feat: Add meshing tools and stats (#81)

* Move vtkUtils and multiblockInspectorTreeFunctions + update dependencies

* Add SplitMesh filters

* Add array transfer from parent to child mesh and tests

* add helpers to create mesh with multiple cells

* add MeshIdCard class and tests + linting

* create vtk filters to compute mesh stats

* create Paraview plugins to wrap vtk filters

* upgrade github actions

* Merge helpers

* Addition of data for tests

* vtkUtils tests implemented

* Reorganize utilities & update paths accordingly

* documentation + typing, liniting, formating

---------

Co-authored-by: Paloma Martinez <[email protected]>
Co-authored-by: alexbenedicto <[email protected]>

Author: 3 people

docs/geos_mesh_docs/model.rst

@@ -0,0 +1,13 @@
+Model
+^^^^^^^
+
+The `model` module of `geos-mesh` package contains data model.
+
+
+geos.mesh.model.CellTypeCounts filter
+--------------------------------------
+
+.. automodule:: geos.mesh.model.CellTypeCounts
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/geos_mesh_docs/modules.rst

@@ -11,4 +11,10 @@ GEOS Mesh tools
 
     io
 
+    model
+
+    processing
+
+    stats
+
     utils

docs/geos_mesh_docs/processing.rst

@@ -0,0 +1,13 @@
+Processing filters
+^^^^^^^^^^^^^^^^^^^
+
+The `processing` module of `geos-mesh` package contains filters to process meshes.
+
+
+geos.mesh.processing.SplitMesh filter
+--------------------------------------
+
+.. automodule:: geos.mesh.processing.SplitMesh
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/geos_mesh_docs/stats.rst

@@ -0,0 +1,13 @@
+Mesh stats tools
+^^^^^^^^^^^^^^^^
+
+The `stats` module of `geos-mesh` package contains filter to compute statistics on meshes.
+
+
+geos.mesh.stats.CellTypeCounter filter
+--------------------------------------
+
+.. automodule:: geos.mesh.stats.CellTypeCounter
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/geos_mesh_docs/utils.rst

@@ -1,7 +1,7 @@
 Mesh utilities
 ^^^^^^^^^^^^^^^^
 
-The `utils` module of `geos-mesh` package contains different utilities methods for VTK meshes.
+The `utils` module of `geos-mesh` package contains various utilities for VTK meshes.
 
 
 geos.mesh.utils.genericHelpers module

geos-mesh/pyproject.toml

@@ -29,8 +29,9 @@ dependencies = [
     "networkx >= 2.4",
     "tqdm >= 4.67",
     "numpy >= 2.2",
+    "pandas >= 2.2",
     "meshio >= 5.3",
-    "pandas",
+    "typing_extensions >= 4.12",
 ]
 
 [project.scripts]
@@ -48,7 +49,8 @@ build = [
   "build ~= 1.2"
 ]
 dev = [
-   "mypy", 
+   "mypy",
+   "ruff", 
    "yapf",
 ]
 test = [
@@ -57,7 +59,7 @@ test = [
 ]
 
 [tool.pytest.ini_options]
-addopts="--import-mode=importlib"
+addopts = "--import-mode=importlib"
 console_output_style = "count"
 pythonpath = ["src"]
 python_classes = "Test"
@@ -66,7 +68,3 @@ python_functions = "test*"
 testpaths = ["tests"]
 norecursedirs = "bin"
 filterwarnings = []
-
-[tool.coverage.run]
-branch = true
-source = ["src/geos"]

geos-mesh/src/geos/mesh/doctor/checks/generate_fractures.py

@@ -13,7 +13,8 @@
 from vtkmodules.util.numpy_support import numpy_to_vtk, vtk_to_numpy
 from vtkmodules.util.vtkConstants import VTK_ID_TYPE
 from geos.mesh.doctor.checks.vtk_polyhedron import FaceStream
-from geos.mesh.utils.arrayHelpers import has_invalid_field
+from geos.mesh.utils.arrayHelpers import has_array
+
 from geos.mesh.utils.genericHelpers import to_vtk_id_list, vtk_iter
 from geos.mesh.io.vtkIO import VtkOutput, read_mesh, write_mesh
 """
@@ -558,7 +559,7 @@ def check( vtk_input_file: str, options: Options ) -> Result:
     try:
         mesh = read_mesh( vtk_input_file )
         # Mesh cannot contain global ids before splitting.
-        if has_invalid_field( mesh, [ "GLOBAL_IDS_POINTS", "GLOBAL_IDS_CELLS" ] ):
+        if has_array( mesh, [ "GLOBAL_IDS_POINTS", "GLOBAL_IDS_CELLS" ] ):
             err_msg: str = ( "The mesh cannot contain global ids for neither cells nor points. The correct procedure " +
                              " is to split the mesh and then generate global ids for new split meshes." )
             logging.error( err_msg )

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

@@ -160,6 +160,7 @@ def __write_vtu( mesh: vtkUnstructuredGrid, output: str, toBinary: bool = False
 
 def write_mesh( mesh: vtkPointSet, vtk_output: VtkOutput, canOverwrite: bool = False ) -> int:
     """Write mesh to disk.
+
     Nothing is done if file already exists.
 
     Args:

geos-mesh/src/geos/mesh/model/CellTypeCounts.py

@@ -0,0 +1,107 @@
+# SPDX-License-Identifier: Apache-2.0
+# SPDX-FileCopyrightText: Copyright 2023-2024 TotalEnergies.
+# SPDX-FileContributor: Antoine Mazuyer, Martin Lemay
+import numpy as np
+import numpy.typing as npt
+from typing_extensions import Self
+from vtkmodules.vtkCommonDataModel import ( vtkCellTypes, VTK_TRIANGLE, VTK_QUAD, VTK_TETRA, VTK_VERTEX, VTK_POLYHEDRON,
+                                            VTK_POLYGON, VTK_PYRAMID, VTK_HEXAHEDRON, VTK_WEDGE,
+                                            VTK_NUMBER_OF_CELL_TYPES )
+
+__doc__ = """
+CellTypeCounts stores the number of elements of each type.
+"""
+
+
+class CellTypeCounts():
+
+    def __init__( self: Self ) -> None:
+        """CellTypeCounts stores the number of cells of each type."""
+        self._counts: npt.NDArray[ np.int64 ] = np.zeros( VTK_NUMBER_OF_CELL_TYPES, dtype=float )
+
+    def __str__( self: Self ) -> str:
+        """Overload __str__ method.
+
+        Returns:
+            str: counts as string.
+        """
+        return self.print()
+
+    def __add__( self: Self, other: Self ) -> 'CellTypeCounts':
+        """Addition operator.
+
+        CellTypeCounts addition consists in suming counts.
+
+        Args:
+            other (Self): other CellTypeCounts object
+
+        Returns:
+            Self: new CellTypeCounts object
+        """
+        assert isinstance( other, CellTypeCounts ), "Other object must be a CellTypeCounts."
+        newCounts: CellTypeCounts = CellTypeCounts()
+        newCounts._counts = self._counts + other._counts
+        return newCounts
+
+    def addType( self: Self, cellType: int ) -> None:
+        """Increment the number of cell of input type.
+
+        Args:
+            cellType (int): cell type
+        """
+        self._counts[ cellType ] += 1
+        self._updateGeneralCounts( cellType, 1 )
+
+    def setTypeCount( self: Self, cellType: int, count: int ) -> None:
+        """Set the number of cells of input type.
+
+        Args:
+            cellType (int): cell type
+            count (int): number of cells
+        """
+        prevCount = self._counts[ cellType ]
+        self._counts[ cellType ] = count
+        self._updateGeneralCounts( cellType, count - prevCount )
+
+    def getTypeCount( self: Self, cellType: int ) -> int:
+        """Get the number of cells of input type.
+
+        Args:
+            cellType (int): cell type
+
+        Returns:
+            int: number of cells
+        """
+        return int( self._counts[ cellType ] )
+
+    def _updateGeneralCounts( self: Self, cellType: int, count: int ) -> None:
+        """Update generic type counters.
+
+        Args:
+            cellType (int): cell type
+            count (int): count increment
+        """
+        if ( cellType != VTK_POLYGON ) and ( vtkCellTypes.GetDimension( cellType ) == 2 ):
+            self._counts[ VTK_POLYGON ] += count
+        if ( cellType != VTK_POLYHEDRON ) and ( vtkCellTypes.GetDimension( cellType ) == 3 ):
+            self._counts[ VTK_POLYHEDRON ] += count
+
+    def print( self: Self ) -> str:
+        """Print counts string.
+
+        Returns:
+            str: counts string.
+        """
+        card: str = ""
+        card += "|                                   |              |\n"
+        card += "|               -                   |       -      |\n"
+        card += f"| **Total Number of Vertices**      | {int(self._counts[VTK_VERTEX]):12} |\n"
+        card += f"| **Total Number of Polygon**       | {int(self._counts[VTK_POLYGON]):12} |\n"
+        card += f"| **Total Number of Polyhedron**    | {int(self._counts[VTK_POLYHEDRON]):12} |\n"
+        card += f"| **Total Number of Cells**         | {int(self._counts[VTK_POLYHEDRON]+self._counts[VTK_POLYGON]):12} |\n"
+        card += "|               -                   |       -      |\n"
+        for cellType in ( VTK_TRIANGLE, VTK_QUAD ):
+            card += f"| **Total Number of {vtkCellTypes.GetClassNameFromTypeId(cellType):<13}** | {int(self._counts[cellType]):12} |\n"
+        for cellType in ( VTK_TETRA, VTK_PYRAMID, VTK_WEDGE, VTK_HEXAHEDRON ):
+            card += f"| **Total Number of {vtkCellTypes.GetClassNameFromTypeId(cellType):<13}** | {int(self._counts[cellType]):12} |\n"
+        return card