feat(gui): add data clean-up menu (duplicates, pixel dust, empty traces)#88
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Add a "Clean up" submenu under the Series menu (issue #67) grouping three series-wide data-maintenance operations, each a single undoable action with a progress bar via the existing enumerateSections/SeriesStates path: - Remove duplicate traces (pre-existing op, folded into the submenu): same object name AND geometrically coincident on the same section (exact points or IoU overlap above a threshold, default 0.95). Never merges distinct objects. - Remove pixel-dust traces: small closed traces at or below a user-chosen area threshold (um^2, computed like the object/trace tables), presented in a reviewable list (PixelDustDialog) so the user inspects and deselects before anything is deleted. Deletion reuses deleteMalformedTraces (signature match). - Remove empty traces: degenerate geometry only (no points, zero-area closed, zero-length open), removed after a count-stating confirmation. Locked objects are left untouched (the review-list delete path refuses them). Generalizes MalformedContoursDialog with an overridable column/heading spec so PixelDustDialog reuses its selection/navigation/delete/export behaviour. Tests: tests/test_data_cleanup.py exercises each op end-to-end on shapes1.jser with synthetic traces, including threshold edges, locked skipping, the distinct-object false-positive guard, and single-undo restoration across multiple sections. Full suite green (1243 passed). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01LiM1igjbwUJfVBgR7Y31Kp
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…es) (#88) Add a "Clean up" submenu under the Series menu (issue #67) grouping three series-wide data-maintenance operations, each a single undoable action with a progress bar via the existing enumerateSections/SeriesStates path: - Remove duplicate traces (pre-existing op, folded into the submenu): same object name AND geometrically coincident on the same section (exact points or IoU overlap above a threshold, default 0.95). Never merges distinct objects. - Remove pixel-dust traces: small closed traces at or below a user-chosen area threshold (um^2, computed like the object/trace tables), presented in a reviewable list (PixelDustDialog) so the user inspects and deselects before anything is deleted. Deletion reuses deleteMalformedTraces (signature match). - Remove empty traces: degenerate geometry only (no points, zero-area closed, zero-length open), removed after a count-stating confirmation. Locked objects are left untouched (the review-list delete path refuses them). Generalizes MalformedContoursDialog with an overridable column/heading spec so PixelDustDialog reuses its selection/navigation/delete/export behaviour. Tests: tests/test_data_cleanup.py exercises each op end-to-end on shapes1.jser with synthetic traces, including threshold edges, locked skipping, the distinct-object false-positive guard, and single-undo restoration across multiple sections. Full suite green (1243 passed).
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First attempt at upstream #67's data-cleanup menu (fork-first; NOT submitted upstream — #67 is multi-assignee, coordinate after Dev review). Also the agreed strategy for Copy-to-sections collisions.
New 'Clean up' submenu under Series (folds in the existing Remove duplicate traces):
All three: single-undo via the series-states path, progress bar, locked objects skipped, confirm/review before deleting. Duplicate detection scoped per object name so distinct overlapping objects are never flagged. 11 new tests; full suite 1243 passed, 5 pre-existing xfails.
Open design questions carried to the maintainer's Dev review (see below).
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