dev.azure.com/e0404/matRad/_apis/build/status/e0404.matRad?branchName=dev)](https://dev.azure.com/e0404/matRad)
+[![GitHub Build Status](https://github.com/e0404/matRad/actions/workflows/tests.yml/badge.svg)](https://github.com/e0404/matRad/actions/workflows/tests.yml)
+[![Azure Pipelines Build Status](https://dev.azure.com/e0404/matRad/_apis/build/status/e0404.matRad)](https://dev.azure.com/e0404/matRad)
 
 DOIs:
 - General DOI: [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.3879615.svg)](https://doi.org/10.5281/zenodo.3879615)
@@ -104,9 +104,16 @@ You can cite specific versions of matRad in your work! For example, Here is the
 
 [![DOI](https://zenodo.org/badge/29671667.svg)](https://zenodo.org/badge/latestdoi/29671667)
 
+# Funding Sources
+matRad developments (on this branch) were (in parts) funded by:
+- Grant  No. BA 2279/3-1 (Project No. 265744405) from the German Research Foundation (DFG)
+- Grant No. 70113094 from the German Cancer Aid
+- Grant No. WA 4707/1-1 (Project No. 443188743) from the German Research Foundation (DFG)
+- Mathworks Academic Research Support
+
 ---
 
-Copyright 2020 the matRad development team. 
+Copyright 2022 the matRad development team. 
 
 [email protected]
 

diff --git a/dicom/matRad_importDicom.m b/dicom/matRad_importDicom.m
@@ -142,10 +142,8 @@
     if ~(cellfun(@isempty,files.rtdose(1,1:2))) 
         fprintf('loading Dose files \n', structures(i).structName);
         % parse plan in order to scale dose cubes to a fraction based dose
-        if exist('pln','var')
-            if isfield(pln,'numOfFractions')
-                resultGUI = matRad_importDicomRTDose(ct, files.rtdose, pln);
-            end
+        if exist('pln','var') && ~isempty(pln) && isfield(pln,'numOfFractions')
+            resultGUI = matRad_importDicomRTDose(ct, files.rtdose, pln);
         else
             resultGUI = matRad_importDicomRTDose(ct, files.rtdose);
         end

diff --git a/gui/matRad_MainGUI.m b/gui/matRad_MainGUI.m
@@ -18,6 +18,7 @@
         ViewingWidget
         DVHStatsWidget
         GammaWidget
+
         eventListeners
 
         matRad_cfg = MatRad_Config.instance();
@@ -31,7 +32,9 @@
            folder = fileparts(mfilename('fullpath'));
            loadIcons = load(fullfile(folder,'matRad_iconsGUI.mat'),'icons');
            icons = loadIcons.icons;
+
            icons{end+1} = imread('icons8-gamma-16.png'); 
+
             h60 = uitoolbar(...
                 'Parent',h1,...
                 'Tag','uitoolbar1');
@@ -113,6 +116,7 @@
                 'ClickedCallback',@(hObject, eventdata)uitoggletool8_ClickedCallback(this, hObject, eventdata),...
                 'Separator','on',...
                 'TooltipString','Insert Colorbar' );
+
              h70 = uipushtool(...
                 'Parent',h60,...
                 'BusyAction','cancel',...
@@ -122,6 +126,7 @@
                 'ClickedCallback',@(hObject,eventdata)gammaWidget_ClickedCallback(this,hObject,eventdata),...
                 'Separator','on',...
                 'TooltipString','Gamma index tool' );
+
 
         end
     end
@@ -497,10 +502,12 @@ function toolbarLegend_ClickedCallback(this,hObject, eventdata)
            %set(this.ViewingWidget.legendHandle,'visible',get(hObject,'State'));
         end
 
+
          function gammaWidget_ClickedCallback(this,hObject,eventdata)
             this.GammaWidget = matRad_GammaWidget();
          end 
 
+
         function toolbarZoomIn_ClickedCallback(this,hObject, eventdata)
             set(this.ViewingWidget.zoomHandle,'Enable',char(get(hObject,'State')));
             set(this.ViewingWidget.zoomHandle,'Direction','in');

diff --git a/gui/matRad_Widget.m b/gui/matRad_Widget.m
@@ -1,4 +1,5 @@
 classdef matRad_Widget <  handle 
+
     % matRad_Widget Main Class for GUI widget generation 
     % Describes a standard fluence optimization problem by providing the 
     % implementation of the objective & constraint function/gradient wrappers
@@ -20,6 +21,7 @@
     % LICENSE file.
     %
     % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
 
     properties (GetAccess = public , SetAccess = protected)
         widgetHandle            %Holds parent widget handle

diff --git a/gui/widgets/matRad_3DWidget.m b/gui/widgets/matRad_3DWidget.m
@@ -1,4 +1,5 @@
 classdef matRad_3DWidget < matRad_ViewingWidget
+
     % matRad_3DWidget class to generate GUI widget for 3D plan visualization 
     % Describes a standard fluence optimization problem by providing the 
     % implementation of the objective & constraint function/gradient wrappers
@@ -20,6 +21,7 @@
     % LICENSE file.
     %
     % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
     properties
         viewingWidgetHandle;
     end

diff --git a/gui/widgets/matRad_DVHStatsWidget.m b/gui/widgets/matRad_DVHStatsWidget.m
@@ -1,4 +1,5 @@
 classdef matRad_DVHStatsWidget < matRad_Widget
+
     % matRad_DVHStatsWidget class to generate GUI widget display DVH and
     % stats
     % Describes a standard fluence optimization problem by providing the 
@@ -34,6 +35,7 @@
 
             matRad_cfg = MatRad_Config.instance();
             if nargin<2 %isempty(p.Results.handleParent)
+
                 handleParent = figure(...
                     'Units','normalized',...
                     'Position',[0.005 0.05 0.495 0.9],...
@@ -125,13 +127,10 @@ function removeOverlap(this)
 
             this.dvhWidgetHandle = matRad_DVHWidget([],p1);
             this.statWidgetHandle = matRad_StatisticsWidget([],p2);
-
             this.createHandles();
 
         end
 
-
-
     end
 end
 
diff --git a/gui/widgets/matRad_DVHWidget.m b/gui/widgets/matRad_DVHWidget.m
@@ -55,6 +55,7 @@
         end
 
         function this=update(this,evt)
+
              if this.lockUpdate
             doUpdate = true;
             if nargin == 2
@@ -87,6 +88,7 @@ function removeOverlap(this)
     end
 
     methods
+
         function set.SelectedCube(this,value)
             this.SelectedCube=value;
         end

diff --git a/gui/widgets/matRad_InfoWidget.m b/gui/widgets/matRad_InfoWidget.m
@@ -21,6 +21,7 @@
     % LICENSE file.
     %
     % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
     properties
 
     end

diff --git a/gui/widgets/matRad_LogoWidget.m b/gui/widgets/matRad_LogoWidget.m
@@ -20,6 +20,7 @@
     % LICENSE file.
     %
     % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
     properties
     end
 

diff --git a/gui/widgets/matRad_OptimizationWidget.m b/gui/widgets/matRad_OptimizationWidget.m
@@ -21,6 +21,7 @@
     % LICENSE file.
     %
     % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
     properties
     end