The current spin box could not hold a typed value: the 1 Hz status poll
read LDS and wrote it straight into the spin box, so the operator's number
was replaced by the laser's within a second — before Set could be pressed.
The spin box is now seeded once on connect and belongs to the operator
after that; the poll's reading goes to a read-back label beside the Set
button, so the value about to be sent and the value the laser holds are
separate readouts.
The write itself was also unverified. Section 6 of the operator's manual:
"Commands or set values can be discarded by the controller unintentionally.
It is recommended to query the set value after the command is entered to
confirm the actual value." set_current_ma() wrote LDS and returned True
regardless, so a discarded write looked exactly like a good one.
_write_verified() now writes, reads back, and retries up to three times;
set_current_ma() and set_frequency_hz() use it, and HeliosWorker reports a
refusal on the status line instead of echoing the requested value.
Also from the manual, recorded but not acted on: LDS accepts 0-7000 mA
(the driver's 2000 mA ceiling is this rig's, not the protocol's), LDF has
to be re-sent after LDG changes, and the power-monitor mnemonic is HMP —
which this laser does not implement, per the operator.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
The operator frames a good spot, confirms the two DC levels the detector
reads there, and the rig then measures its own tilt: step 1.5 mm either side
on X and then on Y, and tilt the platform until those levels come back. The
correction that fixes an offset point is the correction that levels the whole
travel — height error and tilt effect are both proportional to the offset —
so the procedure ends by applying it and leaving it applied.
Both directions are measured from the same starting tilt and averaged, which
makes their disagreement a flatness read-out rather than something averaged
away silently.
core/auto_align.py holds the geometry and the search, Qt-free. The three
T-axes' azimuths are the whole geometry: T1 lies along +X so it alone tilts
along X, and T0/T2 move as an equal-and-opposite pair to tilt along Y without
touching X (tilt_response derives that, and the tests pin it — an axis map
that drifts would still converge, on the wrong axis). The search is a secant
null on the split-detector difference: probe once to learn what a microstep
is worth, sign included, then step at the null. It refuses to servo on a
scope that has not re-triggered, escalates a probe that reads as no response
before calling an axis dead, and stops at a per-axis travel limit.
gui/align_bridge.py runs it on a worker thread; stopping is a threading.Event
rather than a queued command, because the worker is inside a long handler for
the whole run. The camera window carries the button and the progress window,
and locks the scan panel and the jog pads while a run owns the stage.
Adds immediate MEAN measurements and an acquisition count to the scope
driver, and read_bias_mv to core/scope_inspect — the one scalar the
inspection state was missing.
KNOWN_ISSUES.md records what only the rig can settle: the probe step, the
travel limit, the hold current, and whether the piston the X phase applies
alongside its tilt matters.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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>
Focusing the T-axis and framing the sample on the XY stage are both done
by eye, but the controls were in the main window and the T3R panel, so
the operator had to look away from the video to move anything.
Adds gui/jog_panel.py with two panels, laid out in a column to the right
of the camera image:
T3RJogPanel per-axis enable, hold-to-jog ◀/▶, live position, and a
per-channel microstep combo (SET_MICROSTEP is per channel
on this controller). Jog velocity and acceleration are
shared by the four axes.
BBDJogPanel an X/Y jog pad, step size, and velocity/acceleration.
The stage runs closed-loop servos, so there is no
microstepping to set — the panel says so rather than
offering a control that does nothing.
The T3R's JOG is a continuous velocity move, so the button holds it and
the release stops it; the BBD has no such command, so a held button
repeats a short relative move the way the main window already does.
Only axes this panel started are ever stopped — closing the window or
hitting "Stop jogging" can't cut a scan's rotation short.
Both panels take the driver and worker the main window already owns, so
a jog here is the same command as a jog there. The BBD202 worker grows
a set_velocity command, and its jog now carries the step with it instead
of the caller writing _jog_step onto the worker from the GUI thread.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
A full multi-angle scan takes hours, and a rig whose angles disagree produces
all of them before anyone finds out. This adds a test mode that acquires one
row per angle — the row-wise middle of the ROI — and a viewer that puts every
angle's SAW frequency on one graph. The default 80×50 mm ROI at 5 angles goes
from 1461 rows to 5.
Why the middle row answers an alignment question at all: build_plan centres
every angle's rotated bounding box on the same nominal ROI centre, so each
angle's middle row crosses that one point on the sample. All the angles
measure the same material, so a spread in their frequencies belongs to the rig
rather than to where each row happened to land. test_every_angles_middle_row_
crosses_the_roi_centre pins that premise, since the whole comparison rests on
it and nothing else in the geometry code would notice it breaking.
core/saw_check.py — both halves of the mode, kept together because neither is
much use alone. middle_row_plan() reduces a ScanPlan to one row per angle
(n_rows // 2, the upper of two centre rows when even); frequency_traces() and
alignment_summary() turn the resulting file back into per-angle frequency
traces and the scalars an operator is actually asking about — the spread of
the per-angle medians, the worst drift along a row, the sparsest row. The
verdict thresholds are labelled as rules of thumb, not physics: an anisotropic
sample genuinely varies with angle, so a wide spread is a prompt to look at
the curves rather than a verdict.
Format v10: byte-identical to v6, one row per angle. The version byte earns
its keep because the two are otherwise indistinguishable — a v6 scan aborted
after its first row is not a check, and a reader guessing from the row count
would read a failed scan as a deliberate measurement. create_scan_file()
enforces the one-row rule at write time, since nothing downstream can recover
from a v10 file that breaks it. ScanEngine gains file_version and is otherwise
untouched: the acquisition, the abort/pause path and the background capture
are the scan's, unchanged.
sras_scan_manager.py now carries the source file's version through an export
instead of stamping v6 on everything, which the wider reader would otherwise
have made a lie.
saw_check_viewer.py — frequency along the row, one curve per angle, over a
common offset axis so the curves lie on the same piece of sample; a summary of
each angle's median ±1σ against angle; and the per-angle numbers in a table.
Analysis parameters (DC threshold, background, time gate) recompute on a
worker thread; display ones (smoothing, axis, MHz↔m/s) only redraw. A full v6
scan opens too — the same middle row is pulled out of it — so a finished scan
can be re-examined with the check's own read-out.
In the app, a check finishes by handing the operator the file and an "Open
Viewer" button rather than shutting the rig down the way a completed scan
does. Burst mode is not offered: one row per angle means every burst would be
a single row, so it buys nothing and still pays for the gate preflight.
137 tests passing, ruff clean.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
A 9-angle scan takes hours, and an angle that responds poorly still produces
rows that look structurally fine in the file — the SAW packet is just not
there. This lets the operator walk the angles first, parking the rig at a
random point in each, and judge the response before committing to the run.
Nothing reads the scope. The operator inspects the instrument directly, so
there is no transfer path, no plotting, and no waveform crossing the module
boundary — test_inspection_never_reads_a_waveform_back pins that, since it is
the kind of premise a later change erodes without noticing.
core/scope_inspect.py — the scope state worth looking at, which is not the
scan's state:
- plain rising-edge trigger on CH2 at 2.0 V, not the scan's logic AND of the
laser pulse and the stage gate, so a stationary stage still triggers
- FastFrame off, SAMPLE (no averaging) — a weak or intermittent response is
exactly what is being looked for, and averaging would hide it
- free-running (STOPAfter RUNSTop + STATE RUN) so the trace keeps updating
while the operator looks at it
- CH1 keeps the acquisition front-end verbatim, so what is on screen is what
a scan would record
- CH3/CH4 become bias monitors sharing one scale and position, since the
comparison is by eye and only works if a division means the same on each.
100 mV/div with ground 3.5 divisions below centre puts 0–700 mV on screen
with headroom on an 8- or 10-division graticule (the signal never goes
negative, hence moving the trace down).
core/angle_inspect.py — AngleInspector, headless and Qt-free like ScanEngine.
Points are drawn from the angle's own bounding box: Y from its actual row
positions and X uniformly across its data window, so the point is somewhere
the scan would really sample rather than merely inside the box. New Point
re-rolls without rotating, which is what separates a bad spot on the sample
from a bad angle. The stage gate is held off throughout, and the rotator goes
home on stop.
gui/inspect_bridge.py — QtAngleInspector on the existing QueueWorker base.
Inspection is click-driven rather than one long run, so the worker blocks on
its queue between commands and an open window costs nothing. BBD position
polling is suppressed while inspecting, for the same reason the scan does it:
the shared TX queue.
sc3_aui_app.py — AngleInspectWindow (angle list, prev/next, New Point) driven
off the plan currently entered in the scan panel, so it inspects exactly the
scan about to be run. Navigation locks while the stage moves. The list syncs
via itemClicked rather than currentRowChanged, so echoing the worker's
position back does not re-trigger the move it is reporting.
README picks up the new modules, and scope_burst.py which the previous merge
left out of the structure listing. 114 tests passing, ruff clean.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
A mis-triggered row cannot be written as it arrived — v6 declares n_frames per
row in the header and has no per-row length field, so a short or long row
would shift every later row in the file. Until now the only policy was to
square it up, which keeps the scan running but leaves the affected row
indistinguishable from a good one afterwards: nothing in the file records that
it was padded.
strict_rows selects the other trade. On any frame-count mismatch the scan
stops instead of writing the row, so a data run either produces rows that mean
what the header says they mean or fails loudly. Default stays pad, so existing
behaviour is unchanged.
_warn_frame_delta becomes _check_frame_delta, since it now decides rather than
just reports. Both acquisition paths already call it before writing anything
for the row (CH1 leads SCAN_CHANNELS, and the burst path checks every row up
front), so an abort leaves the file on a whole-row boundary rather than a
half-written row — test_strict_row_packing_writes_nothing_for_the_failed_row
pins that.
Plumbed through QtScanController to a checkbox in the scan panel, persisted in
ScanDefaults alongside burst_mode. scan_format.md documents both policies and
notes that the choice is not recorded in the file.
The row-clipping setup in the padding test is now a _clip_one_row helper,
reused by the strict tests. 92 tests passing, ruff clean.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Wires the burst_mode flag through QtScanController to ScanEngine and adds a
checkbox to the scan panel. The setting persists via ScanDefaults like the
other scan fields, defaulting to off — per-row acquisition stays the default
path until burst mode has run on the rig and the gate-off preflight has
settled which TRIGOUT value idles the pin low.
scan_format.md — the acquisition settings table had drifted from the code it
claimed to describe: it attributed the settings to sc3_aui_app.py (they moved
to core/scope_sras.py in the Phase 2 extraction), listed a 1.24 V trigger
level and 0 % offset where the code sets 0.500 V and HORizontal:POSition 30,
and did not mention the logic-AND scan trigger at all. Corrected, pointed at
the module that actually owns them, and noted that none of it affects byte
layout — only where the acoustic packet lands inside a frame.
Added an acquisition-paths section: the two paths write byte-identical files
and the choice is a runtime flag that is not recorded in the file, so a
reader never needs to care which produced it. Documents where row boundaries
come from in a burst and that either path squares rows up to n_frames.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
- Collapsed Args:/Returns:/Raises: blocks that only restated the
signature (364 lines): tektronix_base 48% -> ~20% doc density,
helios_laser and uc480_camera likewise. Only docstrings whose entire
body was those sections were touched.
- Preserved verbatim the comments that carry hardware knowledge the code
can't express: uc480's USB split-transaction contention note (with its
measured fps), the IS_ALLOW_STARTER_FW_UPLOAD segfault explanation, the
QImage-copy rationale, and tektronix's NUMFRAMESACQuired warning.
- README: project structure, quick start, and every usage example now
describe code that exists (they referenced hardware/bbd202.py,
CoherentHOPSLaser, get_curve_binary, and 'python -m scanengine.app',
none of which do). Added a headless-scan example and a read-a-scan-file
example, since reuse without the GUI is the point of the refactor.
- SETUP: structure section defers to README instead of keeping a second
stale copy; documents the vendored uEye SDK and the Genesis quarantine.
- ruff is now clean repo-wide: fixed the remaining raise-from, unused
loop variables, placeholder f-strings, and a non-strict zip; the
widget-layout semicolon idiom is an explicit config ignore rather than
22 standing warnings.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
gui/qt_workers.py — one QueueWorker base replaces the per-device command
queue + dispatch + signal boilerplate. The loop blocks on the queue
instead of waking 10-20x/second forever (test_idle_worker_does_not_spin
asserts an idle worker burns ~no CPU). PollingQueueWorker adds
self-rescheduling polling: the next poll is queued only after the
previous finishes, so a device slower than the interval can't accumulate
a backlog (test_polling_never_overlaps_or_backs_up).
Helios responsiveness — the concrete bug that motivated the above: a free
running 1 s QTimer queued a status poll that took ~2 s, so the queue grew
for as long as the panel stayed connected.
- helios_laser._query reads until the CR terminator instead of sleeping a
fixed 0.05 + 0.2 s per query
- one _query_int() helper replaces five copies of parse-with-logging
- polling is now driven by the worker; HeliosWindow's QTimer is gone
- dropped __del__, which disabled the laser and wrote to the serial port
from the garbage collector at an unpredictable time
helios_test_app.py — the worker was moveToThread'd but every call site
invoked its methods directly, so all serial I/O (including the sleeps)
ran on the GUI thread; Query All froze the UI for ~2 s. Calls now go
through a queued signal to a pyqtSlot. Also: connect/disconnect cycles
leaked a QThread + worker + 9 connections each time; 16 copies of the
not-connected guard collapse to _require_connection(); the Query Power
button called a method that has never existed (AttributeError popup) and
is now disabled and documented in KNOWN_ISSUES.
DCBiasImageWidget preallocates its image and uses set_data/set_clim, so
the live preview stops rebuilding the array and the whole artist tree per
row (O(rows^2) over a scan).
bbd20x: connect() now raises when no bays respond instead of reporting
success on the wrong port; disconnect() joins with a timeout so a wedged
reader can't hang shutdown; one _channel_for() helper replaces four
copy-pasted axis mappings; hardcoded travel limits become TRAVEL_MM; the
joke error strings are gone.
gui/widgets.py adds the shared ConnectionBar / PortSelector / bounded
LogConsole / StatusGrid for the test benches to adopt. 65 tests passing.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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>
- core/sras_format.py: THE v6 implementation — create_scan_file (writer,
byte-identical to the old one, enforced against the Phase-0 goldens),
SrasFile parser with frontier/truncation walk, and zero-copy mmap
load_angle/load_row views for multi-GB files
- core/scan_geometry.py: ScanPlan/AngleGeometry dataclasses, build_plan
(rotated-bbox trig from MainWindow._build_scan_params), travel-limit
validate_plan (limits now a StageLimits dataclass, not literals buried
in the worker), format_eta + EtaEstimator (bounded deque)
- core/config.py: ScanDefaults dataclass replaces the module-import-time
dict globals. FIXES: editing any main-window port used to rewrite
aui_defaults.json without helios_port, silently reverting the Helios
port every time (test_helios_port_survives_partial_update covers it).
Also drops the inert laser_freq_hz plumbing — scans always used the
LASER_FREQ_HZ constant.
- hardware/serial_util.py: shared 8N1 open + scored port enumeration
(promoted from t3r_control_panel); helios_laser and the panel use it
- sc3_aui_app.py and sras_scan_manager.py migrated onto core (three
format implementations down to one); ScanWorker now takes a ScanPlan
- tests: byte-identical writer vs golden, frontier over every truncation
variant, mmap==eager, geometry vs golden fixtures + invariants, config
round-trip. 28 passing.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
- uc480_camera: drop never-called _capture_paused/get_framerate (the
hardware question _capture_paused encoded is now in KNOWN_ISSUES.md)
- t3r_protocol: drop read_reg/write_reg/decode_reg/Reg (commands never
wired into the driver)
- bbd20x: drop _update0x0212 (never dispatched) and 8 of 9 unused
trigger convenience wrappers; apt_constants: drop TriggerBitsStepper
(servo-only rig)
- ruff --fix: 35 unused imports across all apps; drop unused T3R_BAUD
- genesis_core.py: quarantine warning header; docs/genesis_verification.md
bench checklist for the 7 divergences vs tools/genesis_laser_gui.py
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Thomas Ales