[WIP] FILTER: RemoveFlaggedTriangles.

src/Plugins/ComplexCore/CMakeLists.txt

@@ -97,6 +97,7 @@ set(FilterList
   ReadVolumeGraphicsFileFilter
   RegularGridSampleSurfaceMeshFilter
   RemoveFlaggedFeaturesFilter
+  RemoveFlaggedTrianglesFilter
   RemoveFlaggedVertices
   RemoveMinimumSizeFeaturesFilter
   RenameDataObject
@@ -183,6 +184,7 @@ set(AlgorithmList
   ReadVolumeGraphicsFile
   RegularGridSampleSurfaceMesh
   RemoveFlaggedFeatures
+  RemoveFlaggedTriangles
   ReplaceElementAttributesWithNeighborValues
   ResampleImageGeom
   ResampleRectGridToImageGeom

src/Plugins/ComplexCore/docs/RemoveFlaggedTrianglesFilter.md

@@ -0,0 +1,51 @@
+# 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.  
+Specifically, **Triangles** flagged as _true_ are removed from the **Geometry**.  A new reduced **Triangle 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 **Data Container** be created to contain the reduced **Triangle Geometry**.  
+This new **Data Container** will NOT contain copies of any **Feature** or **Ensemble** **Attribute Matrices** from the original **Data Container**.  
+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 **Data Container**.
+
+_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.
+
+## Parameters ##
+
+None
+
+## Required Geometry ###
+
+**Triangle Geometry**
+
+## Required Objects ##
+
+| Kind | Default Name | Type | Component Dimensions | Description                                                         |
+|------|--------------|------|----------------------|---------------------------------------------------------------------|
+| **Data Container** | TriangleDataContainer | N/A | N/A | **Data Container** holding the **Triangle Geometry** to reduce      |
+| **Triangle Attribute Array** | Mask | bool | (1) | Mask array specifying which **Triangles** to remove                 |
+
+## Created Objects ##
+
+| Kind                       | Default Name               | Type | Component Dimensions | Description                                                |
+|----------------------------|----------------------------|------|----------------------|------------------------------------------------------------|
+| Reduced **Data Container** | ReducedVertexDataContainer | N/A  | N/A                  | **Data Container** holding the reduced **Vertex Geometry** |
+
+## Example Pipelines ##
+
+
+
+## License & Copyright ##
+
+Please see the description file distributed with this plugin.
+
+## DREAM3D Mailing Lists ##
+
+If you need more help with a filter, please consider asking your question on the DREAM3D Users mailing list:

src/Plugins/ComplexCore/src/ComplexCore/ComplexCoreLegacyUUIDMapping.hpp

@@ -4,17 +4,26 @@
 #include <string>
 
 // clang-format off
+#include "ComplexCore/Filters/WriteAbaqusHexahedronFilter.hpp"
+#include "ComplexCore/Filters/AddBadDataFilter.hpp"
 #include "ComplexCore/Filters/AlignGeometries.hpp"
 #include "ComplexCore/Filters/AlignSectionsFeatureCentroidFilter.hpp"
 #include "ComplexCore/Filters/AlignSectionsListFilter.hpp"
+#include "ComplexCore/Filters/AppendImageGeometryZSliceFilter.hpp"
+#include "ComplexCore/Filters/ApplyTransformationToGeometryFilter.hpp"
 #include "ComplexCore/Filters/ApplyTransformationToGeometryFilter.hpp"
 #include "ComplexCore/Filters/ApproximatePointCloudHull.hpp"
 #include "ComplexCore/Filters/ArrayCalculatorFilter.hpp"
+#include "ComplexCore/Filters/WriteAvizoRectilinearCoordinateFilter.hpp"
+#include "ComplexCore/Filters/WriteAvizoUniformCoordinateFilter.hpp"
 #include "ComplexCore/Filters/CalculateArrayHistogramFilter.hpp"
 #include "ComplexCore/Filters/CalculateFeatureSizesFilter.hpp"
 #include "ComplexCore/Filters/CalculateTriangleAreasFilter.hpp"
 #include "ComplexCore/Filters/ChangeAngleRepresentation.hpp"
 #include "ComplexCore/Filters/CombineAttributeArraysFilter.hpp"
+#include "ComplexCore/Filters/CombineStlFilesFilter.hpp"
+#include "ComplexCore/Filters/ComputeFeatureRectFilter.hpp"
+#include "ComplexCore/Filters/ComputeMomentInvariants2DFilter.hpp"
 #include "ComplexCore/Filters/ConditionalSetValue.hpp"
 #include "ComplexCore/Filters/ConvertColorToGrayScaleFilter.hpp"
 #include "ComplexCore/Filters/ConvertDataFilter.hpp"
@@ -28,31 +37,37 @@
 #include "ComplexCore/Filters/CropImageGeometry.hpp"
 #include "ComplexCore/Filters/CropVertexGeometry.hpp"
 #include "ComplexCore/Filters/DeleteData.hpp"
+#include "ComplexCore/Filters/ErodeDilateBadDataFilter.hpp"
 #include "ComplexCore/Filters/ErodeDilateCoordinationNumberFilter.hpp"
 #include "ComplexCore/Filters/ErodeDilateMaskFilter.hpp"
-#include "ComplexCore/Filters/ErodeDilateBadDataFilter.hpp"
+#include "ComplexCore/Filters/ExecuteProcessFilter.hpp"
 #include "ComplexCore/Filters/ExecuteProcessFilter.hpp"
 #include "ComplexCore/Filters/WriteDREAM3DFilter.hpp"
 #include "ComplexCore/Filters/ExtractComponentAsArrayFilter.hpp"
 #include "ComplexCore/Filters/ExtractInternalSurfacesFromTriangleGeometry.hpp"
 #include "ComplexCore/Filters/WriteFeatureDataCSVFilter.hpp"
 #include "ComplexCore/Filters/FillBadDataFilter.hpp"
 #include "ComplexCore/Filters/FindArrayStatisticsFilter.hpp"
-#include "ComplexCore/Filters/FindBoundaryCellsFilter.hpp"
 #include "ComplexCore/Filters/FindBiasedFeaturesFilter.hpp"
+#include "ComplexCore/Filters/FindBoundaryCellsFilter.hpp"
+#include "ComplexCore/Filters/FindBoundaryElementFractionsFilter.hpp"
 #include "ComplexCore/Filters/FindDifferencesMap.hpp"
 #include "ComplexCore/Filters/FindEuclideanDistMapFilter.hpp"
 #include "ComplexCore/Filters/FindFeatureCentroidsFilter.hpp"
-#include "ComplexCore/Filters/FindFeaturePhasesFilter.hpp"
+#include "ComplexCore/Filters/FindFeatureClusteringFilter.hpp"
 #include "ComplexCore/Filters/FindFeaturePhasesBinaryFilter.hpp"
+#include "ComplexCore/Filters/FindFeaturePhasesFilter.hpp"
+#include "ComplexCore/Filters/FindLargestCrossSectionsFilter.hpp"
 #include "ComplexCore/Filters/FindNeighborhoodsFilter.hpp"
 #include "ComplexCore/Filters/FindNeighborListStatistics.hpp"
 #include "ComplexCore/Filters/FindNeighbors.hpp"
 #include "ComplexCore/Filters/FindNumFeaturesFilter.hpp"
 #include "ComplexCore/Filters/FindSurfaceAreaToVolumeFilter.hpp"
 #include "ComplexCore/Filters/FindSurfaceFeatures.hpp"
+#include "ComplexCore/Filters/FindVertexToTriangleDistancesFilter.hpp"
 #include "ComplexCore/Filters/FindVolFractionsFilter.hpp"
 #include "ComplexCore/Filters/GenerateColorTableFilter.hpp"
+#include "ComplexCore/Filters/GenerateVectorColorsFilter.hpp"
 #include "ComplexCore/Filters/IdentifySample.hpp"
 #include "ComplexCore/Filters/ReadBinaryCTNorthstarFilter.hpp"
 #include "ComplexCore/Filters/ReadCSVFileFilter.hpp"
@@ -64,36 +79,39 @@
 #include "ComplexCore/Filters/InitializeData.hpp"
 #include "ComplexCore/Filters/InterpolatePointCloudToRegularGridFilter.hpp"
 #include "ComplexCore/Filters/IterativeClosestPointFilter.hpp"
+#include "ComplexCore/Filters/KMeansFilter.hpp"
+#include "ComplexCore/Filters/KMedoidsFilter.hpp"
 #include "ComplexCore/Filters/LaplacianSmoothingFilter.hpp"
+#include "ComplexCore/Filters/WriteLosAlamosFFTFilter.hpp"
 #include "ComplexCore/Filters/MapPointCloudToRegularGridFilter.hpp"
 #include "ComplexCore/Filters/MinNeighbors.hpp"
 #include "ComplexCore/Filters/MoveData.hpp"
 #include "ComplexCore/Filters/MultiThresholdObjects.hpp"
+#include "ComplexCore/Filters/NearestPointFuseRegularGridsFilter.hpp"
 #include "ComplexCore/Filters/PointSampleTriangleGeometryFilter.hpp"
 #include "ComplexCore/Filters/QuickSurfaceMeshFilter.hpp"
 #include "ComplexCore/Filters/ReadRawBinaryFilter.hpp"
+#include "ComplexCore/Filters/RemoveFlaggedTrianglesFilter.hpp"
 #include "ComplexCore/Filters/RemoveFlaggedVertices.hpp"
 #include "ComplexCore/Filters/RemoveMinimumSizeFeaturesFilter.hpp"
 #include "ComplexCore/Filters/RenameDataObject.hpp"
 #include "ComplexCore/Filters/ReplaceElementAttributesWithNeighborValuesFilter.hpp"
 #include "ComplexCore/Filters/ResampleImageGeomFilter.hpp"
+#include "ComplexCore/Filters/ResampleRectGridToImageGeomFilter.hpp"
+#include "ComplexCore/Filters/ReverseTriangleWindingFilter.hpp"
 #include "ComplexCore/Filters/RobustAutomaticThreshold.hpp"
 #include "ComplexCore/Filters/RotateSampleRefFrameFilter.hpp"
 #include "ComplexCore/Filters/ScalarSegmentFeaturesFilter.hpp"
 #include "ComplexCore/Filters/SetImageGeomOriginScalingFilter.hpp"
+#include "ComplexCore/Filters/SilhouetteFilter.hpp"
 #include "ComplexCore/Filters/SplitAttributeArrayFilter.hpp"
 #include "ComplexCore/Filters/ReadStlFileFilter.hpp"
 #include "ComplexCore/Filters/TriangleCentroidFilter.hpp"
 #include "ComplexCore/Filters/TriangleDihedralAngleFilter.hpp"
 #include "ComplexCore/Filters/TriangleNormalFilter.hpp"
+#include "ComplexCore/Filters/UncertainRegularGridSampleSurfaceMeshFilter.hpp"
+#include "ComplexCore/Filters/WriteVtkRectilinearGridFilter.hpp"
 #include "ComplexCore/Filters/WriteASCIIDataFilter.hpp"
-#include "ComplexCore/Filters/RemoveFlaggedFeaturesFilter.hpp"
-#include "ComplexCore/Filters/ComputeMomentInvariants2DFilter.hpp"
-#include "ComplexCore/Filters/ExecuteProcessFilter.hpp"
-#include "ComplexCore/Filters/FindVertexToTriangleDistancesFilter.hpp"
-#include "ComplexCore/Filters/ApplyTransformationToGeometryFilter.hpp"
-#include "ComplexCore/Filters/ComputeFeatureRectFilter.hpp"
-#include "ComplexCore/Filters/FindLargestCrossSectionsFilter.hpp"
 #include "ComplexCore/Filters/WriteStlFileFilter.hpp"
 #include "ComplexCore/Filters/AddBadDataFilter.hpp"
 #include "ComplexCore/Filters/AppendImageGeometryZSliceFilter.hpp"
@@ -114,6 +132,8 @@
 #include "ComplexCore/Filters/KMedoidsFilter.hpp"
 #include "ComplexCore/Filters/KMeansFilter.hpp"
 #include "ComplexCore/Filters/SilhouetteFilter.hpp"
+#include "ComplexCore/Filters/RemoveFlaggedFeaturesFilter.hpp"
+#include "ComplexCore/Filters/RemoveFlaggedTrianglesFilter.hpp"
 // @@__HEADER__TOKEN__DO__NOT__DELETE__@@
 
 namespace complex
@@ -237,6 +257,7 @@ namespace complex
     {complex::Uuid::FromString("f7486aa6-3049-5be7-8511-ae772b70c90b").value(), complex::FilterTraits<KMedoidsFilter>::uuid}, // KMedoids
     {complex::Uuid::FromString("b56a04de-0ca0-509d-809f-52219fca9c98").value(), complex::FilterTraits<KMeansFilter>::uuid}, // KMeans
     {complex::Uuid::FromString("f84d4d69-9ea5-54b6-a71c-df76d76d50cf").value(), complex::FilterTraits<SilhouetteFilter>::uuid}, // Silhouette
+    {complex::Uuid::FromString("379ccc67-16dd-530a-984f-177db9351bac").value(), complex::FilterTraits<RemoveFlaggedTrianglesFilter>::uuid}, // RemoveFlaggedTriangles
     // @@__MAP__UPDATE__TOKEN__DO__NOT__DELETE__@@
   };
 

src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/RemoveFlaggedTriangles.cpp

@@ -0,0 +1,161 @@
+#include "RemoveFlaggedTriangles.hpp"
+
+#include "complex/DataStructure/DataArray.hpp"
+#include "complex/DataStructure/DataGroup.hpp"
+#include "complex/DataStructure/Geometry/TriangleGeom.hpp"
+#include "complex/Utilities/ParallelDataAlgorithm.hpp"
+
+using namespace complex;
+
+namespace
+{
+/**
+ * @brief The PopulateReducedGeometryTrianglesImpl pulls the vertices associated with a triangle then locates the indices in
+ * the new VertexList then assigns that "new" triangle to Reduced Geometry
+ */
+class PopulateReducedGeometryTrianglesImpl
+{
+public:
+  PopulateReducedGeometryTrianglesImpl(const TriangleGeom& originalTriangle, TriangleGeom& reducedTriangle, const std::vector<usize>& newTrianglesIndex, const std::vector<usize>& newVerticesIndex)
+  : m_OriginalTriangle(originalTriangle)
+  , m_ReducedTriangle(reducedTriangle)
+  , m_NewTrianglesIndex(newTrianglesIndex)
+  , m_NewVerticesIndex(newVerticesIndex)
+  {
+  }
+  ~PopulateReducedGeometryTrianglesImpl() = default;
+
+  void generate(usize start, usize end) const
+  {
+    for(usize index = start; index < end; index++)
+    {
+      // pull old vertices
+      Point3Df oldVertexIndices = m_OriginalTriangle.getVertexCoordinate(m_NewTrianglesIndex[index]);
+
+      // locate new vertex index for each vertex index
+      usize newVertexIndices[3] = {0, 0, 0};
+      for(usize vertIndex = 0; vertIndex < 3; vertIndex++)
+      {
+        const auto& itr = lower_bound(m_NewVerticesIndex.begin(), m_NewVerticesIndex.end(), oldVertexIndices[vertIndex]); // find first instance of value as iterator
+        usize indexOfTarget = std::distance(m_NewVerticesIndex.begin(), itr);
+        newVertexIndices[vertIndex] = indexOfTarget;
+      }
+
+      // set the triangle in reduced
+      m_ReducedTriangle.setFacePointIds(index, newVertexIndices);
+    }
+  }
+
+  void operator()(const Range& range) const
+  {
+    generate(range.min(), range.max());
+  }
+
+private:
+  const TriangleGeom& m_OriginalTriangle;
+  TriangleGeom& m_ReducedTriangle;
+  const std::vector<usize>& m_NewTrianglesIndex;
+  const std::vector<usize>& m_NewVerticesIndex;
+};
+} // namespace
+
+// -----------------------------------------------------------------------------
+RemoveFlaggedTriangles::RemoveFlaggedTriangles(DataStructure& dataStructure, const IFilter::MessageHandler& mesgHandler, const std::atomic_bool& shouldCancel,
+                                               RemoveFlaggedTrianglesInputValues* inputValues)
+: m_DataStructure(dataStructure)
+, m_InputValues(inputValues)
+, m_ShouldCancel(shouldCancel)
+, m_MessageHandler(mesgHandler)
+{
+}
+
+// -----------------------------------------------------------------------------
+const std::atomic_bool& RemoveFlaggedTriangles::getCancel()
+{
+  return m_ShouldCancel;
+}
+
+// -----------------------------------------------------------------------------
+Result<> RemoveFlaggedTriangles::operator()()
+{
+  // Remove Triangles from reduced according to removeTrianglesIndex
+  const auto& originalTriangle = m_DataStructure.getDataRefAs<TriangleGeom>(m_InputValues->TriangleGeometry);
+  const auto& mask = m_DataStructure.getDataRefAs<BoolArray>(m_InputValues->MaskArrayPath);
+  auto& reducedTriangle = m_DataStructure.getDataRefAs<TriangleGeom>(m_InputValues->ReducedTriangleGeometry);
+
+  // Set up allocated masks
+  usize size = originalTriangle.getNumberOfFaces();
+  std::vector<usize> newTrianglesIndexList;
+  newTrianglesIndexList.reserve(size);
+
+  // parse mask Triangles list and load a list of indices for triangles to keep
+  for(usize index = 0; index < size; index++)
+  {
+    if(!mask[index])
+    {
+      newTrianglesIndexList.push_back(index);
+    }
+  }
+  newTrianglesIndexList.shrink_to_fit();
+
+  if(getCancel())
+  {
+    return {};
+  }
+  if(newTrianglesIndexList.empty())
+  {
+    return MakeErrorResult(-67880, "Re-evaluate mask conditions - with current configuration all triangles will be stripped!");
+  }
+
+  // flatten a list of the indices of vertices used by the triangles
+  std::vector<usize> pseudoVertexList; // also used as a pseudo look up table in PopulateReducedGeometryTrianglesImpl
+  for(usize& index : newTrianglesIndexList)
+  {
+    usize vertIDs[3] = {0, 0, 0};
+    originalTriangle.getFacePointIds(index, vertIDs);
+    pseudoVertexList.push_back(vertIDs[0]);
+    pseudoVertexList.push_back(vertIDs[1]);
+    pseudoVertexList.push_back(vertIDs[2]);
+  }
+  if(getCancel())
+  {
+    return {};
+  }
+
+  if(pseudoVertexList.empty())
+  {
+    return MakeErrorResult(-67881, "Re-evaluate mask conditions - with current configuration all vertices will be dumped!");
+  }
+
+  // clear duplicate values out of vector
+  std::sort(pseudoVertexList.begin(), pseudoVertexList.end()); // orders ascending !!!!! Basis for later search !!!!!
+  auto dupes = std::unique(pseudoVertexList.begin(), pseudoVertexList.end());
+  pseudoVertexList.erase(dupes, pseudoVertexList.end());
+
+  // define new sizing
+  size = pseudoVertexList.size();
+  reducedTriangle.resizeVertexList(size); // resize accordingly
+
+  // load reduced Geometry Vertex list according to used vertices
+  Point3Df coords = {0.0f, 0.0f, 0.0f};
+  for(usize i = 0; i < size; i++)
+  {
+    coords = originalTriangle.getVertexCoordinate(pseudoVertexList[i]);
+    reducedTriangle.setVertexCoordinate(i, coords);
+  }
+
+  if(getCancel())
+  {
+    return {};
+  }
+
+  // Set up preprocessing conditions (allocation for parallelization)
+  reducedTriangle.resizeFaceList(newTrianglesIndexList.size()); // resize accordingly
+
+  // parse triangles and reassign indexes to match new vertex list
+  ParallelDataAlgorithm dataAlg;
+  dataAlg.setRange(0, size);
+  dataAlg.execute(PopulateReducedGeometryTrianglesImpl(originalTriangle, reducedTriangle, newTrianglesIndexList, pseudoVertexList));
+
+  return {};
+}