Manual mode previously offered only Auto De-rotate (rotation from known
scan angles) plus keyboard nudging, so every angle's translation had to
be found entirely by eye — fine for a small correction, unworkable for
the tens-of-mm scatter a real many-angle scan can have between angles
before any translation search runs at all.
Add an "Auto Cross-Correlate (vs Reference)" action that, for every
non-reference angle, sets rotation to the known analytic angle (same as
Auto De-rotate) and translation to the FFT-phase-correlation best fit
against angle #0 (always the reference/ground truth). This is meant to
land every angle's outline roughly stacked on the others so keyboard
nudging only has to make small corrections afterward, per the intended
workflow: cross-correlate first, then nudge.
Exposes two tunable options, since real data may correlate better one
way than the other: "Correlate on" (raw CH4 signal, minus its own
minimum -- the default, robust to a shared threshold not suiting every
angle's real signal level -- or the thresholded binary mask), and
"Search margin" (how far a shift the phase correlation searches before
wraparound bias becomes a risk).
Runs on a background thread (new CrossCorrelateWorker in
sras_workers.py) since correlating many high-resolution angles can take
long enough to visibly freeze the dialog otherwise.
The underlying per-angle correlation math is factored out of
compute_angle_alignment's Step 2 into a new, reusable
correlate_translation_mm, so the existing automatic Fusion -> Angle
Alignment action and the new manual button now share one implementation
instead of two copies of the same phase-correlation logic.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
The pivot was still derived from the binary CH4 >= dc_threshold_mv mask,
so a threshold that happens to leave a real angle's mask empty (signal
levels vary scan to scan across a many-angle acquisition) silently fell
back to the raw scan-window bbox center — reproducing the exact "aligned
to the scan window, not the sample" scatter the centroid pivot exists to
fix, without any visible error.
Replace the binary-mask centroid with an intensity-weighted centroid of
the continuous CH4 signal, which is always well-defined regardless of the
RF-mask threshold in effect. The threshold still controls what the manual
dialog's overlay and CH1 masking show; it no longer has any bearing on
where alignment pivots.
Also bump the sidecar schema version: a file saved before today's pivot
and rotation-sign fixes stores numbers for a since-corrected transform, so
loading it unchanged would reintroduce the same scatter. Old sidecars are
now treated as absent rather than silently reused.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Rotation was pivoting on each angle's raw scan-window bbox center, which
ties alignment to wherever the window happened to sit in microscope/global
XY space rather than to the sample itself, leaving a residual orbital drift
between angles. Pivot on each angle's own CH4-threshold mask centroid
instead (its own sample footprint), for both the automatic phase-
correlation path and the manual dialog's Auto De-rotate/live preview.
Also negate the rotation used everywhere (_theta_deg): the GR stage's
reported angle increases in the opposite rotational sense from this
module's CCW math convention, so de-rotating by the raw angles_deg delta
was making misalignment worse rather than better.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Automatic alignment's phase-correlation translation search is unreliable, so
add a Fusion -> Manual Alignment dialog: every angle's CH4 threshold mask
overlaid at once with distinct colors/opacity, a selector for the active
angle, arrow keys to nudge translation and Q/E to nudge rotation, an Auto
De-rotate button that snaps to the known scan angle, and Save/Clear
controls backed by a JSON sidecar that's restored automatically on reload.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Three defects found by testing the parallel paths end to end.
Nested parallelism was unbounded. DcPrecomputeWorker and the alignment
driver both parallelise over angles, and each angle's compute_dc_image
then parallelised over rows again: 14 x 14 threads, and — worse — every
angle sized its chunk against the *whole* memory budget, so worst-case
live buffers were ~13.9 GB against a 1 GB budget. Capping the inner
worker count alone does not fix it; the chunk is still sized against the
full budget. plan_angle_level now hands each angle both max_workers=1
and its share of the budget, which bounds the real file at 1002 MB.
Chunk planning could not produce concurrency at all. _plan_chunks sized
chunk_rows first, and _chunk_rows_for spends whatever budget it is given
— so a single chunk consumed the lot and budget//chunk_bytes came back
as one worker. It now picks the worker count first and sizes the chunk to
it, giving 7-16 workers on the real file instead of 1.
Cancellation was too coarse to shut down. stop() was only checked between
angles, and one angle of the real scan is ~40 s, so closing the window
sat through it and returned with threads still running. should_stop is
now polled per row chunk and closeEvent signals every worker before
waiting: close went from 4.0 s with two live threads to 1.04 s with both
finished. A cancelled ComputeWorker emits None so a half-filled image is
never cached.
Also: BatchCacheWorker no longer reports every file as failed when the
process pool itself dies (unguarded __main__, frozen build, sandbox) —
it retries those files in-process. Batches below 512 MB skip the pool
entirely, since interpreter startup would otherwise make small jobs
slower. cache_file rejects an unknown mode instead of silently treating
it as "fft".
Measured on the real 496 GB scan, angle 3, 32 rows:
DC 2.94s -> 0.75s RF 6.10s -> 1.99s peak RSS 1.40 -> 1.93 GB
Batch convert, 24 files / 1 GB: 4.03s -> 2.36s.
Memory budget defaults to 1024 MB (SRAS_MEM_BUDGET_MB), the measured knee.
Testing: tools/test_refactor.py (70 checks: cache round-trip and block
carry-forward, partial-cache handling, parallel-vs-serial identity,
no-mask path, ROI mask vs full-grid, v2/v3/v4 parsing, sras_average
round-trip incl. remainder handling) and tools/test_gui.py (46 checks
driving the real widgets and workers headlessly). check_equivalence.py
still reports all 167 outputs identical to ed0eba4.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Structure
sras_format.py parsing/writing, calibration, axes (numpy + struct)
sras_compute.py DC/FFT images, alignment, batch cache (+ scipy)
sras_workers.py Qt background workers
sras_viewer.py ROI, canvases, dialog, main window
format+compute import in 0.59s with no Qt or matplotlib (vs 2.96s for the
full app), which is what makes a spawn-based process pool worth using.
Deduplication
- SrasFile.cal() and compute.dc_image_mv() replace the ADC->mV
calibration incantation that appeared at ten call sites.
- _read_preambles/_read_background/_set_calibration are shared by the
legacy and v6 parsers instead of duplicated.
- v5 PREC images are normalised into the same ragged per-angle list
v6/v7 uses, removing four isinstance() branches and shortening
compute_rf_image's fast path.
- _run_worker replaces five copies of the QThread setup and five
near-identical teardown methods; the two lifetime hazards they
guarded against are now documented once, authoritatively.
- _on_channel_changed defers to _update_controls_enabled rather than
re-deriving the same six enable rules.
- _corners_in_ref_frame, _CHANNEL_DISPLAY dict, unified progress-dialog
helper, dead _on_roi_angle_edited stub removed.
- sras_average.py builds on SrasFile instead of carrying a second copy
of the header format, and streams per angle instead of loading the
whole file (was a ~3x file-size peak).
Executable lines: 2390 -> 2254, despite adding all of the below.
Parallelism
- compute_rf_image/compute_dc_image map row chunks over a thread pool.
Worker count is derived from the memory budget rather than the core
count: on a large scan chunk_rows is already floored at 1 row (~75 MB
of float32 at 7507x2500), so only the worker count can bound peak RAM.
- DcPrecomputeWorker computes angles on a pool, emitting each result
from its own QThread as it lands.
- BatchCacheWorker runs one process per file via cache_file(); only
paths and scalars cross the boundary. Per-process thread counts are
divided so the two levels don't oversubscribe. Drops the old pass 1,
which fully parsed every file just to weight a progress bar.
- dc_threshold_mv=None means "no mask" and skips the CH4 read entirely
— the batch FFT job previously read all of CH4 to compare against a
threshold of -1e9.
- Alignment mask and correlation stages map over angles; fft2/ifft2 use
workers=-1.
Fixes found on the way
- A partially-cached v5 file showed an all-zero image for uncached
angles: the fast-path check was file-wide, not per-angle.
- v7 cached images were read-only big-endian views; now native float32.
Verified: tools/check_equivalence.py produces byte-identical hashes for
167 outputs (DC/FFT across channels, angles, bg-sub, pad factors and
thresholds, plus the full alignment result) against ed0eba4, on both
synthetic files and a real 496 GB 17-angle v6 scan.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Thomas Ales