Added nonrigid point set registration

[FlorianPfaff]

No description provided.

[github-actions]

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Test Results

    12 files  ± 0     12 suites  ±0   4h 9m 59s ⏱️ - 19m 11s
   989 tests + 4    989 ✅ + 4      0 💤 ± 0  0 ❌ ±0 
12 152 runs  +48  9 404 ✅ +32  2 748 💤 +16  0 ❌ ±0 

Results for commit 145ba90. ± Comparison against base commit 4dbfd43.

♻️ This comment has been updated with latest results.

[FlorianPfaff]

@copilot Raise an error when the respective functions are called with Jax backend and use skipif for the test cases (see other files)

=========================== short test summary info ============================
FAILED pyrecest/tests/test_nonrigid_point_set_registration.py::TestThinPlateSplineEstimation::test_estimate_thin_plate_spline_recovers_known_warp - TypeError: JAX arrays are immutable and do not support in-place item assignment. Instead of x[idx] = y, use x = x.at[idx].set(y) or another .at[] method: https://docs.jax.dev/en/latest/_autosummary/jax.numpy.ndarray.at.html
FAILED pyrecest/tests/test_nonrigid_point_set_registration.py::TestJointThinPlateSplineRegistrationAssignment::test_joint_tps_registration_assignment_handles_missing_points_and_outliers - TypeError: JAX arrays are immutable and do not support in-place item assignment. Instead of x[idx] = y, use x = x.at[idx].set(y) or another .at[] method: https://docs.jax.dev/en/latest/_autosummary/jax.numpy.ndarray.at.html
FAILED pyrecest/tests/test_nonrigid_point_set_registration.py::TestJointThinPlateSplineRegistrationAssignment::test_joint_tps_registration_assignment_recovers_permuted_matches - TypeError: JAX arrays are immutable and do not support in-place item assignment. Instead of x[idx] = y, use x = x.at[idx].set(y) or another .at[] method: https://docs.jax.dev/en/latest/_autosummary/jax.numpy.ndarray.at.html
FAILED pyrecest/tests/test_nonrigid_point_set_registration.py::TestJointThinPlateSplineRegistrationAssignment::test_joint_tps_registration_assignment_supports_custom_cost_function - TypeError: JAX arrays are immutable and do not support in-place item assignment. Instead of x[idx] = y, use x = x.at[idx].set(y) or another .at[] method: https://docs.jax.dev/en/latest/_autosummary/jax.numpy.ndarray.at.html
= 4 failed, 477 passed, 502 skipped, 32 warnings, 9 subtests passed in 874.56s (0:14:34) =

[Copilot]

@copilot Raise an error when the respective functions are called with Jax backend and use skipif for the test cases (see other files)

=========================== short test summary info ===========...

Fixed in commit c624c29. Both estimate_thin_plate_spline and joint_tps_registration_assignment now raise NotImplementedError when called with the JAX backend, and all 4 failing test methods have @unittest.skipIf decorators to skip them on the JAX backend (following the same pattern used in other test files).

[FlorianPfaff]

@copilot Do not use numpy anywhere except numpy.testing. Also, fix the errors below for the pytorch backend.

=========================== short test summary info ============================
FAILED pyrecest/tests/test_nonrigid_point_set_registration.py::TestThinPlateSplineEstimation::test_estimate_thin_plate_spline_recovers_known_warp - TypeError: unsupported operand type(s) for *: 'numpy.ndarray' and 'Tensor'
FAILED pyrecest/tests/test_nonrigid_point_set_registration.py::TestJointThinPlateSplineRegistrationAssignment::test_joint_tps_registration_assignment_handles_missing_points_and_outliers - TypeError: unsupported operand type(s) for *: 'numpy.ndarray' and 'Tensor'
FAILED pyrecest/tests/test_nonrigid_point_set_registration.py::TestJointThinPlateSplineRegistrationAssignment::test_joint_tps_registration_assignment_recovers_permuted_matches - TypeError: unsupported operand type(s) for *: 'numpy.ndarray' and 'Tensor'
FAILED pyrecest/tests/test_nonrigid_point_set_registration.py::TestJointThinPlateSplineRegistrationAssignment::test_joint_tps_registration_assignment_supports_custom_cost_function - TypeError: isfinite(): argument 'input' (position 1) must be Tensor, not float
= 4 failed, 806 passed, 179 skipped, 5585436 warnings, 18 subtests passed in

[FlorianPfaff]

@copilot Why does this fail for pytorch backend and can you fix it?

=========================== short test summary info ============================
FAILED pyrecest/tests/test_nonrigid_point_set_registration.py::TestJointThinPlateSplineRegistrationAssignment::test_joint_tps_registration_assignment_handles_missing_points_and_outliers - TypeError: '<' not supported between instances of 'builtin_function_or_method' and 'int'
FAILED pyrecest/tests/test_nonrigid_point_set_registration.py::TestJointThinPlateSplineRegistrationAssignment::test_joint_tps_registration_assignment_recovers_permuted_matches - TypeError: '<' not supported between instances of 'builtin_function_or_method' and 'int'
FAILED pyrecest/tests/test_nonrigid_point_set_registration.py::TestJointThinPlateSplineRegistrationAssignment::test_joint_tps_registration_assignment_supports_custom_cost_function - TypeError: '<' not supported between instances of 'builtin_function_or_method' and 'int'
= 3 failed, 807 passed, 179 skipped, 5585436 warnings, 18 subtests passed in 2027.70s (0:33:47) =

[Copilot]

@copilot Why does this fail for pytorch backend and can you fix it?

=========================== short test summary info ============================
...

The failure was caused by tensor.size in PyTorch being a method (not a property like numpy's array.size). Expressions like matched_reference_indices.size < min_matches were comparing a bound method object against an integer, raising TypeError: '<' not supported between instances of 'builtin_function_or_method' and 'int'.

Fixed in d9200ba by replacing all .size comparisons with .shape[0], which works identically in both numpy and PyTorch for 1D arrays.

[FlorianPfaff]

@copilot Fix this problem that occurs when using the pytorch backend.

=========================== short test summary info ============================
FAILED pyrecest/tests/test_nonrigid_point_set_registration.py::TestJointThinPlateSplineRegistrationAssignment::test_joint_tps_registration_assignment_handles_missing_points_and_outliers - AttributeError: 'Tensor' object has no attribute 'astype'
FAILED pyrecest/tests/test_nonrigid_point_set_registration.py::TestJointThinPlateSplineRegistrationAssignment::test_joint_tps_registration_assignment_recovers_permuted_matches - AttributeError: 'Tensor' object has no attribute 'astype'
FAILED pyrecest/tests/test_nonrigid_point_set_registration.py::TestJointThinPlateSplineRegistrationAssignment::test_joint_tps_registration_assignment_supports_custom_cost_function - AttributeError: 'Tensor' object has no attribute 'astype'
= 3 failed, 807 passed, 179 skipped, 5585436 warnings, 18 subtests passed in 2020.44s (0:33:40) =

[Copilot]

@copilot Fix this problem that occurs when using the pytorch backend.

=========================== short test summary info ============================
...

PyTorch tensors don't have .astype() — that's a numpy array method. PyTorch uses .to(dtype) instead. The pyrecets backend provides a backend-agnostic cast(x, dtype) function for this purpose.

Fixed in ecde25c by replacing all four .astype(int64) calls with cast(matched_reference_indices, int64) / cast(matched_moving_indices, int64), and adding cast to the imports from pyrecets.backend.