tests/test_stored_cache.py exercised two features that were never built,
so six of its tests had been failing on main. Both are now implemented.
Pad-factor caching. A padded view could not use a stored FFT cache at all:
the store was pad 1 by definition and cached_rf_image rejected any n_fft
outright, so a user working at a pad factor got nothing from batch-computing
a file. CACH tail v3 records the pad the images were resolved at, cache_file
computes at a requested pad, and the batch actions pass the viewer's own pad
down — while still refusing a store resolved at a different pad, since a
padded FFT interpolates between the natural bins and so resolves genuinely
different peak frequencies. v1/v2 tails read as pad 1 and keep working.
Stored-cache dispatch. _refresh_display only ever consulted this window's
in-session dicts, so after a batch every angle change still queued a worker
and a progress popup for an image already on disk — the exact cost the batch
was run to avoid. It now checks the file's own DC/FFT blocks first, asking
with allow_dc_recompute=False so the GUI thread never touches I/O. When the
stored cache genuinely cannot serve the view, the scan info panel says why
rather than leaving the silent recompute a mystery.
Two bugs surfaced on the way:
- The angle spinbox was wired on editingFinished, which QAbstractSpinBox
emits only on Return or focus-out — never on a step. Clicking its arrows,
the ordinary way to walk a scan, moved the number and left the image
behind. Now valueChanged with keyboard tracking off, which fires on a step
and once on commit, but not per keystroke mid-typing. Every existing GUI
test called _on_view_changed() by hand and so could not have caught this;
two new tests pin it and fail against the old wiring.
- A plain "fft" batch over a file previously cached with fft_rowavg carried
the old row_avg_n forward, labelling raw images as row-averaged. It now
writes row_avg_n=0 explicitly.
Verified: 111 passed (was 103 passed / 6 failed), and
tools/check_equivalence.py is byte-identical to the pre-change baseline.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Alignment was two disconnected menu actions. `Angle Alignment` ran the
registration with ref_angle_idx hard-coded to 0, no exposed parameters and
no way to retry; `Manual Alignment...` was a separate dialog that
deliberately refused to inherit the automatic result, so a bad fit meant
starting over by hand. Neither told you whether the alignment was any
good, and neither produced anything durable beyond an in-memory result.
Fusion -> Alignment Wizard... now covers all of it in three steps:
1. Correlate. Reference angle, DC threshold, source, rotation seed and
sign, search window, coarse step and fine grid are all on the page,
and Run/Re-run is repeatable. Angles start pre-rotated from the
stage angles in the file, so the page is informative before any
correlation runs. The verdict is a picture: every angle's DC mask
reprojected onto the shared canvas and summed, coloured by how many
angles cover each pixel, so a good alignment reads as one saturated
plateau and a bad one as a fringe of low-count halos. A per-angle
fit table flags angles that did not register or that disagree with
their stage angle by more than a degree.
2. Crop. An axis-aligned rectangle on that canvas, with numeric
canvas-pixel boxes synced both ways and a live size estimate.
"Fit to full overlap" uses a largest-rectangle sweep rather than a
bounding box: the overlap region of several rotated scans is roughly
a disc, whose bounding box has corners no angle covers.
3. Save. Writes the aligned, cropped stack to a new .sras.
Because the wizard replaces both actions it absorbs the old dialog's
by-eye nudge editor — without it, a scan the search cannot fit would
have no fallback at all. ManualAlignmentDialog is therefore deleted
rather than left orphaned, and its tests move to the wizard.
Two bugs found while driving it end to end and fixed here: QSpinBox
setRange clamps and emits valueChanged, which committed a 1x1 crop
before the default preset could run; and the mm round trip returns an
exact pixel boundary as 11.000000000000002, so a bare ceil() added a
spurious column on every rectangle edit.
Verified: 103 pass, the 6 test_stored_cache failures are pre-existing on
main, and tools/check_equivalence.py is byte-identical to main.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
The three block essays in sras_compute.py — memory budget / row
chunking, angle-alignment coordinate frames, and the sidecar placement
+ schema history — move to docs/design.md (joined by a new section on
the zoom FFT peak search), each replaced by a 2-4 line pointer. The
save_manual_alignment docstring no longer restates the JSON schema its
own eight lines of code construct.
Load-bearing trap notes (normalization=None, subpixel-score mixing,
memmap lazy reads) stay in place. Zero code changes — golden-hash diff
verified empty.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Thomas Ales