API: Standardize I/O Naming to Read/Write (#753)

* AbaqusHexahedronWriter -> WriteAbaqusHexahedron * AvizoRectilinearCoordinateWriter -> WriteAvizoRectilinearCoordinate * AvizoUniformCoordinateWriter -> WriteAvizoUniformCoordinate * ComplexCore Algorithm renaming * Complete complexcore io rename update * Rename OrientationAnalysis i/o * Sort cmake lists alphabetical * Update ITK I/O human names * Update version to 1.2.0 * Fixing various python related codes * FindFeaturePhases: Change k_FeaturePhasesArrayName_Key value * Python: Adjust release notes structure to separate versions. * Rename the ImportHDFDatasetParameter to ReadHDF5DataSetParameter * Rename the H5EbsdReaderParameter to ReadH5EbsdFileParameter * Upate python codes to WriteDREAM3DFilter * Fix runtime exception when parent file path is empty. Signed-off-by: Michael Jackson <[email protected]> --------- Signed-off-by: Michael Jackson <[email protected]> Co-authored-by: Michael Jackson <[email protected]>
BlueQuartzSoftware · Nov 13, 2023 · 8b7b55d · 8b7b55d
1 parent 461f0a2
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -63,7 +63,7 @@ option(COMPLEX_ENABLE_INSTALL "Enables COMPLEX install rules" ON)
 file(TO_CMAKE_PATH "${CMAKE_COMMAND}" CMAKE_COMMAND_NORM)
 
 project(complex
-  VERSION 1.1.0
+  VERSION 1.2.0
   DESCRIPTION "SIMPL Redesign"
   HOMEPAGE_URL "https://github.com/BlueQuartzSoftware/complex"
   LANGUAGES CXX
@@ -262,7 +262,7 @@ set(CoreParameters
   NumberParameter
   NumericTypeParameter
   ReadCSVFileParameter
-  ImportHDF5DatasetParameter
+  ReadHDF5DatasetParameter
   StringParameter
   VectorParameter
 )

diff --git a/cmake/Summary.cmake b/cmake/Summary.cmake
@@ -76,7 +76,7 @@ message(STATUS "* -------------- Complex Python Configuration Options ----------
 message(STATUS "* COMPLEX_BUILD_PYTHON: ${COMPLEX_BUILD_PYTHON}")
 message(STATUS "* COMPLEX_EMBED_PYTHON: ${COMPLEX_EMBED_PYTHON}")
 message(STATUS "* Python3_EXECUTABLE: ${Python3_EXECUTABLE}")
-message(STATUS "* MKDOCS_EXECUTABLE: ${MKDOCS_EXECUTABLE}")
+message(STATUS "* COMPLEX_ENABLE_SPHINX_DOCS: ${COMPLEX_ENABLE_SPHINX_DOCS}")
 
 message(STATUS "* -------------- Known Plugins ------------------------------------------------------")
 foreach(plugin ${COMPLEX_PLUGIN_LIST})

diff --git a/conda/meta.yaml b/conda/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "complex" %}
-{% set version = "1.1.0" %}
+{% set version = "1.2.0" %}
 
 package:
   name: {{ name|lower }}

diff --git a/conda/recipe.yaml b/conda/recipe.yaml
@@ -1,5 +1,5 @@
 context:
-  version: "1.1.0"
+  version: "1.2.0"
   name: complex
 
 package:

diff --git a/pipelines/Combo-EBSD-osc_r0c0.d3dpipeline b/pipelines/Combo-EBSD-osc_r0c0.d3dpipeline
@@ -335,7 +335,7 @@
         "cell_features_attribute_matrix_path": "DataContainer/CellFeatureData",
         "cell_phases_array_path": "DataContainer/CellData/Phases",
         "feature_ids_path": "DataContainer/CellData/FeatureIds",
-        "feature_phases_array_path": "Phases"
+        "feature_phases_array_name": "Phases"
       },
       "comments": "",
       "filter": {
@@ -405,7 +405,7 @@
       },
       "comments": "",
       "filter": {
-        "name": "complex::ExportDREAM3DFilter",
+        "name": "complex::WriteDREAM3DFilter",
         "uuid": "b3a95784-2ced-41ec-8d3d-0242ac130003"
       },
       "isDisabled": false

diff --git a/pipelines/PorosityAnalysis.d3dpipeline b/pipelines/PorosityAnalysis.d3dpipeline
@@ -154,7 +154,7 @@
         "cell_features_attribute_matrix_path": "RoboMet.3D Image Stack/Pore Data",
         "cell_phases_array_path": "RoboMet.3D Image Stack/Optical Data/Phases",
         "feature_ids_path": "RoboMet.3D Image Stack/Optical Data/FeatureIds",
-        "feature_phases_array_path": "Phases"
+        "feature_phases_array_name": "Phases"
       },
       "comments": "",
       "filter": {
@@ -248,7 +248,7 @@
       },
       "comments": "",
       "filter": {
-        "name": "complex::ExportDREAM3DFilter",
+        "name": "complex::WriteDREAM3DFilter",
         "uuid": "b3a95784-2ced-41ec-8d3d-0242ac130003"
       },
       "isDisabled": false

diff --git a/src/Plugins/ComplexCore/CMakeLists.txt b/src/Plugins/ComplexCore/CMakeLists.txt
@@ -7,7 +7,6 @@ set(${PLUGIN_NAME}_SOURCE_DIR ${complex_SOURCE_DIR}/src/Plugins/${PLUGIN_NAME})
 # These are all the filters in the plugin. All filters should be kept in the
 # PLUGIN_NAME/src/PLUGIN_NAME/Filters/ directory.
 set(FilterList
-  AbaqusHexahedronWriterFilter
   AddBadDataFilter
   AlignGeometries
   AlignSectionsFeatureCentroidFilter
@@ -16,16 +15,14 @@ set(FilterList
   ApplyTransformationToGeometryFilter
   ApproximatePointCloudHull
   ArrayCalculatorFilter
-  AvizoRectilinearCoordinateWriterFilter
-  AvizoUniformCoordinateWriterFilter
   CalculateArrayHistogramFilter
   CalculateFeatureSizesFilter
   CalculateTriangleAreasFilter
   ChangeAngleRepresentation
   CombineAttributeArraysFilter
   CombineStlFilesFilter
-  ComputeMomentInvariants2DFilter
   ComputeFeatureRectFilter
+  ComputeMomentInvariants2DFilter
   ConditionalSetValue
   ConvertColorToGrayScaleFilter
   ConvertDataFilter
@@ -44,11 +41,9 @@ set(FilterList
   ErodeDilateCoordinationNumberFilter
   ErodeDilateMaskFilter
   ExecuteProcessFilter
-  ExportDREAM3DFilter
   ExtractComponentAsArrayFilter
   ExtractInternalSurfacesFromTriangleGeometry
   ExtractVertexGeometryFilter
-  FeatureDataCSVWriterFilter
   FeatureFaceCurvatureFilter
   FillBadDataFilter
   FindArrayStatisticsFilter
@@ -59,8 +54,8 @@ set(FilterList
   FindEuclideanDistMapFilter
   FindFeatureCentroidsFilter
   FindFeatureClusteringFilter
-  FindFeaturePhasesFilter
   FindFeaturePhasesBinaryFilter
+  FindFeaturePhasesFilter
   FindLargestCrossSectionsFilter
   FindNeighborhoodsFilter
   FindNeighborListStatistics
@@ -74,22 +69,14 @@ set(FilterList
   FindVolFractionsFilter
   GenerateColorTableFilter
   GenerateVectorColorsFilter
-  ImageContouringFilter
   IdentifySample
-  ImportBinaryCTNorthstarFilter
-  ReadCSVFileFilter
-  ImportDeformKeyFileV12Filter
-  ImportDREAM3DFilter
-  ImportHDF5Dataset
-  ReadTextDataArrayFilter
-  ImportVolumeGraphicsFileFilter
+  ImageContouringFilter
   InitializeData
   InterpolatePointCloudToRegularGridFilter
   IterativeClosestPointFilter
   KMeansFilter
   KMedoidsFilter
   LaplacianSmoothingFilter
-  LosAlamosFFTWriterFilter
   MapPointCloudToRegularGridFilter
   MinNeighbors
   MoveData
@@ -98,7 +85,15 @@ set(FilterList
   PartitionGeometryFilter
   PointSampleTriangleGeometryFilter
   QuickSurfaceMeshFilter
-  RawBinaryReaderFilter
+  ReadBinaryCTNorthstarFilter
+  ReadCSVFileFilter
+  ReadDeformKeyFileV12Filter
+  ReadDREAM3DFilter
+  ReadHDF5Dataset
+  ReadRawBinaryFilter
+  ReadStlFileFilter
+  ReadTextDataArrayFilter
+  ReadVolumeGraphicsFileFilter
   RegularGridSampleSurfaceMeshFilter
   RemoveFlaggedFeaturesFilter
   RemoveFlaggedVertices
@@ -115,37 +110,39 @@ set(FilterList
   SharedFeatureFaceFilter
   SilhouetteFilter
   SplitAttributeArrayFilter
-  StlFileReaderFilter
   SurfaceNetsFilter
   TriangleCentroidFilter
   TriangleDihedralAngleFilter
   TriangleNormalFilter
   UncertainRegularGridSampleSurfaceMeshFilter
-  VtkRectilinearGridWriterFilter
+  WriteAbaqusHexahedronFilter
   WriteASCIIDataFilter
+  WriteAvizoRectilinearCoordinateFilter
+  WriteAvizoUniformCoordinateFilter
   WriteBinaryDataFilter
+  WriteDREAM3DFilter
+  WriteFeatureDataCSVFilter
+  WriteLosAlamosFFTFilter
   WriteStlFileFilter
+  WriteVtkRectilinearGridFilter
 )
 
 set(ActionList
 )
 
 set(AlgorithmList
-  AbaqusHexahedronWriter
   AddBadData
   AlignSectionsFeatureCentroid
   AlignSectionsList
   AppendImageGeometryZSlice
   ApplyTransformationToGeometry
   ArrayCalculator
-  AvizoRectilinearCoordinateWriter
-  AvizoUniformCoordinateWriter
   CalculateArrayHistogram
   CalculateTriangleGroupCurvatures
   CombineAttributeArrays
   CombineStlFiles
-  ComputeMomentInvariants2D
   ComputeFeatureRect
+  ComputeMomentInvariants2D
   ConvertColorToGrayScale
   ConvertData
   ErodeDilateBadData
@@ -171,18 +168,18 @@ set(AlgorithmList
   GenerateColorTable
   GenerateVectorColors
   ImageContouring
-  ImportDeformKeyFileV12
-  ImportVolumeGraphicsFile
-  ImportBinaryCTNorthstar
   KMeans
   KMedoids
   LaplacianSmoothing
-  LosAlamosFFTWriter
   NearestPointFuseRegularGrids
   PartitionGeometry
   PointSampleTriangleGeometry
   QuickSurfaceMesh
-  RawBinaryReader
+  ReadBinaryCTNorthstar
+  ReadDeformKeyFileV12
+  ReadRawBinary
+  ReadStlFile
+  ReadVolumeGraphicsFile
   RegularGridSampleSurfaceMesh
   RemoveFlaggedFeatures
   ReplaceElementAttributesWithNeighborValues
@@ -192,13 +189,16 @@ set(AlgorithmList
   SharedFeatureFace
   Silhouette
   SplitAttributeArray
-  StlFileReader
   SurfaceNets
   TriangleCentroid
   TupleTransfer
   UncertainRegularGridSampleSurfaceMesh
-  VtkRectilinearGridWriter
+  WriteAbaqusHexahedron
+  WriteAvizoRectilinearCoordinate
+  WriteAvizoUniformCoordinate
+  WriteLosAlamosFFT
   WriteStlFile
+  WriteVtkRectilinearGrid
 )
 
 create_complex_plugin(NAME ${PLUGIN_NAME}

diff --git a/...ore/docs/ImportBinaryCTNorthstarFilter.md → ...xCore/docs/ReadBinaryCTNorthstarFilter.md b/...ore/docs/ImportBinaryCTNorthstarFilter.md → ...xCore/docs/ReadBinaryCTNorthstarFilter.md
diff --git a/src/Plugins/ComplexCore/docs/ReadCSVFileFilter.md b/src/Plugins/ComplexCore/docs/ReadCSVFileFilter.md
@@ -1,16 +1,16 @@
-# Read CSV File 
+# Read CSV File
 
-## Group (Subgroup) ##
+## Group (Subgroup)
 
 IO (Input)
 
-## Description ##
+## Description
 
 This **Filter** reads text data from any text-based file and imports the data into DREAM3D-NX-style arrays.  The user specifies which file to import, how the data is formatted, what to call each array, and what type each array should be.
 
 *Note:* This **Filter** is intended to read data that is column-oriented, such that each created DREAM3D-NX array corresponds to a column of data in the text file. Therefore, this **Filter** will only import scalar arrays. If multiple columns are in fact different components of the same array, then the columns may be imported as separate arrays and then combined in the correct order using the Combine Attribute Arrays **Filter**.
 
-### Filling Out The Inputs ###
+### Filling Out The Inputs
 
 The user first selects the **Input Text File** path, which then enables the rest of the interface.
 
@@ -54,40 +54,12 @@ Afterwards, you end up with a data structure that looks like this:
 
 ![Input Text File Field](Images/Read_CSV_10.png)
 
-## Parameters ##
+% Auto generated parameter table will be inserted here
 
-| Name                                                           | Type             | Description                                                                                                                                                                                                                                                 |
-|----------------------------------------------------------------|------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| Importer Data Object                                           | ReadCSVData  | The object that holds all data relevant to importing the data, such as input file path, custom headers, start import line number, data types for all the imported arrays, headers line number, header mode, imported array tuple dimensions, delimiters, etc. |
-| Use Existing Attribute Matrix                                  | bool             | Determines whether or not to store the imported data arrays in an existing attribute matrix                                                                                                                                                                 |
-| Existing Attribute Matrix (Use Existing Attribute Matrix - ON) | DataPath         | The data path to the existing attribute matrix where the imported arrays will be stored                                                                                                                                                                     |
-| New Attribute Matrix (Use Existing Attribute Matrix - OFF)     | DataPath         | The data path to the newly created attribute matrix where the imported arrays will be stored                                                                                                                                                                |
-
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
-
-| Kind | Default Name | Description |
-|------|--------------|------|
-| **Attribute Matrix** | None | The existing attribute matrix to store the imported data arrays (only if Existing Attribute Matrix is turned ON) |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description                                                    |
-|------|--------------|------|----------------------|----------------------------------------------------------------|
-| One or more **Element/Feature/Ensemble/etc. Data Arrays** | None | Any | 1 | One or more arrays that are created due to importing text data |
-
-## Example Pipelines ##
-
-
-## License & Copyright ##
+## License & Copyright
 
 Please see the description file distributed with this plugin.
 
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
 
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/...s/ComplexCore/docs/ImportDREAM3DFilter.md → ...ins/ComplexCore/docs/ReadDREAM3DFilter.md b/...s/ComplexCore/docs/ImportDREAM3DFilter.md → ...ins/ComplexCore/docs/ReadDREAM3DFilter.md
@@ -1,4 +1,4 @@
-# ImportDREAM3DFilter
+# ReadDREAM3DFilter
 
 ## Description
 

diff --git a/...Core/docs/ImportDeformKeyFileV12Filter.md → ...exCore/docs/ReadDeformKeyFileV12Filter.md b/...Core/docs/ImportDeformKeyFileV12Filter.md → ...exCore/docs/ReadDeformKeyFileV12Filter.md
diff --git a/...ins/ComplexCore/docs/ImportHDF5Dataset.md → ...ugins/ComplexCore/docs/ReadHDF5Dataset.md b/...ins/ComplexCore/docs/ImportHDF5Dataset.md → ...ugins/ComplexCore/docs/ReadHDF5Dataset.md
diff --git a/...ComplexCore/docs/RawBinaryReaderFilter.md → ...s/ComplexCore/docs/ReadRawBinaryFilter.md b/...ComplexCore/docs/RawBinaryReaderFilter.md → ...s/ComplexCore/docs/ReadRawBinaryFilter.md
diff --git a/...s/ComplexCore/docs/StlFileReaderFilter.md → ...ins/ComplexCore/docs/ReadStlFileFilter.md b/...s/ComplexCore/docs/StlFileReaderFilter.md → ...ins/ComplexCore/docs/ReadStlFileFilter.md
diff --git a/...re/docs/ImportVolumeGraphicsFileFilter.md → ...Core/docs/ReadVolumeGraphicsFileFilter.md b/...re/docs/ImportVolumeGraphicsFileFilter.md → ...Core/docs/ReadVolumeGraphicsFileFilter.md
diff --git a/...Core/docs/AbaqusHexahedronWriterFilter.md → ...xCore/docs/WriteAbaqusHexahedronFilter.md b/...Core/docs/AbaqusHexahedronWriterFilter.md → ...xCore/docs/WriteAbaqusHexahedronFilter.md
diff --git a/...AvizoRectilinearCoordinateWriterFilter.md → .../WriteAvizoRectilinearCoordinateFilter.md b/...AvizoRectilinearCoordinateWriterFilter.md → .../WriteAvizoRectilinearCoordinateFilter.md
diff --git a/...ocs/AvizoUniformCoordinateWriterFilter.md → ...docs/WriteAvizoUniformCoordinateFilter.md b/...ocs/AvizoUniformCoordinateWriterFilter.md → ...docs/WriteAvizoUniformCoordinateFilter.md
diff --git a/...s/ComplexCore/docs/ExportDREAM3DFilter.md → ...ns/ComplexCore/docs/WriteDREAM3DFilter.md b/...s/ComplexCore/docs/ExportDREAM3DFilter.md → ...ns/ComplexCore/docs/WriteDREAM3DFilter.md
@@ -1,4 +1,4 @@
-# ExportDREAM3DFilter
+# WriteDREAM3DFilter
 
 ## Description
 

diff --git a/...exCore/docs/FeatureDataCSVWriterFilter.md → ...lexCore/docs/WriteFeatureDataCSVFilter.md b/...exCore/docs/FeatureDataCSVWriterFilter.md → ...lexCore/docs/WriteFeatureDataCSVFilter.md
diff --git a/...plexCore/docs/LosAlamosFFTWriterFilter.md → ...mplexCore/docs/WriteLosAlamosFFTFilter.md b/...plexCore/docs/LosAlamosFFTWriterFilter.md → ...mplexCore/docs/WriteLosAlamosFFTFilter.md
diff --git a/...re/docs/VtkRectilinearGridWriterFilter.md → ...ore/docs/WriteVtkRectilinearGridFilter.md b/...re/docs/VtkRectilinearGridWriterFilter.md → ...ore/docs/WriteVtkRectilinearGridFilter.md
diff --git a/src/Plugins/ComplexCore/pipelines/AppendImageGeometryZSlice.d3dpipeline b/src/Plugins/ComplexCore/pipelines/AppendImageGeometryZSlice.d3dpipeline
@@ -190,7 +190,7 @@
       },
       "comments": "",
       "filter": {
-        "name": "complex::ExportDREAM3DFilter",
+        "name": "complex::WriteDREAM3DFilter",
         "uuid": "b3a95784-2ced-41ec-8d3d-0242ac130003"
       },
       "isDisabled": false

diff --git a/src/Plugins/ComplexCore/pipelines/ApplyTransformation_Image.d3dpipeline b/src/Plugins/ComplexCore/pipelines/ApplyTransformation_Image.d3dpipeline
@@ -379,7 +379,7 @@
       },
       "comments": "",
       "filter": {
-        "name": "complex::ExportDREAM3DFilter",
+        "name": "complex::WriteDREAM3DFilter",
         "uuid": "b3a95784-2ced-41ec-8d3d-0242ac130003"
       },
       "isDisabled": false

diff --git a/src/Plugins/ComplexCore/pipelines/ApplyTransformation_Node.d3dpipeline b/src/Plugins/ComplexCore/pipelines/ApplyTransformation_Node.d3dpipeline
@@ -12,7 +12,7 @@
       },
       "comments": "",
       "filter": {
-        "name": "complex::StlFileReaderFilter",
+        "name": "complex::ReadStlFileFilter",
         "uuid": "2f64bd45-9d28-4254-9e07-6aa7c6d3d015"
       },
       "isDisabled": false
@@ -26,7 +26,7 @@
       },
       "comments": "",
       "filter": {
-        "name": "complex::StlFileReaderFilter",
+        "name": "complex::ReadStlFileFilter",
         "uuid": "2f64bd45-9d28-4254-9e07-6aa7c6d3d015"
       },
       "isDisabled": false
@@ -97,7 +97,7 @@
       },
       "comments": "",
       "filter": {
-        "name": "complex::StlFileReaderFilter",
+        "name": "complex::ReadStlFileFilter",
         "uuid": "2f64bd45-9d28-4254-9e07-6aa7c6d3d015"
       },
       "isDisabled": false
@@ -168,7 +168,7 @@
       },
       "comments": "",
       "filter": {
-        "name": "complex::StlFileReaderFilter",
+        "name": "complex::ReadStlFileFilter",
         "uuid": "2f64bd45-9d28-4254-9e07-6aa7c6d3d015"
       },
       "isDisabled": false
@@ -237,7 +237,7 @@
       },
       "comments": "",
       "filter": {
-        "name": "complex::ExportDREAM3DFilter",
+        "name": "complex::WriteDREAM3DFilter",
         "uuid": "b3a95784-2ced-41ec-8d3d-0242ac130003"
       },
       "isDisabled": false