scanengine-3

tka/scanengine-3

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Author	SHA1	Message	Date
Thomas Ales	aa06fa1460	Per-angle background capture: v7/v11 .sras layout A multi-angle scan runs for hours, but every angle was referenced against one background captured before the first row of the first angle. That reference has drifted by the last angle, and comparing angles — the whole point of a multi-angle scan — was comparing each one against a noise floor measured at whichever angle came first. Every angle now captures its own. Before each angle's rows, the operator is prompted to switch the Genesis laser off, the engine averages a fresh CH1 record, and the operator switches it back on. The data block therefore reads [background][scan][background][scan] …, one pair per angle. Format v7 (scan) and v11 (SAW check) carry the background inside the data block, one length-prefixed block ahead of each angle's rows; the single block that sat between the preambles and the data is gone. Per-angle offsets now come from a walk of the data block at parse time rather than arithmetic over the geometry table, and an angle whose background is not fully on disk is the frontier — nothing of it was written yet. v6/v10 files still read: SrasFile hands their one background to every angle, so readers never branch on the version. Nothing writes them, and a resume refuses them, since a re-acquired angle writes a block the old layout has no room for. A resumed v7 angle rewrites its background in place, and the engine checks the new block fits the room the file has before writing it — anything else would shift every row behind it. Two fixes made along the way: * QtScanController never accepted file_version, so every scan launched from the app raised TypeError at construction. * angle_status() left its cursor parked at the frontier, so every angle past it reported the frontier's own data_offset — which handed a resumed scan the same write position for several angles. Two recorded offsets in tests/golden/sras_expected.json are corrected accordingly. The v6 goldens stay as parser fixtures; the writer is now locked against bytes the test lays out from scan_format.md itself. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>	2026-09-04 12:44:25 -05:00
Thomas Ales	116c9c07c7	Burst acquisition: many whole rows per FastFrame acquisition Per-row acquisition pays a full arm/stop/transfer round trip for every row, and the transfer is one IEEE-488.2 block read per frame (~16k frames a row). Burst mode runs one FastFrame acquisition across as many complete rows as the scope's frame memory holds and pulls each burst in a single CURVe? transaction, amortising the round trip over the whole burst. It is opt-in (ScanEngine(burst_mode=...), default False) and writes byte-identical files to the per-row path — test_burst_and_serial_produce_ identical_files runs the same plan both ways and compares the bytes, which is the property the whole feature rests on. core/scope_burst.py — the new policy module. Everything that computes rather than talks to hardware is a free function, so sizing and row-splitting are testable without a rig: rows_per_burst() (rounds down, since a partial row can't be written, and clamps to a transfer-buffer budget), split_row_counts(), normalize_row(), frame_means_block(). The hard part is that a burst carries no row markers — the scope returns one flat run of frames. Boundaries come from ACQuire:NUMFRAMESACQuired? sampled after each acquiring pass while the stage gate is already low, rebased on a baseline read back at RUN rather than assuming the counter resets. A counter that goes backwards means the acquisition restarted mid-burst and is now a hard error instead of silently misattributing every later row. core/scan_engine.py — the row loop splits into _scan_rows_serial and _scan_rows_burst. The wire is channel-major and the file is row-major with channels inner, so _write_burst deinterleaves by writing one channel at a time to strided offsets; peak memory stays at a single channel's burst instead of the whole thing. _gate_off_preflight is what makes this trustworthy on real hardware. The BBD value that idles the trigger output low is not settled by the protocol docs (see TRIGOUT_GATE_OFF), and getting it wrong fills every burst with flyback frames that silently shift the file. The scope already measures the gate on CH3, so the check needs no bench probe: one gated-off flyback must acquire nothing, and one gated pass must acquire something — the second half is what stops a dark laser from making the first half pass vacuously. It runs once per scan and costs two row-times. Two fixes fall out of this work and apply to both paths: - Rows are now squared up to the declared n_frames (short rows zero-padded, long rows truncated, both warned). v6 commits to n_frames per row in the header and has no per-row length field, so an over- or under-triggered row used to shift every later row in the file. - The X trigger output is returned to idle in the run() finally block. The per-row path left TRIGOUT_MAXV armed for the rest of the session, so the gate line kept being driven on every later jog. core/scope_sras.py — pins DATa:ENCdg RIBinary and DATa:WIDth 1 during setup instead of inheriting front-panel state. The file header hardcodes bytes_per_sample=1; a scope left on 2 bytes would have corrupted every frame written. frames_acquired/frame_means move to scope_burst, where the offset- based variants serve both paths. tests/fakes.py — FakeStage and FakeScope are now wired together the way the rig is: a gated X move at scan velocity feeds frames into a running acquisition at the real 20 kHz / 100 mm/s rate, direction-agnostic. Both paths therefore derive frame counts from one model, which is what makes the byte-identity comparison meaningful, and a gate the engine forgets to drop shows up as extra frames instead of passing silently. Frame content is a function of (channel, index) alone, so the same frame sequence yields the same bytes however it is chopped into transfers. 87 tests passing, ruff clean. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>	2026-09-02 12:17:24 -05:00
Thomas Ales	afe33249d1	Phase 4: extract headless ScanEngine; de-Qt the T3R driver The headline of the refactor. Scan orchestration no longer lives inside a QObject that reaches through Qt workers for its hardware handles. core/scan_engine.py — ScanEngine(stage, scope, rotator, plan, out_path, resume, callbacks). Takes the concrete drivers, blocks in run(), reports via plain callables, and prompts through an injected blocking callable. No Qt import anywhere in the path (test_engine_imports_without_qt proves it), so a simpler GUI or a CLI can drive the identical acquisition. Supporting extractions, all Qt-free: - core/scope_sras.py — SCPI policy: channel profiles, trigger programming, background average, per-row FastFrame transfer - core/rotation.py — RotationAxis + RotationSettings (the GR_* constants) - core/scan_resume.py — frontier contiguity rule + settings compatibility - gui/scan_bridge.py — QtScanController, exposing exactly the signal surface the old ScanWorker had, so MainWindow's connections are unchanged hardware/t3r_driver.py is now Qt-free: a plain Signal class, a threading reader, and a polling thread instead of QObject/QThread/QTimer. gui/qt_t3r.py re-emits its callbacks as queued Qt signals for the panels. Fixes carried by the extraction: - rotation waits on the driver's MOTION_DONE event instead of time.sleep(estimate + 0.5) - abort during an operator prompt now takes effect; the old _prompt_event.wait() had no timeout and could not be interrupted - the poll timer is a thread, so an I/O error tearing down the driver no longer calls QTimer.stop() from the wrong thread - T3RDriver.disconnect() renamed close(); it shadowed QObject.disconnect() - per-frame DC means use np.frombuffer over the joined block instead of struct.unpack per frame (~16k tuple allocations per row) tests/fakes.py + test_scan_engine.py (14 tests) assert the exact command sequence, file layout, resume seeking, abort/pause, and geometry rejection before any hardware call; test_scan_resume.py covers the frontier rule. 58 passing. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>	2026-07-28 11:11:09 -05:00

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Thomas Ales

aa06fa1460

Per-angle background capture: v7/v11 .sras layout

A multi-angle scan runs for hours, but every angle was referenced against
one background captured before the first row of the first angle. That
reference has drifted by the last angle, and comparing angles — the whole
point of a multi-angle scan — was comparing each one against a noise floor
measured at whichever angle came first.

Every angle now captures its own. Before each angle's rows, the operator is
prompted to switch the Genesis laser off, the engine averages a fresh CH1
record, and the operator switches it back on. The data block therefore reads
[background][scan][background][scan] …, one pair per angle.

Format v7 (scan) and v11 (SAW check) carry the background inside the data
block, one length-prefixed block ahead of each angle's rows; the single
block that sat between the preambles and the data is gone. Per-angle offsets
now come from a walk of the data block at parse time rather than arithmetic
over the geometry table, and an angle whose background is not fully on disk
is the frontier — nothing of it was written yet.

v6/v10 files still read: SrasFile hands their one background to every angle,
so readers never branch on the version. Nothing writes them, and a resume
refuses them, since a re-acquired angle writes a block the old layout has no
room for. A resumed v7 angle rewrites its background in place, and the
engine checks the new block fits the room the file has before writing it —
anything else would shift every row behind it.

Two fixes made along the way:

  * QtScanController never accepted file_version, so every scan launched
    from the app raised TypeError at construction.
  * angle_status() left its cursor parked at the frontier, so every angle
    past it reported the frontier's own data_offset — which handed a resumed
    scan the same write position for several angles. Two recorded offsets in
    tests/golden/sras_expected.json are corrected accordingly.

The v6 goldens stay as parser fixtures; the writer is now locked against
bytes the test lays out from scan_format.md itself.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

2026-09-04 12:44:25 -05:00

Thomas Ales

116c9c07c7

Burst acquisition: many whole rows per FastFrame acquisition

Per-row acquisition pays a full arm/stop/transfer round trip for every row,
and the transfer is one IEEE-488.2 block read per frame (~16k frames a row).
Burst mode runs one FastFrame acquisition across as many complete rows as the
scope's frame memory holds and pulls each burst in a single CURVe?
transaction, amortising the round trip over the whole burst.

It is opt-in (ScanEngine(burst_mode=...), default False) and writes
byte-identical files to the per-row path — test_burst_and_serial_produce_
identical_files runs the same plan both ways and compares the bytes, which is
the property the whole feature rests on.

core/scope_burst.py — the new policy module. Everything that computes rather
than talks to hardware is a free function, so sizing and row-splitting are
testable without a rig: rows_per_burst() (rounds down, since a partial row
can't be written, and clamps to a transfer-buffer budget), split_row_counts(),
normalize_row(), frame_means_block().

The hard part is that a burst carries no row markers — the scope returns one
flat run of frames. Boundaries come from ACQuire:NUMFRAMESACQuired? sampled
after each acquiring pass while the stage gate is already low, rebased on a
baseline read back at RUN rather than assuming the counter resets. A counter
that goes backwards means the acquisition restarted mid-burst and is now a
hard error instead of silently misattributing every later row.

core/scan_engine.py — the row loop splits into _scan_rows_serial and
_scan_rows_burst. The wire is channel-major and the file is row-major with
channels inner, so _write_burst deinterleaves by writing one channel at a
time to strided offsets; peak memory stays at a single channel's burst
instead of the whole thing.

_gate_off_preflight is what makes this trustworthy on real hardware. The BBD
value that idles the trigger output low is not settled by the protocol docs
(see TRIGOUT_GATE_OFF), and getting it wrong fills every burst with flyback
frames that silently shift the file. The scope already measures the gate on
CH3, so the check needs no bench probe: one gated-off flyback must acquire
nothing, and one gated pass must acquire something — the second half is what
stops a dark laser from making the first half pass vacuously. It runs once
per scan and costs two row-times.

Two fixes fall out of this work and apply to both paths:
- Rows are now squared up to the declared n_frames (short rows zero-padded,
  long rows truncated, both warned). v6 commits to n_frames per row in the
  header and has no per-row length field, so an over- or under-triggered row
  used to shift every later row in the file.
- The X trigger output is returned to idle in the run() finally block. The
  per-row path left TRIGOUT_MAXV armed for the rest of the session, so the
  gate line kept being driven on every later jog.

core/scope_sras.py — pins DATa:ENCdg RIBinary and DATa:WIDth 1 during setup
instead of inheriting front-panel state. The file header hardcodes
bytes_per_sample=1; a scope left on 2 bytes would have corrupted every frame
written. frames_acquired/frame_means move to scope_burst, where the offset-
based variants serve both paths.

tests/fakes.py — FakeStage and FakeScope are now wired together the way the
rig is: a gated X move at scan velocity feeds frames into a running
acquisition at the real 20 kHz / 100 mm/s rate, direction-agnostic. Both
paths therefore derive frame counts from one model, which is what makes the
byte-identity comparison meaningful, and a gate the engine forgets to drop
shows up as extra frames instead of passing silently. Frame content is a
function of (channel, index) alone, so the same frame sequence yields the
same bytes however it is chopped into transfers.

87 tests passing, ruff clean.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

2026-09-02 12:17:24 -05:00

Thomas Ales

afe33249d1

Phase 4: extract headless ScanEngine; de-Qt the T3R driver

The headline of the refactor. Scan orchestration no longer lives inside a
QObject that reaches through Qt workers for its hardware handles.

core/scan_engine.py — ScanEngine(stage, scope, rotator, plan, out_path,
resume, callbacks). Takes the concrete drivers, blocks in run(), reports
via plain callables, and prompts through an injected blocking callable.
No Qt import anywhere in the path (test_engine_imports_without_qt proves
it), so a simpler GUI or a CLI can drive the identical acquisition.

Supporting extractions, all Qt-free:
- core/scope_sras.py  — SCPI policy: channel profiles, trigger programming,
  background average, per-row FastFrame transfer
- core/rotation.py    — RotationAxis + RotationSettings (the GR_* constants)
- core/scan_resume.py — frontier contiguity rule + settings compatibility
- gui/scan_bridge.py  — QtScanController, exposing exactly the signal
  surface the old ScanWorker had, so MainWindow's connections are unchanged

hardware/t3r_driver.py is now Qt-free: a plain Signal class, a threading
reader, and a polling thread instead of QObject/QThread/QTimer.
gui/qt_t3r.py re-emits its callbacks as queued Qt signals for the panels.

Fixes carried by the extraction:
- rotation waits on the driver's MOTION_DONE event instead of
  time.sleep(estimate + 0.5)
- abort during an operator prompt now takes effect; the old
  _prompt_event.wait() had no timeout and could not be interrupted
- the poll timer is a thread, so an I/O error tearing down the driver no
  longer calls QTimer.stop() from the wrong thread
- T3RDriver.disconnect() renamed close(); it shadowed QObject.disconnect()
- per-frame DC means use np.frombuffer over the joined block instead of
  struct.unpack per frame (~16k tuple allocations per row)

tests/fakes.py + test_scan_engine.py (14 tests) assert the exact command
sequence, file layout, resume seeking, abort/pause, and geometry
rejection before any hardware call; test_scan_resume.py covers the
frontier rule. 58 passing.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

2026-07-28 11:11:09 -05:00

3 Commits