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PoC / Paraview integration for mesh_doctor #2790

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a237118
First steps of meshDoctor as a Programmable filter
jafranc Nov 1, 2023
1fb80f5
Update src/docs/sphinx/pythonTools/mesh_doctor.rst
jafranc Nov 1, 2023
1e16393
adding PoC pv plugin
jafranc Mar 27, 2024
bfc11fe
doc for pv plugin
jafranc Mar 27, 2024
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57 changes: 57 additions & 0 deletions src/docs/sphinx/pythonTools/mesh_doctor.rst
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Expand Up @@ -122,3 +122,60 @@ It will also verify that the ``VTK_POLYHEDRON`` cells can effectively get conver

.. command-output:: python mesh_doctor.py supported_elements --help
:cwd: ../../../coreComponents/python/modules/geosx_mesh_doctor

``Using mesh_doctor in paraview``
""""""""""""""""""""""""""""""""""
To use ``mesh_doctor`` in Paraview as a python programmable filter, a python package install is required first in Paraview python resolved
path. Paraview is storing its python ressources under its *lib/pythonX.X* depending on the paraview version, *e.g* Paraview 5.11 is working
with python 3.9. As a results the following command will install ``mesh_doctor`` package into Paraview resolved path.

.. command-output:: python3 -m pip install --index-url https://test.pypi.org/simple/ --no-deps --upgrade --target /path/to/Paraview/lib/python3.9/ mesh_doctor

.. note::
``pip`` is installing the ``mesh_doctor`` package from the test.pypi repo, which is intended to test package deployment.
Once stabilized and ``mesh_doctor`` uploaded onto the main package repo, this should be dropped out.
Comment on lines +138 to +140
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image 😱 🤣

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Hacky I said 😝

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is installing it like this working for you? When I tried it seemed to me that there were some issue in the setup.py that did not allow for this to work. Basically I could not find the modules when trying to import them.

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@jafranc jafranc Nov 1, 2023 •
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I got this output

Looking in indexes: https://test.pypi.org/simple/
Collecting mesh_doctor
  Downloading https://test-files.pythonhosted.org/packages/97/cc/1ece6916f6e87f95cff4b887f2e6ce50488b146a2e025a959c3665a12d6e/mesh_doctor-0.0.1-py3-none-any.whl (42 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 42.4/42.4 KB 2.1 MB/s eta 0:00:00
Installing collected packages: mesh_doctor
Successfully installed mesh_doctor-0.0.1

and I can checked afterwards that checks is in `/path/to/Paraview/lib/PythonX.X' but this need refactor/cleanup obv.

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As a workaround you can try while being in mesh_doctor directory conatining the .toml

python3 -m pip install --upgrade build
python3 -m build

which should produce de dist/ directory with .whl and .tar.gz.

The install command on the .tar.gz might also work, as

python3 -m pip install dist/mesh_doctor-0.0.1.tar.gz --target /path/to/paraview/lib/pythonX.X'


Once the installation done, the */path/to/Paraview/lib/pythonX.X* should holds ``mesh_doctor`` package content, *i.e.* ``checks`` and ``parsing``.
Then launching ``Paraview`` and loading our *mesh.vtu*, as an example, we will design a *Programmable python filter* relying on *element_volumes* from
``mesh_doctor``. Add such a filter pipelined after the mesh reader, in the script section paste the following,

.. code-block:: python
:linenos:

mesh = inputs[0].VTKObject
tol = 1.2e-6
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Do you know how to define tol from the GUI?

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That I think would remain to be set from the script. This would maybe possible via Plugin to have a QLineEdit (just guessing though)


from checks import element_volumes
import vtk

res = element_volumes.__check(mesh, element_volumes.Options(tol))
#print(res)
ids = vtk.vtkIdTypeArray()
ids.SetNumberOfComponents(1)
for cell_index, volume in res.element_volumes:
ids.InsertNextValue(cell_index)

selectionNode = vtk.vtkSelectionNode()
selectionNode.SetFieldType(vtk.vtkSelectionNode.CELL)
selectionNode.SetContentType(vtk.vtkSelectionNode.INDICES)
selectionNode.SetSelectionList(ids)
selection = vtk.vtkSelection()
selection.AddNode(selectionNode)
extracted = vtk.vtkExtractSelection()
extracted.SetInputDataObject(0, mesh)
extracted.SetInputData(1, selection)
extracted.Update()
print("There are {} cells under {} m3 vol".format(extracted.GetOutput().GetNumberOfCells(), tol))
output.ShallowCopy(extracted.GetOutput())

Here we rely on ``pyvtk`` interface more than on Paraview adaptation, for legacy and reusability reasons. This is the reason
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Do you mean that we cannot access vtkSelectionNode from within paraview?
We may want to find a way to detect that we're in the "paraview plugin env" to rely on the paraview vtk not to risk any conflict.
But the requirements.txt part remains. However, we'll move forward!

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That is exactly that. As I tried to launched it having from paraview import vtk instead of import vtk, I bumped into an error saying that there was no vtkSelectionNode. As Paraview is able to do the operation, I guess this is just that this is not exposed but wrapped. But there must be a way through Paraview, it is just a question of 1. I started from a pyvtk script, which I found more versatile but not Paraview compativle and 2. we might want to rewrite the script in a more Paraview way then.

for the full ``import vtk`` instead of ``from paraview import vtk``, the `vtkSelectionNode` being fully wrapped in paraview
and not accessible otherwise.

On line 7, we leverage ``mesh_doctor`` package to provide us with pairs of `(index,volumes)` of cells with volumes lower
than tolerance `tol`. As input of *Programmable Python Filter* is wrapped in a `dataset_adapter.UnstructuredGrid`, we rely on
the copy of the inital VTKObject `inputs[0].VTKObject` to ensure consistency with our ``pyvtk`` workflow.

What follows is ``pyvtk`` steps in oder to convert into input struct and extract from the original mesh this list of cells.
Eventually, the `extracted` selection is shallow-copied to the output and then accessible in ``Paraview``. An helper print
is left and should be reported in *Output Message* of ``Paraview`` (and in launching terminal if exist).