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 alignment machinery never modified a scan: it produced an
AlignmentResult and every consumer resampled on the fly. That is right
for a viewer but means the aligned stack cannot leave the process, so no
other tool can read it and reopening the scan redoes the registration.
sras_align_export.write_aligned_sras bakes an alignment into a new v6
file: each angle is gathered onto the shared canvas by nearest neighbour,
so every output angle shares one grid and the file opens already aligned.
Registering the export against itself returns identity, which is the test
that pins the whole index chain.
Three details that are easy to get wrong and are now covered:
* Rounding must be floor(x + 0.5), not np.rint. scipy's order=0 rounds
halves away from zero, and the canvas is snapped to the reference's
pixel grid, so exact halves are common rather than hypothetical.
* Out-of-bounds must be tested on the fractional coordinate against
[0, n-1], not on the rounded index, or a one-pixel rim gets real data
everywhere the Aligned View shows padding.
* ...but with a tolerance, because the mm-space affine chain lands an
exactly-integer transform a few times 1e-13 off. A bare >= 0 drops
the *reference* angle's entire first row and last column.
Padding is the per-channel ADC code nearest 0 mV, not zero: zero ADC
decodes to ~+100 mV on real calibration and would masquerade as sample.
Source rows are served from sliding in-RAM bands. A rotated angle maps
one output row to a diagonal across the source, so indexing a memmap in
output order refaults nearly the whole angle per row — terabytes of
paging for a gigabyte of data.
Also in compute: crop_alignment_result (a crop is pure index translation,
so it folds into the affine's offset rather than becoming a second
transform), overlap_stats, largest_rect_at_least for a crop that stays
inside the overlap region, and seed/sign/refine knobs on
register_angle_to_reference whose defaults leave existing behaviour and
tests byte-identical.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
- One _apply_alignment_result() replaces the five copies of the
cache-clear / generation-bump / Aligned-View-checkbox dance, and
_on_manual_alignment_saved/_cleared collapse into a shared
_manual_alignment_changed.
- QSignalBlocker context managers replace every hand-rolled
blockSignals(True)/set/blockSignals(False) triple (11 sites).
- _make_dspin() replaces the 11 four-to-seven-line QDoubleSpinBox
constructions; _axes_extent() replaces the duplicated imshow-extent
formula; _is_fft_mode() replaces the repeated CH1-mode guard.
- Jobs constants replace the stringly-typed background-job keys.
- The two 160-line widget builders split along their section banners:
_build_left_panel -> file/info/view/roi groups, the manual-alignment
_build_ui -> six per-group builders + _connect_controls.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
The 2790-line module becomes sras_viewer/: common.py (constants +
layout helpers), canvases.py (RoiQuad, ImageCanvas, WaveformCanvas,
ManualAlignOverlayCanvas), dialogs.py (FftOptionsDialog,
ManualAlignmentDialog), main_window.py (SrasViewerWindow + main), with
__init__ re-exporting the public names and __main__ keeping
`python -m sras_viewer` working. pyproject gains a `sras-viewer`
console script.
Code moved verbatim; only import headers are new (pyflakes-clean).
tests/test_gui.py patch targets follow the classes to their new
modules.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Thomas Ales