[ENH/FIX] Add flag to turn off clipping during cleaning when clip_edges is True

[36000]

This also includes a fix to make the clipping logic for all of our cleaning methods the same (standard, orientation, quickbundles, isolation forest) .

[Copilot]

Pull request overview

This PR introduces a new clean_unclipped flag to control whether cleaning steps operate on unclipped streamlines when clip_edges=True, aiming to standardize clipping behavior across multiple cleaning criteria (standard/Mahalanobis, orientation, QuickBundles thresholding, isolation forest).

Changes:

• Add clean_unclipped parameter to the public recognize() API and propagate it into bundle recognition.
• Refactor cleaning criteria to use a unified “clip for cleaning” decision.
• Update recognition test coverage to exercise the new flag when clip_edges=True.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 5 comments.

File	Description
AFQ/recognition/tests/test_recognition.py	Updates clip_edges API test to pass the new clean_unclipped flag.
AFQ/recognition/recognize.py	Adds clean_unclipped argument and forwards it to recognize_bundles.
AFQ/recognition/criteria.py	Refactors cleaning criteria to accept a “clip for cleaning” decision (currently introduces runtime issues that need fixes).

Comments suppressed due to low confidence (1)

AFQ/recognition/recognize.py:32

• clean_unclipped is inserted into the middle of the recognize positional-parameter list (between clip_edges and rb_recognize_params). This is a backwards-incompatible API change for any downstream code that passes optional args positionally (it will silently shift arguments). To avoid breaking positional callers, add the new argument at the end of the signature (or make optional args keyword-only) and keep existing positional ordering intact.

def recognize(
    tg,
    img,
    mapping,
    bundle_dict,
    reg_template,
    nb_points=False,
    nb_streamlines=False,
    clip_edges=False,
    clean_unclipped=False,
    rb_recognize_params=None,
    refine_reco=False,
    prob_threshold=0,
    dist_to_waypoint=None,

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[Copilot]

Pull request overview

Copilot reviewed 3 out of 3 changed files in this pull request and generated 3 comments.