DataArrayUtilities completed

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

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

@@ -271,7 +271,7 @@ class ComputeArrayStatisticsByIndexImpl
                 histogram[m_NumBins - 1]++;
               }
             } // end of numTuples loop
-          }   // end of increment else
+          } // end of increment else
 
           if(m_ModalBinRanges)
           {

src/Plugins/SimplnxCore/src/SimplnxCore/Filters/AlignSectionsListFilter.hpp

@@ -2,9 +2,8 @@
 
 #include "SimplnxCore/SimplnxCore_export.hpp"
 
-
-#include "simplnx/Filter/IFilter.hpp"
 #include "simplnx/Filter/FilterTraits.hpp"
+#include "simplnx/Filter/IFilter.hpp"
 
 namespace nx::core
 {

src/Plugins/SimplnxCore/src/SimplnxCore/utils/nanoflann.hpp

@@ -2205,7 +2205,7 @@ struct KDTreeEigenMatrixAdaptor
   /** @} */
 
 }; // end of KDTreeEigenMatrixAdaptor
-   /** @} */
+/** @} */
 
 /** @} */ // end of grouping
 } // namespace nanoflann

src/Plugins/SimplnxCore/wrapping/python/simplnxpy.cpp

@@ -584,8 +584,7 @@ PYBIND11_MODULE(simplnx, mod)
   parameters.def("insert_linkable_parameter", &PyInsertLinkableParameter<ChoicesParameter>);
   parameters.def("link_parameters", [](Parameters& self, std::string groupKey, std::string childKey, BoolParameter::ValueType value) { self.linkParameters(groupKey, childKey, value); });
   parameters.def("link_parameters", [](Parameters& self, std::string groupKey, std::string childKey, ChoicesParameter::ValueType value) { self.linkParameters(groupKey, childKey, value); });
-  parameters.def(
-      "__getitem__", [](Parameters& self, std::string_view key) { return self.at(key).get(); }, py::return_value_policy::reference_internal);
+  parameters.def("__getitem__", [](Parameters& self, std::string_view key) { return self.at(key).get(); }, py::return_value_policy::reference_internal);
 
   py::class_<IArrayThreshold, std::shared_ptr<IArrayThreshold>> iArrayThreshold(mod, "IArrayThreshold");
 
@@ -1422,12 +1421,10 @@ PYBIND11_MODULE(simplnx, mod)
       "path"_a);
   pipeline.def_property("name", &Pipeline::getName, &Pipeline::setName);
   pipeline.def("execute", &ExecutePipeline);
-  pipeline.def(
-      "__getitem__", [](Pipeline& self, Pipeline::index_type index) { return self.at(index); }, py::return_value_policy::reference_internal);
+  pipeline.def("__getitem__", [](Pipeline& self, Pipeline::index_type index) { return self.at(index); }, py::return_value_policy::reference_internal);
   pipeline.def("__len__", &Pipeline::size);
   pipeline.def("size", &Pipeline::size);
-  pipeline.def(
-      "__iter__", [](Pipeline& self) { return py::make_iterator(self.begin(), self.end()); }, py::keep_alive<0, 1>());
+  pipeline.def("__iter__", [](Pipeline& self) { return py::make_iterator(self.begin(), self.end()); }, py::keep_alive<0, 1>());
   pipeline.def(
       "insert",
       [internals](Pipeline& self, Pipeline::index_type index, const IFilter& filter, const py::dict& args) {
@@ -1441,10 +1438,8 @@ PYBIND11_MODULE(simplnx, mod)
   pipeline.def("remove", &Pipeline::removeAt, "index"_a);
 
   pipelineFilter.def("get_args", [internals](PipelineFilter& self) { return ConvertArgsToDict(*internals, self.getParameters(), self.getArguments()); });
-  pipelineFilter.def(
-      "set_args", [internals](PipelineFilter& self, py::dict& args) { self.setArguments(ConvertDictToArgs(*internals, self.getParameters(), args)); }, "args"_a);
-  pipelineFilter.def(
-      "get_filter", [](PipelineFilter& self) { return self.getFilter(); }, py::return_value_policy::reference_internal);
+  pipelineFilter.def("set_args", [internals](PipelineFilter& self, py::dict& args) { self.setArguments(ConvertDictToArgs(*internals, self.getParameters(), args)); }, "args"_a);
+  pipelineFilter.def("get_filter", [](PipelineFilter& self) { return self.getFilter(); }, py::return_value_policy::reference_internal);
   pipelineFilter.def(
       "name",
       [](const PipelineFilter& self) {

src/simplnx/DataStructure/IO/Generic/DataIOCollection.cpp

@@ -59,11 +59,11 @@ std::unique_ptr<IDataStore> DataIOCollection::createDataStore(const std::string&
   return nullptr;
 }
 
-void DataIOCollection::checkStoreDataFormat(uint64 dataSize, std::string& dataFormat) const
+std::string DataIOCollection::checkStoreDataFormat(uint64 dataSize, std::string dataFormat) const
 {
   if(!dataFormat.empty())
   {
-    return;
+    return dataFormat;
   }
   const Preferences* preferences = Application::GetOrCreateInstance()->getPreferences();
   const uint64 largeDataSize = preferences->valueAs<uint64>(Preferences::k_LargeDataSize_Key);
@@ -72,6 +72,7 @@ void DataIOCollection::checkStoreDataFormat(uint64 dataSize, std::string& dataFo
   {
     dataFormat = largeDataFormat;
   }
+  return dataFormat;
 }
 
 std::vector<std::string> DataIOCollection::getFormatNames() const

src/simplnx/DataStructure/IO/Generic/DataIOCollection.hpp

@@ -1,10 +1,9 @@
 #pragma once
 
-#include "simplnx/DataStructure/AbstractDataStore.hpp"
-#include "simplnx/simplnx_export.hpp"
-
 #include "simplnx/Common/Types.hpp"
 #include "simplnx/Common/TypesUtility.hpp"
+#include "simplnx/DataStructure/AbstractDataStore.hpp"
+#include "simplnx/simplnx_export.hpp"
 
 #include <map>
 #include <memory>
@@ -63,7 +62,7 @@ class SIMPLNX_EXPORT DataIOCollection
   /**
    * @brief Checks the
    */
-  void checkStoreDataFormat(uint64 dataSize, std::string& dataFormat) const;
+  std::string checkStoreDataFormat(uint64 dataSize, std::string dataFormat) const;
 
   iterator begin();
   iterator end();

src/simplnx/Filter/FilterTraits.hpp

@@ -1,6 +1,6 @@
 #pragma once
 
-//#include "simplnx/Common/StringLiteral.hpp"
+// #include "simplnx/Common/StringLiteral.hpp"
 #include "simplnx/Filter/IFilter.hpp"
 
 #include <type_traits>

src/simplnx/Utilities/DataArrayUtilities.cpp

@@ -2,6 +2,8 @@
 
 #include "simplnx/Common/Types.hpp"
 #include "simplnx/Common/TypesUtility.hpp"
+#include "simplnx/Core/Application.hpp"
+#include "simplnx/DataStructure/IO/Generic/DataIOCollection.hpp"
 #include "simplnx/Utilities/FilterUtilities.hpp"
 
 #include <set>
@@ -32,6 +34,24 @@ struct InitializeNeighborListFunctor
 
 namespace nx::core
 {
+
+std::string GetDataFormatFromPreferences()
+{
+  std::string dataFormat;
+
+  auto* preferencesPtr = Application::GetOrCreateInstance()->getPreferences();
+  if(preferencesPtr->forceOocData())
+  {
+    dataFormat = preferencesPtr->largeDataFormat();
+  }
+  return dataFormat;
+}
+
+std::shared_ptr<DataIOCollection> GetDataCollectionInstance()
+{
+  return Application::GetOrCreateInstance()->getIOCollection();
+}
+
 //-----------------------------------------------------------------------------
 Result<> CheckValueConverts(const std::string& value, NumericType numericType)
 {

src/simplnx/Utilities/DataArrayUtilities.hpp

@@ -2,7 +2,6 @@
 
 #include "simplnx/Common/Array.hpp"
 #include "simplnx/Common/Result.hpp"
-#include "simplnx/Core/Application.hpp"
 #include "simplnx/DataStructure/AttributeMatrix.hpp"
 #include "simplnx/DataStructure/DataArray.hpp"
 #include "simplnx/DataStructure/DataStore.hpp"
@@ -12,6 +11,7 @@
 #include "simplnx/DataStructure/NeighborList.hpp"
 #include "simplnx/DataStructure/StringArray.hpp"
 #include "simplnx/Filter/Actions/CreateArrayAction.hpp"
+#include "simplnx/Filter/IFilter.hpp"
 #include "simplnx/Filter/Output.hpp"
 #include "simplnx/Parameters/MultiArraySelectionParameter.hpp"
 #include "simplnx/Utilities/MemoryUtilities.hpp"
@@ -345,6 +345,18 @@ uint64 CalculateDataSize(const IDataStore::ShapeType& tupleShape, const IDataSto
   return numValues * numComponents * sizeof(T);
 }
 
+/**
+ *
+ * @return
+ */
+std::string GetDataFormatFromPreferences();
+
+/**
+ *
+ * @return
+ */
+std::shared_ptr<DataIOCollection> GetDataCollectionInstance();
+
 /**
  * @brief Creates a DataStore with the given properties
  * @tparam T Primitive Type (int, float, ...)
@@ -364,13 +376,9 @@ std::shared_ptr<AbstractDataStore<T>> CreateDataStore(const typename IDataStore:
   }
   case IDataAction::Mode::Execute: {
     uint64 dataSize = CalculateDataSize<T>(tupleShape, componentShape);
-    auto* preferencesPtr = Application::GetOrCreateInstance()->getPreferences();
-    if(preferencesPtr->forceOocData())
-    {
-      dataFormat = preferencesPtr->largeDataFormat();
-    }
-    auto ioCollection = Application::GetOrCreateInstance()->getIOCollection();
-    ioCollection->checkStoreDataFormat(dataSize, dataFormat);
+    dataFormat = GetDataFormatFromPreferences();
+    auto ioCollection = GetDataCollectionInstance();
+    dataFormat = ioCollection->checkStoreDataFormat(dataSize, dataFormat);
     return ioCollection->createDataStoreWithType<T>(dataFormat, tupleShape, componentShape);
   }
   default: {
@@ -476,7 +484,7 @@ std::shared_ptr<AbstractDataStore<T>> ConvertDataStore(const AbstractDataStore<T
     return nullptr;
   }
 
-  auto ioCollection = Application::GetOrCreateInstance()->getIOCollection();
+  auto ioCollection = GetDataCollectionInstance();
   std::shared_ptr<AbstractDataStore<T>> newStore = ioCollection->createDataStoreWithType<T>(dataFormat, dataStore.getTupleShape(), dataStore.getComponentShape());
   if(newStore == nullptr)
   {

src/simplnx/Utilities/SIMPLConversion.hpp

@@ -6,24 +6,18 @@
 #include "simplnx/Common/TypesUtility.hpp"
 #include "simplnx/Parameters/ArrayCreationParameter.hpp"
 #include "simplnx/Parameters/ArraySelectionParameter.hpp"
-#ifdef SIMPL_PARAM_CONVERT_ARRAY_THRESHOLD
 #include "simplnx/Parameters/ArrayThresholdsParameter.hpp"
-#endif
 #include "simplnx/Parameters/AttributeMatrixSelectionParameter.hpp"
 #include "simplnx/Parameters/BoolParameter.hpp"
 #include "simplnx/Parameters/CalculatorParameter.hpp"
 #include "simplnx/Parameters/ChoicesParameter.hpp"
-#ifdef SIMPL_PARAM_CONVERT_CREATE_COLOR_MAP
 #include "simplnx/Parameters/CreateColorMapParameter.hpp"
-#endif
 #include "simplnx/Parameters/DataGroupCreationParameter.hpp"
 #include "simplnx/Parameters/DataGroupSelectionParameter.hpp"
 #include "simplnx/Parameters/DataObjectNameParameter.hpp"
 #include "simplnx/Parameters/DataTypeParameter.hpp"
 #include "simplnx/Parameters/Dream3dImportParameter.hpp"
-#ifdef SIMPL_PARAM_CONVERT_DYNAMIC_TABLE
 #include "simplnx/Parameters/DynamicTableParameter.hpp"
-#endif
 #include "simplnx/Parameters/EnsembleInfoParameter.hpp"
 #include "simplnx/Parameters/FileSystemPathParameter.hpp"
 #include "simplnx/Parameters/GeneratedFileListParameter.hpp"
@@ -32,17 +26,11 @@
 #include "simplnx/Parameters/MultiPathSelectionParameter.hpp"
 #include "simplnx/Parameters/NumberParameter.hpp"
 #include "simplnx/Parameters/NumericTypeParameter.hpp"
-#ifdef SIMPL_PARAM_CONVERT_READ_CSV
 #include "simplnx/Parameters/ReadCSVFileParameter.hpp"
-#endif
-#ifdef SIMPL_PARAM_CONVERT_READ_HDF5_DATASET
 #include "simplnx/Parameters/ReadHDF5DatasetParameter.hpp"
-#endif
 #include "simplnx/Parameters/StringParameter.hpp"
 #include "simplnx/Parameters/VectorParameter.hpp"
 
-// #include "OrientationAnalysis/Parameters/H5EbsdReaderParameter.h"
-
 #include <nlohmann/json.hpp>
 
 #include <string_view>
@@ -1267,7 +1255,6 @@ struct ChoiceFilterParameterConverter
   }
 };
 
-#ifdef SIMPL_PARAM_CONVERT_DYNAMIC_TABLE
 struct DynamicTableFilterParameterConverter
 {
   using ParameterType = DynamicTableParameter;
@@ -1321,9 +1308,7 @@ struct DynamicTableFilterParameterConverter
     return {std::move(table)};
   }
 };
-#endif
 
-#ifdef SIMPL_PARAM_CONVERT_DYNAMIC_TABLE
 struct ArrayToDynamicTableFilterParameterConverter
 {
   using ParameterType = DynamicTableParameter;
@@ -1358,7 +1343,6 @@ struct ArrayToDynamicTableFilterParameterConverter
     return {std::move(table)};
   }
 };
-#endif
 
 struct AttributeMatrixCreationFilterParameterConverter
 {
@@ -1689,7 +1673,7 @@ struct EnsembleInfoFilterParameterConverter
     return {std::move(value)};
   }
 };
-#ifdef SIMPL_PARAM_CONVERT_CREATE_COLOR_MAP
+
 struct CreateColorMapFilterParameterConverter
 {
   using ParameterType = CreateColorMapParameter;
@@ -1720,9 +1704,7 @@ struct CreateColorMapFilterParameterConverter
     return {std::move(value)};
   }
 };
-#endif
 
-#ifdef SIMPL_PARAM_CONVERT_READ_CSV
 struct ReadASCIIWizardDataFilterParameterConverter
 {
   using ParameterType = ReadCSVFileParameter;
@@ -1801,9 +1783,7 @@ struct ReadASCIIWizardDataFilterParameterConverter
     return {std::move(value)};
   }
 };
-#endif
 
-#ifdef SIMPL_PARAM_CONVERT_READ_HDF5_DATASET
 struct ImportHDF5DatasetFilterParameterConverter
 {
   using ParameterType = ReadHDF5DatasetParameter;
@@ -1857,7 +1837,6 @@ struct ImportHDF5DatasetFilterParameterConverter
     return {std::move(value)};
   }
 };
-#endif
 
 struct DataArraysToRemoveConverter
 {
@@ -2122,7 +2101,6 @@ struct DataContainerReaderFilterParameterConverter
   }
 };
 
-#ifdef SIMPL_PARAM_CONVERT_ARRAY_THRESHOLD
 struct ComparisonSelectionFilterParameterConverter
 {
   using ParameterType = ArrayThresholdsParameter;
@@ -2337,6 +2315,4 @@ struct ComparisonSelectionAdvancedFilterParameterConverter
     return {std::move(value)};
   }
 };
-#endif
-
 } // namespace nx::core::SIMPLConversion

test/DataArrayTest.cpp

@@ -3,6 +3,7 @@
 #include "simplnx/DataStructure/DataStore.hpp"
 #include "simplnx/DataStructure/DataStructure.hpp"
 #include "simplnx/Utilities/DataArrayUtilities.hpp"
+#include "simplnx/Core/Application.hpp"
 
 #include <catch2/catch.hpp>