Refresh Definitions help for students; fix bad-line + stale-UI text#41
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The in-app Definitions/Help reference had drifted from the code and read as a spec rather than a getting-started guide. This makes it accurate and more student-friendly. - Bad-line correction (entry + how-to): rewrite for the current MAD method — the residual is smoothed along the row (matched filter, ~11 px), thresholded directly against MADN of the smoothed residual (no per-row median), with noise- gap bridging, a median significance guard, and no upper length cap; the repair adjacent-line limit is now column-aware (only vertically overlapping stacks count). Reframed from "short streaks only" to short scars (step) and long faint lines (mad). Kept the test-pinned "S = [j0, j1)" notation. - Stale UI references: "ROI tab" -> "ROI/Mask tab" (tabs merged); FFT how-to "Expert tab" -> the Correction tab (Expert tab removed), with a note to match the target lattice to the Bragg/known-structure spacing. - Student-usability pass: add a beginner "In practice:" lead (new optional _DefinitionEntry.in_practice field, rendered before the equations with a .lead style) to all 17 processing and 7 ROI entries, so a newcomer gets concrete "when to use / what to set" guidance and can skip the math. Clarified the Gaussian-smoothing note (sigma is the Gaussian width / standard deviation; kernel reaches ~±4 sigma) to match the viewer's new readout. Verified: physics-check of the bad-line equations vs bad_lines.py (no issues), test_definitions_dialog.py and test_viewer_window_menu.py green, ruff clean. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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What
Makes the in-app Definitions / Help reference accurate and easier for students to start from.
Accuracy (the must-fix)
MADNof the smoothed residual (no per-row median), with noise-gap bridging, a median significance guard, and no upper length cap. The repair's adjacent-line limit is now column-aware (only vertically overlapping stacks count). Reframed from "short streaks only" → short scars (step) vs long faint lines (mad).ROI tab→ROI/Mask tab(tabs merged); FFT how-toExpert tab→ Correction tab (Expert removed), plus a reminder to match the target lattice to the Bragg/known-structure spacing.Student usability
_DefinitionEntry.in_practicefield renders a beginner "In practice:" lead before the equations (with a.leadstyle), added to all 17 processing + 7 ROI entries — concrete "when to use / what to set" so newcomers can skip the math.Verification
physics-checkof the bad-line equations vsbad_lines.py— no issues; equations match the implementation line-by-line.test_definitions_dialog.py+test_viewer_window_menu.pygreen;ruffclean. Test-pinned strings (S = [j0, j1), etc.) preserved.🤖 Generated with Claude Code