BUG: Various small bug fixes and corrections (#1131)

* BUG: Fix various spelling mistakes in customer facing error messages

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

* DOC: Fix spelling mistakes

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

* DOC: Fix some python code snippets

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

* BUG: Removes EbsdLib header dependency in CreateAMScanPaths.

It was never dependent on it anyways.

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

* ENH: Update filter human names for surface meshing filters. Update Docs.

- Update QuickMesh and SurfaceNets surface meshing filter human names
- Update the documentation for each filter.

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

* BUG: Broken external links for the SimplnxCore filters within the python docs

Signed-off-by: Michael Jackson <[email protected]>
(cherry picked from commit 41ee443)

* Improve error message for missing parameter version key

(cherry picked from commit 75f2321)

---------

Signed-off-by: Michael Jackson <[email protected]>
Co-authored-by: Jessica Marquis <[email protected]>

cmake/Summary.cmake

@@ -72,6 +72,7 @@ message(STATUS "* SIMPLNX_ENABLE_PACKAGING: ${SIMPLNX_ENABLE_PACKAGING}")
 message(STATUS "* SIMPLNX_BUILD_DOCS: ${SIMPLNX_BUILD_DOCS}")
 message(STATUS "* DREAM3D_DATA_DIR: ${DREAM3D_DATA_DIR}")
 
+
 message(STATUS "* -------------- Simplnx Python Configuration Options -------------------------------------")
 message(STATUS "* Pybind11 (${pybind11_VERSION}) ${pybind11_DIR}")
 message(STATUS "* Python3_EXECUTABLE: ${Python3_EXECUTABLE}")
@@ -87,7 +88,10 @@ message(STATUS "* SIMPLNX_EMBED_PYTHON: ${SIMPLNX_EMBED_PYTHON}")
 #     message(STATUS "* SIMPLNX_PLUGIN_ENABLE_${plugin}: ${SIMPLNX_PLUGIN_ENABLE_${plugin}}")
 # endforeach()
 
+
 message(STATUS "* -------------- Plugins ------------------------------------------------------")
+message(STATUS "* SIMPLNX_ENABLE_OrientationAnalysis: ${SIMPLNX_ENABLE_OrientationAnalysis}")
+
 get_property(simplnxPluginTargets GLOBAL PROPERTY simplnxPluginTargets)
 foreach(d3dPlugin ${SIMPLNX_PLUGIN_LIST})
     get_property(PluginNumFilters GLOBAL PROPERTY ${d3dPlugin}_filter_count)

src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/ReadAngDataFilter.cpp

@@ -5,6 +5,7 @@
 #include "simplnx/DataStructure/DataPath.hpp"
 #include "simplnx/DataStructure/Geometry/ImageGeom.hpp"
 #include "simplnx/Filter/Actions/CreateArrayAction.hpp"
+#include "simplnx/Filter/Actions/CreateAttributeMatrixAction.hpp"
 #include "simplnx/Filter/Actions/CreateDataGroupAction.hpp"
 #include "simplnx/Filter/Actions/CreateImageGeometryAction.hpp"
 #include "simplnx/Filter/Actions/CreateStringArrayAction.hpp"
@@ -175,14 +176,14 @@ IFilter::PreflightResult ReadAngDataFilter::preflightImpl(const DataStructure& d
   }
 
   // Create the Ensemble AttributeMatrix
+  std::vector<std::shared_ptr<AngPhase>> angPhases = reader.getPhaseVector();
+  tupleDims = {angPhases.size() + 1}; // Always create 1 extra slot for the phases.
   DataPath ensembleAttributeMatrixPath = pImageGeometryPath.createChildPath(pCellEnsembleAttributeMatrixNameValue);
   {
-    auto createDataGroupAction = std::make_unique<CreateDataGroupAction>(ensembleAttributeMatrixPath);
-    resultOutputActions.value().appendAction(std::move(createDataGroupAction));
+    auto createAttributeMatrixAction = std::make_unique<CreateAttributeMatrixAction>(ensembleAttributeMatrixPath, tupleDims);
+    resultOutputActions.value().appendAction(std::move(createAttributeMatrixAction));
   }
 
-  std::vector<std::shared_ptr<AngPhase>> angPhases = reader.getPhaseVector();
-  tupleDims = {angPhases.size() + 1}; // Always create 1 extra slot for the phases.
   // Create the Crystal Structures Array
   {
     cDims[0] = 1;

src/Plugins/SimplnxCore/docs/QuickSurfaceMeshFilter.md

@@ -1,9 +1,13 @@
-# Quick Surface Mesh
+# Create Surface Mesh (QuickMesh Nets)
 
 ## Group (Subgroup)
 
 Surface Meshing (Generation)
 
+## Deprecation Notice
+
+The "SurfaceNets" filter should be used instead. Search the filter list for "Surface Nets".
+
 ## Description
 
 This **Filter** generates a **Triangle Geometry** from a grid **Geometry** (either an **Image Geometry** or a **RectGrid Geometry**) that represents a surface mesh of the present **Features**. The algorithm proceeds by creating a pair of **Triangles** for each face of the **Cell** where the neighboring **Cells** have a different **Feature** Id value. The meshing operation is extremely quick but can result in a surface mesh that is very "stair stepped". The user is encouraged to use a smoothing operation to reduce this "blockiness".
@@ -59,6 +63,14 @@ One of the arrays to come out of the algorithm is the "Node Type" vertex array.
 | 13 | Node that is on the exterior of the mesh and is a triple line  |
 | 14 | Node that is on the exterior of the mesh and is a quadruple point   |
 
+## Notes
+
+The Quickmesh algorithm is very crude and naive in its implementation. This filter 
+along with the Laplacian Smoothing filter can give you reasonable results. The
+newer filter that should replace both the quick mesh and the Laplacian Smoothing
+filter is the "SurfaceNets" surface meshing algorithm. This will create the surface
+mesh and smooth in a single filter and give subjectively better results.
+
 % Auto generated parameter table will be inserted here
 
 ## Example Pipelines

src/Plugins/SimplnxCore/docs/SurfaceNetsFilter.md

@@ -1,4 +1,4 @@
-# SurfaceNets Meshing Filter
+# Create Surface Mesh (Surface Nets)
 
 ## Group (Subgroup)
 
@@ -58,6 +58,11 @@ Nodes that appear on the exterior of a volume have Node Type values starting at
 
 ![Exterior Node Types](Images/SurfaceNets_NodeType_Exterior.png)
 
+## Notes
+
+This filter should be used in place of the "QuickMesh Surface Filter".
+
+
 % Auto generated parameter table will be inserted here
 
 ## Example Pipelines

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

@@ -5,8 +5,6 @@
 #include "simplnx/DataStructure/Geometry/EdgeGeom.hpp"
 #include "simplnx/Utilities/ImageRotationUtilities.hpp"
 
-#include <EbsdLib/Core/Orientation.hpp>
-
 using namespace nx::core;
 
 namespace

src/Plugins/SimplnxCore/src/SimplnxCore/Filters/QuickSurfaceMeshFilter.cpp

@@ -41,7 +41,7 @@ Uuid QuickSurfaceMeshFilter::uuid() const
 //------------------------------------------------------------------------------
 std::string QuickSurfaceMeshFilter::humanName() const
 {
-  return "Quick Surface Mesh";
+  return "Create Surface Mesh (QuickMesh Nets)";
 }
 
 //------------------------------------------------------------------------------

src/Plugins/SimplnxCore/src/SimplnxCore/Filters/SurfaceNetsFilter.cpp

@@ -43,21 +43,21 @@ Uuid SurfaceNetsFilter::uuid() const
 //------------------------------------------------------------------------------
 std::string SurfaceNetsFilter::humanName() const
 {
-  return "SurfaceNets Meshing Filter";
+  return "Create Surface Mesh (Surface Nets)";
 }
 
 //------------------------------------------------------------------------------
 std::vector<std::string> SurfaceNetsFilter::defaultTags() const
 {
-  return {"Surface Meshing", "Generation"};
+  return {className(), "Surface Meshing", "Generation", "Create", "Triangle", "Geometry"};
 }
 
 //------------------------------------------------------------------------------
 Parameters SurfaceNetsFilter::parameters() const
 {
   Parameters params;
   params.insertSeparator(Parameters::Separator{"Input Parameter(s)"});
-  params.insertLinkableParameter(std::make_unique<BoolParameter>(k_ApplySmoothing_Key, "Apply smoothing operations", "Use the built in smmothing operation.", false));
+  params.insertLinkableParameter(std::make_unique<BoolParameter>(k_ApplySmoothing_Key, "Apply smoothing operations", "Use the built in smoothing operation.", false));
 
   params.insert(std::make_unique<Int32Parameter>(k_SmoothingIterations_Key, "Relaxation Iterations", "Number of relaxation iterations to perform. More iterations causes more smoothing.", 20));
   params.insert(

src/simplnx/Filter/IParameter.cpp

@@ -44,7 +44,7 @@ Result<std::any> IParameter::fromJson(const nlohmann::json& json) const
   }
   else
   {
-    warnings.push_back(Warning{-1, fmt::format("{}: Parameter key '{}' does not exist. Assuming version={}", name(), k_VersionKey, version)});
+    warnings.push_back(Warning{-1, fmt::format("{}: Parameter key '{}' does not exist. Assuming version={}. To fix this, save the pipeline file.", name(), k_VersionKey, version)});
   }
 
   nlohmann::json valueJson;

src/simplnx/Parameters/FileSystemPathParameter.cpp

@@ -38,7 +38,7 @@ Result<> ValidateInputFile(const FileSystemPathParameter::ValueType& path)
     }
   } catch(const fs::filesystem_error& exception)
   {
-    return MakeErrorResult(-9, fmt::format("Filesystem excpetion: {}", exception.what()));
+    return MakeErrorResult(-9, fmt::format("Filesystem exception: {}", exception.what()));
   }
   return {};
 }
@@ -59,7 +59,7 @@ Result<> ValidateInputDir(const FileSystemPathParameter::ValueType& path)
     }
   } catch(const fs::filesystem_error& exception)
   {
-    return MakeErrorResult(-10, fmt::format("Filesystem excpetion: {}", exception.what()));
+    return MakeErrorResult(-10, fmt::format("Filesystem exception: {}", exception.what()));
   }
 
   return {};
@@ -86,7 +86,7 @@ Result<> ValidateOutputFile(const FileSystemPathParameter::ValueType& path)
     }
   } catch(const fs::filesystem_error& exception)
   {
-    return MakeErrorResult(-11, fmt::format("Filesystem excpetion: {}", exception.what()));
+    return MakeErrorResult(-11, fmt::format("Filesystem exception: {}", exception.what()));
   }
 
   return {};
@@ -108,7 +108,7 @@ Result<> ValidateOutputDir(const FileSystemPathParameter::ValueType& path)
     }
   } catch(const fs::filesystem_error& exception)
   {
-    return MakeErrorResult(-12, fmt::format("Filesystem excpetion: {}", exception.what()));
+    return MakeErrorResult(-12, fmt::format("Filesystem exception: {}", exception.what()));
   }
   return {};
 }
@@ -265,7 +265,7 @@ Result<> FileSystemPathParameter::validatePath(const ValueType& path) const
     }
   } catch(const fs::filesystem_error& exception)
   {
-    return MakeErrorResult(-9, fmt::format("Filesystem excpetion: {}", exception.what()));
+    return MakeErrorResult(-9, fmt::format("Filesystem exception: {}", exception.what()));
   }
 
   return {};

wrapping/python/docs/generate_sphinx_docs.cpp

@@ -640,6 +640,7 @@ void GeneratePythonRstFiles()
   for(const auto& plugin : pluginListPtr)
   {
     std::string plugName = plugin->getName();
+    std::string fullPluginName = plugName;
     const std::string pluginRootDir = fmt::format("{}", s_PluginDirMap[plugName]);
     if(pluginRootDir.empty())
     {
@@ -711,7 +712,7 @@ void GeneratePythonRstFiles()
       rstStream << "   " << rstDescription << "\n\n";
 
       // Tack on the link to the web address for the full documentation
-      const std::string webAddress = fmt::format("{}/{}/{}/{}.html", k_WebServerAddress, k_WebServerFilterFolder, plugName, filterClassName);
+      const std::string webAddress = fmt::format("{}/{}/{}/{}.html", k_WebServerAddress, k_WebServerFilterFolder, fullPluginName, filterClassName);
       rstStream << "   `Link to the full online documentation for " << filterClassName << " <" << webAddress << ">`_ \n\n";
 
       const auto& parameters = filter->parameters();

wrapping/python/docs/source/Python_Introduction.rst

@@ -178,7 +178,7 @@ In order to import a .dream3d file, we need to tell **simplnx** which data to im
     # import EVERY piece of data from the file.
     import_data.data_paths = None
     # Instantiate and execte the filter immediately.
-    result = nx.ReadDREAM3DFilter.execute(data_structure=data_structure, import_file_data=import_data)
+    result = nx.ReadDREAM3DFilter.execute(data_structure=data_structure, import_data_object=import_data)
     # Check for any execution warnings or errors
     if len(result.errors) != 0:
         print('Errors: {}', result.errors)

wrapping/python/docs/source/User_API.rst

@@ -457,7 +457,7 @@ General Parameters
    import_data = nx.Dream3dImportParameter.ImportData()
    import_data.file_path = "/private/tmp/basic_ebsd.dream3d"
    import_data.data_paths = None
-   result = nx.ReadDREAM3DFilter.execute(data_structure=data_structure, import_file_data=import_data)
+   result = nx.ReadDREAM3DFilter.execute(data_structure=data_structure, import_data_object=import_data)
 
 .. _DynamicTableParameter:
 .. py:class:: DynamicTableParameter