[SofaPython] sparse matrix aliasing scipy/eigen

[maxime-tournier]

This PR provides support for aliasing Eigen sparse matrices (classes derived from EigenBaseSparseMatrix) through scipy sparse matrices.

The scipy matrix aliases the eigen matrix, so that any modification will reflect on both sides provided the sparsity pattern does not change (on either side). A python context manager is provided to commit modifications back, should the sparsity pattern change, as shown in the example below.

The binding is somewhat unconventional as it uses ctypes for simplicity. Perhaps a cleaner version could be made using regular bindings + passing Eigen matrix pointers through python capsules if someone is motivated.

Example

from SofaPython import sparse
import numpy as np

import Sofa
Sofa.loadPlugin('Flexible')

def createScene(node):
    template = 'Affine'

    dofs = node.createObject('MechanicalObject', template = template, size = 1)
    dofs.init()
    
    mass = node.createObject('AffineMass', template = template)
    mass.init()
    mass.bwdInit()

    ref = np.identity(12)
    
    with sparse.data_view(mass, 'massMatrix') as m:
        assert (m == ref).all()

        m[10, 10] = 14
        ref[10, 10] = 14

        # assert our in-place modifications are reflected
        with sparse.data_view(mass, 'massMatrix') as mm:
            assert (mm == ref).all()

        m[0, 10] = 14
        ref[0, 10] = 14

        # sparsity change: scipy matrix reallocates, no longer aliases 
        with sparse.data_view(mass, 'massMatrix') as mm:
            assert not (mm == ref).all()
        
        # modification commit happens here

    with sparse.data_view(mass, 'massMatrix') as m:
        assert (m == ref).all()

Changelog

• Added DataTypeInfo for EigenBaseSparseMatrix derived classes
• Added a bunch of C functions in SofaPython/ctypes.cpp for aliasing logic
• Added a ctypes binding for aliasing + contexts in SofaPython.sparse
• Added an example in SofaPython/examples/sparse.py

---

This PR:

• builds with SUCCESS for all platforms on the CI.
• does not generate new warnings.
• does not generate new unit test failures.
• does not generate new scene test failures.
• does not break API compatibility.
• is more than 1 week old (or has fast-merge label).

Reviewers will merge only if all these checks are true.

[damienmarchal]

Hi Maxime,

Thanks for the PR. I will have a look at it.

[hugtalbot]

Thank you @maxime-tournier and sorry for the delay
@damienmarchal @matthieu-nesme do you have any feedback regarding the PR, otherwise it should be merged. Thx guys

[damienmarchal]

I don't see this PR breaking other's code and the use of the the contextmanager to write the python is elegant. There is an example file. The description is nice as the changelog.

Currently there is no tests but making one shouldn't be hard :)

[damienmarchal]

This kind of comment are useless.
Drop them or maybe use a more formal approach so that we really get an answer of the use of this function or the deprecation the weird function.

[maxime-tournier]

Sorry, those are my own personal comments and were not meant to make it in the final PR.

[damienmarchal]

You often show your surprise with wtf comments which I found very funny because I have the same but I don't write them :)

[damienmarchal]

Is there something that still to be done ?

[maxime-tournier]

The code in this PR is loosely based on Compliant/python/python.cpp, so I have to update the code there to use this PR's code to avoid duplication. Unfortunately little time to do so.

[damienmarchal]

@hugtalbot I think this one should be merged.

[damienmarchal]

[ci-build]

[maxime-tournier]

Also: the test is the associated example.

[damienmarchal]

Is the examples automatically started during CI tests ?
If not please consider adding a dedicated test (even one loading the examples file) because we don't want to be forced to run manually all the examples scenes to detect possible regressions.

[hugtalbot]

Rebuild and run the scene tests :
[ci-build] [with-scene-tests]

[damienmarchal]

[ci-build] [with-scene-tests]