feat: Add mesh statistic tools

.ruff.toml

@@ -1,5 +1,6 @@
 # Exclude a variety of commonly ignored directories.
-extend-exclude = ["tests/data"]
+extend-exclude = ["tests/data", "geos-mesh/src/geos/mesh/model/_bar_label.py"]
+
 
 line-length = 120
 indent-width = 4
@@ -21,12 +22,12 @@ select = [
     "W",    # pycodestyle warnings
     "F",    # pyflakes
 #    "UP",   # pyupgrade deactivate since python39
-    "B",    # flake8-bugbear        
-    "SIM",  # flake8-simplify        
-    "ANN",  # flake8-annotations        
-    "C4",   # flake8-comprehensions    
+    "B",    # flake8-bugbear
+    "SIM",  # flake8-simplify
+    "ANN",  # flake8-annotations
+    "C4",   # flake8-comprehensions
 #    "I",    # isort - manage by yapf
-    "D",    # pydocstyle    
+    "D",    # pydocstyle
 ]
 
 ignore = [

README.md

@@ -17,7 +17,7 @@ Package summary
 * `geos-ats` package includes tools for managing integrated tests for GEOS.
 * `pygeos-tools` package adds a variety of tools for working with *pygeosx* objects.
 
-The next packages are dedicated to pre- and post-process GEOS inputs/outputs. 
+The next packages are dedicated to pre- and post-process GEOS inputs/outputs.
 
 The following packages contain basic utilities used by the other ones:
 
@@ -110,7 +110,7 @@ Installation
 
 * *Manual installation:*
 
-  GEOS Python packages can be manually installed with pip using `python` >= 3.10. 
+  GEOS Python packages can be manually installed with pip using `python` >= 3.10.
 
     To install any package, run the following commands from the geosPythonPackage directory:
 
@@ -131,21 +131,28 @@ Installation
   [!WARNING]
    Due to local package conflicts with `pip install`, it is recommended to use the `--upgrade` option when building packages, or to use the script `install_packages.sh` located at the root of the repository.
   [!NOTE]
-  geos-pv package cannot be build alone, but together with Paraview ([see Paraview compilation guide](https://gitlab.kitware.com/paraview/paraview/-/blob/master/Documentation/dev/build.md)). It is recommended to use Paraview v5.12+, which is based on python 3.10+. Alternatively, plugins from geos-pv/PVplugins can be manually loaded into Paraview ([see documentation](https://docs.paraview.org/en/latest/ReferenceManual/pythonProgrammableFilter.html#python-algorithm)).
+  geos-pv package cannot be build alone, but together with Paraview ([see Paraview compilation guide](https://gitlab.kitware.com/paraview/paraview/-/blob/master/Documentation/dev/build.md)). It is recommended to use Paraview v5.12+, which is based on python 3.10+. Alternatively, plugins from `geos-pv/src/geos/pv/plugins` can be manually loaded into Paraview ([see documentation](https://docs.paraview.org/en/latest/ReferenceManual/pythonProgrammableFilter.html#python-algorithm)).
 
 
 Contributions
 -------------
 
 GEOS Python packages repository gathers python scripts from any GEOS developpers and users. Feel free to share any scripts that may benefit to the GEOS community.
 
-If you would like to report a bug, please submit an [issue](https://github.com/GEOS-DEV/geosPythonPackages/issues/new). 
+If you would like to report a bug, please submit an [issue](https://github.com/GEOS-DEV/geosPythonPackages/issues/new).
 
 If you would like to contribute to GEOS Python packages, please respect the following guidelines:
 
 1. Create a new branch named from this template: `[CONTRIBUTOR]/[TYPE]/[TITLE]` where CONTRIBUTOR is the name of the contributor, TYPE is the type of contribution among 'feature', 'refactor', 'doc', 'ci', TITLE is a short title for the branch.
 2. Add your code trying to integrate into the current code architecture.
-3. Push the branch, open a new PR respecting naming [semantics](https://gist.github.com/joshbuchea/6f47e86d2510bce28f8e7f42ae84c716), and add reviewers
+3. Run mypy, ruff and yapf in this order
+  ```
+  python -m pip install --upgrade mypy ruff yapf
+  python -m mypy --config-file ./.mypy.ini --check-untyped-defs ./<PACKAGE_NAME>
+  python -m ruff check --fix --config .ruff.toml ./<PACKAGE_NAME>
+  python -m yapf -r -i --style .style.yapf ./<PACKAGE_NAME>
+  ```
+4. Push the branch, open a new PR respecting naming [semantics](https://gist.github.com/joshbuchea/6f47e86d2510bce28f8e7f42ae84c716), and add reviewers
 
 If you do not have the rights to push the code and open new PRs, consider opening a new issue to explain what you want to do and ask for the dev rights.
 

docs/geos-pv.rst

@@ -7,6 +7,10 @@ GEOS Paraview plugins
 
    ./geos_pv_docs/home.rst
 
-   ./geos_pv_docs/modules.rst
+   ./geos_pv_docs/utilities.rst
 
-   ./geos_pv_docs/readers.rst
+   ./geos_pv_docs/readers.rst
+
+   ./geos_pv_docs/meshQuality.rst
+
+   ./geos_pv_docs/processing.rst

docs/geos_mesh_docs/model.rst

@@ -4,10 +4,18 @@ Model
 The `model` module of `geos-mesh` package contains data model.
 
 
-geos.mesh.model.CellTypeCounts filter
+geos.mesh.model.CellTypeCounts module
 --------------------------------------
 
 .. automodule:: geos.mesh.model.CellTypeCounts
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+geos.mesh.model.QualityMetricSummary module
+--------------------------------------------
+
+.. automodule:: geos.mesh.model.QualityMetricSummary
     :members:
     :undoc-members:
     :show-inheritance:

docs/geos_mesh_docs/processing.rst

@@ -4,6 +4,14 @@ Processing filters
 The `processing` module of `geos-mesh` package contains filters to process meshes.
 
 
+geos.mesh.processing.meshQualityMetricHelpers module
+-----------------------------------------------------
+
+.. automodule:: geos.mesh.processing.meshQualityMetricHelpers
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 geos.mesh.processing.SplitMesh filter
 --------------------------------------
 

docs/geos_mesh_docs/stats.rst

@@ -4,10 +4,18 @@ Mesh stats tools
 The `stats` module of `geos-mesh` package contains filter to compute statistics on meshes.
 
 
-geos.mesh.stats.CellTypeCounter filter
---------------------------------------
+geos.mesh.stats.CellTypeCounterEnhanced filter
+-----------------------------------------------
 
-.. automodule:: geos.mesh.stats.CellTypeCounter
+.. automodule:: geos.mesh.stats.CellTypeCounterEnhanced
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+geos.mesh.stats.MeshQualityEnhanced filter
+-------------------------------------------
+
+.. automodule:: geos.mesh.stats.MeshQualityEnhanced
     :members:
     :undoc-members:
     :show-inheritance:

docs/geos_pv_docs/geosLogReaderUtils.rst

@@ -4,42 +4,42 @@ GeosLogReaderUtils functions
 This package define functions dedicated to the GeosLogReader.
 
 
-geos.pv.geosLogReaderUtils.GeosLogReaderAquifers module
+GeosLogReaderAquifers module
 -------------------------------------------------------------------
 
 .. automodule:: geos.pv.geosLogReaderUtils.GeosLogReaderAquifers
    :members:
    :undoc-members:
    :show-inheritance:
 
-geos.pv.geosLogReaderUtils.geosLogReaderConvergence module
+geosLogReaderConvergence module
 ---------------------------------------------------------------------
 
 .. automodule:: geos.pv.geosLogReaderUtils.GeosLogReaderConvergence
    :members:
    :undoc-members:
    :show-inheritance:
 
-geos.pv.geosLogReaderUtils.GeosLogReaderFlow module
+GeosLogReaderFlow module
 ---------------------------------------------------------------
 
 .. automodule:: geos.pv.geosLogReaderUtils.GeosLogReaderFlow
    :members:
    :undoc-members:
    :show-inheritance:
 
-geos.pv.geosLogReaderUtils.GeosLogReaderFunctions module
+GeosLogReaderFunctions module
 --------------------------------------------------------------------
 
 .. automodule:: geos.pv.geosLogReaderUtils.geosLogReaderFunctions
    :members:
    :undoc-members:
    :show-inheritance:
 
-geos.pv.geosLogReaderUtils.GeosLogReaderWells module
+GeosLogReaderWells module
 --------------------------------------------------------------------
 
 .. automodule:: geos.pv.geosLogReaderUtils.GeosLogReaderWells
    :members:
    :undoc-members:
-   :show-inheritance:
+   :show-inheritance:

docs/geos_pv_docs/home.rst

@@ -1,18 +1,21 @@
 Home
 ====
 
-**geos-pv** is a Python package that gathers `Paraview <https://www.paraview.org/>`_ plugins of GEOS python tools. 
+**geos-pv** is a Python package that gathers `Paraview <https://www.paraview.org/>`_ plugins of GEOS python tools.
 
 It includes:
 
 * Paraview readers allowing to load data;
-* generic tools to processes meshes;
+* generic tools to process meshes;
 * GEOS pre-processing tools to clean and check GEOS input mesh;
 * GEOS post-processing tools to clean GEOS output mesh, compute additional properties, or create specific plots such as Mohr's circle plot.
 
-The packages can be loaded into Paraview using the Plugin Manager from `Tools > Plugin Manager`. On success, you will 
-see the selected plugin in the `Filters`` menu (see `Paraview documentation <https://docs.paraview.org/en/latest/ReferenceManual/pythonProgrammableFilter.html>`.
+The packages can be loaded into Paraview using the Plugin Manager from `Tools > Plugin Manager`. On success, you will
+see the selected plugin in the `Filters`` menu (see `Paraview documentation <https://docs.paraview.org/en/latest/ReferenceManual/pythonProgrammableFilter.html>`_).
 
-Alternatively, geos-pv package can be build together with Paraview ([see Paraview compilation guide](https://gitlab.kitware.com/paraview/paraview/-/blob/master/Documentation/dev/build.md)). 
+Alternatively, geos-pv package can be build together with Paraview (see `Paraview compilation guide <https://gitlab.kitware.com/paraview/paraview/-/blob/master/Documentation/dev/build.md>`_).
 It is recommended to use Paraview v5.12+, which is based on python 3.10+. If you need to build geos-pv package with the paraview dependency, use the command:
-`pip install Path/To/geosPythonPackages/geos-pv[paraview]`
+
+.. code-block:: bash
+
+    pip install path/to/geosPythonPackages/geos-pv[paraview]

docs/geos_pv_docs/meshQuality.rst

@@ -0,0 +1,13 @@
+Mesh Quality
+================
+
+
+PVCellTypeCounterEnhanced
+----------------------------------
+
+.. automodule:: geos.pv.plugins.PVCellTypeCounterEnhanced
+
+PVMeshQualityEnhanced
+---------------------------
+
+.. automodule:: geos.pv.plugins.PVMeshQualityEnhanced

docs/geos_pv_docs/processing.rst

@@ -0,0 +1,7 @@
+Post-/Pre-processing
+=========================
+
+PVSplitMesh
+----------------------------------
+
+.. automodule:: geos.pv.plugins.PVSplitMesh

docs/geos_pv_docs/readers.rst

@@ -1,7 +1,7 @@
-Paraview readers
-================
+Readers
+=============
 
-readers.PVGeosLogReader module
-----------------------------------
+PVGeosLogReader
+--------------------
 
-.. automodule:: readers.PVGeosLogReader
+.. automodule:: geos.pv.plugins.PVGeosLogReader

docs/geos_pv_docs/modules.rst → docs/geos_pv_docs/utilities.rst

@@ -1,4 +1,4 @@
-Processing
+Utilities
 ==========
 
 .. toctree::
@@ -8,4 +8,4 @@ Processing
 
    pyplotUtils
 
-   utils
+   utils

geos-mesh/pyproject.toml

@@ -32,6 +32,7 @@ dependencies = [
     "pandas >= 2.2",
     "meshio >= 5.3",
     "typing_extensions >= 4.12",
+    "geos-utils",
 ]
 
 [project.scripts]

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

@@ -10,6 +10,21 @@
 
 __doc__ = """
 CellTypeCounts stores the number of elements of each type.
+
+To use the filter:
+
+.. code-block:: python
+
+    from geos.mesh.model.CellTypeCounts import CellTypeCounts
+
+    counts: CellTypeCounts = CellTypeCounts()
+
+    # set data
+    counts.addType( cellType )
+    counts.setTypeCount( cellType, count )
+
+    # get data
+    count: int counts.getTypeCount( cellType )
 """
 
 
@@ -43,6 +58,22 @@ def __add__( self: Self, other: Self ) -> 'CellTypeCounts':
         newCounts._counts = self._counts + other._counts
         return newCounts
 
+    def getCounts( self: Self ) -> npt.NDArray[ np.int64 ]:
+        """Get all counts.
+
+        Returns:
+            npt.NDArray[ np.int64 ]: counts
+        """
+        return self._counts
+
+    def getTotalCount( self: Self ) -> int:
+        """Get the total number of cells.
+
+        Returns:
+            int: Total number of cells
+        """
+        return self._counts[ VTK_POLYHEDRON ] + self._counts[ VTK_POLYGON ]
+
     def addType( self: Self, cellType: int ) -> None:
         """Increment the number of cell of input type.
 
@@ -74,6 +105,10 @@ def getTypeCount( self: Self, cellType: int ) -> int:
         """
         return int( self._counts[ cellType ] )
 
+    def reset( self: Self ) -> None:
+        """Reset counts."""
+        self._counts = np.zeros( VTK_NUMBER_OF_CELL_TYPES, dtype=float )
+
     def _updateGeneralCounts( self: Self, cellType: int, count: int ) -> None:
         """Update generic type counters.
 
@@ -98,7 +133,7 @@ def print( self: Self ) -> str:
         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 += f"| **Total Number of Cells**         | {int(self.getTotalCount()):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"