FILTER: Label Triangle Geometry and Remove Flagged Triangles Filters (#…

…842)

Signed-off-by: Michael Jackson <[email protected]>
Co-authored-by: Matthew Marine <[email protected]>
Co-authored-by: Michael Jackson <[email protected]>

src/Plugins/SimplnxCore/CMakeLists.txt

@@ -78,6 +78,7 @@ set(FilterList
   IterativeClosestPointFilter
   KMeansFilter
   KMedoidsFilter
+  LabelTriangleGeometryFilter
   LaplacianSmoothingFilter
   MapPointCloudToRegularGridFilter
   MinNeighbors
@@ -98,6 +99,7 @@ set(FilterList
   ReadVolumeGraphicsFileFilter
   RegularGridSampleSurfaceMeshFilter
   RemoveFlaggedFeaturesFilter
+  RemoveFlaggedTrianglesFilter
   RemoveFlaggedVertices
   RemoveMinimumSizeFeaturesFilter
   RenameDataObject
@@ -173,6 +175,7 @@ set(AlgorithmList
   ImageContouring
   KMeans
   KMedoids
+  LabelTriangleGeometry
   LaplacianSmoothing
   NearestPointFuseRegularGrids
   PartitionGeometry
@@ -185,6 +188,7 @@ set(AlgorithmList
   ReadVolumeGraphicsFile
   RegularGridSampleSurfaceMesh
   RemoveFlaggedFeatures
+  RemoveFlaggedTriangles
   ReplaceElementAttributesWithNeighborValues
   ResampleImageGeom
   ResampleRectGridToImageGeom
@@ -428,7 +432,7 @@ if(EXISTS "${DREAM3D_DATA_DIR}" AND SIMPLNX_DOWNLOAD_TEST_FILES)
 
   download_test_data(DREAM3D_DATA_DIR ${DREAM3D_DATA_DIR}
     ARCHIVE_NAME STL_Models.tar.gz
-    SHA512 14d5bbb1dcc241a5ad9b17e7647144926f22fca9af5e426798c2ed423d8d3b5d89d8c66ce9e6854bfcdbaea7f72b69980477ab837498e3dca89b5cd2870e2cff
+    SHA512 6a17caa1c5b60740a18d30732b10139b5864e12abd5009ce482972f4070f86e1762a3bf2bbceb8f178187b4d70bedbde1516f32397c3d4424404557b320dde9d
     INSTALL
     COPY_DATA
   )

src/Plugins/SimplnxCore/docs/LabelTriangleGeometryFilter.md

@@ -0,0 +1,35 @@
+# Label Triangle Geometry
+
+## Group (Subgroup)
+
+Surface Meshing (Geometry)
+
+## Description
+
+This **Filter** accepts a **Triangle Geometry** and checks the connectivity of **Triangles** and assigns them **region ID**s in a mask accordingly as well as providing a count for the number of **Triangles** in each **Region**.
+
+Note: Our connectivity is different from other connectivity algorithms, in that it is dependent on the dimensionality of the geometry it is run on. A triangle geometry is two dimensional thus it must share one edge with another triangle to be considered connected. Only one shared vertex will not be enough to count triangles as connected. See the following image for reference:
+
+![Connectivity Image](Images/connectivity_image.png)
+
+The image in question demonstrates what geometric shapes would be considered connected according to matching color scheme. The colors are relative to the shapes dimensionality. Thus the fact there is a yellow triangle and a yellow cube does not mean they are related.
+
+- 1D Geometry: Two edges are considered connected if they share a vertex.
+- 2D Geometry: Triangle and Quad Geometries are considered connected if they share an entire edge. As shown in the image above, Triangles 1 & 2 are connected while triangles 2 & 3 are **not** connected.
+- 3D Geometry: Hexahedron/Tetrahedron: In the image above the hexahedrons 4,5, and 6 are **not** considered connected while 6 & 7 are considered connected.
+
+## Example Output
+
+The image below shows a single STL file that contains 12 different geometries. This filter labeled each geometry with a unique "Region ID" and the visualization is colored by those "Region Ids"
+
+![Filter Output](Images/LabelTriangleGeometry_1.png)
+
+% Auto generated parameter table will be inserted here
+
+## License & Copyright
+
+Please see the description file distributed with this plugin.
+
+## DREAM3D-NX Help
+
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.

src/Plugins/SimplnxCore/docs/RegularGridSampleSurfaceMesh.md

@@ -13,31 +13,7 @@ This **Filter** "samples" a triangulated surface mesh on a rectilinear grid. The
 3. For each bounding box a **Cell** falls in, check against that **Feature's** **Triangle** list to determine if the **Cell** falls within that n-sided polyhedra (*Note:* if the surface mesh is conformal, then each **Cell** will only belong to one **Feature**, but if not, the last **Feature** the **Cell** is found to fall inside of will *own* the **Cell**)
 4. Assign the **Feature** number that the **Cell** falls within to the *Feature Ids* array in the new rectilinear grid geometry
 
-## Parameters
-
-| Name | Type | Description |
-|------------|------| --------------------------------- |
-| Dimensions | uint64 | Number of **Cells** along each axis |
-| Resolution | float32 (3x) | The resolution values (dx, dy, dz) |
-| Origin | float32 (3x) | The origin of the sampling volume |
-
-## Required Geometry
-
-Triangle
-
-## Required Objects
-
-| Type | Default Name | Type | Comp Dims | Description |
-|------|--------------|-----|-----|-----------------------------------|
-| Data Array | Face Labels | int32 | (2) | Specifies which **Features** are on either side of each **Face**. |
-
-## Created
-
-| Kind                      | Default Name | Type     | Comp Dims | Description                                 |
-|---------------------------|--------------|----------|--------|---------------------------------------------|
-| Image Geometry | Image Geometry | N/A | N/A | Created **Image Geometry** name and *DataPath* |
-|   Attribute Matrix   | Cell Data | Cell | N/A | Created **Cell Attribute Matrix** name |
-| Data Array | Feature Ids | int32 | (1) | Specifies to which **Feature** each **Cell** belongs |
+% Auto generated parameter table will be inserted here
 
 ## License & Copyright
 

src/Plugins/SimplnxCore/docs/RemoveFlaggedFeaturesFilter.md

@@ -6,11 +6,11 @@ Processing (Cleanup)
 
 ## Description
 
-This **Filter** will remove **Features** that have been flagged by another **Filter** from the structure.  The **Filter**
-requires that the user point to a boolean array at the **Feature** level that tells the **Filter** whether the **Feature**
-should remain in the structure.  If the boolean array is *false* for a **Feature**, then all **Cells** that belong to that
-**Feature** are temporarily *unassigned*. Optionally, after all *undesired* **Features** are removed, the remaining **Features** are
-isotropically coarsened to fill in the gaps left by the removed **Features**.
+This **Filter** will remove **Features** that have been flagged by another **Filter** from the structure.  The **Filter** requires that the user point to a boolean array at the **Feature** level that tells the **Filter** whether the **Feature** should remain in the structure.  If the boolean array is *false* for a **Feature**, then all **Cells** that belong to that **Feature** are temporarily *unassigned*. Optionally, after all *undesired* **Features** are removed, the remaining **Features** are isotropically coarsened to fill in the gaps left by the removed **Features**.
+
+## Caveats
+
+This filter will **ONLY** run on an Image Geometry.
 
 % Auto generated parameter table will be inserted here
 

src/Plugins/SimplnxCore/docs/RemoveFlaggedTrianglesFilter.md

@@ -0,0 +1,38 @@
+# Remove Flagged Triangles
+
+## Group (Subgroup)
+
+Surface Meshing (Misc)
+
+## Description
+
+This **Filter** removes **Triangles** from the supplied **Triangle Geometry** that are flagged by a boolean mask array as **true**.  A new reduced **Geometry** is created that contains all the remaining **Triangles**.  It is unknown until run time how many **Triangles** will be removed from the **Geometry**. Therefore, this **Filter** requires that a new **TriangleGeom** be created to contain the reduced **Triangle Geometry**. This new **Geometry** will *NOT* contain copies of any **Feature Attribute Matrix** or **Ensemble Attribute Matrix** from the original **Geometry**. 
+
+- Additionally, all **Vertex** data will be copied, with tuples *removed* for any **Vertices** removed by the **Filter**.  The user must supply a name for the reduced **Geometry**.
+
+The mask is expected to be over the triangles themselves so it should be based on something from the ***Face Data*** **Attribute Matrix**, generally we suggest basing the mask on the created **Region Ids** array from the *Label Triangle Geometry Filter*.
+
+*Note:* Since it cannot be known before run time how many **Vertices** will be removed, the new **Vertex Geometry** and
+all associated **Vertex** data to be copied will be initialized to have size 0.
+
+## Example Output
+
+- The next figure shows a triangle geometry that has had a mask generated. Yellow parts are flagged as true.
+
+![Masked triangle geometries for removal.](Images/RemoveFlaggedTriangles_1.png)
+
+- The next figure shows the result of running the filter.
+
+![Resulting triangle geometry](Images/RemoveFlaggedTriangles_2.png)
+
+% Auto generated parameter table will be inserted here
+
+## Example Pipelines
+
+## License & Copyright
+
+Please see the description file distributed with this plugin.
+
+## DREAM3D-NX Help
+
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.

src/Plugins/SimplnxCore/pipelines/Remove_Triangles.d3dpipeline

@@ -0,0 +1,113 @@
+{
+  "isDisabled": false,
+  "name": "Untitled Pipeline",
+  "pipeline": [
+    {
+      "args": {
+        "face_attribute_matrix": "Face Data",
+        "face_normals_data_path": "Face Normals",
+        "scale_factor": 1.0,
+        "scale_output": false,
+        "stl_file_path": "Data/STL_Models/Example_Triangle_Geometry.stl",
+        "triangle_geometry_name": "TriangleDataContainer",
+        "vertex_attribute_matrix": "Vertex Data"
+      },
+      "comments": "",
+      "filter": {
+        "name": "nx::core::ReadStlFileFilter",
+        "uuid": "2f64bd45-9d28-4254-9e07-6aa7c6d3d015"
+      },
+      "isDisabled": false
+    },
+    {
+      "args": {
+        "created_region_ids_path": "TriangleDataContainer/Face Data/Region Ids",
+        "num_triangles_name": "NumTriangles",
+        "triangle_attribute_matrix_name": "CAD Part Data",
+        "triangle_geom_path": "TriangleDataContainer"
+      },
+      "comments": "",
+      "filter": {
+        "name": "nx::core::LabelTriangleGeometryFilter",
+        "uuid": "7a7a2c6f-3b03-444d-8b8c-5976b0e5c82e"
+      },
+      "isDisabled": false
+    },
+    {
+      "args": {
+        "array_thresholds": {
+          "inverted": false,
+          "thresholds": [
+            {
+              "array_path": "TriangleDataContainer/Face Data/Region Ids",
+              "comparison": 0,
+              "inverted": false,
+              "type": "array",
+              "union": 0,
+              "value": 9.0
+            }
+          ],
+          "type": "collection",
+          "union": 0
+        },
+        "created_data_path": "Mask",
+        "created_mask_type": 1,
+        "custom_false_value": 0.0,
+        "custom_true_value": 1.0,
+        "use_custom_false_value": false,
+        "use_custom_true_value": false
+      },
+      "comments": "",
+      "filter": {
+        "name": "nx::core::MultiThresholdObjects",
+        "uuid": "4246245e-1011-4add-8436-0af6bed19228"
+      },
+      "isDisabled": false
+    },
+    {
+      "args": {
+        "array_thresholds": {
+          "inverted": false,
+          "thresholds": [
+            {
+              "array_path": "TriangleDataContainer/Face Data/Region Ids",
+              "comparison": 0,
+              "inverted": false,
+              "type": "array",
+              "union": 0,
+              "value": 9.0
+            }
+          ],
+          "type": "collection",
+          "union": 0
+        },
+        "created_data_path": "Mask2",
+        "created_mask_type": 10,
+        "custom_false_value": 0.0,
+        "custom_true_value": 1.0,
+        "use_custom_false_value": false,
+        "use_custom_true_value": false
+      },
+      "comments": "",
+      "filter": {
+        "name": "nx::core::MultiThresholdObjects",
+        "uuid": "4246245e-1011-4add-8436-0af6bed19228"
+      },
+      "isDisabled": false
+    },
+    {
+      "args": {
+        "input_geometry": "TriangleDataContainer",
+        "mask_array_path": "TriangleDataContainer/Face Data/Mask2",
+        "output_geometry": "Part 10"
+      },
+      "comments": "",
+      "filter": {
+        "name": "nx::core::RemoveFlaggedTrianglesFilter",
+        "uuid": "38155c61-2709-4731-be95-43745bb3f8d8"
+      },
+      "isDisabled": false
+    }
+  ],
+  "version": 1
+}

src/Plugins/SimplnxCore/src/SimplnxCore/Filters/Algorithms/LabelTriangleGeometry.cpp

@@ -0,0 +1,111 @@
+#include "LabelTriangleGeometry.hpp"
+
+#include "simplnx/DataStructure/DataArray.hpp"
+#include "simplnx/DataStructure/DataGroup.hpp"
+#include "simplnx/DataStructure/Geometry/TriangleGeom.hpp"
+
+using namespace nx::core;
+
+// -----------------------------------------------------------------------------
+LabelTriangleGeometry::LabelTriangleGeometry(DataStructure& dataStructure, const IFilter::MessageHandler& mesgHandler, const std::atomic_bool& shouldCancel,
+                                             LabelTriangleGeometryInputValues* inputValues)
+: m_DataStructure(dataStructure)
+, m_InputValues(inputValues)
+, m_ShouldCancel(shouldCancel)
+, m_MessageHandler(mesgHandler)
+{
+}
+
+// -----------------------------------------------------------------------------
+LabelTriangleGeometry::~LabelTriangleGeometry() noexcept = default;
+
+// -----------------------------------------------------------------------------
+const std::atomic_bool& LabelTriangleGeometry::getCancel()
+{
+  return m_ShouldCancel;
+}
+
+// -----------------------------------------------------------------------------
+Result<> LabelTriangleGeometry::operator()()
+{
+  // Scope other values since underlying arrays will be changed by the time they are need again
+  std::vector<uint32> triangleCounts = {0, 0};
+  auto& triangle = m_DataStructure.getDataRefAs<TriangleGeom>(m_InputValues->TriangleGeomPath);
+
+  {
+    usize numTris = triangle.getNumberOfFaces();
+
+    auto check = triangle.findElementNeighbors(); // use auto since return time is a class declared typename
+    if(check < 0)
+    {
+      return MakeErrorResult(check, fmt::format("Error finding element neighbors for {} geometry", triangle.getName()));
+    }
+
+    const TriangleGeom::ElementDynamicList* triangleNeighborsPtr = triangle.getElementNeighbors();
+
+    auto& regionIds = m_DataStructure.getDataRefAs<Int32Array>(m_InputValues->RegionIdsPath);
+
+    usize chunkSize = 1000;
+    std::vector<int32> triList(chunkSize, -1);
+    // first identify connected triangle sets as features
+    int32 regionCount = 1;
+    for(usize i = 0; i < numTris; i++)
+    {
+      if(regionIds[i] == 0)
+      {
+        regionIds[i] = regionCount;
+        triangleCounts[regionCount]++;
+
+        usize size = 0;
+        triList[size] = static_cast<int32>(i);
+        size++;
+        while(size > 0)
+        {
+          TriangleGeom::MeshIndexType tri = triList[size - 1];
+          size -= 1;
+          uint16_t tCount = triangleNeighborsPtr->getNumberOfElements(tri);
+          TriangleGeom::MeshIndexType* dataPtr = triangleNeighborsPtr->getElementListPointer(tri);
+          for(int j = 0; j < tCount; j++)
+          {
+            TriangleGeom::MeshIndexType neighTri = dataPtr[j];
+            if(regionIds[neighTri] == 0)
+            {
+              regionIds[neighTri] = regionCount;
+              triangleCounts[regionCount]++;
+              triList[size] = static_cast<int32>(neighTri);
+              size++;
+              if(size >= triList.size())
+              {
+                size = triList.size();
+                triList.resize(size + chunkSize);
+                for(usize k = size; k < triList.size(); ++k)
+                {
+                  triList[k] = -1;
+                }
+              }
+            }
+          }
+        }
+        regionCount++;
+        triangleCounts.push_back(0);
+      }
+    }
+
+    // Resize the Triangle Region AttributeMatrix
+    m_DataStructure.getDataAs<AttributeMatrix>(m_InputValues->TriangleAMPath)->resizeTuples(std::vector<usize>{triangleCounts.size()});
+  }
+
+  // Clear ElementDynamicLists so write out is possible
+  triangle.deleteElementNeighbors();
+  // Remove elements containing vertices, because Element neighbors created it quietly under the covers
+  triangle.deleteElementsContainingVert();
+
+  // copy triangleCounts into the proper DataArray "NumTriangles" in the Feature Attribute Matrix
+  auto& numTriangles = m_DataStructure.getDataRefAs<UInt64Array>(m_InputValues->NumTrianglesPath);
+  for(usize index = 0; index < numTriangles.getSize(); index++)
+  {
+    numTriangles[index] = static_cast<uint64>(triangleCounts[index]);
+  }
+
+  return {};
+}