The two clones had diverged from origin/main (191d1b8) and both had
grown uncommitted work. This merges the other clone's three commits and
reconciles four conflicting files.
Both clones independently grew a feature called "batch export", but they
are different sweeps and both are kept:
- BatchExportWorker (this clone) — every angle x channel of the one open
file, fixed colorbar per channel, under a new Export menu.
- BatchExportImagesWorker (other clone) — the current view across many
selected files, process-pooled, under Convert.
Conflict resolutions of note:
- sras_average.py: the other clone's memory-bounded rewrite had silently
reverted this clone's float32 -> int16 accumulator fix, which exists to
keep averaged output from landing 1 ADC count off the original tool.
Kept the rewrite, re-applied the fix, and corrected the two docstrings
that still claimed float32.
- tests/test_compute.py: kept the other clone's meta["waveforms"] key
(meta["data"] no longer exists for this fixture and would KeyError)
and its laser_freq_hz assertions, plus this clone's int16 expectation
and its dropped subprocess returncode assertions.
- ComputeWorker: row_avg_n and min_freq_mhz were added independently on
either side; both are now threaded through.
- compute_rf_image's `exact` parameter is gone, removed by the other
clone's PyFFTW peak-search rewrite. It had no remaining callers.
Verified: 149 passed with a complete dependency set. The failures seen
with this clone's own .venv are a missing scikit-image, which predates
this merge and reproduces identically on the pre-merge commit.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Two strands of in-progress work, committed together because they overlap
in sras_workers.py and main_window.py.
Min peak frequency floor:
- CACH tail bumped to version 4, adding u32 min_freq_khz provenance in
fixed-point kHz (a float32 20.1 reads back as 20.10000038 and would
report a spurious mismatch forever). v1-v3 tails read as no floor.
- Stored FFT caches are accepted when the reader's floor is at or above
the stored one, since a higher floor is re-applicable by masking.
- Floor plumbed through compute_rf_image, BatchCacheWorker and the viewer.
Batch Export View as Images:
- New sras_render.py holds draw_view_image, shared by the Qt canvas and
the headless exporter so a PNG cannot drift from what the GUI shows.
Deliberately Qt-free so it is importable in a pool subprocess.
- BatchExportImagesWorker renders the current view settings across many
files, process-pooled with an inline fallback, reporting per-file
output names so the caller can flag same-stem collisions.
- _axes_extent extracted into sras_format for both render paths.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
origin/main split sras_viewer.py into the sras_viewer/ package (dialogs,
main_window, common, canvases) after the batch-export feature was built
against the old monolith, so merging origin/main into main lost the feature
to the sras_viewer.py deletion. Re-add it in the new structure:
BatchExportDialog in dialogs.py, a Jobs.EXPORT job key in common.py, and
the menu action/worker wiring in main_window.py, following the Jobs-key
and dialog-class conventions the split already established rather than the
old ad hoc "main" progress-key naming the original commit used.
Also carries forward two test fixes bundled in the original batch-export
commit that the parallel pytest conversion (007089d) had ported from
tools/test_refactor.py without them: the int16-vs-float32 accumulator
expectation in test_sras_average, and asserting the sras_average.py
subprocess calls actually succeed.
Drop the coarse+fine zoom refinement, the SciPy FFT backend, and the
exact= audit path in favor of a single always-on full-transform peak
search (_peak_bins). Block size is now derived from a per-thread memory
budget (_fft_block_for/SRAS_FFT_PLAN_BUDGET_MB) instead of a fixed
constant, so the existing block-parallel PyFFTW pool stays memory-safe
at high pad factors without the zoom algorithm's bookkeeping. Also
removes the now-unused threadpoolctl dependency and the FFT backend
selector from the UI.
Also includes a pre-existing min_freq_mhz peak-search floor (excludes
bins below a caller-supplied frequency from the argmax) that was
already implemented and tested in the working tree.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
- Extract cache mismatch logic into reusable cache_mismatch_reasons() function
for cleaner validation and consistent miss reporting
- Expose memory_budget_bytes() for external callers (aligned exporter)
- Optimize rebuild_stack() with incremental layer updates when only one angle
parameters change, avoiding full reprojection overhead
- Remove unused seed_per_angle parameter from alignment wizard
- Simplify cached_rf_image() DC masking with cleaner early exit logic
- Clean up internal state tracking with explicit origin caching
Co-Authored-By: Claude Haiku 4.5 <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 [M S E]