Merge branch 'dev_FREDengine_release' of https://github.com/remocrist…

…oforetti/matRad into pr/800

.github/workflows/test-results.yml

@@ -36,5 +36,10 @@ jobs:
               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
 

.gitlab-ci.yml

@@ -0,0 +1,51 @@
+variables:
+  GIT_SUBMODULE_STRATEGY: recursive
+  GIT_SUBMODULE_DEPTH: 1
+  GIT_SUBMODULE_PATH: submodules/MOxUnit submodules/MOcov
+
+.matlab_defaults:
+  image:
+    name: '${CUSTOM_MATLAB_IMAGE}:r2024b'  # Replace the value with the name of the MATLAB container image you want to use
+    entrypoint: [""]
+  variables:
+    MLM_LICENSE_FILE: $E040_MATLAB_LICENSE_SERVER  # Replace the value with the port number and DNS address for your network license manager
+  resource_group: matlab
+
+test:
+  stage: test
+  extends: .matlab_defaults
+  script: matlab -batch "assert(matRad_runTests('test',true));"
+  artifacts:
+    reports:
+      junit: "./testresults.xml"
+      coverage_report:
+        coverage_format: cobertura
+        path: "./coverage.xml"
+    paths:
+      - "./*.xml"
+      - "./*.json"
+  coverage: '/TOTAL.*? (100(?:\.0+)?%|[1-9]?\d(?:\.\d+)?%)/'
+
+
+package:
+  stage: deploy
+  extends: .matlab_defaults
+  script: 
+    - |
+      if [ -n "$CI_COMMIT_TAG" ]; then        
+        matlab -batch "matRad_buildStandalone('isRelease', true);"
+        PACKAGE_NAME="$CI_COMMIT_TAG"        
+      else
+        matlab -batch "matRad_buildStandalone();"
+        PACKAGE_NAME="$CI_COMMIT_BRANCH"
+      fi
+      INSTALLER_NAME="matRad_installerLinux64_$PACKAGE_NAME"
+    - tar -czvf $INSTALLER_NAME.tar.gz build/installer
+    - 'curl --header "JOB-TOKEN: $CI_JOB_TOKEN" --upload-file $INSTALLER_NAME.tar.gz "$CI_API_V4_URL/projects/$CI_PROJECT_ID/packages/generic/matRad_linux64/$CI_COMMIT_BRANCH/matRad/$PACKAGE_NAME/$INSTALLER_NAME.tar.gz"'
+    # - echo "$CI_REGISTRY_PASSWORD" | docker login $CI_REGISTRY -u $CI_REGISTRY_USER --password-stdin
+    # - docker image tag matRad:develop $CI_REGISTRY/$CI_PROJECT_NAMESPACE/$CI_PROJECT_NAME/matRad:develop
+    # - docker push $CI_REGISTRY/$CI_PROJECT_NAMESPACE/$CI_PROJECT_NAME/matRad:develop
+  rules:
+    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
+    - if: $CI_COMMIT_BRANCH == "dev"
+    - if: $CI_COMMIT_TAG

CHANGELOG.md

@@ -1,5 +1,15 @@
 # Changelog
 
+## Development Changes
+
+### Bug Fixes
+- DICOM Import widget allow selection of multiple RTDose files.
+- DICOM Import Widget and importer handle selected patient more consistently and robustly. 
+- DICOM Exporter writes quantities beyond dose, importer tries to import them correctly.
+- DICOM Exporter now always writes ReferencedRTPlanSequence. Importer can now survive without it.
+- DVH widget does not throw a warning in updates, handle scenarios correctly / more robustly and missing xlabel axesHandle parameter.
+
+
 ## Version 3.1.0 - "Cleve"
 
 ### Major Changes and New Features

matRad/dicom/@matRad_DicomExporter/matRad_exportDicomRTDoses.m

@@ -44,15 +44,12 @@
 
 meta.Modality = 'RTDOSE';
 meta.Manufacturer = '';
-meta.DoseUnits = 'GY';
 
 %Reference
 %ID of the CT
 meta.StudyInstanceUID = obj.StudyInstanceUID;
 meta.StudyID = obj.StudyID; 
 
-
-
 %Dates & Times
 currDate = now;
 currDateStr = datestr(currDate,'yyyymmdd');
@@ -99,10 +96,11 @@
 meta.GridFrameOffsetVector = transpose(ct.z - ct.z(1));
 
 %Referenced Plan
-%This does currently not work due to how Matlab creates UIDs by itself,
-%we can not know the reference before it is written by the RTPlanExport,
-%which itself needs the RTDose UIDs
-%{
+%This does currently not work well due to how Matlab creates UIDs by
+%itself, we can not know the reference before it is written by the 
+%RTPlanExport, which itself needs the RTDose UIDs.
+%However, we need to set the ReferencedRTPlanSequence, because it is a
+%conditionally required field according to the DICOM standard
 try
     rtPlanUID = obj.rtPlanMeta.SOPInstanceUID;   
 catch
@@ -111,38 +109,34 @@
     obj.rtPlanMeta.SOPClassUID = obj.rtPlanClassUID;
     rtPlanUID = obj.rtPlanMeta.SOPInstanceUID;
 end
-%}
-
-
-%meta.ReferencedRTPlanSequence.Item_1.ReferencedSOPClassUID = obj.rtPlanClassUID;
-%meta.ReferencedRTPlanSequence.Item_1.ReferencedSOPInstanceUID = rtPlanUID;
-
-if nargin < 4 || isempty(doseFieldNames)
-    doseFieldNames = cell(0);
-    fn = fieldnames(obj.resultGUI);
-    for i = 1:numel(fn)
-        if numel(size(obj.resultGUI.(fn{i}))) == 3
-            doseFieldNames{end+1} = fn{i};
-        end
+
+meta.ReferencedRTPlanSequence.Item_1.ReferencedSOPClassUID = obj.rtPlanClassUID;
+meta.ReferencedRTPlanSequence.Item_1.ReferencedSOPInstanceUID = rtPlanUID;
+
+doseFieldNames = cell(0);
+fn = fieldnames(obj.resultGUI);
+for i = 1:numel(fn)
+    if numel(size(obj.resultGUI.(fn{i}))) == 3
+        doseFieldNames{end+1} = fn{i};
     end
 end
 
-
-
-
-
 obj.rtDoseMetas = struct([]);
 obj.rtDoseExportStatus = struct([]);
 
 for i = 1:numel(doseFieldNames)
-    doseName = doseFieldNames{i};
+    doseName = doseFieldNames{i};    
+    doseUnits = 'GY';
 
     %Now check if we export physical or RBE weighted dose, they are known
     %to dicom
-    if strncmp(doseName,'physicalDose',12)
+    if strncmp(doseName,'physicalDose',12) || strncmp(doseName,'LET',3)
         doseType = 'PHYSICAL';
-    elseif strncmp(doseName,'RBExDose',8)
+    elseif strncmp(doseName,'RBExDose',8) || strncmp(doseName,'BED',3) || strncmp(doseName,'alpha',3) || strncmp(doseName,'beta',3) || strncmp(doseName,'effect',6) || strncmp(doseName,'RBE',3)
         doseType = 'EFFECTIVE';
+        if strncmp(doseName,'RBE',3)
+            doseUnits = 'RELATIVE';
+        end
     else
         matRad_cfg.dispInfo('Dose Cube ''%s'' of unknown type for DICOM. Not exported!\n',doseName);
         continue;
@@ -174,6 +168,8 @@
     metaCube = meta;
     metaCube.DoseType = doseType;
     metaCube.DoseSummationType = deliveryType;
+    metaCube.DoseComment = doseName;
+    metaCube.DoseUnits = doseUnits;
 
     %ID of the RTDose
     metaCube.SeriesInstanceUID = dicomuid;    

matRad/dicom/@matRad_DicomImporter/matRad_DicomImporter.m

@@ -26,7 +26,8 @@
 
        % lists of all files
        allfiles;
-       patient;
+       patients;
+       selectedPatient;
        importFiles; % all the names (directories) of files, that will be imported
 
        % properties with data for import functions

matRad/dicom/@matRad_DicomImporter/matRad_importDicomRTDose.m

@@ -62,11 +62,24 @@
     else
         doseInstanceHelper = [];
     end
-
+
+    doseComment = '';
+    if isfield(dose.(itemName).dicomInfo,'DoseComment')
+        doseComment = dose.(itemName).dicomInfo.DoseComment;
+    end
+
     if strncmpi(doseTypeHelper,'PHYSICAL',6)
-        doseTypeHelper = 'physicalDose';
+        if any(strcmp(doseComment,{'physicalDose','LET'}))
+            doseTypeHelper = doseComment;
+        else
+            doseTypeHelper = 'physicalDose';
+        end
     elseif strncmpi(doseTypeHelper,'EFFECTIVE',6)
-        doseTypeHelper = 'RBExDose';
+        if any(strcmp(doseComment,{'RBExDose','BED','alpha','beta','effect','RBE'}))
+            doseTypeHelper = doseComment;
+        else
+            doseTypeHelper = 'RBExDose';
+        end
     end
 
     %If given as plan and not per fraction

matRad/dicom/@matRad_DicomImporter/matRad_interpDicomDoseCube.m

@@ -102,7 +102,9 @@
 %always given
 obj.importRTDose.dose.dicomInfo.SOPClassUID             = doseInfo.SOPClassUID;
 obj.importRTDose.dose.dicomInfo.SOPInstanceUID          = doseInfo.SOPInstanceUID;
-obj.importRTDose.dose.dicomInfo.ReferencedRTPlanSequence = doseInfo.ReferencedRTPlanSequence;
+if isfield(doseInfo,'ReferencedRTPlanSequence')
+    obj.importRTDose.dose.dicomInfo.ReferencedRTPlanSequence = doseInfo.ReferencedRTPlanSequence;
+end
 
 end
 

matRad/dicom/@matRad_DicomImporter/matRad_scanDicomImportFolder.m

@@ -246,9 +246,9 @@
     close(h)
 
     if ~isempty(obj.allfiles)
-        obj.patient = unique(obj.allfiles(:,3));
+        obj.patients = unique(obj.allfiles(:,3));
 
-        if isempty(obj.patient)
+        if isempty(obj.patients)
              matRad_cfg.dispError('No patient found with DICOM CT _and_ RT structure set in patient directory!');
         end
     else

matRad/gui/widgets/matRad_DVHWidget.m

@@ -109,15 +109,24 @@ function showDVH(this)
             resultGUI = evalin('base','resultGUI');
             pln = evalin('base','pln');
             cst = evalin('base','cst');
+            ct  = evalin('base','ct');
+
             % Calculate and show DVH
             doseCube = resultGUI.(this.selectedCube);
             dvh = matRad_calcDVH(cst,doseCube,'cum');
 
             matRad_showDVH(dvh,cst,pln,'axesHandle',this.dvhAx);
+
+            if ~isfield(pln,'multScen')
+                multScen = matRad_NominalScenario(ct);
+            else
+                multScen = pln.multScen;
+            end
+            multScen = matRad_ScenarioModel.create(multScen,ct);
 
             %check scenarios
-            if pln.multScen.totNumScen > 1
-                for i = 1:pln.multScen.totNumScen
+            if multScen.totNumScen > 1
+                for i = 1:multScen.totNumScen
                     scenFieldName = sprintf('%s_scen%d',this.selectedCube,i);
                     if isfield(resultGUI,scenFieldName)
                         tmpDvh = matRad_calcDVH(cst,resultGUI.(scenFieldName),'cum'); % Calculate cumulative scenario DVH

matRad/gui/widgets/matRad_importDicomWidget.m

@@ -174,8 +174,8 @@
             % to pass only selected objects to the matRad_importDicom
             % selected patient
             if ~isempty(handles.patient_listbox)
-                selected_patient = this.importer.patient{get(handles.patient_listbox,'Value')};
-                this.importer.patient = selected_patient;
+                selected_patient = get(handles.patient_listbox,'Value');
+                this.importer.selectedPatient = selected_patient;
             end
 
             % selected CT serie
@@ -211,7 +211,7 @@
             % selected dose serie
             allRTDoses = this.importer.importFiles.rtdose;
             if ~isempty(allRTDoses) && ~isempty(handles.doseseries_listbox.Value)
-                UIDSelected_rtdose = handles.doseseries_listbox.String{get(handles.doseseries_listbox,'Value'), 1};
+                UIDSelected_rtdose = handles.doseseries_listbox.String(get(handles.doseseries_listbox,'Value'));
                 selectedRTDose = allRTDoses(strcmp(allRTDoses(:, 4), UIDSelected_rtdose), :);
                 this.importer.importFiles.rtdose = selectedRTDose;
             else 
@@ -222,7 +222,7 @@
 
             %% save ct, cst, pln, dose
             matRad_cfg = MatRad_Config.instance();
-            matRadFileName = fullfile(matRad_cfg.userfolders{1},[this.importer.patient '.mat']); % use default from dicom
+            matRadFileName = fullfile(matRad_cfg.userfolders{1},[this.importer.patients{this.importer.selectedPatient} '.mat']); % use default from dicom
             [FileName,PathName] = uiputfile('*.mat','Save as...',matRadFileName);
             ct = this.importer.ct;
             cst = this.importer.cst;
@@ -970,13 +970,15 @@
 
             this.importer = matRad_DicomImporter(get(handles.dir_path_field,'String'));
 
-            if iscell(this.importer.patient)
-                handles.fileList =  this.importer.allfiles;
-                %handles.patient_listbox.String = patient_listbox;
-                set(handles.patient_listbox,'String',this.importer.patient,'Value',1);
-                % guidata(hObject, handles);
-                this.handles = handles;
+            handles.fileList =  this.importer.allfiles;
+            %handles.patient_listbox.String = patient_listbox;
+            if isempty(this.importer.selectedPatient) || this.importer.selectedPatient > numel(this.importer.patients)
+                this.importer.selectedPatient = 1;
             end
+
+            set(handles.patient_listbox,'String',this.importer.patients,'Value',this.importer.selectedPatient);
+            % guidata(hObject, handles);
+            this.handles = handles;
         end
     end
 

matRad/planAnalysis/matRad_showDVH.m

@@ -163,7 +163,7 @@ function matRad_showDVH(dvh,cst,varargin)
     pln.bioModel = matRad_BiologicalModel.validate(pln.bioModel,pln.radiationMode);
 
     if strcmp(pln.bioModel.model,'none')
-        xlabel('Dose [Gy]','FontSize',fontSizeValue);
+        xlabel(axesHandle,'Dose [Gy]','FontSize',fontSizeValue);
     else
         xlabel(axesHandle,'RBE x Dose [Gy(RBE)]','FontSize',fontSizeValue);
     end