Merge branch 'ALive-research:develop' into feature/Resectogram-Resect…

…ionVolumetry
RuoyanMeng · Oct 9, 2024 · 49ca1ec · 49ca1ec
2 parents 2ccac63 + 6295b47
commit 49ca1ec
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diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml
@@ -0,0 +1,23 @@
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: Paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: Paper/paper.pdf
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -7,13 +7,14 @@ project(SlicerLiver)
 set(EXTENSION_HOMEPAGE "https://github.com/ALive-research/Slicer-Liver")
 set(EXTENSION_CATEGORY "IGT")
 set(EXTENSION_STATUS "Beta")
-set(EXTENSION_CONTRIBUTORS "Rafael Palomar (Oslo University Hospital / NTNU), Ole Vegard Solberg (SINTEF), Geir Arne Tangen (SINTEF), Egidijus Pelanis (Oslo University Hospital), Davit Aghayan (Oslo University Hospital), Gabriella D'Albenzio (Oslo University Hospital) Javier Pérez de Frutos (SINTEF), Ruoyan Meng (NTNU), Héctor Martínez (Universidad de Córdoba), Francisco José Rodríguez Lozano (Universidad de Córdoba), Joaquín Olivares Bueno (Universidad de Córdoba), José Manuel Palomares Muñoz (Universidad de Córdoba)")
+set(EXTENSION_CONTRIBUTORS "Rafael Palomar (Oslo University Hospital / NTNU), Ole Vegard Solberg (SINTEF), Geir Arne Tangen (SINTEF), Egidijus Pelanis (Oslo University Hospital), Davit Aghayan (Oslo University Hospital), Gabriella D'Albenzio (Oslo University Hospital) Javier Pérez de Frutos (SINTEF), Ruoyan Meng (NTNU)")
 set(EXTENSION_DESCRIPTION "3D Slicer extension for liver analysis and therapy planning")
 set(EXTENSION_ICONURL "https://raw.githubusercontent.com/ALive-research/Slicer-Liver/master/SlicerLiver.png")
 set(EXTENSION_SCREENSHOTURLS "https://raw.githubusercontent.com/ALive-research/Slicer-Liver/master/Screenshots/Slicer-Liver_screenshot_01.png https://raw.githubusercontent.com/ALive-research/Slicer-Liver/master/Screenshots/Slicer-Liver_screenshot_02.png https://raw.githubusercontent.com/ALive-research/Slicer-Liver/master/Screenshots/Slicer-Liver_screenshot_03.png https://raw.githubusercontent.com/ALive-research/Slicer-Liver/master/Screenshots/Slicer-Liver_screenshot_04.png https://raw.githubusercontent.com/ALive-research/Slicer-Liver/master/Screenshots/Slicer-Liver_screenshot_05.png https://raw.githubusercontent.com/ALive-research/Slicer-Liver/master/Screenshots/Slicer-Liver_screenshot_06.png https://raw.githubusercontent.com/ALive-research/Slicer-Liver/master/Screenshots/Slicer-Liver_screenshot_07.png https://raw.githubusercontent.com/ALive-research/Slicer-Liver/master/Screenshots/Slicer-Liver_screenshot_08.png")
 set(EXTENSION_DEPENDS
-  Markups
   SlicerVMTK
+  SegmentEditorExtraEffects
+  ExtraMarkups
   )
 
 #-----------------------------------------------------------------------------

diff --git a/LiverMarkups/VTKWidgets/vtkBezierSurfaceSource.cxx b/LiverMarkups/VTKWidgets/vtkBezierSurfaceSource.cxx
@@ -382,7 +382,7 @@ void vtkBezierSurfaceSource::ComputeBinomialCoefficients()
   unsigned int yGrid = this->NumberOfControlPoints[1];
 
 #pragma omp parallel for
-  for (int i=0; i<xGrid; i++)
+  for (unsigned int i=0; i<xGrid; i++)
     {
     this->BinomialCoefficientsX[i] =
       Factorial(xGrid-1) /
@@ -393,7 +393,7 @@ void vtkBezierSurfaceSource::ComputeBinomialCoefficients()
   if (xGrid != yGrid)
     {
 #pragma omp parallel for
-    for (int i=0; i<yGrid; i++)
+    for (unsigned int i=0; i<yGrid; i++)
       {
       this->BinomialCoefficientsY[i] =
         Factorial(yGrid-1) /
@@ -403,7 +403,7 @@ void vtkBezierSurfaceSource::ComputeBinomialCoefficients()
   else
     {
 #pragma omp parallel for
-    for (int i=0; i<xGrid; i++)
+    for (unsigned int i=0; i<xGrid; i++)
       {
       this->BinomialCoefficientsY[i] = this->BinomialCoefficientsX[i];
       }
@@ -436,7 +436,7 @@ void vtkBezierSurfaceSource::EvaluateBezierSurface(vtkPoints *points)
   unsigned int yRes = this->Resolution[1];
 
 #pragma omp parallel for
-  for (int i=0; i<xRes; i++)
+  for (unsigned int i=0; i<xRes; i++)
     {
     double u;
     u = i / static_cast<double>(xRes - 1);

diff --git a/LiverMarkups/VTKWidgets/vtkBezierSurfaceSource.h b/LiverMarkups/VTKWidgets/vtkBezierSurfaceSource.h
@@ -75,7 +75,7 @@ class VTK_SLICER_LIVERMARKUPS_MODULE_VTKWIDGETS_EXPORT vtkBezierSurfaceSource :
    * @param os ouptut stream to print the properties to.
    * @param indent indentation value.
    */
-  void PrintSelf(ostream &os, vtkIndent indent);
+  void PrintSelf(ostream &os, vtkIndent indent) override;
 
   /**
    * Set the control points.
@@ -164,7 +164,7 @@ class VTK_SLICER_LIVERMARKUPS_MODULE_VTKWIDGETS_EXPORT vtkBezierSurfaceSource :
    *
    * @return return code.
    */
-  int RequestData(vtkInformation *, vtkInformationVector **, vtkInformationVector *);
+  int RequestData(vtkInformation *, vtkInformationVector **, vtkInformationVector *) override;
 
  private:
   vtkBezierSurfaceSource(const vtkBezierSurfaceSource&);  // Not implemented.

diff --git a/LiverResections/MRML/vtkMRMLLiverResectionNode.h b/LiverResections/MRML/vtkMRMLLiverResectionNode.h
@@ -94,7 +94,7 @@ class VTK_SLICER_LIVERRESECTIONS_MODULE_MRML_EXPORT vtkMRMLLiverResectionNode
   vtkMRMLCopyContentDefaultMacro(vtkMRMLLiverResectionNode);
 
   /// Create default storage node or nullptr if does not have one
-  vtkMRMLStorageNode* CreateDefaultStorageNode();
+  vtkMRMLStorageNode* CreateDefaultStorageNode() override;
 
 
   // TODO: Review the need for this further down the road
@@ -371,16 +371,16 @@ class VTK_SLICER_LIVERRESECTIONS_MODULE_MRML_EXPORT vtkMRMLLiverResectionNode
   bool GridVisibility;
   float GridDivisions;
   float GridThickness;
-  bool Grid3DVisibility;
   bool ShowResection2D;
-  bool EnableFlexibleBoundary;
-  bool Grid2DVisibility;
   double HepaticContourThickness; //Resection margin in mm
   double PortalContourThickness; //Uncertainty margin in mm
   float HepaticContourColor[3];
   float PortalContourColor[3];
   int TextureNumComps;
+  bool EnableFlexibleBoundary;
   bool MirrorDisplay;
+  bool Grid3DVisibility;
+  bool Grid2DVisibility;
 
  private:
   vtkMRMLLiverResectionNode(const vtkMRMLLiverResectionNode&);

diff --git a/LiverResections/MRMLDM/vtkMRMLLiverResectionsDisplayableManager2D.h b/LiverResections/MRMLDM/vtkMRMLLiverResectionsDisplayableManager2D.h
@@ -80,7 +80,7 @@ vtkMRMLLiverResectionsDisplayableManager2D
 
 // Description:
 // VTK-specific function for print out information
-  void PrintSelf(ostream& os, vtkIndent indent);
+  void PrintSelf(ostream& os, vtkIndent indent) override;
 
  protected:
 
@@ -92,12 +92,12 @@ vtkMRMLLiverResectionsDisplayableManager2D
 
 // Description:
 // MRML virtual functions
-  virtual void SetMRMLSceneInternal(vtkMRMLScene *newScene);
-  virtual void ProcessMRMLNodesEvents(vtkObject *caller, unsigned long event, void *callData);
-  virtual void OnMRMLSceneNodeAdded(vtkMRMLNode *node);
-  virtual void OnMRMLNodeModified(vtkMRMLNode *node);
-  virtual void OnMRMLSceneNodeRemoved(vtkMRMLNode *node);
-  virtual void OnMRMLSceneEndClose();
+  virtual void SetMRMLSceneInternal(vtkMRMLScene *newScene) override;
+  virtual void ProcessMRMLNodesEvents(vtkObject *caller, unsigned long event, void *callData) override;
+  virtual void OnMRMLSceneNodeAdded(vtkMRMLNode *node) override;
+  virtual void OnMRMLNodeModified(vtkMRMLNode *node) override;
+  virtual void OnMRMLSceneNodeRemoved(vtkMRMLNode *node) override;
+  virtual void OnMRMLSceneEndClose() override;
 
  protected:
 
@@ -120,4 +120,4 @@ vtkMRMLLiverResectionsDisplayableManager2D
 
 };
 
-#endif
+#endif
diff --git a/LiverResections/MRMLDM/vtkMRMLLiverResectionsDisplayableManagerHelper2D.cpp b/LiverResections/MRMLDM/vtkMRMLLiverResectionsDisplayableManagerHelper2D.cpp
@@ -87,9 +87,9 @@ vtkMRMLLiverResectionsDisplayableManagerHelper2D::
 //---------------------------------------------------------------------------
 void vtkMRMLLiverResectionsDisplayableManagerHelper2D::
 PrintSelf(ostream &os,
-          vtkIndent vtkNotUsed(indent))
+          vtkIndent indent)
 {
-
+    this->vtkObject::PrintSelf(os, indent);
 }
 
 //---------------------------------------------------------------------------

diff --git a/LiverResections/MRMLDM/vtkMRMLLiverResectionsDisplayableManagerHelper2D.h b/LiverResections/MRMLDM/vtkMRMLLiverResectionsDisplayableManagerHelper2D.h
@@ -80,7 +80,7 @@ vtkMRMLLiverResectionsDisplayableManagerHelper2D
 
 // Description:
 // VTK-specific function for printing information
-  void PrintSelf(ostream &os, vtkIndent indent);
+  void PrintSelf(ostream &os, vtkIndent indent) override;
 
 // Description:
 // Add surface contour to the 2D views

diff --git a/LiverSegments/CMakeLists.txt b/LiverSegments/CMakeLists.txt
@@ -24,6 +24,29 @@ slicerMacroBuildScriptedModule(
   WITH_GENERIC_TESTS
   )
 
+
+# #-----------------------------------------------------------------------------
+# set(MODULE_EXPORT_DIRECTIVE "Q_SLICER_QTMODULES_${MODULE_NAME_UPPER}_EXPORT")
+
+# set(MODULE_INCLUDE_DIRECTORIES
+#   ${CMAKE_CURRENT_SOURCE_DIR}/Logic
+#   ${CMAKE_CURRENT_BINARY_DIR}/Logic
+#   )
+
+# #-----------------------------------------------------------------------------
+# slicerMacroBuildLoadableModule(
+#   NAME ${MODULE_NAME}
+#   TITLE ${MODULE_TITLE}
+#   EXPORT_DIRECTIVE ${MODULE_EXPORT_DIRECTIVE}
+#   INCLUDE_DIRECTORIES ${MODULE_INCLUDE_DIRECTORIES}
+#   SRCS ${MODULE_SRCS}
+#   MOC_SRCS ${MODULE_MOC_SRCS}
+#   UI_SRCS ${MODULE_UI_SRCS}
+#   TARGET_LIBRARIES ${MODULE_TARGET_LIBRARIES}
+#   RESOURCES ${MODULE_RESOURCES}
+#   # WITH_GENERIC_TESTS
+#   )
+
 #-----------------------------------------------------------------------------
 if(BUILD_TESTING)