feat: VTK filters for mesh-doctor Part 01 Base classes and io by alexbenedicto · Pull Request #143 · GEOS-DEV/geosPythonPackages

alexbenedicto · 2025-09-29T22:32:45Z

This PR aims to split the large PR #124 into multiple steps while still keeping the same logic to resolve #80
I am considering following this PR by at least three other PRs completing this work, the last one being the complete .rst documentation.

Once done, I will close PR #124

This first part involves:

rework of vtkIO to be more robust and have a dedicated function for mesh-doctor that will only read vtkUnstructuredGrid because mesh-doctor has been designed for that purpose
add the base class for all upcoming vtk filters of mesh-doctor features
add a function that will help in future developments for mesh mapping

RomainBaville

It seems good for me, thanks for having split your pr, it is easier to review.
You just may add unit case to your test for generic helper in order test more cases.

RomainBaville · 2025-09-30T07:57:38Z

geos-mesh/src/geos/mesh/doctor/filters/MeshDoctorFilterBase.py

+        self: Self,
+        mesh: vtkUnstructuredGrid,
+        filterName: str,
+        useExternalLogger: bool = False,


To be more specific, users can use an external Handler more than an external logger

As this refers to the same variable that is called speHandler in the other filters, it is a bit confusing to change it only here... I suggest to keep that same name here and dedicate a specific PR to change this name in all files if needed.

RomainBaville · 2025-09-30T08:00:25Z

geos-mesh/src/geos/mesh/doctor/filters/MeshDoctorFilterBase.py

+
+        Args:
+            filepath (str): /path/to/your/file.vtu
+            isDataModeBinary (bool, optional): Writes the file in binary format or ascii. Defaults to True.


Suggested change

isDataModeBinary (bool, optional): Writes the file in binary format or ascii. Defaults to True.

isDataModeBinary (bool, optional): Writes the file in binary format (True) or ascii (False). Defaults to True.

RomainBaville · 2025-09-30T08:02:14Z

geos-mesh/src/geos/mesh/doctor/filters/MeshDoctorFilterBase.py

+                                           Defaults to False.
+        """
+        if self.mesh:
+            vtk_output = VtkOutput( filepath, isDataModeBinary )


Why do you use snake case and not camel case here and after?

RomainBaville · 2025-09-30T08:05:08Z

geos-mesh/src/geos/mesh/doctor/filters/MeshDoctorFilterBase.py

+
+        Args:
+            filepath (str): /path/to/your/file.vtu
+            isDataModeBinary (bool, optional): Writes the file in binary format or ascii. Defaults to True.


Suggested change

isDataModeBinary (bool, optional): Writes the file in binary format or ascii. Defaults to True.

isDataModeBinary (bool, optional): Writes the file in binary format (True) or ascii (False). Defaults to True.

RomainBaville · 2025-09-30T08:13:53Z

geos-mesh/src/geos/mesh/io/vtkIO.py

+        mesh (vtkPointSet): The grid data to write.
+        writer_class (VtkWriterClass): The VTK writer class to use.
+        output (str): The output file path.
+        is_binary (bool): Whether to write the file in binary mode.


Suggested change

is_binary (bool): Whether to write the file in binary mode.

is_binary (bool): Whether to write the file in binary mode (True) or ASCII (False).

RomainBaville · 2025-09-30T08:16:58Z

geos-mesh/src/geos/mesh/io/vtkIO.py

-    # If it does not match, then test all the others.
-    for reader in extension_to_reader.values():
-        output_mesh = reader( vtk_input_file )
+    filepath_path: Path = Path( filepath )


Why not directly ask for a Path instead of str ?

RomainBaville · 2025-09-30T08:21:23Z

geos-mesh/src/geos/mesh/io/vtkIO.py

+        io_logger.warning( f"Unknown file extension '{filepath_path.suffix}'. Trying all available readers." )
+
+    # 2. Add all other unique readers as fallbacks
+    for reader_cls in READER_MAP.values():


Why not use vtkXMLGenericDataObjectReader ?

RomainBaville · 2025-09-30T09:04:20Z

geos-mesh/tests/test_genericHelpers.py

+
+
+def test_findUniqueCellCenterCellIds() -> None:
+    """Test of findUniqueCellCenterCellIds method."""


You may test your function with two cells sharing a center but with diferents shape for example with a tetra with the following coordinate [ [ -1, -1, -1 ], [ 4, -1, -1 ], [ -1, 4, -1 ], [ -1, -1, 4 ] ] or [ [ 0, 0, 0 ], [ 2, 0, 0 ], [ 0, 0, 2 ], [ -1, -1, 4 ] ] to be sure to catch all the possibilities

paloma-martinez · 2025-09-30T11:54:01Z

geos-mesh/src/geos/mesh/doctor/filters/MeshDoctorFilterBase.py

+MeshDoctorFilterBase serves as the foundation class for filters that process existing meshes,
+while MeshDoctorGenerator is for filters that generate new meshes from scratch.
+
+These base classes provide common functionality including:


Suggested change

These base classes provide common functionality including:

These base classes provide common functionalities including:

paloma-martinez · 2025-09-30T11:59:07Z

geos-mesh/src/geos/mesh/doctor/filters/MeshDoctorFilterBase.py

+        """Writes a .vtu file of the vtkUnstructuredGrid at the specified filepath.
+
+        Args:
+            filepath (str): /path/to/your/file.vtu


Suggested change

filepath (str): /path/to/your/file.vtu

filepath (str): The path for the output mesh file.

paloma-martinez · 2025-09-30T12:24:59Z

geos-mesh/src/geos/mesh/doctor/filters/MeshDoctorFilterBase.py

+        if not useExternalLogger:
+            self.logger = getLogger( filterName, True )
+        else:
+            import logging


I suggest to move this import at the top of the file as it better for readability of the code. The logging package is one of the most common and 'cheap' package, the import without actually using it will not be too bothersome.

paloma-martinez · 2025-09-30T12:31:36Z

geos-mesh/src/geos/mesh/doctor/filters/MeshDoctorFilterBase.py

+class MeshDoctorGeneratorBase:
+    """Base class for mesh doctor generator filters (no input mesh required).
+
+    This class provides functionality for filters that generate meshes


Suggested change

This class provides functionality for filters that generate meshes

This class provides functionalities for filters that generate meshes

paloma-martinez · 2025-09-30T12:37:09Z

geos-mesh/src/geos/mesh/doctor/filters/MeshDoctorFilterBase.py

+    def copyMesh( self: Self, sourceMesh: vtkUnstructuredGrid ) -> vtkUnstructuredGrid:
+        """Helper method to create a copy of a mesh with structure and attributes.
+
+        Args:
+            sourceMesh (vtkUnstructuredGrid): Source mesh to copy from.
+
+        Returns:
+            vtkUnstructuredGrid: New mesh with copied structure and attributes.
+        """
+        output_mesh: vtkUnstructuredGrid = sourceMesh.NewInstance()
+        output_mesh.CopyStructure( sourceMesh )
+        output_mesh.CopyAttributes( sourceMesh )
+        return output_mesh


This function is generic and could be moved to geos-mesh.utils.

paloma-martinez · 2025-09-30T13:01:30Z

geos-mesh/src/geos/mesh/doctor/filters/MeshDoctorFilterBase.py

+        self: Self,
+        mesh: vtkUnstructuredGrid,
+        filterName: str,
+        useExternalLogger: bool = False,


As this refers to the same variable that is called speHandler in the other filters, it is a bit confusing to change it only here... I suggest to keep that same name here and dedicate a specific PR to change this name in all files if needed.

paloma-martinez · 2025-09-30T13:22:14Z

geos-mesh/src/geos/mesh/doctor/filters/MeshDoctorFilterBase.py

+        """Writes a .vtu file of the vtkUnstructuredGrid at the specified filepath.
+
+        Args:
+            filepath (str): /path/to/your/file.vtu


Suggested change

filepath (str): /path/to/your/file.vtu

filepath (str): The path for the output mesh file.

paloma-martinez · 2025-09-30T13:29:01Z

geos-mesh/src/geos/mesh/io/vtkIO.py

+        is_binary (bool): Whether to write the file in binary mode.
+
+    Returns:
+        int: The result of the write operation.


Suggested change

int: The result of the write operation.

int: 1 if success, 0 otherwise.

alexbenedicto · 2025-10-07T18:20:57Z

Closing this PR for the work suggested in #145 and done in #146 .
I will still take into account the reviews made here for upcoming PRs.

alexbenedicto added 3 commits September 29, 2025 15:19

Update vtkIO for better robustness and clearer logic

56060eb

Add findUniqueCellCenterCellIds function for next PRs

6a14167

Create base class for all future vtk filters

32ba668

alexbenedicto self-assigned this Sep 29, 2025

alexbenedicto added the type: feature label Sep 29, 2025

alexbenedicto requested review from RomainBaville, jafranc and paloma-martinez September 29, 2025 22:33

RomainBaville approved these changes Sep 30, 2025

View reviewed changes

paloma-martinez reviewed Sep 30, 2025

View reviewed changes

This was referenced Oct 7, 2025

Create a mesh-doctor package #145

Closed

refactor: mesh-doctor Convert snake_case to camelCase & Update old formatted function docString #146

Merged

alexbenedicto closed this Oct 7, 2025

	isDataModeBinary (bool, optional): Writes the file in binary format or ascii. Defaults to True.
	isDataModeBinary (bool, optional): Writes the file in binary format (True) or ascii (False). Defaults to True.

	is_binary (bool): Whether to write the file in binary mode.
	is_binary (bool): Whether to write the file in binary mode (True) or ASCII (False).



		def test_findUniqueCellCenterCellIds() -> None:
		"""Test of findUniqueCellCenterCellIds method."""

	These base classes provide common functionality including:
	These base classes provide common functionalities including:

	filepath (str): /path/to/your/file.vtu
	filepath (str): The path for the output mesh file.

	This class provides functionality for filters that generate meshes
	This class provides functionalities for filters that generate meshes

	int: The result of the write operation.
	int: 1 if success, 0 otherwise.

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alexbenedicto commented Oct 7, 2025

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alexbenedicto commented Sep 29, 2025 •

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edited by paloma-martinez

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RomainBaville Sep 30, 2025 •

edited by paloma-martinez

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