[WIP] FILTER: Merge Colonies

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

@@ -148,6 +148,20 @@
     return MakeErrorResult(-84500, fmt::format("Keeping the original geometry is not supported."));
   }
 
+  auto* imageGeometryPtr = m_DataStructure.getDataAs<ImageGeom>(m_InputValues->SelectedGeometryPath);
+  const bool isNodeBased = (imageGeometryPtr == nullptr);
+
+  ImageRotationUtilities::Matrix4fR translationToGlobalOriginMat = ImageRotationUtilities::Matrix4fR::Identity();
+  ImageRotationUtilities::Matrix4fR translationFromGlobalOriginMat = ImageRotationUtilities::Matrix4fR::Identity();
+  if(isNodeBased)
+  {
+    auto& nodeGeometry0D = m_DataStructure.getDataRefAs<INodeGeometry0D>(m_InputValues->SelectedGeometryPath);
+    auto boundingBox = nodeGeometry0D.getBoundingBox();
+    Point3Df minPoint = boundingBox.getMinPoint();
+    translationToGlobalOriginMat = ImageRotationUtilities::GenerateTranslationTransformationMatrix({-minPoint[0], -minPoint[1], -minPoint[2]});
+    translationFromGlobalOriginMat = ImageRotationUtilities::GenerateTranslationTransformationMatrix({minPoint[0], minPoint[1], minPoint[2]});
+  }
+
   switch(m_InputValues->TransformationSelection)
   {
   case k_NoTransformIdx: // No-Op
@@ -168,6 +182,12 @@
   case k_RotationIdx: // Rotation via axis-angle
   {
     m_TransformationMatrix = ImageRotationUtilities::GenerateRotationTransformationMatrix(m_InputValues->Rotation);
+    if(isNodeBased)
+    {
+      // Translate the geometry to/from the global origin
+      m_TransformationMatrix = translationFromGlobalOriginMat * m_TransformationMatrix * translationToGlobalOriginMat;
+    }
+
     break;
   }
   case k_TranslationIdx: // Translation
@@ -178,12 +198,17 @@
   case k_ScaleIdx: // Scale
   {
     m_TransformationMatrix = ImageRotationUtilities::GenerateScaleTransformationMatrix(m_InputValues->Scale);
+    if(isNodeBased)
+    {
+      // Translate the geometry to/from the global origin
+      m_TransformationMatrix = translationFromGlobalOriginMat * m_TransformationMatrix * translationToGlobalOriginMat;
+    }
     break;
   }
   }
 
   // Apply geometry transformation
   auto* imageGeometryPtr = m_DataStructure.getDataAs<ImageGeom>(m_InputValues->SelectedGeometryPath);
   if(imageGeometryPtr == nullptr)
   {
     if(m_InputValues->TranslateGeometryToGlobalOrigin)
@@ -191,8 +216,8 @@
       auto& nodeGeometry0D = m_DataStructure.getDataRefAs<INodeGeometry0D>(m_InputValues->SelectedGeometryPath);
       auto boundingBox = nodeGeometry0D.getBoundingBox();
       Point3Df minPoint = boundingBox.getMinPoint();
       const ImageRotationUtilities::Matrix4fR translationToGlobalOriginMat = ImageRotationUtilities::GenerateTranslationTransformationMatrix({-minPoint[0], -minPoint[1], -minPoint[2]});
       const ImageRotationUtilities::Matrix4fR translationFromGlobalOriginMat = ImageRotationUtilities::GenerateTranslationTransformationMatrix({minPoint[0], minPoint[1], minPoint[2]});
       m_TransformationMatrix = translationFromGlobalOriginMat * m_TransformationMatrix * translationToGlobalOriginMat;
     }
 

src/Plugins/OrientationAnalysis/CMakeLists.txt

@@ -65,6 +65,7 @@ set(FilterList
   ImportH5EspritDataFilter
   ImportH5OimDataFilter
   INLWriterFilter
+  MergeColoniesFilter
   MergeTwinsFilter
   NeighborOrientationCorrelationFilter
   ReadAngDataFilter
@@ -199,6 +200,7 @@ set(filter_algorithms
   ImportH5EspritData
   ImportH5OimData
   INLWriter
+  MergeColonies
   MergeTwins
   NeighborOrientationCorrelation
   ReadAngData

src/Plugins/OrientationAnalysis/docs/MergeColoniesFilter.md

@@ -0,0 +1,69 @@
+# Merge Colonies #
+
+## Group (Subgroup) ##
+
+Reconstruction (Grouping)
+
+## Description ##
+
+This **Filter** groups neighboring **Features** that have a *special* misorientation that is associated with *alpha* variants that transformed from the same *beta* grain in titanium.  The algorithm for grouping the **Features** is analogous to the algorithm for segmenting the **Features**, except the average orientation of the **Features** are used instead of the orientations of the individual **Elements** and the criterion for grouping is specific to the *alpha-beta transformation*.  The user can specify a tolerance on both the *axis* and the *angle* that defines the misorientation relationship (i.e., a tolerance of 1 degree for both tolerances would allow the neighboring **Features** to be grouped if their misorientation was between 59-61 degrees about an axis within 1 degree of a2, as given by the 3rd *special* misorientation below).
+
+The list of *special* misorientations can be found in the paper by Germain et al.<sup>1</sup> and are listed here:
+
+| Angle | Axis |
+|------|------|
+| 0 | Identity |
+| 10.529 | c = <0001> |
+| 60 | a2 = <-12-10> |
+| 60.832 | d1 at 80.97 degrees from c in the plane of (d3,c) |
+| 63.262 | d2 at 72.73 degrees from c in the plane of (a2,c) |
+| 90 | d3 at 5.26 degrees from a2 in the basal plane |
+
+## Parameters ##
+
+| Name | Type | Description |
+|------|------| ----------- |
+| Use Seed | bool | Whether a seed shouold be used for random generation |
+| Seed | uint64 | This is the value fed into the random generator |
+| Axis Tolerance (Degrees) | float32 | Tolerance allowed when comparing the axis part of the axis-angle representation of the misorientation to the *special* misorientations listed above |
+| Angle Tolerance (Degrees) | float32 | Tolerance allowed when comparing the angle part of the axis-angle representation of the misorientation to the *special* misorientations listed above |
+| Use Non-Contiguous Neighbors | bool | Whether to use a non-contiguous neighbor list during the merging process |
+
+## Required Geometry ##
+
+Not Applicable
+
+## Required Objects ##
+
+| Kind | Default Name | Type | Component Dimensions | Description |
+|------|--------------|------|----------------------|-------------|
+| **Feature Attribute Array** | NonContiguousNeighbors | Int32NeighborList | (1) | List of non-contiguous neighbors for each **Feature**. Only needed if *Use Non-Contiguous Neighbors* is checked |
+| **Feature Attribute Array** | NeighborList | Int32NeighborList | (1) | List of neighbors for each **Feature** |
+| **Element Attribute Array** | FeatureIds | int32 | (1) | Specifies to which **Feature** each **Element** belongs |
+| **Element Attribute Array** | Phases | int32 | (1) | Specifies to which **Ensemble** each **Element** belongs |
+| **Feature Attribute Array** | Phases | int32 | (1) | Specifies to which **Ensemble** each **Feature** belongs |
+| **Feature Attribute Array** | AvgQuats | float32 | (4) | Specifies the average orientation of the **Feature** in quaternion representation |
+| **Ensemble Attribute Array** | CrystalStructures | uint32 | (1) | Enumeration representing the crystal structure for each **Ensemble** |
+
+## Created Objects ##
+
+| Kind | Default Name | Type | Component Dimensions | Description |
+|------|--------------|------|----------------------|-------------|
+| **Element Attribute Array** | ParentIds | int32 | (1) | Specifies to which *parent* each **Element** belongs |
+| **Attribute Matrix** | NewFeatureData | Feature | N/A | Created **Feature Attribute Matrix** name |
+| **Feature Attribute Array** | ParentIds | int32 | (1) | Specifies to which *parent* each **Feature** belongs |
+| **Feature Attribute Array** | Active | bool | (1) | Specifies if the **Feature** is still in the sample (*true* if the **Feature** is in the sample and *false* if it is not). At the end of the **Filter**, all **Features** will be *Active* |
+
+## References ##
+
+[1] L. Germain, N. Gey and M. Humbert, Reliability of reconstructed Beta orientation maps in titanium alloys, Ultramicrscopy, 2007, 1129-1135.
+
+## Example Pipelines ##
+
+## License & Copyright ##
+
+Please see the description file distributed with this **Plugin**
+
+## DREAM.3D Mailing Lists ##
+
+If you need more help with a **Filter**, please consider asking your question on the [DREAM.3D Users Google group!](https://groups.google.com/forum/?hl=en#!forum/dream3d-users)