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