Merge tag 'v0.5.0.0' into maintenance

nlambriICH · Apr 29, 2024 · 7acac49 · 7acac49
2 parents 2fd1d7e + addddb0
commit 7acac49
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diff --git a/.github/workflows/reusable_build.yml b/.github/workflows/reusable_build.yml
@@ -13,6 +13,18 @@ jobs:
     steps:
       - name: Check out repository
         uses: actions/checkout@v2
+      - name: Install Python
+        uses: actions/setup-python@v4
+        with:
+            python-version: '3.11'
+      - name: Setup env
+        run: |
+            cd TMIAutomation\Server
+            pip install . -r requirements.txt
+      - name: Build server app
+        run: |
+            cd TMIAutomation\Server
+            pyinstaller --clean --noconfirm --add-data "models;models" --add-data "config.yml;." --collect-submodules=pydicom src/app.py
       - name: Add nuget to PATH
         uses: nuget/setup-nuget@v1
       - name: Add msbuild to PATH

diff --git a/.gitignore b/.gitignore
@@ -366,4 +366,5 @@ FodyWeavers.xsd
 TMIAutomation.Tests/Configuration/SensitiveData.txt
 TMIAutomation/Library/
 Docs/*
-!Docs/*.pdf
+!Docs/*.pdf
+TMIAutomation.Tests/Dicoms/
diff --git a/Docs/TMIAutomation.pdf b/Docs/TMIAutomation.pdf
diff --git a/README.md b/README.md
@@ -2,12 +2,15 @@
 
 Plug-in script for the Eclipse Treatment Planning System to automate Total Marrow (Lymph-node) Irradiation (TMI/TMLI).
 
-The script was introduced and validated in [this paper](https://doi.org/10.1007/s00066-022-02014-0).
+The script was introduced and validated in [this paper](https://doi.org/10.1007/s00066-022-02014-0) on Strahlentherapie und Onkologie.
+
+The generation of the field geometry of TMI/TMLI with deep-learning was introduced in [this paper](https://aapm.onlinelibrary.wiley.com/doi/10.1002/mp.17089) on Medical Physics.
 
 If you liked/used this project, don't forget to give it a star! :star:
 
 ## Key features
 
+* Field geometry for the TMI/TMLI upper-body generated with deep-learning models
 * Automatic planning of the lower-extremities for TMI/TMLI
 * Extendible to VMAT-TBI (Total Body Irradiation delivered with Volumetric Modulated Arc Therapy)
 
@@ -37,9 +40,6 @@ If you are on a research workstation (_TBox_), you can immediately run the scrip
 by setting the database in research mode from the RT Administration module of Eclipse.
 Otherwise, the plug-in script `TMIAutomation.esapi.dll` needs to be **approved** in the Eclipse application.
 
-The `Configuration` folder contains config files with objectives and parameters to optimize the lower-extremities plan.
-Example values are provided in order for the script to execute properly.
-
 ## Contributing
 
 Any contribution/feedback is **greatly appreciated**!

diff --git a/TMIAutomation.Runner/TMIAutomation.Runner.csproj b/TMIAutomation.Runner/TMIAutomation.Runner.csproj
@@ -179,6 +179,12 @@
 IF %25ERRORLEVEL%25 GEQ 8 exit 1
 IF $(ConfigurationName) == Debug-15.6 robocopy $(SolutionDir)$(SolutionName)\Configuration\ESAPI15 $(TargetDir)Configuration /mir
 IF %25ERRORLEVEL%25 GEQ 8 exit 1
+robocopy $(SolutionDir)$(SolutionName)\Configuration $(TargetDir)Configuration OARNames.txt
+IF %25ERRORLEVEL%25 GEQ 8 exit 1
+robocopy $(SolutionDir)$(SolutionName)\Configuration $(TargetDir)Configuration DCMExport.txt
+IF %25ERRORLEVEL%25 GEQ 8 exit 1
+robocopy $(SolutionDir)$(SolutionName)\Server\dist $(TargetDir)dist /mir /ns /nc /nfl /ndl
+IF %25ERRORLEVEL%25 GEQ 8 exit 1
 exit 0</PostBuildEvent>
   </PropertyGroup>
 </Project>
diff --git a/TMIAutomation.Tests/Configuration/ESAPI15/OptimizationOptions.txt b/TMIAutomation.Tests/Configuration/ESAPI15/OptimizationOptions.txt
@@ -1,5 +1,9 @@
 # Values must be tab separated
 # Lines starting with a hash sign '#' are ignored
 # Empty lines are ignored
-OptimizationAlgorithm	DoseAlgorithm	MLCID	DosePerFraction	NumberOfFractions
-PO_15.6.06	AAA 15.06.06	MLC0010	2	1
+OptimizationAlgorithm	PO_15.6.06
+DoseAlgorithm	AAA 15.06.06
+MLCID	MLC0010
+DosePerFraction	2
+NumberOfFractions	1
+TreatmentMachine	TrueBeamSN1015
diff --git a/TMIAutomation.Tests/Configuration/ESAPI16/OptimizationOptions.txt b/TMIAutomation.Tests/Configuration/ESAPI16/OptimizationOptions.txt
@@ -1,5 +1,9 @@
 # Values must be tab separated
 # Lines starting with a hash sign '#' are ignored
 # Empty lines are ignored
-OptimizationAlgorithm	DoseAlgorithm	MLCID	DosePerFraction	NumberOfFractions
-PO 16.1.0	AAA 15.06.06	MLC0010	2	1
+OptimizationAlgorithm	PO 16.1.0
+DoseAlgorithm	AAA 15.06.06
+MLCID	MLC0010
+DosePerFraction	2
+NumberOfFractions	1
+TreatmentMachine	TrueBeamSN1015
diff --git a/TMIAutomation.Tests/Configuration/OARNames.txt b/TMIAutomation.Tests/Configuration/OARNames.txt
@@ -0,0 +1,12 @@
+# Lines starting with a hash sign '#' are ignored
+# Empty lines are ignored
+brain
+encefalo
+lung
+polmone
+liver
+fegato
+bowel
+intestino
+bladder
+vescica
diff --git a/TMIAutomation.Tests/EntryPoint.cs b/TMIAutomation.Tests/EntryPoint.cs
@@ -17,30 +17,28 @@ internal class EntryPoint
         [STAThread]
         public static void Main(string[] args)
         {
+            ConfigOptOptions.Init();
+
             using (EclipseApp = Application.CreateApplication())
             {
                 string patientID = testData["PatientID"];
                 Patient patient = EclipseApp.OpenPatientById(patientID);
                 Course course = patient.Courses.FirstOrDefault(c => c.Id == testData["CourseID"]);
-                PlanSetup planSetup = course.PlanSetups.FirstOrDefault(ps => ps.Id == testData["PlanID"]);
-                PluginScriptContext scriptContext = new PluginScriptContext
-                {
-                    Patient = patient,
-                    Course = course,
-                    PlanSetup = planSetup,
-                    StructureSet = planSetup.StructureSet
-                };
-                EsapiWorker esapiWorker = new EsapiWorker(scriptContext);
+                PlanSetup planSetupLower = course.PlanSetups.FirstOrDefault(ps => ps.Id == testData["PlanIDLower"]);
+                PlanSetup planSetupUpper = course.PlanSetups.FirstOrDefault(ps => ps.Id == testData["PlanIDUpper"]);
+
+                SetUpContext(patient, course, planSetupLower, out PluginScriptContext scriptContextLower, out EsapiWorker esapiWorkerLower);
 
                 patient.BeginModifications();
                 try
                 {
                     TestBuilder.Create()
-                            .Add<ModelBaseTests>(new ModelBase(esapiWorker), scriptContext)
-                            .Add<ObjectiveSetupTests>(scriptContext.PlanSetup.OptimizationSetup, scriptContext.PlanSetup)
-                            .Add<CalculationTests>(scriptContext.PlanSetup, scriptContext)
-                            .Add<IsocenterTests>(scriptContext.PlanSetup, scriptContext)
-                            .Add<StructureHelperTests>(scriptContext.StructureSet);
+                            .Add<ModelBaseTests>(new ModelBase(esapiWorkerLower), scriptContextLower)
+                            .Add<ObjectiveSetupTests>(scriptContextLower.PlanSetup.OptimizationSetup, scriptContextLower.PlanSetup)
+                            .Add<CalculationTests>(scriptContextLower.PlanSetup, scriptContextLower)
+                            .Add<IsocenterTests>(scriptContextLower.PlanSetup, planSetupUpper, scriptContextLower)
+                            .Add<StructureHelperTests>(scriptContextLower.StructureSet)
+                            .AddStatic<ClientTests>(patientID);
                     TestBase.RunTests();
                 }
                 catch (Exception e)
@@ -54,6 +52,18 @@ public static void Main(string[] args)
             }
         }
 
+        private static void SetUpContext(Patient patient, Course course, PlanSetup planSetupLower, out PluginScriptContext scriptContextLower, out EsapiWorker esapiWorkerLower)
+        {
+            scriptContextLower = new PluginScriptContext
+            {
+                Patient = patient,
+                Course = course,
+                PlanSetup = planSetupLower,
+                StructureSet = planSetupLower.StructureSet
+            };
+            esapiWorkerLower = new EsapiWorker(scriptContextLower);
+        }
+
         private static Dictionary<string, string> InitializeTestData()
         {
             Dictionary<string, string> dict = new Dictionary<string, string>();

diff --git a/TMIAutomation.Tests/TMIAutomation.Tests.csproj b/TMIAutomation.Tests/TMIAutomation.Tests.csproj
@@ -64,6 +64,7 @@
     <Compile Include="Attributes\TheoryAttribute.cs" />
     <Compile Include="EntryPoint.cs" />
     <Compile Include="Tests\CalculationTests.cs" />
+    <Compile Include="Tests\ClientTests.cs" />
     <Compile Include="Tests\IsocenterTests.cs" />
     <Compile Include="Tests\ObjectiveSetupTests.cs" />
     <Compile Include="TestRunner\ITestBase.cs" />
@@ -105,6 +106,7 @@
     <Content Include="Configuration\EUDOptimizationObjectives.txt" />
     <Content Include="Configuration\ESAPI15\OptimizationOptions.txt" />
     <Content Include="Configuration\ESAPI16\OptimizationOptions.txt" />
+    <Resource Include="Configuration\OARNames.txt" />
     <Content Include="Configuration\PointOptimizationObjectives.txt" />
     <Content Include="Configuration\SensitiveData.txt">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
@@ -121,7 +123,11 @@
     <PostBuildEvent>IF $(ConfigurationName) == Debug-16.1 robocopy $(ProjectDir)Configuration\ESAPI16 $(TargetDir)Configuration /mir
 IF %25ERRORLEVEL%25 GEQ 8 exit 1
 IF $(ConfigurationName) == Debug-15.6 robocopy $(ProjectDir)Configuration\ESAPI15 $(TargetDir)Configuration /mir
-robocopy $(ProjectDir)Configuration $(TargetDir)Configuration PointOptimizationObjectives.txt EUDOptimizationObjectives.txt SensitiveData.txt 
+robocopy $(ProjectDir)Configuration $(TargetDir)Configuration PointOptimizationObjectives.txt EUDOptimizationObjectives.txt SensitiveData.txt OARNames.txt
+IF %25ERRORLEVEL%25 GEQ 8 exit 1
+robocopy $(SolutionDir)$(SolutionName)\Server\dist $(TargetDir)dist /mir /ns /nc /nfl /ndl
+IF %25ERRORLEVEL%25 GEQ 8 exit 1
+robocopy $(ProjectDir)Dicoms $(TargetDir)Dicoms /mir /ns /nc /nfl /ndl
 IF %25ERRORLEVEL%25 GEQ 8 exit 1
 exit 0</PostBuildEvent>
   </PropertyGroup>

diff --git a/TMIAutomation.Tests/TestBuilder/TestBuilder.cs b/TMIAutomation.Tests/TestBuilder/TestBuilder.cs
@@ -38,5 +38,12 @@ public static TestBuilder Create()
                 throw new ArgumentException($"Could not find a private testObject of type {testObject.GetType()} in {testBase.GetType()}");
             }
         }
+
+        public TestBuilder AddStatic<T>(params object[] optParams) where T : ITestBase, new()
+        {
+            T testBase = new T();
+            testBase.Init(null, optParams).DiscoverTests();
+            return testBuilderInstance;
+        }
     }
 }
diff --git a/TMIAutomation.Tests/Tests/CalculationTests.cs b/TMIAutomation.Tests/Tests/CalculationTests.cs
@@ -19,11 +19,11 @@ public override ITestBase Init(object testObject, params object[] optParams)
 
         [Theory]
         [InlineData("LowerBase")]
-        [InlineData("LowerBase1")]
-        private void AddBaseDosePlan(string expectedPlanId)
+        [InlineData("LowerBase")]
+        private void GetOrCreateBaseDosePlan(string expectedPlanId)
         {
             Course targetCourse = externalPlanSetup.Course;
-            ExternalPlanSetup newPlan = targetCourse.AddBaseDosePlan(externalPlanSetup.StructureSet);
+            ExternalPlanSetup newPlan = targetCourse.GetOrCreateBaseDosePlan(externalPlanSetup.StructureSet);
             try
             {
                 Assert.Equal(expectedPlanId, newPlan.Id);