algorithm almost complete - randomness pending

src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/MergeColonies.cpp

@@ -138,6 +138,12 @@ MergeColonies::MergeColonies(DataStructure& dataStructure, const IFilter::Messag
 , m_ShouldCancel(shouldCancel)
 , m_MessageHandler(mesgHandler)
 , m_OrientationOps(LaueOps::GetAllOrientationOps())
+, m_FeatureParentIds(dataStructure.getDataRefAs<Int32Array>(inputValues->FeatureParentIdsPath))
+, m_FeaturePhases(dataStructure.getDataRefAs<Int32Array>(inputValues->FeaturePhasesPath))
+, m_AvgQuats(dataStructure.getDataRefAs<Float32Array>(inputValues->AvgQuatsPath))
+, m_CrystalStructures(dataStructure.getDataRefAs<UInt32Array>(inputValues->CrystalStructuresPath))
+, m_AxisToleranceRad(inputValues->AxisTolerance * Constants::k_PiF / 180.0f)
+, m_AngleTolerance(inputValues->AngleTolerance)
 {
 }
 
@@ -153,14 +159,6 @@ const std::atomic_bool& MergeColonies::getCancel()
 // -----------------------------------------------------------------------------
 Result<> MergeColonies::operator()()
 {
-  m_FeatureParentIds = m_DataStructure.getDataRefAs<Int32Array>(m_InputValues->FeatureParentIdsPath);
-  m_FeaturePhases = m_DataStructure.getDataRefAs<Int32Array>(m_InputValues->FeaturePhasesPath);
-  m_AvgQuats = m_DataStructure.getDataRefAs<Float32Array>(m_InputValues->AvgQuatsPath);
-  m_CrystalStructures = m_DataStructure.getDataRefAs<UInt32Array>(m_InputValues->CrystalStructuresPath);
-
-  m_AxisToleranceRad = m_InputValues->AxisTolerance * Constants::k_PiF / 180.0f;
-  m_AngleTolerance = m_InputValues->AngleTolerance;
-
   GroupFeatures::execute();
 
   auto active = m_DataStructure.getDataRefAs<BoolArray>(m_InputValues->ActivePath);
@@ -187,6 +185,10 @@ Result<> MergeColonies::operator()()
   }
   numParents += 1;
 
+  m_MessageHandler({IFilter::Message::Type::Info, "Characterizing Colonies Starting"});
+  characterize_colonies();
+  m_MessageHandler({IFilter::Message::Type::Info, "Characterizing Colonies Complete"});
+
   if(m_InputValues->RandomizeParentIds)
   {
     m_MessageHandler({IFilter::Message::Type::Info, "Randomizing Parent Ids...."});
@@ -355,3 +357,10 @@ bool MergeColonies::determineGrouping(int32 referenceFeature, int32 neighborFeat
   }
   return false;
 }
+
+// -----------------------------------------------------------------------------
+//
+// -----------------------------------------------------------------------------
+void MergeColonies::characterize_colonies()
+{
+}

src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/MergeColonies.hpp

@@ -18,9 +18,6 @@ namespace complex
 {
 struct ORIENTATIONANALYSIS_EXPORT MergeColoniesInputValues
 {
-  bool UseNonContiguousNeighbors;
-  DataPath NonContiguousNLPath;
-  DataPath ContiguousNLPath;
   float32 AxisTolerance;
   float32 AngleTolerance;
   DataPath FeaturePhasesPath;
@@ -47,7 +44,8 @@ class ORIENTATIONANALYSIS_EXPORT MergeColonies : public GroupFeatures
   using LaueOpsContainer = std::vector<LaueOpsShPtrType>;
 
 public:
-  MergeColonies(DataStructure& dataStructure, const IFilter::MessageHandler& mesgHandler, const std::atomic_bool& shouldCancel, MergeColoniesInputValues* inputValues);
+  MergeColonies(DataStructure& dataStructure, const IFilter::MessageHandler& mesgHandler, const std::atomic_bool& shouldCancel, MergeColoniesInputValues* inputValues,
+                GroupFeaturesInputValues* groupInputValues);
   ~MergeColonies() noexcept;
 
   MergeColonies(const MergeColonies&) = delete;
@@ -61,6 +59,7 @@ class ORIENTATIONANALYSIS_EXPORT MergeColonies : public GroupFeatures
 
   int getSeed(int32 newFid) override;
   bool determineGrouping(int32 referenceFeature, int32 neighborFeature, int32 newFid) override;
+  void characterize_colonies();
 
 private:
   DataStructure& m_DataStructure;

src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/MergeColoniesFilter.cpp

@@ -99,11 +99,6 @@ IFilter::UniquePointer MergeColoniesFilter::clone() const
 IFilter::PreflightResult MergeColoniesFilter::preflightImpl(const DataStructure& dataStructure, const Arguments& filterArgs, const MessageHandler& messageHandler,
                                                             const std::atomic_bool& shouldCancel) const
 {
-  auto pUseNonContiguousNeighborsValue = filterArgs.value<bool>(k_UseNonContiguousNeighbors_Key);
-  auto pNonContiguousNeighborListArrayPathValue = filterArgs.value<DataPath>(k_NonContiguousNeighborListArrayPath_Key);
-  auto pContiguousNeighborListArrayPathValue = filterArgs.value<DataPath>(k_ContiguousNeighborListArrayPath_Key);
-  auto pAxisToleranceValue = filterArgs.value<float32>(k_AxisTolerance_Key);
-  auto pAngleToleranceValue = filterArgs.value<float32>(k_AngleTolerance_Key);
   auto pFeaturePhasesArrayPathValue = filterArgs.value<DataPath>(k_FeaturePhasesArrayPath_Key);
   auto pAvgQuatsArrayPathValue = filterArgs.value<DataPath>(k_AvgQuatsArrayPath_Key);
   auto pFeatureIdsArrayPathValue = filterArgs.value<DataPath>(k_FeatureIdsArrayPath_Key);
@@ -128,21 +123,24 @@ Result<> MergeColoniesFilter::executeImpl(DataStructure& dataStructure, const Ar
 {
   MergeColoniesInputValues inputValues;
 
-  inputValues.UseNonContiguousNeighbors = filterArgs.value<bool>(k_UseNonContiguousNeighbors_Key);
-  inputValues.NonContiguousNeighborListArrayPath = filterArgs.value<DataPath>(k_NonContiguousNeighborListArrayPath_Key);
-  inputValues.ContiguousNeighborListArrayPath = filterArgs.value<DataPath>(k_ContiguousNeighborListArrayPath_Key);
   inputValues.AxisTolerance = filterArgs.value<float32>(k_AxisTolerance_Key);
   inputValues.AngleTolerance = filterArgs.value<float32>(k_AngleTolerance_Key);
-  inputValues.FeaturePhasesArrayPath = filterArgs.value<DataPath>(k_FeaturePhasesArrayPath_Key);
-  inputValues.AvgQuatsArrayPath = filterArgs.value<DataPath>(k_AvgQuatsArrayPath_Key);
-  inputValues.FeatureIdsArrayPath = filterArgs.value<DataPath>(k_FeatureIdsArrayPath_Key);
-  inputValues.CellPhasesArrayPath = filterArgs.value<DataPath>(k_CellPhasesArrayPath_Key);
-  inputValues.CrystalStructuresArrayPath = filterArgs.value<DataPath>(k_CrystalStructuresArrayPath_Key);
-  inputValues.CellParentIdsArrayName = filterArgs.value<DataPath>(k_CellParentIdsArrayName_Key);
-  inputValues.NewCellFeatureAttributeMatrixName = filterArgs.value<DataPath>(k_NewCellFeatureAttributeMatrixName_Key);
-  inputValues.FeatureParentIdsArrayName = filterArgs.value<DataPath>(k_FeatureParentIdsArrayName_Key);
-  inputValues.ActiveArrayName = filterArgs.value<DataPath>(k_ActiveArrayName_Key);
-
-  return MergeColonies(dataStructure, messageHandler, shouldCancel, &inputValues)();
+  inputValues.FeaturePhasesPath = filterArgs.value<DataPath>(k_FeaturePhasesArrayPath_Key);
+  inputValues.AvgQuatsPath = filterArgs.value<DataPath>(k_AvgQuatsArrayPath_Key);
+  inputValues.FeatureIdsPath = filterArgs.value<DataPath>(k_FeatureIdsArrayPath_Key);
+  inputValues.CellPhasesPath = filterArgs.value<DataPath>(k_CellPhasesArrayPath_Key);
+  inputValues.CrystalStructuresPath = filterArgs.value<DataPath>(k_CrystalStructuresArrayPath_Key);
+  inputValues.CellParentIdsPath = filterArgs.value<DataPath>(k_CellParentIdsArrayName_Key);
+  inputValues.CellFeatureAMPath = filterArgs.value<DataPath>(k_NewCellFeatureAttributeMatrixName_Key);
+  inputValues.FeatureParentIdsPath = filterArgs.value<DataPath>(k_FeatureParentIdsArrayName_Key);
+  inputValues.ActivePath = filterArgs.value<DataPath>(k_ActiveArrayName_Key);
+
+  GroupFeaturesInputValues gpInputValues;
+
+  gpInputValues.UseNonContiguousNeighbors = filterArgs.value<bool>(k_UseNonContiguousNeighbors_Key);
+  gpInputValues.NonContiguousNeighborListArrayPath = filterArgs.value<DataPath>(k_NonContiguousNeighborListArrayPath_Key);
+  gpInputValues.ContiguousNeighborListArrayPath = filterArgs.value<DataPath>(k_ContiguousNeighborListArrayPath_Key);
+
+  return MergeColonies(dataStructure, messageHandler, shouldCancel, &inputValues, &gpInputValues)();
 }
 } // namespace complex