ENH: Misc doc and filter updates for ITK, ExtractInternalSurfaces and…

… SurfaceNets (#898)


- DOC: Fix Human labels in a few ITK filters
- ENH: ExtractInternalSurfacesFromTriangleGeometry now allows user defined NodeType ranges
- DOC: Improve SurfaceNets filter documentation with images.

Signed-off-by: Michael Jackson <[email protected]>

src/Plugins/ITKImageProcessing/src/ITKImageProcessing/Filters/ITKClosingByReconstructionImage.cpp

@@ -87,7 +87,7 @@ Parameters ITKClosingByReconstructionImage::parameters() const
                                                 "For objects that are 1 pixel wide, use True.",
                                                 false));
   params.insert(std::make_unique<BoolParameter>(
-      k_PreserveIntensities_Key, "PreserveIntensities",
+      k_PreserveIntensities_Key, "Preserve Intensities",
       "Set/Get whether the original intensities of the image retained for those pixels unaffected by the opening by reconstruction. If Off, the output pixel contrast will be reduced.", false));
 
   params.insertSeparator(Parameters::Separator{"Required Input Cell Data"});

src/Plugins/ITKImageProcessing/src/ITKImageProcessing/Filters/ITKOpeningByReconstructionImage.cpp

@@ -87,7 +87,7 @@ Parameters ITKOpeningByReconstructionImage::parameters() const
                                                 "For objects that are 1 pixel wide, use True.",
                                                 false));
   params.insert(std::make_unique<BoolParameter>(
-      k_PreserveIntensities_Key, "PreserveIntensities",
+      k_PreserveIntensities_Key, "Preserve Intensities",
       "Set/Get whether the original intensities of the image retained for those pixels unaffected by the opening by reconstruction. If Off, the output pixel contrast will be reduced.", false));
 
   params.insertSeparator(Parameters::Separator{"Required Input Cell Data"});

src/Plugins/SimplnxCore/docs/ExtractInternalSurfacesFromTriangleGeometry.md

@@ -6,7 +6,9 @@ Geometry
 
 ## Description
 
-This **Filter** extracts any **Triangles** from the supplied **Triangle Geometry** that contain any *internal nodes*, then uses these extracted **Triangles** to create a new **Data Container** with the reduced **Triangle Geometry**.  This operation is the same as removing all **Triangles** that only lie of the outer surface of the supplied **Triangle Geometry**.  The user must supply a **Vertex Attribute Array** that defines the type for each node of the **Triangle Geometry**.  Node types may take the following values:
+This **Filter** extracts any **Triangles** from the supplied **Triangle Geometry** that contain any *internal nodes*, then uses these extracted **Triangles** to create a new **Data Container** with the reduced **Triangle Geometry**.  This operation is the same as removing all **Triangles** that only lie of the outer surface of the supplied **Triangle Geometry**.  The user must supply a "Node Type" **Vertex Attribute Array** that defines the type for each node of the **Triangle Geometry**.  Node types may take the following values:
+
+### Quick Surface Mesh
 
 | Id Value | Node Type |
 |----------|-----------|
@@ -17,7 +19,18 @@ This **Filter** extracts any **Triangles** from the supplied **Triangle Geometry
 | 13 | Triple Line on the outer surface |
 | 14 | Quadruple Point on the outer surface |
 
-This **Filter** has the effect of removing any **Triangles** that only contain **Vertices** whose node Id values are 12, 13, or 14.  In general, this *node type* array is created when the original surface mesh is created.
+### SurfaceNets Mesh
+
+| Id Value | Node Type |
+|----------|-----------|
+| 0 | Normal **Vertex |
+| 3 | Triple Line |
+| 4-8 | Quadruple Point |
+| 13 | Normal **Vertex** on the outer surface |
+| 14 | Triple Line on the outer surface |
+| 15-18 | Quadruple Point on the outer surface |
+
+This **Filter** has the effect of removing any **Triangles** that only contain **Vertices** whose node Id values fall outside of the min and max that the user sets.  In general, this *node type* array is created when the original surface mesh is created.
 
 It is unknown until runtime how the **Geometry** will be changed by removing certain **Vertices** and **Triangles**.
 

src/Plugins/SimplnxCore/docs/SurfaceNetsFilter.md

@@ -35,6 +35,29 @@ SurfaceNets output **with** the built-in smoothing operation applied.
 
 ---------------
 
+## Node Types
+
+During the meshing process, each vertex, or node, will get a "Node Type" value assigned to it. These will range from 0 to 6. The value is an internal representation from the SurfaceNets algorithm. They are roughly equivelent to the Node Types from the Quick Surface Mesh algorithm but not strictly the same.
+
+- Node Type = 0: This is a node that ONLY has 2 features connected to the node.
+- Node Type = 2: This is a node that has 3 features connected to the node, such as a triple line
+- Node Type = 3-6: These nodes have 4 or more features connected to the node.
+
+
+| Node Type | Example Image                                |
+|-----------|----------------------------------------------|
+| 0 | ![Node Type 0](Images/SurfaceNets_NodeType_0.png)|
+| 2 |  ![Node Type 2](Images/SurfaceNets_NodeType_2.png)|
+| 3 |  ![Node Type 3](Images/SurfaceNets_NodeType_3.png)|
+| 4 | ![Node Type 4](Images/SurfaceNets_NodeType_4.png)|
+| 6 |  ![Node Type 6](Images/SurfaceNets_NodeType_6.png)|
+
+### Exterior or Boundary Nodes
+
+Nodes that appear on the exterior of a volume have Node Type values starting at 10 and going up from there. For instance, a triple line that is also on the exterior of the volume should have a value of 12.
+
+![Exterior Node Types](Images/SurfaceNets_NodeType_Exterior.png)
+
 % Auto generated parameter table will be inserted here
 
 ## Example Pipelines

src/Plugins/SimplnxCore/src/SimplnxCore/Filters/ExtractInternalSurfacesFromTriangleGeometry.cpp

@@ -135,8 +135,11 @@ Parameters ExtractInternalSurfacesFromTriangleGeometry::parameters() const
   params.insertSeparator(Parameters::Separator{"Input Vertex Data"});
   params.insert(std::make_unique<ArraySelectionParameter>(k_NodeTypesPath_Key, "Node Types Array", "Path to the Node Types array", DataPath(), ArraySelectionParameter::AllowedTypes{DataType::int8},
                                                           ArraySelectionParameter::AllowedComponentShapes{{1}}));
+  params.insert(std::make_unique<VectorInt8Parameter>(k_NodeTypeRange_Key, "Internal Surface Node Type Min & Max",
+                                                      "The min and max (inclusive) Node Type values that distinguish an internal surface from an external surface", std::vector<int8>{0, 8},
+                                                      std::vector<std::string>{"Min", "Max"}));
 
-  params.insertSeparator(Parameters::Separator{"Create Data Objects"});
+  params.insertSeparator(Parameters::Separator{"Created Data Objects"});
   params.insert(std::make_unique<DataGroupCreationParameter>(k_InternalTriangleGeom_Key, "Created Triangle Geometry Path", "Path to create the new Triangle Geometry", DataPath()));
   params.insert(std::make_unique<DataObjectNameParameter>(k_VertexDataName_Key, "Vertex Data Attribute Matrix", "Created vertex data AttributeMatrix name", INodeGeometry0D::k_VertexDataName));
   params.insert(std::make_unique<DataObjectNameParameter>(k_FaceDataName_Key, "Face Data Attribute Matrix", "Created face data AttributeMatrix name", INodeGeometry2D::k_FaceDataName));
@@ -263,6 +266,8 @@ Result<> ExtractInternalSurfacesFromTriangleGeometry::executeImpl(DataStructure&
   auto vertexDataName = args.value<std::string>(k_VertexDataName_Key);
   auto faceDataName = args.value<std::string>(k_FaceDataName_Key);
 
+  auto minMaxNodeValues = args.value<VectorInt8Parameter::ValueType>(k_NodeTypeRange_Key);
+
   auto& triangleGeom = data.getDataRefAs<TriangleGeom>(triangleGeomPath);
   auto& internalTriangleGeom = data.getDataRefAs<TriangleGeom>(internalTrianglesPath);
   auto& vertices = *triangleGeom.getVertices();
@@ -298,7 +303,8 @@ Result<> ExtractInternalSurfacesFromTriangleGeometry::executeImpl(DataStructure&
     MeshIndexType v1Index = triangles[3 * triIndex + 1];
     MeshIndexType v2Index = triangles[3 * triIndex + 2];
     // Check if the NodeType is either 2, 3, 4
-    if((nodeTypes[v0Index] >= 2 && nodeTypes[v0Index] <= 4) && (nodeTypes[v1Index] >= 2 && nodeTypes[v1Index] <= 4) && (nodeTypes[v2Index] >= 2 && nodeTypes[v2Index] <= 4))
+    if((nodeTypes[v0Index] >= minMaxNodeValues[0] && nodeTypes[v0Index] <= minMaxNodeValues[1]) && (nodeTypes[v1Index] >= minMaxNodeValues[0] && nodeTypes[v1Index] <= minMaxNodeValues[1]) &&
+       (nodeTypes[v2Index] >= minMaxNodeValues[0] && nodeTypes[v2Index] <= minMaxNodeValues[1]))
     {
       // All Nodes are the correct type
       triNewIndex[triIndex] = currentNewTriIndex;

src/Plugins/SimplnxCore/src/SimplnxCore/Filters/ExtractInternalSurfacesFromTriangleGeometry.hpp

@@ -28,6 +28,7 @@ class SIMPLNXCORE_EXPORT ExtractInternalSurfacesFromTriangleGeometry : public IF
   static inline constexpr StringLiteral k_CopyTrianglePaths_Key = "copy_triangle_array_paths";
   static inline constexpr StringLiteral k_VertexDataName_Key = "vertex_data_name";
   static inline constexpr StringLiteral k_FaceDataName_Key = "face_data_name";
+  static inline constexpr StringLiteral k_NodeTypeRange_Key = "node_type_range";
 
   /**
    * @brief Reads SIMPL json and converts it simplnx Arguments.