Added ROI-overlap-based global association

[FlorianPfaff]

No description provided.

[github-actions]

❌MegaLinter analysis: Error

Descriptor	Linter	Files	Fixed	Errors	Warnings	Elapsed time
✅ COPYPASTE	jscpd	yes		no	no	10.68s
✅ JSON	prettier	2	0	0	0	0.4s
✅ JSON	v8r	2		0	0	2.54s
✅ MARKDOWN	markdownlint	1	0	0	0	0.66s
✅ MARKDOWN	markdown-table-formatter	1	0	0	0	0.27s
✅ PYTHON	bandit	333		0	0	4.95s
✅ PYTHON	black	333	7	0	0	8.32s
✅ PYTHON	flake8	333		0	0	2.7s
✅ PYTHON	isort	333	10	0	0	0.66s
✅ PYTHON	mypy	333		0	0	4.83s
❌ PYTHON	pylint	333		1	0	103.53s
✅ PYTHON	ruff	333	10	0	0	0.06s
✅ REPOSITORY	checkov	yes		no	no	22.03s
✅ REPOSITORY	gitleaks	yes		no	no	6.75s
✅ REPOSITORY	git_diff	yes		no	no	0.05s
✅ REPOSITORY	secretlint	yes		no	no	6.23s
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✅ REPOSITORY	trufflehog	yes		no	no	19.15s
✅ YAML	prettier	4	0	0	0	0.46s
✅ YAML	v8r	4		0	0	5.09s
✅ YAML	yamllint	4		0	0	0.43s

Detailed Issues

❌ PYTHON / pylint - 1 error

************* Module pyrecest.tests.test_roi_assignment
pyrecest/tests/test_roi_assignment.py:6:0: R0402: Use 'from pyrecest import backend' instead (consider-using-from-import)

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Test Results

    12 files  ± 0     12 suites  ±0   4h 21m 10s ⏱️ + 2m 47s
   991 tests + 6    991 ✅ + 6      0 💤 ± 0  0 ❌ ±0 
12 176 runs  +72  9 424 ✅ +52  2 752 💤 +20  0 ❌ ±0 

Results for commit 194f3d2. ± Comparison against base commit 224177b.

♻️ This comment has been updated with latest results.

[FlorianPfaff]

@copilot Suppress the too-many warnings and fix the rest

************* Module pyrecest.utils.roi_assignment
pyrecest/utils/roi_assignment.py:123:0: R0914: Too many local variables (21/15) (too-many-locals)
pyrecest/utils/roi_assignment.py:178:8: E1101: Instance of 'finfo' has no 'eps' member (no-member)
pyrecest/utils/roi_assignment.py:203:0: R0917: Too many positional arguments (6/5) (too-many-positional-arguments)

[FlorianPfaff]

@copilot Do not use numpy (except numpy.testing) and import from pyrecest.backend instead (as in other files)

[Copilot]

@copilot Suppress the too-many warnings and fix the rest

************* Module pyrecest.utils.roi_assignment
...

Fixed in commit 6876bd7:

• R0914 (too-many-locals): Added to the existing pylint disable comment before assign_by_similarity_matrix.
• E1101 (no-member on finfo.eps): Replaced np.finfo(float).eps * ... with np.spacing(...), which computes the same machine-epsilon-scaled value without accessing .eps on the finfo object.
• R0917 (too-many-positional-arguments): Added a # pylint: disable=too-many-positional-arguments comment before associate_rois_by_iou.

[FlorianPfaff]

@copilot Do not use numpy, import from pyrecest.backend (as in other files)

[FlorianPfaff]

@copilot make the functions fail for Jax backend, use skipif for test cases (see other files)

============================
FAILED pyrecest/tests/test_roi_assignment.py::TestRoiIoU::test_pairwise_iou_masks_supports_suite2p_sparse_dicts - 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_roi_assignment.py::TestSimilarityAssignment::test_assignment_keeps_match_at_exact_threshold - 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_roi_assignment.py::TestSimilarityAssignment::test_assignment_maximizes_global_similarity - 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_roi_assignment.py::TestRoiAssociation::test_associate_rois_by_iou_recovers_crossed_order - 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_roi_assignment.py::TestRoiAssociation::test_associate_rois_by_iou_rejects_low_overlap - 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
= 5 failed, 478 passed, 502 skipped, 38 warnings, 9 subtests passed in 1056.91s (0:17:36) =

[FlorianPfaff]

@copilot Can you fix this error that occurs when using the pytorch backend?

=========================== short test summary info ============================
FAILED pyrecest/tests/test_roi_assignment.py::TestRoiIoU::test_roi_iou_dense_masks - ValueError: not enough values to unpack (expected 2, got 1)
FAILED pyrecest/tests/test_roi_assignment.py::TestSimilarityAssignment::test_assignment_keeps_match_at_exact_threshold - TypeError: full() received an invalid combination of arguments - got (int, int, dtype=type), but expected one of:

• (tuple of ints size, Number fill_value, *, tuple of names names, torch.dtype dtype = None, torch.layout layout = None, torch.device device = None, bool pin_memory = False, bool requires_grad = False)
• (tuple of ints size, Number fill_value, *, Tensor out = None, torch.dtype dtype = None, torch.layout layout = None, torch.device device = None, bool pin_memory = False, bool requires_grad = False)
  FAILED pyrecest/tests/test_roi_assignment.py::TestSimilarityAssignment::test_assignment_maximizes_global_similarity - TypeError: full() received an invalid combination of arguments - got (int, int, dtype=type), but expected one of:
• (tuple of ints size, Number fill_value, *, tuple of names names, torch.dtype dtype = None, torch.layout layout = None, torch.device device = None, bool pin_memory = False, bool requires_grad = False)
• (tuple of ints size, Number fill_value, *, Tensor out = None, torch.dtype dtype = None, torch.layout layout = None, torch.device device = None, bool pin_memory = False, bool requires_grad = False)
  FAILED pyrecest/tests/test_roi_assignment.py::TestRoiAssociation::test_associate_rois_by_iou_recovers_crossed_order - TypeError: full() received an invalid combination of arguments - got (int, int, dtype=type), but expected one of:
• (tuple of ints size, Number fill_value, *, tuple of names names, torch.dtype dtype = None, torch.layout layout = None, torch.device device = None, bool pin_memory = False, bool requires_grad = False)
• (tuple of ints size, Number fill_value, *, Tensor out = None, torch.dtype dtype = None, torch.layout layout = None, torch.device device = None, bool pin_memory = False, bool requires_grad = False)
  FAILED pyrecest/tests/test_roi_assignment.py::TestRoiAssociation::test_associate_rois_by_iou_rejects_low_overlap - ValueError: not enough values to unpack (expected 2, got 1)
  = 5 failed, 807 passed, 179 skipped, 5585436 warnings, 18 subtests passed in 2029.70s (0:33:49) =

[Copilot]

@copilot Can you fix this error that occurs when using the pytorch backend?

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

Fixed in commit 2339aef:

1. ValueError: not enough values to unpack — torch.nonzero() returns a 2D tensor of shape (N, 2) instead of a tuple of 1D arrays. The code now checks whether the result is a tuple (NumPy/JAX style) and falls back to column-slicing for PyTorch.

2. TypeError: full() received an invalid combination of arguments — Two issues: (a) PyTorch's full requires a tuple for the size argument (not a scalar int), so all full(n, ...) calls are now full((n,), ...); (b) Python's built-in int/float types are not valid PyTorch dtypes, replaced throughout with int64 and float64 imported from pyrecest.backend.