Merge branch 'dev' into pr/842

Author: wahln

.gitattributes

@@ -0,0 +1,13 @@
+# Auto-detect text files and normalize (LF in repo).
+* text=auto
+
+# Force files to be binary
+*.mat binary
+*.pdf binary
+*.mex* binary
+*.zip binary
+*.dll binary
+*.exe binary
+
+# Ensure .m files are never marked as executable
+*.m -x

.github/before_install_linux.sh

@@ -7,4 +7,4 @@ mv matRad/optimization/optimizer/ipopt.m optimization/optimizer/ipopt.m.bak
 
 octave --no-gui --eval "pkg install -forge dicom"
 octave --no-gui --eval "pkg install -forge nan"
-octave --no-gui --eval "pkg install -forge image"
+octave --no-gui --eval "pkg install \"https://downloads.sourceforge.net/project/octave/Octave%20Forge%20Packages/Individual%20Package%20Releases/image-2.14.0.tar.gz\""

.github/workflows/coverage-report.yml

@@ -15,6 +15,10 @@ jobs:
         runs-on: ubuntu-latest
 
         steps:
+            - name: Checkout Repository
+              uses: actions/checkout@v4 # Checks-out repository under $GITHUB_WORKSPACE
+              with:
+                  submodules: 'false'
 
             - name: Download Coverage Artifact
               uses: actions/download-artifact@v4
@@ -30,10 +34,10 @@ jobs:
                   format: coveralls
 
             - name: Upload to Codecov
-              uses: codecov/codecov-action@v4
+              uses: codecov/codecov-action@v5
               with:
                   token: ${{ secrets.CODECOV_TOKEN }}
-                  file: coverage/coverage.xml
+                  files: coverage/coverage.json,coverage/coverage.xml
                   fail_ci_if_error: false
 
             - name: Publish Coverage Report

.github/workflows/test-results.yml

@@ -1,45 +1,62 @@
 name: Test Report
 
-permissions:
-    checks: write
-    pull-requests: write
-
 on:
-    workflow_call:
+    workflow_run:
+        workflows: ["Tests"]
+        types:
+            - completed
 
 jobs:
-    test_report:
+    test-report:
+        if: github.event.workflow_run.conclusion == 'success' || github.event.workflow_run.conclusion == 'failure'
         runs-on: ubuntu-latest
+        permissions:
+            checks: write
+            pull-requests: write
+
 
-        steps:
-            
+        steps:            
             - name: Download Results for Matlab R2022b
               uses: actions/download-artifact@v4
               with:
+                  run-id: ${{ github.event.workflow_run.id }}
                   name: test-results-matlab-R2022b
                   path: test-results/matlab-R2022b
+                  github-token: ${{ secrets.GITHUB_TOKEN }}
 
             - name: Download Results for Matlab Latest
               uses: actions/download-artifact@v4
               with:
+                  run-id: ${{ github.event.workflow_run.id }}
                   name: test-results-matlab-latest
                   path: test-results/matlab-latest
+                  github-token: ${{ secrets.GITHUB_TOKEN }}
 
             - name: Download Results for Octave
               uses: actions/download-artifact@v4
               with:
+                  run-id: ${{ github.event.workflow_run.id }}
                   name: test-results-octave
                   path: test-results/octave
-            
+                  github-token: ${{ secrets.GITHUB_TOKEN }}
+
+            - name: Download Event File
+              uses: actions/download-artifact@v4
+              with:
+                  run-id: ${{ github.event.workflow_run.id }}
+                  name: event-file
+                  path: event-file
+                  github-token: ${{ secrets.GITHUB_TOKEN }}
+
             - name: Publish Test Results
               uses: EnricoMi/publish-unit-test-result-action@v2
               with:
-                  files: |
-                      test-results/*/testresults.xml
-            
-            - name: Publish Test Results on Codecov
-              uses: codecov/test-results-action@v1
-              with:
-                  token: ${{ secrets.CODECOV_TOKEN }}
-                  files: test-results/matlab-R2022b/testresults.xml,test-results/matlab-latest/testresults.xml,test-results/octave/testresults.xml
+                  commit: ${{ github.event.workflow_run.head_sha }}
+                  files: "test-results/**/testresults.xml"
+                  event_file: event-file/event.json
+                  event_name: ${{ github.event.workflow_run.event}}
+                  comment_mode: ${{ (github.event.workflow_run.event == 'pull_request' || github.event_name == 'pull_request') && 'always' || 'off' }}
+                  check_name: "Test Results"
+
+
 

.github/workflows/tests.yml

@@ -38,15 +38,19 @@ jobs:
         with:
           submodules: 'true'
       - uses: ./.github/actions/test-octave
-
-  test-report:
-    name: Collect Test Results
-    needs: [test-matlab-stable, test-matlab-latest, test-octave-6]
-    uses: ./.github/workflows/test-results.yml
-    secrets: inherit
 
   coverage-report:
     name: Collect Coverage Report
     needs: [test-matlab-stable]
     uses: ./.github/workflows/coverage-report.yml
-    secrets: inherit
+    secrets: inherit
+
+  event_file:
+    name: Event File
+    runs-on: ubuntu-latest
+    steps:
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        with:
+          name: event-file
+          path: ${{ github.event_path }}

AUTHORS.txt

@@ -1,4 +1,4 @@
-List of all matRad developers that contributed code (alphabetical)
+List of all matRad developers that contributed code (alphabetical)
 
 * Nelly Abbani
 * Nabe Al-Hasnawi
@@ -26,6 +26,7 @@
 * Navid Khaledi
 * Thomas Klinge
 * Jeremias Kunz
+* Mariia Lapaeva
 * Paul Anton Meder
 * Henning Mescher
 * Lucas-Raphael Müller

CITATION.cff

@@ -61,6 +61,8 @@ authors:
   given-names: "Thomas"
 - family-names: "Kunz"
   given-names: "Jeremias"
+- family-names: "Lapaeva"
+  given-names: "Mariia"
 - family-names: "Mairani"
   given-names: "Andrea"
 - family-names: "Meder"

README.md

@@ -1,6 +1,7 @@
 [![Current Release](https://img.shields.io/github/v/release/e0404/matRad)](https://github.com/e0404/matRad/releases) 
 [![Downloads](https://img.shields.io/github/downloads/e0404/matRad/total)](https://github.com/e0404/matRad/releases) 
 [![Contributors](https://img.shields.io/github/contributors/e0404/matRad)](https://github.com/e0404/matRad/graphs/contributors)
+![Citations](https://img.shields.io/endpoint?url=https%3A%2F%2Fapi.juleskreuer.eu%2Fcitation-badge.php%3Fshield%26doi%3D10.1002%2Fmp.12251&style=flat&color=blue)
 
 [![GitHub Build Status](https://github.com/e0404/matRad/actions/workflows/tests.yml/badge.svg)](https://github.com/e0404/matRad/actions/workflows/tests.yml)
 [![codecov](https://codecov.io/gh/e0404/matRad/graph/badge.svg?token=xQhUQLu4FK)](https://codecov.io/gh/e0404/matRad)

examples/matRad_example10_4DphotonRobust.m

@@ -192,7 +192,7 @@
 stf = matRad_generateStf(ct,cst,pln);
 
 %% Dose Calculation
-dij = matRad_calcPhotonDose(ct,stf,pln,cst);
+dij =  matRad_calcDoseInfluence(ct,cst,stf,pln);
 
 %% Inverse Optimization  for IMPT based on RBE-weighted dose
 % The goal of the fluence optimization is to find a set of bixel/spot 
@@ -241,30 +241,38 @@
 maxDose       = max([max(resultGUI.([pln.propOpt.quantityOpt])(:,:,slice)) max(resultGUIrobust.([pln.propOpt.quantityOpt])(:,:,slice))])+1e-4;
 doseIsoLevels = linspace(0.1 * maxDose,maxDose,10);
 figure,
-subplot(121),matRad_plotSliceWrapper(gca,ct,cst,1,resultGUI.([pln.propOpt.quantityOpt '_' 'beam1'])      ,plane,slice,[],[],colorcube,[],[0 maxDose],doseIsoLevels);title('conventional plan - beam1')
-subplot(122),matRad_plotSliceWrapper(gca,ct,cst,1,resultGUI.([pln.propOpt.quantityOpt])      ,plane,slice,[],[],colorcube,[],[0 maxDose],doseIsoLevels);title('conventional plan')
+subplot(121),matRad_plotSlice(ct, 'axesHandle', gca, 'cst', cst, 'cubeIdx', 1, 'dose', resultGUI.([pln.propOpt.quantityOpt '_' 'beam1'])    ,'plane', plane, 'slice', slice, 'contourColorMap', colorcube, 'doseWindow', [0 maxDose], 'doseIsoLevels', doseIsoLevels);title('conventional plan - beam1')
+subplot(122),matRad_plotSlice(ct, 'axesHandle', gca, 'cst', cst, 'cubeIdx', 1, 'dose', resultGUI.([pln.propOpt.quantityOpt])                ,'plane', plane, 'slice', slice, 'contourColorMap', colorcube, 'doseWindow', [0 maxDose], 'doseIsoLevels', doseIsoLevels);title('conventional plan')
+%subplot(121),matRad_plotSliceWrapper(gca,ct,cst,1,resultGUI.([pln.propOpt.quantityOpt '_' 'beam1'])      ,plane,slice,[],[],colorcube,[],[0 maxDose],doseIsoLevels);title('conventional plan - beam1')
+%subplot(122),matRad_plotSliceWrapper(gca,ct,cst,1,resultGUI.([pln.propOpt.quantityOpt])      ,plane,slice,[],[],colorcube,[],[0 maxDose],doseIsoLevels);title('conventional plan')
 
 figure
-subplot(121),matRad_plotSliceWrapper(gca,ct,cst,1,resultGUIrobust.([pln.propOpt.quantityOpt '_' 'beam1']),plane,slice,[],[],colorcube,[],[0 maxDose],doseIsoLevels);title('robust plan - beam1')
-subplot(122),matRad_plotSliceWrapper(gca,ct,cst,1,resultGUIrobust.([pln.propOpt.quantityOpt]),plane,slice,[],[],colorcube,[],[0 maxDose],doseIsoLevels);title('robust plan')
+subplot(121),matRad_plotSlice(ct, 'axesHandle', gca, 'cst', cst, 'cubeIdx', 1, 'dose', resultGUIrobust.([pln.propOpt.quantityOpt '_' 'beam1'])  ,'plane', plane, 'slice', slice, 'contourColorMap', colorcube, 'doseWindow', [0 maxDose], 'doseIsoLevels', doseIsoLevels);title('robust plan - beam1')
+subplot(122),matRad_plotSlice(ct, 'axesHandle', gca, 'cst', cst, 'cubeIdx', 1, 'dose', resultGUIrobust.([pln.propOpt.quantityOpt])              ,'plane', plane, 'slice', slice, 'contourColorMap', colorcube, 'doseWindow', [0 maxDose], 'doseIsoLevels', doseIsoLevels);title('robust plan')
+%subplot(121),matRad_plotSliceWrapper(gca,ct,cst,1,resultGUIrobust.([pln.propOpt.quantityOpt '_' 'beam1']),plane,slice,[],[],colorcube,[],[0 maxDose],doseIsoLevels);title('robust plan - beam1')
+%subplot(122),matRad_plotSliceWrapper(gca,ct,cst,1,resultGUIrobust.([pln.propOpt.quantityOpt]),plane,slice,[],[],colorcube,[],[0 maxDose],doseIsoLevels);title('robust plan')
 
 
 figure
-subplot(131),matRad_plotSliceWrapper(gca,ct,cst,1,resultGUIrobust4D.([pln.propOpt.quantityOpt]),plane,slice,[],[],colorcube,[],[0 maxDose],doseIsoLevels);title('robust plan')
-subplot(132),matRad_plotSliceWrapper(gca,ct,cst,1,resultGUIrobust4D.('accPhysicalDose'),plane,slice,[],[],colorcube,[],[0 maxDose],doseIsoLevels);title('robust plan dose accumulation')
+subplot(131),matRad_plotSlice(ct, 'axesHandle', gca, 'cst', cst, 'cubeIdx', 1, 'dose', resultGUIrobust4D.([pln.propOpt.quantityOpt])  ,'plane', plane, 'slice', slice, 'contourColorMap', colorcube, 'doseWindow', [0 maxDose], 'doseIsoLevels', doseIsoLevels);title('robust plan')
+subplot(132),matRad_plotSlice(ct, 'axesHandle', gca, 'cst', cst, 'cubeIdx', 1, 'dose', resultGUIrobust4D.('accPhysicalDose')  ,'plane', plane, 'slice', slice, 'contourColorMap', colorcube, 'doseWindow', [0 maxDose], 'doseIsoLevels', doseIsoLevels);title('robust plan dose accumulation')
+%subplot(131),matRad_plotSliceWrapper(gca,ct,cst,1,resultGUIrobust4D.([pln.propOpt.quantityOpt]),plane,slice,[],[],colorcube,[],[0 maxDose],doseIsoLevels);title('robust plan')
+%subplot(132),matRad_plotSliceWrapper(gca,ct,cst,1,resultGUIrobust4D.('accPhysicalDose'),plane,slice,[],[],colorcube,[],[0 maxDose],doseIsoLevels);title('robust plan dose accumulation')
 
 % create an interactive plot to slide through individual scnearios
 f       = figure; title('individual scenarios');
 numScen = 1;
 maxDose       = max(max(resultGUIrobust.([pln.propOpt.quantityOpt '_scen' num2str(round(numScen))])(:,:,slice)))+0.2;
 doseIsoLevels = linspace(0.1 * maxDose,maxDose,10);
-matRad_plotSliceWrapper(gca,ct,cst,1,resultGUIrobust.([pln.propOpt.quantityOpt '_scen' num2str(round(numScen))]),plane,slice,[],[],colorcube,[],[0 maxDose],doseIsoLevels);
+matRad_plotSlice(ct, 'axesHandle', gca, 'cst', cst, 'cubeIdx', 1, 'dose', resultGUIrobust.([pln.propOpt.quantityOpt '_scen' num2str(round(numScen))]) ,'plane', plane, 'slice', slice, 'contourColorMap', colorcube, 'doseWindow', [0 maxDose], 'doseIsoLevels', doseIsoLevels);
+%matRad_plotSliceWrapper(gca,ct,cst,1,resultGUIrobust.([pln.propOpt.quantityOpt '_scen' num2str(round(numScen))]),plane,slice,[],[],colorcube,[],[0 maxDose],doseIsoLevels);
 
 [env,envver] = matRad_getEnvironment();
 if strcmp(env,'MATLAB') || str2double(envver(1)) >= 5
     b = uicontrol('Parent',f,'Style','slider','Position',[50,5,419,23],...
         'value',numScen, 'min',1, 'max',pln.multScen.totNumScen,'SliderStep', [1/(pln.multScen.totNumScen-1) , 1/(pln.multScen.totNumScen-1)]);
-    set(b,'Callback',@(es,ed)  matRad_plotSliceWrapper(gca,ct,cst,round(get(es,'Value')),resultGUIrobust.([pln.propOpt.quantityOpt '_scen' num2str(round(get(es,'Value')))]),plane,slice,[],[],colorcube,[],[0 maxDose],doseIsoLevels));
+    set(b,'Callback',@(es,ed)  matRad_plotSlice(ct, 'axesHandle', gca, 'cst', cst, 'cubeIdx', round(get(es,'Value')), 'dose', resultGUIrobust.([pln.propOpt.quantityOpt '_scen' num2str(round(get(es,'Value')))]) ,'plane', plane, 'slice', slice, 'contourColorMap', colorcube, 'doseWindow', [0 maxDose], 'doseIsoLevels', doseIsoLevels)); 
+    %matRad_plotSliceWrapper(gca,ct,cst,round(get(es,'Value')),resultGUIrobust.([pln.propOpt.quantityOpt '_scen' num2str(round(get(es,'Value')))]),plane,slice,[],[],colorcube,[],[0 maxDose],doseIsoLevels));
 end
 
 %% Indicator calculation and show DVH and QI
@@ -282,10 +290,12 @@
 [cstStatRob, resultGUISampRob, metaRob]                = matRad_samplingAnalysis(ct,cst,plnSampRob,caSampRob, mSampDoseRob, resultGUInomScen);
 
 figure,title('std dose cube based on sampling - conventional')
-matRad_plotSliceWrapper(gca,ct,cst,1,resultGUISamp.stdCube,plane,slice,[],[],colorcube,[],[0 max(resultGUISamp.stdCube(:))]);
+matRad_plotSlice(ct, 'axesHandle', gca, 'cst', cst, 'cubeIdx', 1, 'dose', resultGUISamp.stdCube     ,'plane', plane, 'slice', slice, 'contourColorMap', colorcube, 'doseWindow', [0 max(resultGUISamp.stdCube(:))]);
+%matRad_plotSliceWrapper(gca,ct,cst,1,resultGUISamp.stdCube,plane,slice,[],[],colorcube,[],[0 max(resultGUISamp.stdCube(:))]);
 
 figure,title('std dose cube based on sampling - robust')
-matRad_plotSliceWrapper(gca,ct,cst,1,resultGUISampRob.stdCube,plane,slice,[],[],colorcube,[],[0 max(resultGUISampRob.stdCube(:))]);
+matRad_plotSlice(ct, 'axesHandle', gca, 'cst', cst, 'cubeIdx', 1, 'dose', resultGUISampRob.stdCube  ,'plane', plane, 'slice', slice, 'contourColorMap', colorcube, 'doseWindow', [0 max(resultGUISampRob.stdCube(:))]);
+%matRad_plotSliceWrapper(gca,ct,cst,1,resultGUISampRob.stdCube,plane,slice,[],[],colorcube,[],[0 max(resultGUISampRob.stdCube(:))]);