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merge into: tka/scanengine-3:nonessential-cleanup
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tka/scanengine-3:main tka/scanengine-3:dev-helios-current-setpoint tka/scanengine-3:dev-auto-align tka/scanengine-3:dev-saw-check tka/scanengine-3:dev-angle-inspect tka/scanengine-3:dev-rowpacking tka/scanengine-3:dev-burst-mode tka/scanengine-3:dev-bbdrowpack tka/scanengine-3:refactor-01 tka/scanengine-3:nonessential-cleanup tka/scanengine-3:dev-resumescan tka/scanengine-3:local-llm-add-t3r tka/scanengine-3:new-refactor
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pull from: tka/scanengine-3:dev-saw-check
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tka/scanengine-3:main tka/scanengine-3:dev-helios-current-setpoint tka/scanengine-3:dev-auto-align tka/scanengine-3:dev-saw-check tka/scanengine-3:dev-angle-inspect tka/scanengine-3:dev-rowpacking tka/scanengine-3:dev-burst-mode tka/scanengine-3:dev-bbdrowpack tka/scanengine-3:refactor-01 tka/scanengine-3:nonessential-cleanup tka/scanengine-3:dev-resumescan tka/scanengine-3:local-llm-add-t3r tka/scanengine-3:new-refactor

19 Commits
nonessential-cleanup .. dev-saw-check

Author SHA1 Message Date
Thomas Ales 844fcd0297 SAW quality check: one middle row per angle, and a viewer that overlays them 
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>
 2026-09-04 08:13:54 -05:00
Thomas Ales dfd6c9e2b8 Merge dev-angle-inspect: pre-scan angle inspection 
Walk a plan's angles before committing to the run, parking the rig at a random
point in each so the SAW response can be judged on the oscilloscope. A weak
angle otherwise produces rows that look structurally fine in the file with no
usable packet in them, which is only discoverable hours later.

The app configures the scope and drives the motion; it never reads a waveform
back. That is the feature's premise rather than an omission, so a test asserts
no transfer path exists.

- core/scope_inspect.py  free-running edge trigger on CH2 at 2.0 V, FastFrame
  and averaging off, CH1 on the acquisition front-end, CH3/CH4 rescaled as
  bias monitors sharing one scale and position
- core/angle_inspect.py  headless AngleInspector; points land on the angle's
  own scan grid, and New Point re-rolls without rotating
- gui/inspect_bridge.py  QtAngleInspector on the QueueWorker base
- sc3_aui_app.py         AngleInspectWindow, driven off the entered plan

The bias scaling (100 mV/div, ground 3.5 divisions low) is derived to fit
0-700 mV on an 8- or 10-division graticule, not measured on the rig; expect to
tune BIAS_POSITION_DIV against the bench-tuned values in SRAS_CHANNELS.

114 tests passing, ruff clean.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
 2026-09-04 07:21:56 -05:00
Thomas Ales 23546a03f7 Pre-scan angle inspection: park the rig per angle, read the response on the scope 
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>
 2026-09-02 12:41:52 -05:00
Thomas Ales 817da0160c Merge dev-rowpacking: selectable row packing policy 
Row packing is now a choice rather than a fixed behaviour. Pad (default,
unchanged) squares a mis-triggered row up to the declared n_frames and warns;
strict stops the scan instead, so a data run cannot quietly contain a padded
row that nothing in the file marks as padded.

Both paths check the frame count before writing any of the row's channels, so
a strict abort ends the file on a whole-row boundary.

92 tests passing, ruff clean.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
 2026-09-02 12:32:15 -05:00
Thomas Ales 52fdcdd9f3 Make row packing toggleable: pad (default) or strict abort 
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>
 2026-09-02 12:32:09 -05:00
Thomas Ales ab5f3166f4 Merge dev-burst-mode: opt-in burst acquisition 
Adds a second acquisition path that runs one FastFrame acquisition across as
many whole rows as the scope's frame memory holds, transferring each burst in
a single CURVe? transaction instead of one block read per frame per row.
Off by default; both paths write byte-identical files.

- d6a5626 driver support (bulk transfer, MAXFRames?, per-row trigger gating)
  and two read_raw fixes: a short read on the length digits, and #0
  indeterminate-length blocks, which a raw socket cannot delimit by EOI
- 116c9c0 core/scope_burst.py, the split row loop, and the on-rig gate-off
  preflight that resolves the undocumented BBD trigger-idle value
- ef8c0fe GUI checkbox, persisted default, and corrected scan_format docs

Also fixes, on both paths: rows are squared up to the declared n_frames
(v6 has no per-row length field, so a mis-triggered row shifted every later
row in the file), the transfer format is pinned rather than inherited from
the front panel (the header hardcodes bytes_per_sample=1), and the X trigger
output is returned to idle when a scan ends.

87 tests passing, ruff clean.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
 2026-09-02 12:19:31 -05:00
Thomas Ales ef8c0feb91 Expose burst acquisition in the app; refresh scan_format acquisition docs 
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>
 2026-09-02 12:18:23 -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 d6a56266b7 Driver support for multi-row FastFrame bursts; fix read_raw block parsing 
Groundwork for burst acquisition: the scope needs to report and transfer a
whole multi-row FastFrame acquisition, and the BBD needs to gate its trigger
output per row rather than staying armed for the scan.

tektronix_base
- get_fastframe_max_frames() exposes HORizontal:FASTframe:MAXFRames?, which
  is what sizes a burst once the horizontal settings are fixed.
- transfer_fastframe_bulk() pulls a burst as one contiguous buffer. Unlike
  transfer_fastframe it does not assume how the scope frames the response:
  it accumulates until the expected byte count is reached, so one large IEEE
  block and one block per frame both work.
- set_data_encoding() / set_data_width() make the transfer format settable
  instead of inherited from whatever the front panel was left on.
- read_raw() had two real defects. The length-digit read used a bare recv()
  and only checked the length afterwards, so a short read raised "Failed to
  read data length" on a perfectly good transfer; it now goes through a
  _recv_exact() helper, as does the trailing separator. And a #0
  indeterminate-length block was parsed as int("") -> ValueError. #0 is
  normally delimited by EOI, which a raw socket never sees, so read_raw now
  takes expected_bytes to size it. The bulk transfer relies on this.

pybbd202
- arm_scan_gate(axis, armed) raises and drops the max-velocity trigger
  output the scope's AND-gate uses. A burst spans several rows with the
  scope running throughout, so the gate must be low for the flyback or the
  return move reaches max velocity and injects frames between rows.
- set_trigger_verified() reads the mode back after setting it. set_trigger
  is fire-and-forget over the shared TX queue; burst mode toggles the gate
  between every row, where a dropped change silently corrupts the file
  rather than failing loudly.
- set_trigger_gate_off() so the scan can leave the output idle on exit.
- TRIGOUT_GATE_OFF is deliberately marked unverified. §7.6 of the BBD203
  protocol doc describes `mode` as an enumeration capping at 0x11, which
  contradicts the bitmask this driver actually sends (TRIGOUT_MAXV = 0x90,
  known working), so the doc cannot settle which value idles the pin low.
  The engine's preflight check resolves it on the rig instead.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
 2026-09-02 12:16:20 -05:00
Thomas Ales 278df9411e Ignore macOS .DS_Store files 
hardware/.DS_Store kept showing up as untracked throughout the refactor;
.gitignore had no rule for it. The file itself is left on disk (Finder
regenerates it) — it is simply ignored now.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
 2026-07-28 11:39:51 -05:00
Thomas Ales 709dc529df Phase 6: strip signature-restating docstrings; correct README/SETUP 
- 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>
 2026-07-28 11:27:36 -05:00
Thomas Ales 44febe34b8 Phase 5: shared worker base, self-rescheduling polls, driver robustness 
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>
 2026-07-28 11:21:29 -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
Thomas Ales d2734c45d6 Phase 3: viewer reads v6 via mmap; extract analysis core 
The viewer could only parse v2-v4 headers while the app has been writing
v6 for some time — it could not open ANY file the current app produces.
It now uses core.sras_format directly (v6 only, per user decision).

New core/sras_analysis.py (Qt-free): ChannelCalibration, image reducers,
and SawPipeline. sras_viewer.py keeps only Qt.

Memory (measured, 92 MB synthetic scan, separate processes):
  old eager path  +305 MB   read()+slice-copy+astype+float32 mean
  new mmap path   + 31 MB   zero-copy view + mean(dtype=)
  -> identical DC image; old scaled at ~3.3x file size, new at image size
- load_angle() returns a read-only mmap view instead of reading the whole
  data block, then copying it twice
- SAW sweeps keep one scalar per pixel (process_shot_metrics) instead of
  retaining 5 full arrays x pixel count in a results list
- CH1 float32 materializes only for pixels passing the DC mask
- matched filter caches the template FFT instead of recomputing per pixel
- opening a new file drops every reference to the old one (compute/
  template/diagnostic workers used to pin the previous multi-GB mapping)

Responsiveness:
- 250 ms debounce coalesces spinbox storms into one recompute
- grating change is a display-time scalar multiply, not a full FFT rerun
- colormap/clim reuse the AxesImage (set_data/set_clim) instead of
  clf() + rebuilding the colorbar; draw_idle() throughout
- SAW diagnostics (21 pipeline runs) and CSV export moved off the GUI thread

Also: ragged per-angle geometry is respected (v6 angles differ in rows/
frames), truncated scans show only rows present on disk, dead decimation
path and v2 fallback branch removed, scipy added to viewer requirements.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
 2026-07-28 10:55:38 -05:00
Thomas Ales dff9f69d78 Phase 2: extract headless core modules (sras_format, scan_geometry, config) 
- 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>
 2026-07-28 10:20:44 -05:00
Thomas Ales 67aabde4b6 Phase 1c: prune remaining dead functions, unused imports, quarantine Genesis 
- 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>
 2026-07-28 10:08:48 -05:00
Thomas Ales 5148f0bca2 Phase 1b: prune 45 never-called methods from tektronix_base (~850 lines) 
Verified by repo-wide name search + transitive closure over internal
calls: the live apps use 25 methods (plus raw write/query); everything
else — cosmetic label styling, unused getters/setters, transfer_waveform,
acquire_waveform — had no callers. Also: linear-time chunk join in
read_raw instead of quadratic bytes += concat, and a typed except on its
debug path.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
 2026-07-28 10:04:41 -05:00
Thomas Ales 1d4e65f8ac Phase 1a: delete dead parallel app stack (~4,600 lines) 
app.py was an abandoned skeleton (15 'pass # TODO' handlers, loads a
deleted .qss); everything else was reachable only from it:
ui_mainwindow.py (pyuic6 artifact), sc3-new.ui, motion_worker.py,
genesis_worker.py, coherent_hops_laser.py (stubs), scanning/ (dead C#
port + unused plan generator), config.json, plus helios_diagnostic.py
(sends wrong protocol commands) and helios_terminal.py (worse duplicate
of helios_test_app's Terminal tab).

hardware/__init__.py no longer wildcard-imports every driver, so the
stage driver imports without the uEye camera SDK installed.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
 2026-07-28 10:02:36 -05:00
Thomas Ales d185676130 Phase 0: test scaffolding + golden fixtures 
- ruff config, offscreen smoke tests for all 7 GUI apps/panels
- golden v6 .sras fixtures (complete + 4 truncation variants) generated
  by the pre-refactor writer, with expected header/frontier JSON
- golden geometry fixtures from the pre-refactor _build_scan_params
- consistency tests proving current code reproduces the goldens

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
 2026-07-28 10:01:14 -05:00
84 changed files with 15204 additions and 10406 deletions
Expand all files Collapse all files
.gitignore
Regular → Executable
+3
View File
@@ -177,3 +177,6 @@ cython_debug/
marimo/_static/ marimo/_static/
marimo/_lsp/ marimo/_lsp/
__marimo__/ __marimo__/
# macOS
.DS_Store
KNOWN_ISSUES.md
+50
View File
@@ -0,0 +1,50 @@
# Known issues requiring on-rig verification
Questions that cannot be answered from the code alone. Check these the next
time the hardware is available; each one gates a small code change.
## uC480 camera: gain/exposure during active capture
The driver used to carry an (unused) `_capture_paused` context manager whose
docstring claimed many IDS cameras return `IS_CANT_COMMUNICATE_WITH_DRIVER`
(17) or `IS_NO_SUCCESS` (-1) when gain/exposure commands are issued during
active capture. `set_exposure()` and `set_gain()` never used it, and the
helper was deleted in the Phase-1 cleanup.
**Bench check:** with live streaming running, move the exposure and gain
sliders in `camera_test_app.py` and watch the log for those error codes.
If they appear, the setters need a stop-live/apply/restart sequence
(re-create the helper around the two call sites in
[uc480_camera.py](hardware/uc480_camera.py)).
## Helios: no output-power query
`docs/hardware/HELIOS_DRIVER_README.md` documents `driver.get_power_mw()`,
but `HeliosLaser` has no such method and no output-power mnemonic appears
anywhere in this repo's protocol notes. `helios_test_app.py` called it
anyway and raised `AttributeError` into a popup; the button is now disabled
and the handler reports the gap instead.
**Bench check:** find the power-read command in the Helios manual (the
other reads are three-letter mnemonics like `LDO`, `LDS`, `LTA`). If one
exists, add `get_power_mw()` to `hardware/helios_laser.py` using
`_query_int`, then re-enable the button. If it doesn't, delete the Power
Monitoring group from the test app and fix the README.
## Genesis laser: forked protocol implementations disagree
`hardware/genesis_core.py` and the reference implementation
`tools/genesis_laser_gui.py` disagree on ADC command bytes, LDD enable
polarity, shutter semantics, filtering, and scaling. Do not modify either
until the checklist in [docs/genesis_verification.md](docs/genesis_verification.md)
has been run on the bench.
## `lib/ueye_loader.so` — still needed?
`lib/ueye_loader.c` is an `LD_PRELOAD` shim that dlopens
`/usr/lib/libueye_api.so` — yet nothing in the repo references it, and the
vendored SDK copy is `lib/libueye_api64.so.3.82` (a different file). On the
rig, check whether the camera apps run without the shim; if they do, delete
`lib/ueye_loader.{c,so}`. Either way, record in SETUP.md where
`libueye_api64.so.3.82` came from (IDS SDK version) and how the loader is
meant to be used.
README.md
+218 -93
View File
@@ -9,9 +9,14 @@ scanengine-3 is a unified platform for scanning acoustic microscopy and precisio
### Key Features ### Key Features
- **Stage Control**: ThorLabs BBD202/BBD203 motor controller with 3-axis positioning - **Stage Control**: ThorLabs BBD202/BBD203 motor controller with 3-axis positioning
- **Laser Systems**: Helios and Coherent HOPS laser control - **Laser Systems**: Helios pulsed laser and Genesis CW laser control
- **Data Acquisition**: Tektronix oscilloscope integration with fast-frame support - **Data Acquisition**: Tektronix oscilloscope integration with fast-frame support
- **Scan Planning**: Automated raster scan generation and execution - **Scan Planning**: Automated raster scan generation and execution
- **Angle Inspection**: Park the rig at random points across a plan's angles
to check the SAW response on the scope before committing to a long scan
- **SAW Quality Check**: Acquire one row per angle — the row-wise middle of
the ROI — as a v10 `.sras`, then compare every angle's SAW frequency on one
graph to judge the alignment before a full run
- **Real-time Monitoring**: Live status updates and progress tracking - **Real-time Monitoring**: Live status updates and progress tracking
## Hardware Components ## Hardware Components
@@ -30,11 +35,6 @@ scanengine-3 is a unified platform for scanning acoustic microscopy and precisio
- Multiple pulse modes - Multiple pulse modes
- Temperature and power monitoring - Temperature and power monitoring
- **Coherent HOPS Laser**
- I2C/FTDI interface
- Power and modulation control
- Temperature monitoring
### Data Acquisition ### Data Acquisition
- **Tektronix MSO/DPO Series Oscilloscopes** - **Tektronix MSO/DPO Series Oscilloscopes**
- Direct socket communication (no VISA overhead) - Direct socket communication (no VISA overhead)
@@ -42,69 +42,75 @@ scanengine-3 is a unified platform for scanning acoustic microscopy and precisio
- Multi-channel waveform capture - Multi-channel waveform capture
- Configurable triggering - Configurable triggering
### Microscope Systems ### Rotation / Focus
- **Genesis Microscope** (stub implementation) - **T3R four-channel stepper controller**
- **T3R Timing Device** (stub implementation) - Focus axis plus the GR rotation stage (12.5:1 gear train)
- Custom binary framing protocol over USB serial
## Project Structure ## Project Structure
The codebase is split so that everything needed to run a scan is importable
without PyQt6 or any vendor SDK — `core/` is the headless engine, `gui/` is
the shared Qt layer, and the root scripts are entry points.
``` ```
scanengine-3/ scanengine-3/
├── scanengine/ # Main application package ├── core/ # Headless: no PyQt6, no vendor SDKs
│ ├── __init__.py │ ├── scan_engine.py # ScanEngine — full acquisition sequence
│ ├── app.py # Main application entry point │ ├── scan_geometry.py # ScanPlan, rotated-bbox planning, limits
│ ├── main_launcher.ui # Main launcher UI │ ├── scan_resume.py # Resume planning (frontier rule)
│ ├── new_scan_wizard.ui # Scan wizard UI │ ├── scope_sras.py # Oscilloscope SCPI policy for SRAS
│ └── options.ui # Options dialog UI │ ├── scope_burst.py # Burst-mode FastFrame sizing + row splitting
│ ├── scope_inspect.py # Scope setup for pre-scan angle inspection
│ ├── angle_inspect.py # AngleInspector — park on a point per angle
│ ├── saw_check.py # Middle-row SAW check: plan + alignment read-out
│ ├── rotation.py # GR rotation axis settings + moves
│ ├── sras_format.py # v6/v10 .sras writer/reader (memory-mapped)
│ ├── sras_analysis.py # Image reducers + SAW matched filter
│ └── config.py # ScanDefaults ⇄ aui_defaults.json
│ │
├── hardware/ # Hardware driver package ├── hardware/ # Device drivers (Qt-free)
│ ├── __init__.py │ ├── serial_util.py # Shared 8N1 open + port enumeration
│ ├── bbd202.py # ThorLabs stage controller │ ├── t3r_driver.py # T3R stepper controller
│ ├── uc480_camera.py # IDS/ThorLabs camera │ ├── t3r_protocol.py # T3R frame encode/decode
│ ├── tektronix_base.py # Tektronix oscilloscope │ ├── helios_laser.py # Helios pulsed laser
│ ├── coherent_hops_laser.py # Coherent HOPS laser │ ├── tektronix_base.py # Tektronix oscilloscope (raw SCPI)
│ └── genesis_core.py # Genesis laser core logic │ ├── uc480_camera.py # IDS/ThorLabs uEye camera (returns QImage)
│ ├── genesis_core.py # Genesis laser — QUARANTINED, see below
│ └── pybbd202/ # ThorLabs BBD202 stage (APT protocol)
│ │
├── scanning/ # Scan planning package ├── gui/ # Shared PyQt6 layer
│ ├── __init__.py │ ├── scan_bridge.py # QtScanController over core.scan_engine
│ ├── sc3_scan_model.py # Scan model │ ├── inspect_bridge.py # QtAngleInspector over core.angle_inspect
│ └── stage_scan_plan_generator.py # Scan path planning │ ├── qt_t3r.py # Qt adapter over the T3R driver
│ ├── qt_workers.py # QueueWorker / PollingQueueWorker bases
│ └── widgets.py # ConnectionBar, LogConsole, PortSelector…
│ │
├── tools/ # Standalone executable tools ├── sc3_aui_app.py # Main acquisition application
│ ├── genesis_laser_control.py # Standalone Genesis app ├── sras_viewer.py # Scan data viewer
│ └── genesis_laser_gui.py # Alternative Genesis GUI ├── saw_check_viewer.py # SAW check viewer: every angle's frequency, one graph
├── sras_scan_manager.py # CLI: inspect/export/delete angles
├── t3r_control_panel.py # T3R panel (used by the main app)
├── helios_test_app.py # Per-device test benches
├── bbd202_test_app.py
├── camera_test_app.py
├── sc3-aui-*.ui # Qt Designer files loaded at runtime
│ │
├── tests/ # Test files ├── tests/ # pytest suite
│ ├── __init__.py │ ├── golden/ # v6 .sras + geometry fixtures
│ ├── test_camera_integration.py │ ├── fakes.py # Recording fake stage/scope/rotator
│ ├── test_genesis_connection.py │ └── test_*.py
│ ├── test_genesis_protocol.py
│ ├── test_rotated_aoi.py
│ └── test_temperature_scaling.py
│ │
├── docs/ # Documentation ├── docs/
│ ├── hardware/ # Hardware documentation │ ├── hardware/ # Driver notes
│ │ ├── BBD203_CONNECTION_GUIDE.md │ ├── protocols/ # Vendor protocol PDFs
│ │ ├── BBD203_Communications_Protocol.md │ └── genesis_verification.md # Bench checklist (see KNOWN_ISSUES.md)
│ │ ├── BBD203_DRIVER_README.md
│ │ ├── HELIOS_DRIVER_README.md
│ │ ├── GENESIS_LASER_README.md
│ │ └── laser_control_implementation_guide.md
│ └── protocols/ # Protocol specifications
│ ├── apt_communications_protocol.pdf
│ ├── helios_comms_protocol.pdf
│ └── thorlabs_mls_protocol.pdf
│ │
├── lib/ # Binary libraries (not in git) ├── lib/ # Vendored IDS uEye SDK (not in git)
│ ├── libueye_api64.so.3.82 ├── aui_defaults.json # Persisted ports / scope IP / save dir
│ ├── ueye_loader.c ├── scan_format.md # .sras binary format specification
│ └── ueye_loader.so ├── KNOWN_ISSUES.md # Open questions needing the hardware
│ └── requirements.txt
├── config.json # System configuration
├── requirements.txt # Python dependencies
├── README.md # This file
├── SETUP.md # Setup instructions
└── LICENSE # License file
``` ```
## Quick Start ## Quick Start
@@ -126,14 +132,35 @@ pip install -r requirements.txt
### Running the Application ### Running the Application
```bash ```bash
# Main GUI application # Main acquisition application
python -m scanengine.app python sc3_aui_app.py
# Scan data viewer
python sras_viewer.py
# SAW quality check viewer (every angle's frequency on one graph)
python saw_check_viewer.py path/to/scan-sawcheck.sras
# Inspect / export / delete angles in a .sras file
python sras_scan_manager.py path/to/scan.sras
# Per-device test benches
python helios_test_app.py
python bbd202_test_app.py
python camera_test_app.py
# Genesis laser control tool # Genesis laser control tool
python tools/genesis_laser_control.py python tools/genesis_laser_control.py
```
# Alternative Genesis laser GUI ### Running the tests
python tools/genesis_laser_gui.py
The suite is hardware-free: fake drivers and committed fixtures stand in
for the rig.
```bash
pip install pytest ruff
python -m pytest tests/ -q
``` ```
## Dependencies ## Dependencies
@@ -143,66 +170,164 @@ python tools/genesis_laser_gui.py
- **pyvisa** (>=1.13.0) - VISA instrument control - **pyvisa** (>=1.13.0) - VISA instrument control
- **pyvisa-py** (>=0.7.0) - Pure Python VISA backend - **pyvisa-py** (>=0.7.0) - Pure Python VISA backend
- **pyftdi** (>=0.54.0) - FTDI USB device support - **pyftdi** (>=0.54.0) - FTDI USB device support
- **numpy** (>=1.20.0) - Array processing
- **scipy** (>=1.10) - Signal processing (viewer SAW pipeline)
- **matplotlib** (>=3.7) - Plotting (viewer, live scan preview)
- **pyueye** (>=4.95.0) - IDS uEye camera SDK bindings (camera only)
## Known hardware caveats
`hardware/genesis_core.py` is quarantined: it diverges from the reference
implementation in `tools/genesis_laser_gui.py` in ways that need the laser
on the bench to settle. See [KNOWN_ISSUES.md](KNOWN_ISSUES.md) and
[docs/genesis_verification.md](docs/genesis_verification.md) before
changing either file.
## Usage Examples ## Usage Examples
### Stage Control ### Running a scan without any GUI
The acquisition sequence lives in `core.scan_engine` and takes plain
drivers plus callbacks, so a script (or a future simpler GUI) can drive the
identical scan the main app runs:
```python ```python
from hardware.bbd202 import BBD202Controller from pathlib import Path
from core.scan_engine import ScanCallbacks, ScanEngine
from core.scan_geometry import build_plan
from core.rotation import RotationAxis
from hardware.pybbd202 import ThorlabsServoDriver
from hardware.tektronix_base import TektronixOscilloscopeBase
from hardware.t3r_driver import T3RDriver
# BBD202/BBD203 controller example plan = build_plan(x_start=10.0, y_start=10.0, x_delta=20.0, y_delta=10.0,
controller = BBD202Controller() num_angles=3, row_spacing=0.25,
controller.connect("/dev/ttyUSB0") # Serial port laser_freq_hz=20000.0, velocity_mm_s=100.0)
# Use controller for stage operations
stage = ThorlabsServoDriver(); stage.connect("/dev/ttyUSB0")
scope = TektronixOscilloscopeBase("192.168.100.105"); scope.connect()
t3r = T3RDriver(); t3r.open("/dev/ttyACM0")
engine = ScanEngine(stage, scope, RotationAxis(t3r), plan,
Path("/data/SRAS/demo.sras"),
callbacks=ScanCallbacks(on_status=print,
prompt=lambda t, m: input(f"{t}: {m} ")))
result = engine.run() # blocking; engine.abort() is thread-safe
print(f"wrote {result.rows_written} rows to {result.path}")
``` ```
### Oscilloscope Acquisition ### Running a SAW quality check
Same engine, same hardware sequence — the plan is reduced to one row per
angle and the result is tagged v10 so the viewer knows it is a check rather
than a scan cut short:
```python ```python
from core.saw_check import alignment_summary, frequency_traces, middle_row_plan
from core.sras_format import VERSION_SAW_CHECK, SrasFile
check = middle_row_plan(plan) # the plan above: 163 rows → 3
engine = ScanEngine(stage, scope, RotationAxis(t3r), check,
Path("/data/SRAS/demo-sawcheck.sras"),
callbacks=ScanCallbacks(on_status=print),
file_version=VERSION_SAW_CHECK)
engine.run()
with SrasFile("/data/SRAS/demo-sawcheck.sras") as sras:
traces = frequency_traces(sras, dc_threshold_mv=50.0)
for t in traces:
print(f"{t.angle_deg:+7.1f}° {t.median_mhz:.2f} MHz "
f"drift {t.drift_mhz_per_mm:+.3f} MHz/mm")
print(alignment_summary(traces).describe())
```
`saw_check_viewer.py` is the same read-out with the curves drawn.
### Reading a scan file
`SrasFile` memory-maps the data block, so opening a multi-gigabyte scan
costs only the pages actually touched:
```python
from core.sras_format import SrasFile
from core.sras_analysis import CH4_IDX, ChannelCalibration, compute_dc_image
with SrasFile("/data/SRAS/demo.sras") as sras:
print(sras.header.n_angles, "angles")
for st in sras.angle_status(): # handles aborted/partial files
print(f" angle {st.index}: {st.n_rows_available}/{st.n_rows} rows ({st.status})")
view = sras.load_angle(0) # (rows, channels, frames, samples)
calib = ChannelCalibration.from_preambles(sras.preambles)
dc_mv = calib.adc_to_mv(compute_dc_image(view, CH4_IDX), CH4_IDX)
```
### Stage control
```python
from hardware.pybbd202 import AXIS_X, AXIS_Y, ThorlabsServoDriver
stage = ThorlabsServoDriver()
stage.connect("/dev/ttyUSB0") # raises if no bay responds
stage.enable_axis(AXIS_X)
stage.home_axis(AXIS_X, timeout=120.0)
stage.move_axis_absolute(AXIS_X, 25.0, timeout=30.0)
```
### Oscilloscope acquisition
```python
from core.scope_sras import configure_acquisition, configure_channels
from hardware.tektronix_base import TektronixOscilloscopeBase from hardware.tektronix_base import TektronixOscilloscopeBase
scope = TektronixOscilloscopeBase() scope = TektronixOscilloscopeBase("192.168.100.105", port=4000)
scope.connect("192.168.1.100", 4000) scope.connect()
scope.set_acquire_mode("SAMPLE") configure_channels(scope) # standard SRAS front-end setup
waveform = scope.get_curve_binary(1) # Channel 1 samples_per_frame = configure_acquisition(scope)
``` ```
### Laser Control ### Laser control
```python ```python
from hardware.coherent_hops_laser import CoherentHOPSLaser from hardware.helios_laser import HeliosLaser
laser = CoherentHOPSLaser() laser = HeliosLaser()
laser.connect() laser.connect("/dev/ttyUSB1")
laser.set_power_level(50.0) # 50% power laser.set_current_ma(1200)
laser.enable_output(True) laser.set_laser_enable(True)
print(laser.get_diode_temp_c(), "°C")
laser.disconnect() # always explicit — no __del__
``` ```
### Camera Control ### Camera control
```python ```python
from hardware.uc480_camera import UC480Camera from hardware.uc480_camera import UC480Camera, find_camera_bus_conflicts
camera = UC480Camera(camera_id=0) find_camera_bus_conflicts() # warns about USB bus contention
camera = UC480Camera(camera_id=1)
camera.initialize() camera.initialize()
camera.start_capture() camera.start_capture()
# Camera operations
``` ```
## Configuration ## Configuration
### Stage Settings ### Persisted settings
Stage configuration is stored in `~/.nuescan/stage_settings.json`: `aui_defaults.json` holds the ports, scope IP, and save directory the main
- Velocity and acceleration profiles app last used. It is read and written through `core.config.ScanDefaults`,
- Trigger configuration which always writes every field — see KNOWN_ISSUES.md history for why
- Axis limits and safety parameters partial writes were a problem.
### Serial Port Configuration ### Fixed acquisition settings
Hardware devices are accessed via: Scan velocity, laser frequency, sample rate, and the ramp geometry are
- **BBD202/203**: USB with automatic serial number detection constants in `core/scan_engine.py` and `core/scope_sras.py`, not user
- **Helios**: RS-232 serial port (9600 baud, 8N1) settings; a `.sras` file records them so resume can refuse a mismatch.
- **HOPS Laser**: FTDI USB (I2C interface)
### Serial port configuration
- **BBD202**: USB serial, APT protocol (`/dev/ttyUSB*`)
- **T3R**: USB serial, custom binary framing (`/dev/ttyACM*`)
- **Helios**: RS-232 (9600 baud, 8N1)
- **Genesis**: USB serial, I2C-over-serial
- **Oscilloscope**: Ethernet/LXI (TCP socket on port 4000) - **Oscilloscope**: Ethernet/LXI (TCP socket on port 4000)
## Development ## Development
SETUP.md
+25 -65
View File
@@ -91,11 +91,10 @@ lsusb | grep -i thorlabs
**First-time setup:** **First-time setup:**
```bash ```bash
# Run the stage test application # Run the stage test application
python stage_test_app.py python bbd202_test_app.py
# Enter your BBD203 serial number # Set the serial port, click Connect (it now fails loudly if no bay
# Click "Connect" to test the connection # responds), then Home to verify operation.
# Use "Home All Axes" to verify operation
``` ```
### Helios Laser System ### Helios Laser System
@@ -132,10 +131,15 @@ python -c "from pyftdi.ftdi import Ftdi; Ftdi.show_devices()"
**First-time setup:** **First-time setup:**
```bash ```bash
# Test laser connection # Test the Genesis laser connection
python -c "from hardware.coherent_hops_laser import CoherentHOPSLaser; laser = CoherentHOPSLaser(); print('Connected:', laser.connect())" python tools/genesis_laser_control.py
``` ```
> Before changing any Genesis code, read
> [docs/genesis_verification.md](docs/genesis_verification.md) — the two
> implementations in the repo disagree on ADC scaling, LDD polarity, and
> shutter behaviour, and only the bench can settle it.
### Tektronix Oscilloscope ### Tektronix Oscilloscope
**Connection:** **Connection:**
@@ -228,65 +232,21 @@ Main window settings (geometry, last used values) are stored in Qt settings:
## Project Structure ## Project Structure
``` See the tree in [README.md](README.md#project-structure). In short: `core/`
scanengine-3/ is the headless scan engine and file format (no PyQt6, no vendor SDKs),
│ `hardware/` holds the Qt-free device drivers, `gui/` the shared PyQt6
├── scanengine/ # Main application package adapters and widgets, and the root `*.py` files are the runnable apps.
│ ├── __init__.py
│ ├── app.py # Main application entry point ## Vendored camera SDK (`lib/`)
│ ├── main_launcher.ui # Main launcher UI
│ ├── new_scan_wizard.ui # Scan wizard UI `lib/` is gitignored, so a fresh clone does not have it. The IDS uEye
│ └── options.ui # Options dialog UI runtime (`libueye_api64.so.3.82`) must come from the IDS SDK installation
│ matching the camera firmware on this rig.
├── hardware/ # Hardware driver package
│ ├── __init__.py `lib/ueye_loader.{c,so}` is an `LD_PRELOAD` shim that dlopens
│ ├── bbd202.py # ThorLabs stage controller `/usr/lib/libueye_api.so` before Python starts. Nothing in the repo
│ ├── uc480_camera.py # IDS/ThorLabs camera references it and no launcher sets `LD_PRELOAD`, so whether it is still
│ ├── tektronix_base.py # Tektronix oscilloscope needed is an open question — see [KNOWN_ISSUES.md](KNOWN_ISSUES.md).
│ ├── coherent_hops_laser.py # Coherent HOPS laser
│ └── genesis_core.py # Genesis laser core logic
│
├── scanning/ # Scan planning package
│ ├── __init__.py
│ ├── sc3_scan_model.py # Scan model
│ └── stage_scan_plan_generator.py # Scan path planning
│
├── tools/ # Standalone executable tools
│ ├── genesis_laser_control.py # Standalone Genesis app
│ └── genesis_laser_gui.py # Alternative Genesis GUI
│
├── tests/ # Test files
│ ├── __init__.py
│ ├── test_camera_integration.py
│ ├── test_genesis_connection.py
│ ├── test_genesis_protocol.py
│ ├── test_rotated_aoi.py
│ └── test_temperature_scaling.py
│
├── docs/ # Documentation
│ ├── hardware/ # Hardware documentation
│ │ ├── BBD203_CONNECTION_GUIDE.md
│ │ ├── BBD203_Communications_Protocol.md
│ │ ├── BBD203_DRIVER_README.md
│ │ ├── HELIOS_DRIVER_README.md
│ │ ├── GENESIS_LASER_README.md
│ │ └── laser_control_implementation_guide.md
│ └── protocols/ # Protocol specifications
│ ├── apt_communications_protocol.pdf
│ ├── helios_comms_protocol.pdf
│ └── thorlabs_mls_protocol.pdf
│
├── lib/ # Binary libraries (not in git)
│ ├── libueye_api64.so.3.82
│ ├── ueye_loader.c
│ └── ueye_loader.so
│
├── config.json # System configuration
├── requirements.txt # Python dependencies
├── README.md # Project overview
├── SETUP.md # This file
└── LICENSE # License file
```
## Troubleshooting ## Troubleshooting
app.py
-615
View File
@@ -1,615 +0,0 @@
#!/usr/bin/env python3
"""
Scanengine 3 Main Application
"""
import sys
import json
from pathlib import Path
from PyQt6 import QtWidgets, QtCore
from typing import Optional
import serial.tools.list_ports
from hardware.coherent_hops_laser import CoherentHOPSLaser, DummyLaser
from hardware.helios_laser import HeliosLaser, PulseMode
from hardware.uc480_camera import UC480Camera, CameraStreamThread
from hardware.pybbd202 import ThorlabsServoDriver, AXIS_X, AXIS_Y, TriggerBitsServo
from hardware.t3r_driver import T3RDriver
from motion_worker import MotionWorker
from scanning.stage_scan_plan_generator import StageScanPlanGenerator
from genesis_worker import GenesisWorker, GenesisCommand
from t3r_control_panel import T3RControlPanel
from ui_mainwindow import Ui_MainWindow
# Page indices in stackedWidget
PAGE_START = 0
PAGE_OPTIONS = 1
PAGE_NEWSCAN = 2
PAGE_CONTINUESCAN = 3
PAGE_SCAN_PROGRESS = 4
CONFIG_PATH = Path(__file__).parent / "config.json"
DEFAULT_CONFIG = {
"stage": {
"serial_port": "",
"trigger": "Disabled",
"scan_velocity_mm_s": 200.0,
"scan_acceleration_mm_s2": 500.0,
"optical_axis_x_mm": 0.0,
"optical_axis_y_mm": 0.0,
},
"fpga": {
"serial_port": "",
"pulse_divider": 1,
"rowpack_enabled": False,
},
"t3r": {
"serial_port": "",
"t_axis_current_ma": 0.0,
"gr_axis_current_ma": 0.0,
"t_axis_microstepping": "Full Step",
"gr_axis_microstepping": "Full Step",
},
"oscilloscope": {
"ip_address": "",
},
"generation_laser": {
"serial_port": "",
"pulse_frequency_hz": 125000,
"diode_pump_current_ma": 0.0,
},
"detection_laser": {
"power_mw": 0.0,
},
"genesis_laser": {
"com_port": "/dev/ttyUSB0",
},
}
# Fixed option lists for combo boxes
TRIGGER_OPTIONS = [
"Disabled",
"Trigger Out: In Motion",
"Trigger Out: Motion Complete",
"Trigger Out: Max Velocity",
"Trigger Out: High at Max Velocity",
]
MICROSTEPPING_OPTIONS = [
"Full Step",
"Half Step",
"1/4 Step",
"1/8 Step",
"1/16 Step",
"1/32 Step",
]
class ScanWorker(QtCore.QObject):
"""Worker object for handling scanning in a separate thread."""
scan_started = QtCore.pyqtSignal()
scan_completed = QtCore.pyqtSignal()
scan_failed = QtCore.pyqtSignal(str)
angle_started = QtCore.pyqtSignal(int, int)
line_started = QtCore.pyqtSignal(int, int, float)
current_progress = QtCore.pyqtSignal(int)
overall_progress = QtCore.pyqtSignal(int)
status_message = QtCore.pyqtSignal(str)
def __init__(self, scan_params, motion_worker, t3r_driver=None):
super().__init__()
self.scan_params = scan_params
self.motion_worker = motion_worker
self.t3r_driver = t3r_driver
self.should_stop = False
@QtCore.pyqtSlot()
def run_scan(self):
"""Execute the full scanning process."""
if self.motion_worker:
self.motion_worker.scanning_active = True
try:
self.scan_started.emit()
num_angles = self.scan_params.get("num_angles", 1)
angle_step = 360.0 / num_angles if num_angles > 1 else 0.0
gr_microsteps = self.scan_params.get("gr_axis_microsteps", 16)
for angle_idx in range(num_angles):
if self.should_stop:
break
self.angle_started.emit(angle_idx, num_angles)
self.status_message.emit(
f"Scanning angle {angle_idx + 1}/{num_angles}")
# TODO: execute scan lines for this angle via motion_worker
if angle_idx < num_angles - 1 and angle_step and self.t3r_driver:
if self.t3r_driver.is_open:
self.status_message.emit(
f"Rotating stage {angle_step:.3f}° for next angle…")
self.t3r_driver.rotate_stage(
angle_step,
gr_microsteps,
self.scan_params.get("rotation_velocity", 8000),
self.scan_params.get("rotation_accel", 4000),
)
# TODO: wait for MOTION_DONE event before proceeding
self.scan_completed.emit()
except Exception as e:
self.scan_failed.emit(str(e))
finally:
if self.motion_worker:
self.motion_worker.scanning_active = False
def stop(self):
self.should_stop = True
class MainWindow(QtWidgets.QMainWindow):
def __init__(self):
super().__init__()
self.ui = Ui_MainWindow()
self.ui.setupUi(self)
self.config = self._load_config()
# Hardware objects
self.motion_worker: Optional[MotionWorker] = None
self.motion_thread: Optional[QtCore.QThread] = None
self.genesis_worker: Optional[GenesisWorker] = None
self.genesis_thread: Optional[QtCore.QThread] = None
self.camera: Optional[UC480Camera] = None
self.camera_stream: Optional[CameraStreamThread] = None
self.vis_laser: Optional[CoherentHOPSLaser] = None
self.ir_laser: Optional[HeliosLaser] = None
self.scan_worker: Optional[ScanWorker] = None
self.scan_thread: Optional[QtCore.QThread] = None
# T3R focusing / rotation driver (lives in main thread; reader runs internally)
self.t3r_driver = T3RDriver(self)
self.t3r_panel: Optional[T3RControlPanel] = None
self._connect_signals()
self._init_genesis_worker()
self._init_t3r_menu()
self.ui.stackedWidget.setCurrentIndex(PAGE_START)
# ------------------------------------------------------------------
# Config
# ------------------------------------------------------------------
def _load_config(self) -> dict:
if CONFIG_PATH.exists():
try:
with open(CONFIG_PATH) as f:
cfg = json.load(f)
for section, values in DEFAULT_CONFIG.items():
cfg.setdefault(section, {})
for key, val in values.items():
cfg[section].setdefault(key, val)
return cfg
except Exception:
pass
return {k: dict(v) for k, v in DEFAULT_CONFIG.items()}
def _save_config(self):
with open(CONFIG_PATH, "w") as f:
json.dump(self.config, f, indent=2)
# ------------------------------------------------------------------
# Signal wiring
# ------------------------------------------------------------------
def _connect_signals(self):
# Start page
self.ui.start_new_scan_btn.clicked.connect(self._go_to_newscan)
self.ui.resume_scan_btn.clicked.connect(self._go_to_continuescan)
self.ui.edit_options_btn.clicked.connect(self._go_to_options)
# Options page
self.ui.options_save_settings_btn.clicked.connect(self._on_options_save)
self.ui.options_cancel_btn.clicked.connect(self._go_to_start)
self.ui.stage_test_connection_btn.clicked.connect(self._on_test_stage_connection)
self.ui.fpga_connect_button.clicked.connect(self._on_fpga_connect)
self.ui.fpga_refresh_ports_btn.clicked.connect(self._on_fpga_refresh_ports)
self.ui.refresh_serial_ports_btn.clicked.connect(self._on_refresh_serial_ports)
self.ui.scope_connect_btn.clicked.connect(self._on_scope_connect)
self.ui.generation_connect_button.clicked.connect(self._on_generation_connect)
self.ui.detection_test_btn.clicked.connect(self._on_detection_test)
self.ui.t3r_connect_btn.clicked.connect(self._on_t3r_connect)
self.ui.t3r_refresh_ports_btn.clicked.connect(self._on_t3r_refresh_ports)
# New scan page
self.ui.newscan_browse_folders_btn.clicked.connect(self._on_newscan_browse)
self.ui.newscan_set_current_as_start_btn.clicked.connect(self._on_newscan_set_start)
self.ui.newscan_get_delta_from_current_btn.clicked.connect(self._on_newscan_get_delta)
self.ui.newscan_toggle_vis_laser_btn.clicked.connect(self._on_newscan_toggle_vis_laser)
self.ui.newscan_continue_to_next_btn.clicked.connect(self._on_newscan_start_scan)
self.ui.newscan_jog_x_pos_btn.pressed.connect(self._on_jog_x_pos_pressed)
self.ui.newscan_jog_x_pos_btn.released.connect(self._on_jog_stop)
self.ui.newscan_jog_x_neg_btn.pressed.connect(self._on_jog_x_neg_pressed)
self.ui.newscan_jog_x_neg_btn.released.connect(self._on_jog_stop)
self.ui.newscan_jog_y_pos_btn.pressed.connect(self._on_jog_y_pos_pressed)
self.ui.newscan_jog_y_pos_btn.released.connect(self._on_jog_stop)
self.ui.newscan_jog_y_neg_btn.pressed.connect(self._on_jog_y_neg_pressed)
self.ui.newscan_jog_y_neg_btn.released.connect(self._on_jog_stop)
# Continue scan page
self.ui.continuescan_resume_scans.clicked.connect(self._on_resume_scan)
# Scan progress page
self.ui.abort_scan_button.clicked.connect(self._on_abort_scan)
# ------------------------------------------------------------------
# Navigation
# ------------------------------------------------------------------
def _go_to_start(self):
self.ui.stackedWidget.setCurrentIndex(PAGE_START)
def _go_to_options(self):
self._populate_options_page()
self.ui.stackedWidget.setCurrentIndex(PAGE_OPTIONS)
def _go_to_newscan(self):
self._populate_newscan_page()
self.ui.stackedWidget.setCurrentIndex(PAGE_NEWSCAN)
def _go_to_continuescan(self):
self._populate_continuescan_page()
self.ui.stackedWidget.setCurrentIndex(PAGE_CONTINUESCAN)
def _go_to_scan_progress(self):
self.ui.stackedWidget.setCurrentIndex(PAGE_SCAN_PROGRESS)
# ------------------------------------------------------------------
# Options page
# ------------------------------------------------------------------
def _get_serial_ports(self) -> list[str]:
return sorted(p.device for p in serial.tools.list_ports.comports())
def _populate_combo(self, combo: QtWidgets.QComboBox, items: list[str], current: str):
"""Refill a combo box, re-selecting `current` if present."""
combo.blockSignals(True)
combo.clear()
combo.addItems(items)
idx = combo.findText(current)
if idx >= 0:
combo.setCurrentIndex(idx)
elif current:
combo.insertItem(0, current)
combo.setCurrentIndex(0)
combo.blockSignals(False)
def _populate_options_page(self):
cfg = self.config
ports = self._get_serial_ports()
# ---- Kinematics tab ----
self.ui.scan_velocity_edit.setText(str(cfg["stage"]["scan_velocity_mm_s"]))
self.ui.scan_accel_edit.setText(str(cfg["stage"]["scan_acceleration_mm_s2"]))
self.ui.optical_axis_x_edit.setText(str(cfg["stage"]["optical_axis_x_mm"]))
self.ui.optical_axis_y_edit.setText(str(cfg["stage"]["optical_axis_y_mm"]))
self.ui.stage_serial_edit.setText(cfg["stage"]["serial_port"])
self._populate_combo(self.ui.stage_trigger_combo, TRIGGER_OPTIONS, cfg["stage"]["trigger"])
# ---- Detection / VIS tab ----
self.ui.detection_power_edit.setText(str(cfg["detection_laser"]["power_mw"]))
# ---- Generation / IR tab ----
self._populate_combo(self.ui.comboBox, ports, cfg["generation_laser"]["serial_port"])
self.ui.generation_pulse_freq_edit.setText(str(cfg["generation_laser"]["pulse_frequency_hz"]))
self.ui.diode_pump_current_edit.setText(str(cfg["generation_laser"]["diode_pump_current_ma"]))
# ---- PulseDecimator tab ----
self._populate_combo(self.ui.fpga_serial_port, ports, cfg["fpga"]["serial_port"])
self.ui.fpga_divider_value_edit.setText(str(cfg["fpga"]["pulse_divider"]))
self.ui.checkBox.setChecked(cfg["fpga"]["rowpack_enabled"])
# ---- T3R-SL tab ----
self._populate_combo(self.ui.t3r_serial_port_edit, ports, cfg["t3r"]["serial_port"])
self.ui.lineEdit.setText(str(cfg["t3r"]["t_axis_current_ma"]))
self.ui.lineEdit_2.setText(str(cfg["t3r"]["gr_axis_current_ma"]))
self._populate_combo(self.ui.comboBox_2, MICROSTEPPING_OPTIONS, cfg["t3r"]["t_axis_microstepping"])
self._populate_combo(self.ui.comboBox_3, MICROSTEPPING_OPTIONS, cfg["t3r"]["gr_axis_microstepping"])
# ---- Oscilloscope tab ----
self.ui.scope_ip_address_edit.setText(cfg["oscilloscope"]["ip_address"])
def _on_options_save(self):
try:
# Kinematics
self.config["stage"]["scan_velocity_mm_s"] = float(self.ui.scan_velocity_edit.text())
self.config["stage"]["scan_acceleration_mm_s2"] = float(self.ui.scan_accel_edit.text())
self.config["stage"]["optical_axis_x_mm"] = float(self.ui.optical_axis_x_edit.text())
self.config["stage"]["optical_axis_y_mm"] = float(self.ui.optical_axis_y_edit.text())
self.config["stage"]["serial_port"] = self.ui.stage_serial_edit.text().strip()
self.config["stage"]["trigger"] = self.ui.stage_trigger_combo.currentText()
# Detection / VIS
self.config["detection_laser"]["power_mw"] = float(self.ui.detection_power_edit.text())
# Generation / IR
self.config["generation_laser"]["serial_port"] = self.ui.comboBox.currentText()
self.config["generation_laser"]["pulse_frequency_hz"] = int(self.ui.generation_pulse_freq_edit.text())
self.config["generation_laser"]["diode_pump_current_ma"] = float(self.ui.diode_pump_current_edit.text())
# PulseDecimator
self.config["fpga"]["serial_port"] = self.ui.fpga_serial_port.currentText()
self.config["fpga"]["pulse_divider"] = int(self.ui.fpga_divider_value_edit.text())
self.config["fpga"]["rowpack_enabled"] = self.ui.checkBox.isChecked()
# T3R-SL
self.config["t3r"]["serial_port"] = self.ui.t3r_serial_port_edit.currentText()
self.config["t3r"]["t_axis_current_ma"] = float(self.ui.lineEdit.text())
self.config["t3r"]["gr_axis_current_ma"] = float(self.ui.lineEdit_2.text())
self.config["t3r"]["t_axis_microstepping"] = self.ui.comboBox_2.currentText()
self.config["t3r"]["gr_axis_microstepping"] = self.ui.comboBox_3.currentText()
# Oscilloscope
self.config["oscilloscope"]["ip_address"] = self.ui.scope_ip_address_edit.text().strip()
except ValueError as e:
QtWidgets.QMessageBox.warning(self, "Invalid input", str(e))
return
self._save_config()
self._go_to_start()
def _refresh_serial_ports_for_combos(self, *combos: QtWidgets.QComboBox):
"""Re-populate serial port combos, preserving current selections."""
ports = self._get_serial_ports()
for combo in combos:
self._populate_combo(combo, ports, combo.currentText())
def _on_refresh_serial_ports(self):
self._refresh_serial_ports_for_combos(self.ui.comboBox)
def _on_fpga_refresh_ports(self):
self._refresh_serial_ports_for_combos(self.ui.fpga_serial_port)
def _on_t3r_refresh_ports(self):
self._refresh_serial_ports_for_combos(self.ui.t3r_serial_port_edit)
def _on_test_stage_connection(self):
pass # TODO
def _on_fpga_connect(self):
pass # TODO
def _on_scope_connect(self):
pass # TODO
def _on_generation_connect(self):
pass # TODO
def _on_detection_test(self):
pass # TODO
def _on_t3r_connect(self):
port = self.ui.t3r_serial_port_edit.currentText().split(" ")[0]
self._show_t3r_panel()
if port and not self.t3r_driver.is_open:
try:
self.t3r_driver.connect(port)
except Exception as exc:
QtWidgets.QMessageBox.warning(self, "T3R Connect", str(exc))
# ------------------------------------------------------------------
# New scan page
# ------------------------------------------------------------------
def _populate_newscan_page(self):
self.ui.newscan_save_directory_edit.setText(str(Path.home() / "scans"))
def _on_newscan_browse(self):
directory = QtWidgets.QFileDialog.getExistingDirectory(self, "Select save directory")
if directory:
self.ui.newscan_save_directory_edit.setText(directory)
def _on_newscan_set_start(self):
pass # TODO: capture current stage position as scan start
def _on_newscan_get_delta(self):
pass # TODO: capture current stage position as scan end (compute delta)
def _on_newscan_toggle_vis_laser(self):
pass # TODO: toggle vis laser on/off
def _on_newscan_start_scan(self):
scan_params = self._build_scan_params()
if scan_params is None:
return
self._start_scan(scan_params)
def _build_scan_params(self) -> Optional[dict]:
"""Read newscan page widgets and return scan parameter dict, or None on error."""
try:
x_start = float(self.ui.newscan_start_x_coord_edit.text())
y_start = float(self.ui.newscan_start_y_coord_edit.text())
x_delta = float(self.ui.newscan_delta_x_coord_edit.text())
y_delta = float(self.ui.newscan_delta_y_coord_edit.text())
except ValueError:
QtWidgets.QMessageBox.warning(self, "Invalid input", "Scan coordinates must be numbers.")
return None
pixel_size_map = {
self.ui.newscan_50_micron_radio: 0.05,
self.ui.newscan_100_micron_radio: 0.10,
self.ui.newscan_250_micron_radio: 0.25,
}
row_spacing = next(
(v for btn, v in pixel_size_map.items() if btn.isChecked()), 0.10
)
return {
"x_start_mm": x_start,
"y_start_mm": y_start,
"x_delta_mm": x_delta,
"y_delta_mm": y_delta,
"row_spacing_mm": row_spacing,
"num_angles": int(self.ui.newscan_num_angles_combo.currentText()),
"friendly_name": self.ui.newscan_friendly_name_edit.text(),
"file_prefix": self.ui.newcsan_file_prefix_edit.text(),
"save_directory": self.ui.newscan_save_directory_edit.text(),
"scan_velocity_mm_s": self.config["stage"]["scan_velocity_mm_s"],
"scan_acceleration_mm_s2": self.config["stage"]["scan_acceleration_mm_s2"],
# T3R rotation between angles (GR-axis, ch1)
"gr_axis_microsteps": 16,
"rotation_velocity": 8000,
"rotation_accel": 4000,
}
# ------------------------------------------------------------------
# Jog controls
# ------------------------------------------------------------------
def _on_jog_x_pos_pressed(self):
pass # TODO
def _on_jog_x_neg_pressed(self):
pass # TODO
def _on_jog_y_pos_pressed(self):
pass # TODO
def _on_jog_y_neg_pressed(self):
pass # TODO
def _on_jog_stop(self):
pass # TODO
# ------------------------------------------------------------------
# Continue scan page
# ------------------------------------------------------------------
def _populate_continuescan_page(self):
pass # TODO: populate list of interrupted scans
def _on_resume_scan(self):
pass # TODO: resume selected scan
# ------------------------------------------------------------------
# Scan execution
# ------------------------------------------------------------------
def _start_scan(self, scan_params: dict):
self.scan_thread = QtCore.QThread()
self.scan_worker = ScanWorker(scan_params, self.motion_worker, self.t3r_driver)
self.scan_worker.moveToThread(self.scan_thread)
self.scan_thread.started.connect(self.scan_worker.run_scan)
self.scan_worker.scan_started.connect(self._on_scan_started)
self.scan_worker.scan_completed.connect(self._on_scan_completed)
self.scan_worker.scan_failed.connect(self._on_scan_failed)
self.scan_worker.current_progress.connect(self.ui.scanning_scan_progbar.setValue)
self.scan_worker.overall_progress.connect(self.ui.scanning_overall_progbar.setValue)
self.scan_worker.status_message.connect(self.ui.scanning_stage_state_label.setText)
self._go_to_scan_progress()
self.scan_thread.start()
@QtCore.pyqtSlot()
def _on_scan_started(self):
self.ui.abort_scan_button.setEnabled(True)
@QtCore.pyqtSlot()
def _on_scan_completed(self):
self._cleanup_scan_thread()
QtWidgets.QMessageBox.information(self, "Scan complete", "Scan finished successfully.")
self._go_to_start()
@QtCore.pyqtSlot(str)
def _on_scan_failed(self, error: str):
self._cleanup_scan_thread()
QtWidgets.QMessageBox.critical(self, "Scan failed", error)
self._go_to_start()
def _on_abort_scan(self):
if self.scan_worker:
self.scan_worker.stop()
def _cleanup_scan_thread(self):
if self.scan_thread:
self.scan_thread.quit()
self.scan_thread.wait()
self.scan_thread = None
self.scan_worker = None
# ------------------------------------------------------------------
# T3R focusing / rotation panel
# ------------------------------------------------------------------
def _init_t3r_menu(self):
"""Add a Hardware menu with a T3R panel toggle action."""
hw_menu = self.menuBar().addMenu("Hardware")
self._t3r_action = hw_menu.addAction("T3R Focusing && Rotation…")
self._t3r_action.setCheckable(True)
self._t3r_action.setShortcut("Ctrl+T")
self._t3r_action.triggered.connect(self._on_t3r_action_toggled)
def _show_t3r_panel(self):
if self.t3r_panel is None:
self.t3r_panel = T3RControlPanel(self.t3r_driver, self)
self.t3r_panel.finished.connect(
lambda: self._t3r_action.setChecked(False))
self.t3r_panel.show()
self.t3r_panel.raise_()
self._t3r_action.setChecked(True)
def _on_t3r_action_toggled(self, checked: bool):
if checked:
self._show_t3r_panel()
elif self.t3r_panel is not None:
self.t3r_panel.hide()
# ------------------------------------------------------------------
# Genesis laser worker
# ------------------------------------------------------------------
def _init_genesis_worker(self):
com_port = self.config.get("genesis_laser", {}).get("com_port", "/dev/ttyUSB0")
self.genesis_worker = GenesisWorker(com_port)
self.genesis_thread = QtCore.QThread()
self.genesis_worker.moveToThread(self.genesis_thread)
self.genesis_thread.started.connect(self.genesis_worker.run)
self.genesis_thread.start()
def _cleanup_genesis_worker(self):
if self.genesis_worker:
self.genesis_worker.stop()
if self.genesis_thread:
self.genesis_thread.quit()
self.genesis_thread.wait()
self.genesis_worker = None
self.genesis_thread = None
# ------------------------------------------------------------------
# Lifecycle
# ------------------------------------------------------------------
def closeEvent(self, event):
if self.t3r_driver.is_open:
self.t3r_driver.disconnect()
self._cleanup_genesis_worker()
self._cleanup_scan_thread()
if self.motion_thread:
self.motion_thread.quit()
self.motion_thread.wait()
super().closeEvent(event)
def main():
app = QtWidgets.QApplication(sys.argv)
qss_path = Path(__file__).parent / "app_style.qss"
if qss_path.exists():
app.setStyleSheet(qss_path.read_text())
window = MainWindow()
window.show()
sys.exit(app.exec())
if __name__ == "__main__":
main()
bbd202_test_app.py
+2 -2
View File
@@ -12,10 +12,10 @@ import time
from PyQt6.QtWidgets import ( from PyQt6.QtWidgets import (
QApplication, QMainWindow, QWidget, QVBoxLayout, QHBoxLayout, QApplication, QMainWindow, QWidget, QVBoxLayout, QHBoxLayout,
QGroupBox, QLabel, QLineEdit, QPushButton, QComboBox, QDoubleSpinBox, QGroupBox, QLabel, QLineEdit, QPushButton, QComboBox, QDoubleSpinBox,
QStatusBar, QMessageBox, QGridLayout, QCheckBox, QFrame QStatusBar, QMessageBox, QGridLayout
) )
from PyQt6.QtCore import Qt, QThread, pyqtSignal, QObject, QTimer from PyQt6.QtCore import Qt, QThread, pyqtSignal, QObject, QTimer
from PyQt6.QtGui import QFont, QKeySequence, QShortcut from PyQt6.QtGui import QFont
from hardware.pybbd202 import ThorlabsServoDriver, AXIS_X, AXIS_Y from hardware.pybbd202 import ThorlabsServoDriver, AXIS_X, AXIS_Y
from hardware.pybbd202.apt_constants import TriggerBitsServo from hardware.pybbd202.apt_constants import TriggerBitsServo
camera_test_app.py
+2 -2
View File
@@ -10,9 +10,9 @@ import logging
from PyQt6.QtWidgets import ( from PyQt6.QtWidgets import (
QApplication, QMainWindow, QWidget, QVBoxLayout, QHBoxLayout, QApplication, QMainWindow, QWidget, QVBoxLayout, QHBoxLayout,
QGroupBox, QLabel, QPushButton, QDoubleSpinBox, QSpinBox, QGroupBox, QLabel, QPushButton, QDoubleSpinBox, QSpinBox,
QStatusBar, QSizePolicy QSizePolicy
) )
from PyQt6.QtCore import Qt, QTimer from PyQt6.QtCore import Qt
from PyQt6.QtGui import QPixmap, QImage from PyQt6.QtGui import QPixmap, QImage
from hardware.uc480_camera import UC480Camera, CameraStreamThread from hardware.uc480_camera import UC480Camera, CameraStreamThread
config.json
-31
View File
@@ -1,31 +0,0 @@
{
"genesis_laser": {
"com_port": "/dev/ttyUSB0"
},
"detection_laser": {
"scan_power_mw": "125"
},
"generation_laser": {
"com_port": "/dev/ttyACM0",
"frequency_hz": "20000",
"pump_diode_current_ma": "750",
"focusing_frequency_hz": "20000",
"focusing_pump_current_ma": "300"
},
"scanning_stage": {
"scan_velocity_mm_s": "200",
"scan_acceleration_mm_s2": "1500",
"x_trigger_mode": 6,
"y_trigger_mode": 0,
"optical_axis_x_mm": "55",
"optical_axis_y_mm": "37.5"
},
"t3r": {
"com_port": "/dev/ttyUSB0"
},
"oscilloscope": {
"socket_address": "192.168.0.1",
"scratch_directory": "/opt/",
"save_location": "pc"
}
}
core/__init__.py
+1
View File
@@ -0,0 +1 @@
"""Headless scan-engine core: importable without PyQt6 or any vendor SDK."""
core/angle_inspect.py
+251
View File
@@ -0,0 +1,251 @@
"""Pre-scan angle inspection: park the rig on a point and let the operator look.
A multi-angle scan can take hours, and an angle that responds poorly produces
rows that look fine in the file but carry no usable SAW packet. This drives
the rig through the same angles the scan will use, parking at a random point
inside each angle's own bounding box so the response can be judged on the
oscilloscope before committing to the run.
Headless and Qt-free, like ScanEngine: gui/inspect_bridge.py wraps it.
No waveform ever crosses this boundary. The operator reads the scope screen
directly; this module's job is only to put the hardware in the right place and
the scope in a state worth looking at (see core.scope_inspect).
"""
from __future__ import annotations
import logging
import random
from dataclasses import dataclass
from typing import Callable
from core import scope_inspect
from core.rotation import RotationAxis
from core.scan_engine import (
AXIS_X, AXIS_Y, SCAN_ACCEL_MM_S2, SCAN_VELOCITY_MM_S,
)
from core.scan_geometry import DEFAULT_STAGE_LIMITS, ScanPlan, StageLimits
logger = logging.getLogger(__name__)
# Positioning moves only — no data is taken while moving, so there is no
# reason to cross the tray at full scan velocity.
INSPECT_VELOCITY_MM_S = SCAN_VELOCITY_MM_S / 2.0
@dataclass(frozen=True)
class InspectionPoint:
"""Where the rig is parked, and which angle it is parked for."""
angle_idx: int
angle_deg: float
x_mm: float
y_mm: float
def describe(self) -> str:
return (f"Angle {self.angle_idx + 1} ({self.angle_deg:.1f}°) "
f"X={self.x_mm:.3f} mm Y={self.y_mm:.3f} mm")
@dataclass
class InspectCallbacks:
"""Progress reporting. Defaults are no-ops so the core needs no front end."""
on_status: Callable[[str], None] = lambda msg: None
on_point: Callable[[InspectionPoint], None] = lambda pt: None
on_busy: Callable[[bool], None] = lambda busy: None
@dataclass
class _State:
angle_idx: int = 0
point: InspectionPoint | None = None
started: bool = False
rotator_ready: bool = False
class AngleInspector:
"""Drives stage + rotator to inspection points across a plan's angles."""
def __init__(self, stage, scope, rotator: RotationAxis | None,
plan: ScanPlan,
callbacks: InspectCallbacks | None = None,
limits: StageLimits = DEFAULT_STAGE_LIMITS,
rng: random.Random | None = None):
self._stage = stage
self._scope = scope
self._rotator = rotator
self._plan = plan
self._cb = callbacks if callbacks is not None else InspectCallbacks()
self._limits = limits
# Injectable so tests can pin the point selection.
self._rng = rng if rng is not None else random.Random()
self._st = _State()
# ── Introspection ─────────────────────────────────────────────────────────
@property
def n_angles(self) -> int:
return self._plan.n_angles
@property
def angle_idx(self) -> int:
return self._st.angle_idx
@property
def current_point(self) -> InspectionPoint | None:
return self._st.point
def angle_labels(self) -> list[str]:
return [f"Angle {i + 1}/{self.n_angles} — {pa.angle_deg:.2f}°"
for i, pa in enumerate(self._plan.per_angle)]
# ── Lifecycle ─────────────────────────────────────────────────────────────
def start(self) -> InspectionPoint:
"""Configure the hardware and park on the first angle."""
if self._stage is None:
raise RuntimeError("BBD202 not connected")
if self._scope is None:
raise RuntimeError("Oscilloscope not connected")
self._st.rotator_ready = (self._rotator is not None
and self._rotator.is_available)
if self.n_angles > 1 and not self._st.rotator_ready:
raise RuntimeError(
f"Inspecting {self.n_angles} angles requires the T3R rotation "
"stage (GR-axis), but it is not connected. Connect T3R from "
"the T3R panel, or inspect a single-angle plan."
)
self._cb.on_busy(True)
try:
self._cb.on_status("Configuring stage for inspection …")
ctrl = self._stage
for axis in (AXIS_X, AXIS_Y):
ctrl.set_velocity_params(axis,
max_velocity=INSPECT_VELOCITY_MM_S,
acceleration=SCAN_ACCEL_MM_S2)
# Nothing here is gated, and an armed trigger output would keep
# driving the gate line on every positioning move.
ctrl.set_trigger_gate_off(AXIS_X)
if self._st.rotator_ready:
self._cb.on_status("Configuring GR axis …")
self._rotator.configure()
self._cb.on_status("Configuring oscilloscope for inspection …")
scope_inspect.configure_inspection(self._scope)
self._st.started = True
return self._goto(0, new_point=True)
finally:
self._cb.on_busy(False)
def stop(self) -> None:
"""Stop the sweep and send the rotator home. Safe to call twice."""
if not self._st.started:
return
self._st.started = False
self._cb.on_busy(True)
try:
try:
scope_inspect.stop_inspection(self._scope)
except Exception:
logger.exception("Could not stop the inspection acquisition")
if self._st.rotator_ready and abs(self._rotator.current_deg) > 0.001:
self._cb.on_status("Returning GR to home …")
try:
self._rotator.return_to_zero()
except Exception:
logger.exception("GR return-to-home failed")
self._cb.on_status("Inspection finished.")
finally:
self._cb.on_busy(False)
# ── Navigation ────────────────────────────────────────────────────────────
def goto_angle(self, angle_idx: int) -> InspectionPoint:
"""Rotate to `angle_idx` and park on a fresh random point there."""
self._require_started()
self._cb.on_busy(True)
try:
return self._goto(angle_idx, new_point=True)
finally:
self._cb.on_busy(False)
def next_angle(self) -> InspectionPoint:
"""Advance one angle, wrapping at the end."""
return self.goto_angle((self._st.angle_idx + 1) % self.n_angles)
def prev_angle(self) -> InspectionPoint:
return self.goto_angle((self._st.angle_idx - 1) % self.n_angles)
def new_point(self) -> InspectionPoint:
"""Re-roll the point within the current angle, without rotating.
One point can be unrepresentative — a bad spot on the sample looks the
same as a bad angle. Re-rolling a few times is how you tell them
apart, so this deliberately skips the rotation.
"""
self._require_started()
self._cb.on_busy(True)
try:
return self._goto(self._st.angle_idx, new_point=True, rotate=False)
finally:
self._cb.on_busy(False)
# ── Internals ─────────────────────────────────────────────────────────────
def _require_started(self):
if not self._st.started:
raise RuntimeError("Inspection has not been started")
def _goto(self, angle_idx: int, new_point: bool,
rotate: bool = True) -> InspectionPoint:
if not 0 <= angle_idx < self.n_angles:
raise IndexError(
f"Angle {angle_idx} out of range (plan has {self.n_angles})")
pa = self._plan.per_angle[angle_idx]
self._st.angle_idx = angle_idx
if rotate and self._st.rotator_ready:
delta = pa.angle_deg - self._rotator.current_deg
if abs(delta) > 0.001:
self._cb.on_status(
f"Rotating GR to {pa.angle_deg:.1f}° (Δ{delta:+.1f}°) …")
self._rotator.rotate_to(pa.angle_deg)
point = self._pick_point(angle_idx) if new_point else self._st.point
self._cb.on_status(f"Moving to {point.describe()} …")
# Y first, then X — the same order the scan uses to reach a row.
self._stage.move_axis_absolute(AXIS_Y, point.y_mm, timeout=60.0)
self._stage.move_axis_absolute(AXIS_X, point.x_mm, timeout=60.0)
self._st.point = point
self._cb.on_point(point)
self._cb.on_status(f"Parked at {point.describe()}")
return point
def _pick_point(self, angle_idx: int) -> InspectionPoint:
"""A random point on this angle's scan grid.
Y is drawn from the angle's actual row positions and X uniformly from
its data window, so the point is somewhere the scan would really
sample — not merely inside the bounding box.
"""
pa = self._plan.per_angle[angle_idx]
if not pa.y_positions:
raise ValueError(f"Angle {angle_idx + 1} has no rows to inspect")
y = self._rng.choice(pa.y_positions)
x = self._rng.uniform(pa.x_start, pa.x_start + pa.x_delta)
lim = self._limits
if not (lim.x_min <= x <= lim.x_max and lim.y_min <= y <= lim.y_max):
raise ValueError(
f"Inspection point X={x:.3f} Y={y:.3f} is outside the stage "
f"travel ({lim.x_min}–{lim.x_max} × {lim.y_min}–{lim.y_max} mm)"
)
return InspectionPoint(angle_idx=angle_idx, angle_deg=pa.angle_deg,
x_mm=x, y_mm=y)
core/config.py
+49
View File
@@ -0,0 +1,49 @@
"""Persisted user defaults (ports, scope IP, save directory).
One flat JSON file, one dataclass. ``save()`` always writes every field, so
a partial UI update can never silently drop another field's saved value
(which is exactly what the old dict-based writer did to helios_port).
"""
from __future__ import annotations
import json
import logging
from dataclasses import asdict, dataclass, fields
from pathlib import Path
logger = logging.getLogger(__name__)
DEFAULTS_PATH = Path(__file__).resolve().parent.parent / "aui_defaults.json"
@dataclass
class ScanDefaults:
t3r_port: str = "/dev/ttyUSB0"
bbd_port: str = "/dev/ttyUSB1"
oscope_ip: str = "192.168.0.1"
save_dir: str = str(DEFAULTS_PATH.parent / "scans")
helios_port: str = "/dev/ttyUSB2"
burst_mode: bool = False
strict_rows: bool = False
@classmethod
def load(cls, path: Path = DEFAULTS_PATH) -> "ScanDefaults":
"""Load defaults, tolerating a missing/corrupt file and unknown keys."""
if path.exists():
try:
with open(path) as f:
data = json.load(f)
known = {f.name for f in fields(cls)}
return cls(**{k: v for k, v in data.items() if k in known})
except (OSError, ValueError, TypeError) as e:
logger.warning("Could not load %s (%s); using fallback defaults", path, e)
inst = cls()
inst.save(path)
return inst
def save(self, path: Path = DEFAULTS_PATH) -> None:
try:
with open(path, "w") as f:
json.dump(asdict(self), f, indent=2)
except OSError as e:
logger.warning("Could not save defaults to %s: %s", path, e)
core/rotation.py
+87
View File
@@ -0,0 +1,87 @@
"""GR rotation axis: the T3R configuration and move policy for scanning.
Qt-free façade over hardware.t3r_driver.T3RDriver that owns the drive
settings the scan depends on, so the engine never re-derives them.
"""
from __future__ import annotations
import logging
from dataclasses import dataclass
logger = logging.getLogger(__name__)
@dataclass(frozen=True)
class RotationSettings:
"""Drive settings for the GR axis during a scan."""
microsteps: int = 8 # microsteps/full-step on the GR axis (ch3)
velocity: int = 4000 # steps/s for inter-angle moves
accel: int = 2000 # steps/s² for inter-angle moves
run_current_ma: int = 1200 # drive current while moving
hold_current_ma: int = 400 # standstill current
ihold_delay: int = 6 # run→hold current ramp delay (TMC IHOLDDELAY units)
# The sample rotates CW instead of CCW to clear wiring and avoid a stall.
rotation_sign: int = -1
DEFAULT_ROTATION = RotationSettings()
class RotationAxis:
"""Blocking rotation control for the GR axis.
``configure()`` must run before any move: ``steps_for_angle()`` assumes
the configured microstep setting, so the device has to be told to match
rather than trusting whatever the T3R panel or firmware default left it
at.
"""
def __init__(self, driver, settings: RotationSettings = DEFAULT_ROTATION):
self.driver = driver
self.settings = settings
self._current_deg = 0.0
@property
def is_available(self) -> bool:
return self.driver is not None and self.driver.is_open
@property
def current_deg(self) -> float:
return self._current_deg
def configure(self) -> None:
s = self.settings
ch = self.driver.GR_AXIS_CH
self.driver.set_microstep(ch, s.microsteps)
self.driver.set_current(ch, s.run_current_ma, s.hold_current_ma, s.ihold_delay)
self.driver.enable(ch)
def estimate_move_secs(self, delta_deg: float) -> float:
"""Trapezoidal move time: cruise + accel/decel ramps."""
s = self.settings
steps = abs(self.driver.steps_for_angle(delta_deg, s.microsteps))
return steps / s.velocity + s.velocity / s.accel
def rotate_to(self, angle_deg: float, timeout_margin_s: float = 5.0) -> float:
"""Rotate to an absolute angle and block until the move completes.
Returns the estimated move time (for status reporting). Waits on the
driver's MOTION_DONE event rather than sleeping for a guessed
duration; falls back to the estimate only if the event never arrives.
"""
delta_deg = angle_deg - self._current_deg
if abs(delta_deg) <= 0.001:
return 0.0
s = self.settings
est_secs = self.estimate_move_secs(delta_deg)
self.driver.rotate_stage(delta_deg, s.microsteps, s.velocity, s.accel)
if not self.driver.wait_motion_done(self.driver.GR_AXIS_CH,
est_secs + timeout_margin_s):
logger.warning(
"GR axis did not report MOTION_DONE within %.1f s for a "
"%.1f° move; continuing", est_secs + timeout_margin_s, delta_deg)
self._current_deg = angle_deg
return est_secs
def return_to_zero(self) -> float:
return self.rotate_to(0.0)
core/saw_check.py
+255
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@@ -0,0 +1,255 @@
"""Middle-row SAW quality check: acquire one row per angle, then read the
alignment off the frequencies it produces.
Two halves of one test mode, kept together because neither is much use
without the other:
*Acquisition* — ``middle_row_plan`` reduces a full ScanPlan to a single row
per angle, the row-wise middle of the ROI. ScanEngine runs the result
exactly like any other scan and writes it as a v10 .sras file
(``sras_format.VERSION_SAW_CHECK``), so a check costs one row-time per angle
instead of the hours a full multi-angle scan takes.
*Analysis* — ``frequency_traces`` turns such a file back into one peak-SAW-
frequency trace per angle, and ``alignment_summary`` reduces those to the
numbers the operator is actually asking about. Both are Qt-free; the plotting
lives in saw_check_viewer.py.
Why the middle row answers an alignment question: ``scan_geometry.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. Every angle
therefore measures the same material, and a spread in the per-angle
frequencies is a property of the rig (or of a genuinely anisotropic sample),
not of where each row happened to land.
"""
from __future__ import annotations
from dataclasses import dataclass, field, replace
import numpy as np
from core.scan_geometry import ScanGeometryError, ScanPlan
from core.sras_analysis import ChannelCalibration, compute_rf_image
from core.sras_format import SrasFile
# Rules of thumb for the read-out, not physics. A well-aligned rig on an
# isotropic sample reads the same frequency at every angle, so the spread of
# the per-angle medians is the alignment signal — but an anisotropic sample
# genuinely varies with angle, so a wide spread is a prompt to look at the
# curves, never a verdict on its own.
SPREAD_GOOD_PCT = 1.0
SPREAD_MARGINAL_PCT = 3.0
# Below this fraction of unmasked pixels a trace is too sparse to read.
VALID_FRACTION_FLOOR = 0.5
# ── Acquisition side ─────────────────────────────────────────────────────────
def middle_row_plan(plan: ScanPlan) -> ScanPlan:
"""Reduce a scan plan to its row-wise middle row at every angle.
Each angle keeps the geometry the full scan would have used — same
x_start, x_delta and n_frames from its own rotated bounding box — and
scans only the middle entry of its row list, so the check samples exactly
what the scan would along that row.
An even row count has no exact middle; the upper of the two central rows
is taken (``n_rows // 2``), which is also the row the viewer picks when it
reads the middle row out of a full v6 scan.
"""
if plan.n_angles == 0:
raise ScanGeometryError("Cannot build a SAW check from a plan with no angles")
per_angle = []
for pa in plan.per_angle:
if not pa.y_positions:
raise ScanGeometryError(
f"Angle {pa.angle_deg:.1f}° has no rows, so it has no middle row to check"
)
per_angle.append(replace(pa, n_rows=1,
y_positions=[pa.y_positions[middle_row_index(pa.n_rows)]]))
return replace(plan, per_angle=per_angle)
def middle_row_index(n_rows: int) -> int:
"""The row this check calls the middle one. One rule, two callers."""
return max(0, n_rows // 2)
# ── Analysis side ────────────────────────────────────────────────────────────
@dataclass
class AngleTrace:
"""One angle's peak SAW frequency along its middle row.
``freq_mhz`` is NaN wherever the pixel was masked out (CH4 DC below the
threshold), so the gaps stay gaps instead of reading as 0 MHz.
"""
angle_idx: int
angle_deg: float
row_idx: int
y_mm: float
x_mm: np.ndarray # absolute stage X of each frame
freq_mhz: np.ndarray # NaN where masked
_valid: np.ndarray = field(init=False, repr=False)
def __post_init__(self):
self._valid = np.isfinite(self.freq_mhz)
@property
def offset_mm(self) -> np.ndarray:
"""X relative to the centre of this row.
Every angle's row is centred on the same ROI centre, so plotting
against this puts all the angles' curves over the same piece of
sample — which is the whole point of the comparison.
"""
if len(self.x_mm) == 0:
return self.x_mm
return self.x_mm - 0.5 * (self.x_mm[0] + self.x_mm[-1])
@property
def n_valid(self) -> int:
return int(self._valid.sum())
@property
def valid_fraction(self) -> float:
return self.n_valid / len(self.freq_mhz) if len(self.freq_mhz) else 0.0
@property
def median_mhz(self) -> float:
return float(np.median(self.freq_mhz[self._valid])) if self.n_valid else float("nan")
@property
def std_mhz(self) -> float:
return float(np.std(self.freq_mhz[self._valid])) if self.n_valid > 1 else float("nan")
@property
def drift_mhz_per_mm(self) -> float:
"""Least-squares slope of frequency along the row.
A flat trace means the response did not change across the ROI; a
sloped one is the signature of a tilt or a defocus the angle spread
alone would not show.
"""
if self.n_valid < 2:
return float("nan")
x = self.offset_mm[self._valid]
if np.ptp(x) == 0:
return float("nan")
return float(np.polyfit(x, self.freq_mhz[self._valid], 1)[0])
@dataclass
class AlignmentSummary:
"""What the per-angle traces say about the alignment, in scalars."""
n_angles: int
median_mhz: float
spread_mhz: float # max − min of the per-angle medians
spread_pct: float # that spread as a % of the overall median
best_angle_deg: float # angle reading the highest median
worst_angle_deg: float # angle reading the lowest median
worst_drift_mhz_per_mm: float
worst_drift_angle_deg: float
min_valid_fraction: float
@property
def level(self) -> str:
""""good" / "marginal" / "poor" — see the module's threshold note."""
if self.n_angles == 0 or not np.isfinite(self.spread_pct):
return "poor"
if self.min_valid_fraction < VALID_FRACTION_FLOOR:
return "poor"
if self.spread_pct <= SPREAD_GOOD_PCT:
return "good"
if self.spread_pct <= SPREAD_MARGINAL_PCT:
return "marginal"
return "poor"
def describe(self) -> str:
if self.n_angles == 0:
return "No angle produced a usable frequency trace."
if self.min_valid_fraction < VALID_FRACTION_FLOOR:
return (f"Only {self.min_valid_fraction * 100:.0f} % of the worst angle's row "
f"is above the DC threshold — check the detection beam and the "
f"threshold before reading the spread.")
return (f"Per-angle medians span {self.spread_mhz:.3f} MHz "
f"({self.spread_pct:.2f} % of {self.median_mhz:.3f} MHz), "
f"lowest at {self.worst_angle_deg:.1f}°, highest at {self.best_angle_deg:.1f}°. "
f"Largest drift along a row: {self.worst_drift_mhz_per_mm:+.3f} MHz/mm "
f"at {self.worst_drift_angle_deg:.1f}°.")
def frequency_traces(sras: SrasFile, *, dc_threshold_mv: float = 0.0,
background: np.ndarray | None = None,
gate_start_ns: float | None = None,
gate_end_ns: float | None = None,
calib: ChannelCalibration | None = None,
on_progress=lambda done, total: None) -> list[AngleTrace]:
"""Peak SAW frequency along the middle row of every angle in ``sras``.
Works on a v10 check (one row per angle, so the middle row is the only
row) and on a full v6 scan alike — the same middle row the check would
have acquired is pulled out of the scan, which is what lets a finished
scan be re-examined with the check's own read-out.
Angles with nothing on disk (an aborted file) are skipped rather than
reported as flat zero.
"""
calib = calib if calib is not None else ChannelCalibration.from_preambles(sras.preambles)
freq_axis = sras.freq_axis_mhz(sras.header.samples_per_frame)
time_axis = sras.time_axis_ns()
statuses = sras.angle_status()
traces: list[AngleTrace] = []
for st in statuses:
on_progress(st.index, len(statuses))
if st.n_rows_available < 1:
continue
pa = sras.per_angle[st.index]
row = middle_row_index(st.n_rows_available)
view = sras.load_angle(st.index, n_rows=st.n_rows_available)[row:row + 1]
img = compute_rf_image(view, calib, freq_axis, dc_threshold_mv,
background=background,
gate_start_ns=gate_start_ns, gate_end_ns=gate_end_ns,
time_axis_ns=time_axis)
# compute_rf_image zeroes masked pixels and its FFT never peaks in the
# suppressed DC bin, so 0 MHz means "no reading" and nothing else.
freq = img[0].astype(np.float64)
freq[freq <= 0.0] = np.nan
traces.append(AngleTrace(
angle_idx=st.index, angle_deg=pa.angle_deg, row_idx=row,
y_mm=pa.y_positions[row] if row < len(pa.y_positions) else float("nan"),
x_mm=sras.x_axis_mm(st.index), freq_mhz=freq,
))
on_progress(len(statuses), len(statuses))
return traces
def alignment_summary(traces: list[AngleTrace]) -> AlignmentSummary:
"""Reduce per-angle traces to the alignment read-out."""
usable = [t for t in traces if t.n_valid > 0]
if not usable:
nan = float("nan")
return AlignmentSummary(0, nan, nan, nan, nan, nan, nan, nan, 0.0)
medians = np.array([t.median_mhz for t in usable])
overall = float(np.median(medians))
spread = float(medians.max() - medians.min())
drifts = [(abs(t.drift_mhz_per_mm), t) for t in usable
if np.isfinite(t.drift_mhz_per_mm)]
worst_drift = max(drifts, key=lambda d: d[0])[1] if drifts else None
return AlignmentSummary(
n_angles=len(usable),
median_mhz=overall,
spread_mhz=spread,
spread_pct=spread / overall * 100.0 if overall else float("nan"),
best_angle_deg=usable[int(np.argmax(medians))].angle_deg,
worst_angle_deg=usable[int(np.argmin(medians))].angle_deg,
worst_drift_mhz_per_mm=worst_drift.drift_mhz_per_mm if worst_drift else float("nan"),
worst_drift_angle_deg=worst_drift.angle_deg if worst_drift else float("nan"),
min_valid_fraction=min(t.valid_fraction for t in usable),
)
core/scan_engine.py
+644
View File
@@ -0,0 +1,644 @@
"""Headless SRAS scan engine.
Takes plain hardware drivers, a ScanPlan, and callbacks — no Qt, no
widgets. ``run()`` blocks, so the caller owns the thread; GUIs wrap this
with gui.scan_bridge.QtScanController, which adapts the callbacks to Qt
signals. A CLI or a simpler GUI can drive the same engine with nothing but
functions.
"""
from __future__ import annotations
import logging
import threading
import time
from dataclasses import dataclass, field
from pathlib import Path
from typing import Callable
from core import scope_burst, scope_sras
from core.rotation import RotationAxis
from core.scan_geometry import ScanPlan, validate_plan
from core.sras_format import SCAN_CHANNELS, VERSION, create_scan_file
logger = logging.getLogger(__name__)
SCAN_VELOCITY_MM_S = 100.0
SCAN_ACCEL_MM_S2 = 1500.0
LASER_FREQ_HZ = 20000.0 # laser pulse frequency during data acquisition
# Theoretical ramp distance: d = v² / (2a) = 100² / (2×1500) ≈ 3.33 mm
SCAN_RAMP_MM = SCAN_VELOCITY_MM_S**2 / (2.0 * SCAN_ACCEL_MM_S2)
# Extra buffer added to both ends of the ramp. The BBD202 controller begins
# decelerating slightly before the theoretical point to avoid overshoot,
# which drops TRIGOUT_MAXV early and clips the last few data points.
SCAN_RAMP_BUFFER_MM = 1.0
AXIS_X = 0x21
AXIS_Y = 0x22
class ScanAborted(Exception):
"""Raised inside the engine thread to unwind a scan cleanly."""
@dataclass
class ResumeTarget:
"""One angle selected for (re)acquisition in an existing file."""
angle_idx: int
data_offset: int
n_rows: int
angle_deg: float
@dataclass
class ResumeState:
path: Path
targets: list[ResumeTarget]
samples_per_frame: int
@property
def target_indices(self) -> set[int]:
return {t.angle_idx for t in self.targets}
@dataclass
class ScanCallbacks:
"""Progress reporting hooks. Every one is optional."""
on_status: Callable[[str], None] = lambda msg: None
on_started: Callable[[], None] = lambda: None
on_row_started: Callable[[int, int, int, int], None] = lambda r, nr, a, na: None
on_row_done: Callable[[int, int, int, int], None] = lambda r, nr, a, na: None
on_dc_bias: Callable[[int, list], None] = lambda row, means: None
on_paused_changed: Callable[[bool], None] = lambda paused: None
# Blocking operator prompt: must not return until acknowledged.
prompt: Callable[[str, str], None] = lambda title, msg: None
@dataclass
class ScanResult:
path: Path
rows_written: int = 0
aborted: bool = False
angles_acquired: list[int] = field(default_factory=list)
class ScanEngine:
"""Runs a full SRAS acquisition: stage, rotation, scope, and file output.
Constructed with the concrete drivers (not worker/queue wrappers), so
any front end can reuse it::
engine = ScanEngine(stage, scope, rotator, plan, out_path,
callbacks=ScanCallbacks(on_status=print))
result = engine.run() # blocking
"""
def __init__(self, stage, scope, rotator: RotationAxis | None,
plan: ScanPlan, out_path: Path,
resume: ResumeState | None = None,
callbacks: ScanCallbacks | None = None,
burst_mode: bool = False, strict_rows: bool = False,
file_version: int = VERSION):
self._stage = stage
self._scope = scope
self._rotator = rotator
self._plan = plan
self._out_path = Path(out_path)
self._resume = resume
self._cb = callbacks if callbacks is not None else ScanCallbacks()
# Burst mode acquires as many whole rows per FastFrame acquisition as
# the scope's frame memory holds, instead of one row per acquisition.
self._burst_mode = burst_mode
# Strict row packing stops the scan on a frame-count mismatch
# instead of squaring the row up (see _check_frame_delta).
self._strict_rows = strict_rows
# Which kind of file this run produces. The acquisition is identical
# either way; VERSION_SAW_CHECK only marks a one-row-per-angle plan
# (core.saw_check) as the quality check it is, so a reader does not
# mistake it for a scan that aborted after its first row.
self._file_version = file_version
self._max_frames = 0
self._preflight_done = False
self._abort = threading.Event()
self._resume_event = threading.Event()
self._resume_event.set() # set = running, cleared = pause requested
# ── External control (thread-safe) ────────────────────────────────────────
def abort(self):
self._abort.set()
self._resume_event.set() # unblock a paused scan so it can exit
def pause(self):
"""Request a pause; takes effect at the next row boundary."""
self._resume_event.clear()
def resume(self):
self._resume_event.set()
@property
def aborted(self) -> bool:
return self._abort.is_set()
# ── Internals ─────────────────────────────────────────────────────────────
def _check_abort(self):
if self._abort.is_set():
raise ScanAborted("Scan aborted by user.")
def _pause_point(self):
"""Block here (between rows, hardware idle) while a pause is requested."""
if self._resume_event.is_set():
self._check_abort()
return
self._cb.on_status(
"Scan paused — lasers may be switched off. "
"Turn lasers back on before resuming."
)
self._cb.on_paused_changed(True)
while not self._resume_event.wait(0.2):
if self._abort.is_set():
break
self._cb.on_paused_changed(False)
self._check_abort()
self._cb.on_status("Scan resumed.")
def _prompt(self, title: str, message: str):
self._cb.prompt(title, message)
self._check_abort()
# ── Main sequence ─────────────────────────────────────────────────────────
def run(self) -> ScanResult:
"""Execute the scan. Blocking; returns a ScanResult.
Raises ScanGeometryError for an unrunnable plan, RuntimeError for
missing/mismatched hardware, or ScanAborted if the operator aborts.
"""
plan = self._plan
per_angle = plan.per_angle
n_angles = plan.n_angles
result = ScanResult(path=self._out_path)
validate_plan(plan, SCAN_RAMP_MM, SCAN_RAMP_BUFFER_MM)
geometry_summary = ", ".join(
f"{pa.angle_deg:.1f}°: {pa.n_rows} row(s) × {pa.n_frames} pts/row"
for pa in per_angle
)
self._cb.on_status(
f"Scan geometry: {n_angles} angle(s), {plan.total_rows} row(s) total "
f"(per-angle bounding box) | save → {self._out_path.parent}\n"
f"{geometry_summary}"
)
self._cb.on_started()
if self._stage is None:
raise RuntimeError("BBD202 not connected")
if self._scope is None:
raise RuntimeError("Oscilloscope not connected")
rotator_ready = self._rotator is not None and self._rotator.is_available
if n_angles > 1 and not rotator_ready:
raise RuntimeError(
f"NumAngles={n_angles} requires the T3R rotation stage (GR-axis), "
"but it is not connected. Connect T3R from the T3R panel before "
"starting a multi-angle scan, or set NumAngles to 1."
)
if rotator_ready:
s = self._rotator.settings
self._cb.on_status(
f"Configuring GR axis: {s.microsteps} µsteps, "
f"{s.run_current_ma}/{s.hold_current_ma} mA run/hold …"
)
self._rotator.configure()
time.sleep(0.2)
self._prepare_stage()
samples_per_frame = self._prepare_scope()
scan_file = self._open_output(samples_per_frame, result)
try:
self._scan_loop(scan_file, samples_per_frame, result)
finally:
scan_file.close()
# Leave the X trigger output inactive. Burst mode toggles it every
# row and could exit from either state; the per-row path used to
# leave TRIGOUT_MAXV armed for the rest of the session, which keeps
# driving the gate line on every later jog.
try:
self._stage.set_trigger_gate_off(AXIS_X)
except Exception:
logger.exception("Could not return the X trigger output to idle")
# Return the GR axis home regardless of abort or error
if rotator_ready and abs(self._rotator.current_deg) > 0.001:
self._cb.on_status("Returning GR to home …")
try:
self._rotator.return_to_zero()
except Exception:
logger.exception("GR return-to-home failed")
if self._abort.is_set():
result.aborted = True
raise ScanAborted("Scan aborted by user.")
self._cb.on_status("Scan complete.")
return result
def _prepare_stage(self):
ctrl = self._stage
self._cb.on_status("Enabling stage axes …")
if not ctrl.am_enabled[0]:
ctrl.enable_axis(AXIS_X)
if not ctrl.am_enabled[1]:
ctrl.enable_axis(AXIS_Y)
time.sleep(0.2)
if not ctrl.am_homed[0] or not ctrl.am_homed[1]:
self._cb.on_status("Homing stage (may take up to 2 min) …")
if not ctrl.am_homed[0]:
ctrl.home_axis(AXIS_X, timeout=120.0)
if not ctrl.am_homed[1]:
ctrl.home_axis(AXIS_Y, timeout=120.0)
self._cb.on_status("Setting scan velocity …")
ctrl.set_velocity_params(AXIS_X, max_velocity=SCAN_VELOCITY_MM_S,
acceleration=SCAN_ACCEL_MM_S2)
ctrl.set_velocity_params(AXIS_Y, max_velocity=SCAN_VELOCITY_MM_S,
acceleration=SCAN_ACCEL_MM_S2)
# X trigger: logic-high output while the stage is at maximum velocity.
# Burst mode arms it per acquiring pass instead — a burst spans several
# rows with the scope running throughout, so leaving it armed would let
# the flyback trigger frames between rows.
if self._burst_mode:
ctrl.arm_scan_gate(AXIS_X, False)
else:
ctrl.set_trigger_trigout_maxv(AXIS_X)
def _prepare_scope(self) -> int:
self._cb.on_status("Configuring oscilloscope …")
samples_per_frame = scope_sras.configure_acquisition(self._scope)
if self._resume is None:
self._preambles = scope_sras.read_preambles(self._scope, SCAN_CHANNELS)
self._prompt(
"Background Capture",
"Please ensure the Helios laser is ON and the Genesis laser is OFF,\n"
"then click OK to capture the background waveform."
)
self._background = scope_sras.capture_background(
self._scope, should_abort=self._abort.is_set,
on_status=self._cb.on_status)
self._prompt(
"Begin Scanning",
"Background captured successfully.\n\n"
"Please ensure the Genesis laser is back ON,\n"
"then click OK to begin scanning."
)
else:
# Resuming: the file's existing background waveform and channel
# preambles are reused as-is (the format has no way to replace
# them without rewriting the whole file), so background capture is
# skipped. Sanity-check that this scope still produces the same
# record length the file was started with — a mismatch would
# silently corrupt the ragged per-row byte layout on append.
if samples_per_frame != self._resume.samples_per_frame:
raise RuntimeError(
f"Oscilloscope record length ({samples_per_frame} samples/frame) "
f"does not match the {self._resume.samples_per_frame} samples/frame "
f"this scan file was started with — cannot safely resume."
)
targets = ", ".join(str(t.angle_idx + 1) for t in self._resume.targets)
self._prompt(
"Resume Scan",
f"Resuming {self._resume.path.name} — will (re)acquire "
f"angle(s) {targets} of {self._plan.n_angles}.\n\n"
"Please re-home the GR axis to 0° before continuing — the scan "
"will rotate it directly from angle to angle before scanning resumes.\n\n"
"Please ensure the Genesis laser is ON,\n"
"then click OK to continue scanning."
)
scope_sras.configure_scan_trigger(self._scope)
if self._burst_mode:
# Horizontal settings are fixed by now, so the capacity is stable
# for the whole scan; only rows-per-burst varies (n_frames is
# per-angle).
self._max_frames = scope_burst.max_frames(self._scope)
self._cb.on_status(
f"Burst mode: scope holds {self._max_frames} frames "
f"({samples_per_frame} samples/frame)"
)
return samples_per_frame
def _open_output(self, samples_per_frame: int, result: ScanResult):
if self._resume is not None:
result.path = self._resume.path
self._cb.on_status(
f"Resuming {self._resume.path.name} — "
f"{len(self._resume.targets)} angle(s) to (re)acquire …"
)
return open(self._resume.path, "r+b")
return create_scan_file(
self._out_path, self._plan, samples_per_frame,
scope_sras.SAMPLE_RATE_HZ, self._preambles, self._background,
version=self._file_version,
)
def _scan_loop(self, scan_file, samples_per_frame: int, result: ScanResult):
plan = self._plan
n_angles = plan.n_angles
x_ramp_total = SCAN_RAMP_MM + SCAN_RAMP_BUFFER_MM
scope = self._scope
targets_by_ai = None
if self._resume is not None:
targets_by_ai = {t.angle_idx: t for t in self._resume.targets}
# Both fresh and resumed scans assume the GR axis starts at home (0°)
# — the resume prompt instructs the operator to re-home it — so the
# first move always rotates directly from 0° to the starting angle.
for ai, pa in enumerate(plan.per_angle):
if targets_by_ai is not None and ai not in targets_by_ai:
continue # not selected for (re)acquisition
self._pause_point()
if targets_by_ai is not None:
# Interior angles may already have valid data on either side,
# so seek to this angle's fixed offset rather than relying on
# the file's current position.
scan_file.seek(targets_by_ai[ai].data_offset)
if self._rotator is not None and self._rotator.is_available:
delta = pa.angle_deg - self._rotator.current_deg
if abs(delta) > 0.001:
self._cb.on_status(
f"Rotating GR to {pa.angle_deg:.1f}° (Δ{delta:+.1f}°) …")
self._rotator.rotate_to(pa.angle_deg)
if self._burst_mode:
# Burst mode sizes the FastFrame count from the scope's whole
# capacity instead (see scope_burst.start_burst), so there is
# nothing to re-arm per angle here.
self._scan_rows_burst(scan_file, pa, ai, n_angles,
samples_per_frame, result, x_ramp_total)
else:
# Each angle's bounding box gives it its own points/row count,
# so the scope's FastFrame count must be re-armed per angle.
scope.set_fastframe_count(pa.n_frames)
self._scan_rows_serial(scan_file, pa, ai, n_angles,
samples_per_frame, result, x_ramp_total)
result.angles_acquired.append(ai)
# ── Per-row acquisition (one FastFrame acquisition per row) ───────────────
def _scan_rows_serial(self, scan_file, pa, ai: int, n_angles: int,
samples_per_frame: int, result: ScanResult,
x_ramp_total: float):
ctrl = self._stage
scope = self._scope
for ri, y_pos in enumerate(pa.y_positions):
self._pause_point()
self._cb.on_row_started(ri + 1, pa.n_rows, ai + 1, n_angles)
self._cb.on_status(
f"Angle {ai+1}/{n_angles} Row {ri+1}/{pa.n_rows} "
f"(Y={y_pos:.3f} mm)"
)
# Position the stage one ramp-length + buffer before the data
# window so it is at full velocity before x_start.
ctrl.move_axis_absolute(AXIS_Y, y_pos, timeout=60.0)
ctrl.move_axis_absolute(AXIS_X, pa.x_start - x_ramp_total, timeout=30.0)
scope_sras.arm_row(scope)
# Data window + ramp + buffer run-off, so the stage does not
# begin decelerating before the last point.
x_end = pa.x_start + pa.x_delta + x_ramp_total
ctrl.move_axis_absolute(AXIS_X, x_end, timeout=120.0)
scope_sras.finish_row(scope)
self._write_row(scan_file, samples_per_frame, ri, pa.n_frames)
result.rows_written += 1
self._cb.on_row_done(ri + 1, pa.n_rows, ai + 1, n_angles)
def _write_row(self, scan_file, samples_per_frame: int, row_idx: int,
n_frames: int):
"""Stream every channel from the scope into the file.
CH3 is the max-vel gate signal — no useful waveform data — so zeroed
frames are written to keep the file layout intact.
"""
scope = self._scope
ch_bytes = n_frames * samples_per_frame
for ch in SCAN_CHANNELS:
if ch == 3:
self._cb.on_status("Writing zeroed CH3 frames …")
scan_file.write(bytes(ch_bytes))
continue
self._cb.on_status(f"Fetching CH{ch} data …")
waveforms = scope_sras.transfer_channel(scope, ch)
if ch == SCAN_CHANNELS[0]:
self._check_frame_delta(row_idx, len(waveforms), n_frames)
row = scope_burst.normalize_row(
b"".join(waveforms), 0, len(waveforms), n_frames, samples_per_frame)
if ch == 4:
self._cb.on_dc_bias(row_idx + 1, scope_burst.frame_means_block(
row, 0, n_frames, samples_per_frame))
scan_file.write(row)
# ── Burst acquisition (many whole rows per FastFrame acquisition) ─────────
def _scan_rows_burst(self, scan_file, pa, ai: int, n_angles: int,
samples_per_frame: int, result: ScanResult,
x_ramp_total: float):
"""Acquire the angle in bursts of as many whole rows as the scope holds.
One ACQuire:STATE RUN spans the whole burst, so the gate is armed only
for each acquiring pass and dropped for the flyback — otherwise the
return move would reach max velocity and inject frames between rows.
"""
scope = self._scope
n_frames = pa.n_frames
x_lead_in = pa.x_start - x_ramp_total
x_end = pa.x_start + pa.x_delta + x_ramp_total
if not self._preflight_done:
# Once per scan: the gate wiring can't change between angles, and
# the check costs two row-times.
self._gate_off_preflight(x_lead_in, x_end)
self._preflight_done = True
row = 0
while row < pa.n_rows:
self._pause_point()
n_burst = scope_burst.rows_per_burst(
self._max_frames, n_frames, samples_per_frame, pa.n_rows - row)
self._cb.on_status(
f"Angle {ai+1}/{n_angles} Rows {row+1}-{row+n_burst}/{pa.n_rows} "
f"in one acquisition ({n_burst * n_frames} frames) …"
)
burst_start = scan_file.tell()
cumulative = []
baseline = scope_burst.start_burst(scope, self._max_frames)
try:
for r in range(n_burst):
self._check_abort()
self._cb.on_row_started(row + r + 1, pa.n_rows,
ai + 1, n_angles)
self._acquire_gated_row(pa.y_positions[row + r],
x_lead_in, x_end)
total = scope_burst.frames_acquired(scope)
if total >= self._max_frames:
raise RuntimeError(
f"FastFrame buffer full ({total}/{self._max_frames} "
f"frames) at row {row + r + 1} — later rows in this "
"burst would be misattributed. Raise "
"scope_burst.BURST_FRAME_HEADROOM and rerun."
)
cumulative.append(total - baseline)
finally:
scope_burst.stop_burst(scope)
counts = scope_burst.split_row_counts(cumulative)
self._write_burst(scan_file, burst_start, row, counts,
n_frames, samples_per_frame)
for r in range(n_burst):
result.rows_written += 1
self._cb.on_row_done(row + r + 1, pa.n_rows, ai + 1, n_angles)
row += n_burst
def _acquire_gated_row(self, y_pos: float, x_lead_in: float, x_end: float):
"""One row: step Y, fly back gated off, then acquire on the +X pass."""
ctrl = self._stage
ctrl.move_axis_absolute(AXIS_Y, y_pos, timeout=60.0)
ctrl.move_axis_absolute(AXIS_X, x_lead_in, timeout=30.0)
ctrl.arm_scan_gate(AXIS_X, True)
ctrl.move_axis_absolute(AXIS_X, x_end, timeout=120.0)
ctrl.arm_scan_gate(AXIS_X, False)
time.sleep(scope_burst.BURST_ROW_SETTLE_S)
def _gate_off_preflight(self, x_lead_in: float, x_end: float):
"""Prove the gate really gates before trusting a multi-row burst.
The value that makes the BBD trigger output idle low is not settled by
the protocol docs (see apt_constants.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 this 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.
Leaves the stage parked at x_end, where the burst loop expects it.
"""
ctrl, scope = self._stage, self._scope
self._cb.on_status("Burst preflight: checking the stage gate …")
ctrl.arm_scan_gate(AXIS_X, False)
ctrl.move_axis_absolute(AXIS_X, x_end, timeout=120.0)
baseline = scope_burst.start_burst(scope, self._max_frames)
ctrl.move_axis_absolute(AXIS_X, x_lead_in, timeout=120.0)
scope_burst.stop_burst(scope)
leaked = scope_burst.frames_acquired(scope) - baseline
ctrl.arm_scan_gate(AXIS_X, True)
baseline = scope_burst.start_burst(scope, self._max_frames)
ctrl.move_axis_absolute(AXIS_X, x_end, timeout=120.0)
ctrl.arm_scan_gate(AXIS_X, False)
scope_burst.stop_burst(scope)
gated = scope_burst.frames_acquired(scope) - baseline
if gated <= 0:
raise RuntimeError(
"Burst preflight: no frames acquired with the gate armed. "
"Check that the Genesis laser is pulsing (CH2) and that the "
"BBD X trigger output reaches CH3 before scanning."
)
if leaked:
raise RuntimeError(
f"Burst preflight: {leaked} frame(s) acquired during a flyback "
"that should have been gated off — the BBD trigger output is "
"not idling low. Set apt_constants.TRIGOUT_GATE_OFF to "
"TriggerBitsServo.TRIGOUT_HIGH and retry, or use per-row "
"acquisition."
)
self._cb.on_status(
f"Burst preflight OK ({gated} frames gated on, 0 leaked).")
def _write_burst(self, scan_file, burst_start: int, first_row: int,
counts: list[int], n_frames: int, samples_per_frame: int):
"""Deinterleave one burst into the file's per-row, per-channel blocks.
The wire is channel-major (every row of CH1, then every row of CH4);
the file is row-major with channels inner. Writing one channel at a
time to strided offsets keeps peak memory at a single channel's burst
instead of the whole thing.
"""
scope = self._scope
ch_bytes = n_frames * samples_per_frame
row_bytes = len(SCAN_CHANNELS) * ch_bytes
total_frames = sum(counts)
for r, count in enumerate(counts):
self._check_frame_delta(first_row + r, count, n_frames)
for ch_idx, ch in enumerate(SCAN_CHANNELS):
if ch == 3:
self._cb.on_status("Writing zeroed CH3 frames …")
blob = None
else:
self._cb.on_status(
f"Fetching CH{ch} burst ({total_frames} frames) …")
blob = scope_burst.transfer_burst(scope, ch, total_frames,
samples_per_frame)
src = 0
zeros = bytes(ch_bytes) if blob is None else None
for r, count in enumerate(counts):
scan_file.seek(burst_start + r * row_bytes + ch_idx * ch_bytes)
if blob is None:
scan_file.write(zeros)
else:
row = scope_burst.normalize_row(
blob, src, count, n_frames, samples_per_frame)
if ch == 4:
self._cb.on_dc_bias(
first_row + r + 1,
scope_burst.frame_means_block(
row, 0, n_frames, samples_per_frame))
scan_file.write(row)
src += count * samples_per_frame
del blob
scan_file.seek(burst_start + len(counts) * row_bytes)
def _check_frame_delta(self, row_idx: int, count: int, n_frames: int):
"""Decide what to do with a row that did not acquire n_frames frames.
v6 declares n_frames per row in the header and has no per-row length
field, so a mismatched row cannot just be written as-is — that would
shift every later row in the file. The only two safe options are to
square it up or to stop, which is what strict_rows selects between.
Called before anything for the row is written (CH1 leads
SCAN_CHANNELS), so raising here leaves no partial row behind.
"""
if count == n_frames:
return
verb = "zero-padded" if count < n_frames else "truncated"
if self._strict_rows:
raise RuntimeError(
f"Row {row_idx + 1}: {count} frames acquired, {n_frames} "
f"expected. Strict row packing is on, so the scan stops here "
f"rather than writing a row that would be {verb}."
)
msg = (f"Row {row_idx + 1}: {count} frames acquired, {n_frames} "
f"expected — {verb} to keep the file layout intact.")
logger.warning(msg)
self._cb.on_status(msg)
core/scan_geometry.py
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"""Scan geometry planning: angle sequences, rotated bounding boxes, travel
limits, and ETA math. Pure Python — no Qt, no hardware.
"""
from __future__ import annotations
import math
import time
from collections import deque
from dataclasses import dataclass, field
class ScanGeometryError(ValueError):
"""Scan geometry that cannot be executed (bad inputs or off-stage)."""
@dataclass(frozen=True)
class StageLimits:
"""Usable travel of the scanning stage in mm (MLS203-1)."""
x_min: float = 0.0
x_max: float = 110.0
y_min: float = 0.0
y_max: float = 75.0
DEFAULT_STAGE_LIMITS = StageLimits()
@dataclass
class AngleGeometry:
"""One rotation angle's scan extent — also the on-disk v6 geometry row."""
angle_deg: float
x_start: float
x_delta: float
n_frames: int
n_rows: int
y_positions: list[float] = field(default_factory=list)
@dataclass
class ScanPlan:
x_start_nominal: float
y_start_nominal: float
x_delta_nominal: float
y_delta_nominal: float
row_spacing: float
velocity_mm_s: float
laser_freq_hz: float
per_angle: list[AngleGeometry] = field(default_factory=list)
@property
def n_angles(self) -> int:
return len(self.per_angle)
@property
def angles(self) -> list[float]:
return [pa.angle_deg for pa in self.per_angle]
@property
def total_rows(self) -> int:
return sum(pa.n_rows for pa in self.per_angle)
def build_plan(x_start: float, y_start: float, x_delta: float, y_delta: float,
num_angles: int, row_spacing: float, *,
laser_freq_hz: float, velocity_mm_s: float,
rotation_sign: int = -1) -> ScanPlan:
"""Compute the per-angle scan geometry for a nominal ROI.
Each angle only needs to physically scan the bounding box of the nominal
(x_start, y_start, x_delta, y_delta) rectangle rotated by THAT angle --
not the worst case across all angles -- so the X extent (and therefore
points/row) and the row count are computed per angle.
"""
if x_delta <= 0:
raise ScanGeometryError("XD must be > 0")
if row_spacing <= 0:
raise ScanGeometryError("RowSpacing must be > 0")
if num_angles < 1:
raise ScanGeometryError("NumAngles must be ≥ 1")
# Signed so the recorded/commanded angle sequence reflects the GR
# stage's actual physical rotation direction.
if num_angles > 1:
angles = [rotation_sign * i * 180.0 / (num_angles - 1) for i in range(num_angles)]
else:
angles = [0.0]
cx = x_start + x_delta / 2.0
cy = y_start + y_delta / 2.0
per_angle = []
for a in angles:
r = math.radians(a)
bb_w = abs(x_delta * math.cos(r)) + abs(y_delta * math.sin(r))
bb_h = abs(x_delta * math.sin(r)) + abs(y_delta * math.cos(r))
a_x_start = cx - bb_w / 2.0
a_y_start = cy - bb_h / 2.0
a_n_rows = max(1, round(bb_h / row_spacing) + 1) if bb_h > 0 else 1
a_n_frames = max(1, round(bb_w * laser_freq_hz / velocity_mm_s))
per_angle.append(AngleGeometry(
angle_deg=a,
x_start=a_x_start,
x_delta=bb_w,
n_frames=a_n_frames,
n_rows=a_n_rows,
y_positions=[a_y_start + i * row_spacing for i in range(a_n_rows)],
))
return ScanPlan(
x_start_nominal=x_start, y_start_nominal=y_start,
x_delta_nominal=x_delta, y_delta_nominal=y_delta,
row_spacing=row_spacing,
velocity_mm_s=velocity_mm_s, laser_freq_hz=laser_freq_hz,
per_angle=per_angle,
)
def validate_plan(plan: ScanPlan, ramp_mm: float, ramp_buffer_mm: float,
limits: StageLimits = DEFAULT_STAGE_LIMITS) -> None:
"""Raise ScanGeometryError if any angle's physical move leaves the stage.
The actual X move starts one ramp-length + buffer before x_start and ends
one ramp-length + buffer after x_start + x_delta, so the stage is at full
velocity across the whole data window.
"""
x_ramp_total = ramp_mm + ramp_buffer_mm
for pa in plan.per_angle:
x_move_start = pa.x_start - x_ramp_total
x_move_end = pa.x_start + pa.x_delta + x_ramp_total
if x_move_start < limits.x_min:
raise ScanGeometryError(
f"Angle {pa.angle_deg:.1f}°: scan pre-ramp start ({x_move_start:.3f} mm) "
f"is below the X axis minimum ({limits.x_min:g} mm). Reduce XD/YD or move XS/YS "
f"so every rotation angle's bounding box stays on-stage "
f"(SCAN_RAMP_MM={ramp_mm:.3f} + SCAN_RAMP_BUFFER_MM={ramp_buffer_mm:.3f})."
)
if x_move_end > limits.x_max:
raise ScanGeometryError(
f"Angle {pa.angle_deg:.1f}°: scan run-off end ({x_move_end:.3f} mm) "
f"exceeds the X axis maximum ({limits.x_max:g} mm). Reduce XD/YD or move XS/YS "
f"so every rotation angle's bounding box stays on-stage."
)
y_min = min(pa.y_positions)
y_max = max(pa.y_positions)
if y_min < limits.y_min:
raise ScanGeometryError(
f"Angle {pa.angle_deg:.1f}°: scan Y range starts at {y_min:.3f} mm, "
f"below the Y axis minimum ({limits.y_min:g} mm)."
)
if y_max > limits.y_max:
raise ScanGeometryError(
f"Angle {pa.angle_deg:.1f}°: scan Y range ends at {y_max:.3f} mm, "
f"exceeds the Y axis maximum ({limits.y_max:g} mm)."
)
def format_eta(secs: float) -> str:
secs = max(0.0, secs)
m, s = divmod(int(secs), 60)
h, m = divmod(m, 60)
if h > 0:
return f"{h}h {m:02d}m"
if m > 0:
return f"{m}m {s:02d}s"
return f"{s}s"
class EtaEstimator:
"""Rolling average of recent row durations → remaining-time estimate.
Duration history resets when the angle index changes, since different
angles have different row lengths.
"""
def __init__(self, window: int = 5):
self._durations: deque[float] = deque(maxlen=window)
self._row_start: float | None = None
self._last_angle_idx: int = -1
def reset(self) -> None:
self._durations.clear()
self._row_start = None
self._last_angle_idx = -1
def row_started(self, now: float | None = None) -> None:
self._row_start = time.monotonic() if now is None else now
def row_finished(self, angle_idx: int, now: float | None = None) -> None:
if angle_idx != self._last_angle_idx and self._last_angle_idx != -1:
self._durations.clear()
self._last_angle_idx = angle_idx
if self._row_start is not None:
end = time.monotonic() if now is None else now
self._durations.append(end - self._row_start)
self._row_start = None
def eta_secs(self, rows_left: int) -> float | None:
if not self._durations or rows_left <= 0:
return None
return sum(self._durations) / len(self._durations) * rows_left
core/scan_resume.py
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"""Resume planning: turn a file's frontier into a set of angles to re-acquire.
Pure logic, no Qt and no file I/O beyond what SrasFile already parsed, so
the non-obvious contiguity rule is testable on its own.
"""
from __future__ import annotations
from dataclasses import dataclass, field
from core.scan_engine import ResumeState, ResumeTarget
from core.sras_format import SrasFile
@dataclass
class ResumePlan:
targets: list[ResumeTarget]
auto_added: list[int] = field(default_factory=list) # indices forced in
frontier_idx: int = 0
@property
def total_rows(self) -> int:
return sum(t.n_rows for t in self.targets)
def to_state(self, sras: SrasFile) -> ResumeState:
return ResumeState(path=sras.path, targets=self.targets,
samples_per_frame=sras.header.samples_per_frame)
def plan_resume(statuses, selected: set[int]) -> ResumePlan:
"""Expand an operator's angle selection into a runnable resume plan.
Waveform data is one contiguous append-only stream, so nothing can be
written past a gap: if the operator picks an angle at or beyond the
frontier (the first incomplete angle), every angle from the frontier up
to it must be re-acquired too. Those extras are reported in
``auto_added`` so the UI can say so.
"""
frontier_idx = next((s.index for s in statuses if not s.complete), len(statuses))
at_or_past = {i for i in selected if i >= frontier_idx}
if at_or_past:
final = selected | set(range(frontier_idx, max(at_or_past) + 1))
else:
final = set(selected)
targets = [
ResumeTarget(angle_idx=s.index, data_offset=s.data_offset,
n_rows=s.n_rows, angle_deg=s.angle_deg)
for s in statuses if s.index in final
]
return ResumePlan(targets=targets,
auto_added=sorted(final - set(selected)),
frontier_idx=frontier_idx)
def is_compatible(sras: SrasFile, *, velocity: float, laser_freq: float,
sample_rate: float, n_channels: int) -> bool:
"""Whether appending to this file with the current settings is safe."""
h = sras.header
return (h.bytes_per_sample == 1
and h.n_channels == n_channels
and abs(h.velocity - velocity) <= 1e-3
and abs(h.laser_freq - laser_freq) <= 1e-3
and abs(h.sample_rate - sample_rate) <= 1.0)
core/scope_burst.py
+149
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"""Burst-mode FastFrame acquisition policy.
Per-row acquisition pays a full arm/stop/transfer round trip for every row,
and the transfer alone is one IEEE-488.2 block read per frame (~16k frames a
row). A burst instead runs one FastFrame acquisition across as many complete
rows as the scope's frame memory holds, then pulls the whole thing in a single
transaction — amortising the round trip over `rows_per_burst` rows.
The scope reports its capacity with ``HORizontal:FASTframe:MAXFRames?`` once
the horizontal settings are fixed; ``rows_per_burst`` turns that into a row
count. Everything here that computes rather than talks to hardware is a free
function, so the row-splitting logic is testable without a rig.
The catch is that the burst contains no row markers: the scope hands back one
flat run of frames. Boundaries come from polling ``ACQuire:NUMFRAMESACQuired?``
after each row's acquiring pass, while the stage gate is already low — see
``split_row_counts``.
"""
from __future__ import annotations
import logging
import time
import numpy as np
logger = logging.getLogger(__name__)
# Peak transfer buffer, per channel. The writer holds one channel at a time
# (see ScanEngine._scan_rows_burst), so this is the real high-water mark.
BURST_MEMORY_BUDGET_BYTES = 512 * 1024 * 1024
# Extra frames budgeted per row on top of n_frames. 0 gives the plain
# floor(max_frames / n_frames) row count; raise it if the acquiring pass
# routinely over-triggers (watch the pad/truncate warnings).
BURST_FRAME_HEADROOM = 0
BURST_ARM_SETTLE_S = 0.05 # after ACQuire:STATE RUN, before the first move
BURST_ROW_SETTLE_S = 0.05 # after the gate drops, before reading the counter
# ── Pure helpers ─────────────────────────────────────────────────────────────
def rows_per_burst(max_frames: int, n_frames: int, samples_per_frame: int,
rows_remaining: int,
memory_budget: int = BURST_MEMORY_BUDGET_BYTES,
headroom: int = BURST_FRAME_HEADROOM) -> int:
"""How many complete rows fit in one acquisition.
Rounds down — a partial row is worthless, since a row must be transferred
whole to be written. Clamped by the transfer buffer budget and by the rows
actually left in the angle, and never below 1 (a single row always goes,
even if it exceeds the budget, so the scan can still make progress).
"""
if n_frames < 1 or samples_per_frame < 1:
raise ValueError(f"n_frames={n_frames} samples_per_frame={samples_per_frame}")
by_scope = max_frames // (n_frames + headroom)
by_memory = memory_budget // (n_frames * samples_per_frame)
return max(1, min(by_scope, by_memory, rows_remaining))
def split_row_counts(cumulative: list[int]) -> list[int]:
"""Per-row frame counts from the cumulative counter sampled after each row.
``cumulative`` is ``ACQuire:NUMFRAMESACQuired?`` read once per row, already
rebased on the value at burst start.
"""
counts = []
prev = 0
for i, c in enumerate(cumulative):
if c < prev:
raise RuntimeError(
f"FastFrame counter went backwards at row {i} ({prev} → {c}) — "
"the acquisition was restarted mid-burst"
)
counts.append(c - prev)
prev = c
return counts
def normalize_row(buf, offset: int, count: int, n_frames: int,
samples_per_frame: int):
"""Coerce one row's frames to exactly ``n_frames``.
The v6 format commits to n_frames per row in the header and has no per-row
length field, so a row that over- or under-triggers must be squared up or
every later row in the file shifts. Short rows are zero-padded, long rows
lose their trailing frames. Returns something writable directly.
"""
want = n_frames * samples_per_frame
end = min(offset + count * samples_per_frame, offset + want, len(buf))
chunk = memoryview(buf)[offset:end]
if len(chunk) == want:
return chunk
return bytes(chunk) + bytes(want - len(chunk))
def frame_means_block(buf, offset: int, n_frames: int,
samples_per_frame: int) -> list[float]:
"""Per-frame DC mean over one row's slice of a burst buffer."""
n = n_frames * samples_per_frame
block = np.frombuffer(buf, dtype=np.int8, count=n, offset=offset)
return block.reshape(n_frames, samples_per_frame).mean(
axis=1, dtype=np.float32).tolist()
# ── Instrument control ───────────────────────────────────────────────────────
def max_frames(scope) -> int:
"""Frames the scope can hold under the current horizontal settings."""
try:
m = scope.get_fastframe_max_frames()
except Exception as exc:
raise RuntimeError(
"Scope did not answer HORizontal:FASTframe:MAXFRames? — burst mode "
"cannot size a burst without it. Use per-row acquisition on this "
f"firmware. ({exc})"
) from exc
if m < 1:
raise RuntimeError(f"Scope reports a FastFrame capacity of {m} frames")
return m
def start_burst(scope, frame_count: int) -> int:
"""Arm one burst; returns the counter baseline to subtract from later reads.
Reading the baseline back beats assuming the counter resets to 0 on RUN —
any residual is simply subtracted out instead of being misattributed to the
first row.
"""
scope.set_fastframe_count(frame_count)
scope.write("ACQuire:STATE RUN")
time.sleep(BURST_ARM_SETTLE_S)
return frames_acquired(scope)
def stop_burst(scope) -> None:
time.sleep(BURST_ROW_SETTLE_S)
scope.write("ACQuire:STATE STOP")
def frames_acquired(scope) -> int:
return int(scope.query("ACQuire:NUMFRAMESACQuired?"))
def transfer_burst(scope, ch: int, frame_count: int, samples_per_frame: int):
"""Pull a whole burst for one channel in a single CURVe? transaction."""
scope.set_data_source(ch)
return scope.transfer_fastframe_bulk(frame_count, samples_per_frame)
core/scope_inspect.py
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"""Oscilloscope configuration for pre-scan angle inspection.
Inspection is read-on-the-instrument: nothing in this module transfers or
plots waveform data. The app puts the scope into a free-running, edge-
triggered state and drives the stage to the point being inspected; the
operator judges the SAW response and the bias levels on the scope screen.
That split is deliberate. A scan's acquisition trigger is the logic AND of
the laser pulse and the stage's max-velocity gate, and its transfers are
FastFrame blocks — neither is useful for looking at one point by eye. Here
the trigger is a plain edge on the laser pulse, FastFrame is off, and the
acquisition free-runs, so the display updates continuously while the stage
sits still.
CH1 keeps the acquisition front-end so what is on screen is what a scan would
record. CH3 and CH4 are rescaled as DC bias monitors (see BIAS_* below).
"""
from __future__ import annotations
import logging
from dataclasses import replace
from core.scope_sras import SAMPLE_RATE_HZ, SRAS_CHANNELS, configure_channels
logger = logging.getLogger(__name__)
# CH2 carries the laser pulse. The scan triggers it at 0.5 V as one term of a
# logic AND; inspection triggers well above that so a slow edge or a noisy
# baseline cannot free-run the display.
INSPECT_TRIG_LEVEL_V = 2.0
# CH3/CH4 are the DC bias monitors during inspection. The signal never goes
# negative and spans roughly 0–700 mV, so both channels get the *same* scale
# and position — the point of inspecting them is comparing the two by eye, and
# that only works if a division means the same thing on each.
#
# Ground sits BIAS_POSITION_DIV divisions below centre, which puts the whole
# 0–700 mV range above the centre line with a little room underneath for
# undershoot. With 100 mV/div and ground 3.5 divisions low, the visible window
# runs from about -50 mV to +750 mV on an 8-division display and wider on a
# 10-division one, so 0–700 mV sits comfortably inside either.
BIAS_CHANNELS = (3, 4)
BIAS_WINDOW_V = 0.700
BIAS_SCALE_V_DIV = 0.100
BIAS_POSITION_DIV = -3.5
BIAS_LABELS = {3: "Bias - A", 4: "Bias - B"}
def inspect_channel_profiles() -> dict:
"""Channel front-end config for inspection.
CH1 and CH2 are the acquisition profiles verbatim. CH3 and CH4 differ
only in label, scale and position — termination, coupling and bandwidth
stay as the scan sets them, so the bias reading is the same measurement
the scan records, just displayed usefully.
"""
profiles = dict(SRAS_CHANNELS)
for ch in BIAS_CHANNELS:
profiles[ch] = replace(
SRAS_CHANNELS[ch],
label=BIAS_LABELS[ch],
scale_v_div=BIAS_SCALE_V_DIV,
position_div=BIAS_POSITION_DIV,
)
return profiles
def configure_inspection(scope) -> None:
"""Put the scope into free-running inspection mode.
Leaves the acquisition running, so the display stays live while the
operator moves between angles and points.
"""
configure_channels(scope, inspect_channel_profiles())
# Plain edge trigger on the laser pulse — no logic pattern, so the stage
# gate plays no part and a stationary stage still triggers.
scope.write("TRIGger:A:TYPe EDGE")
scope.set_trigger_source(2)
scope.set_trigger_slope("RISE")
scope.set_trigger_level(2, INSPECT_TRIG_LEVEL_V)
scope.set_trigger_mode("NORMAL")
# No averaging: a weak or intermittent SAW response is exactly what the
# operator is looking for, and averaging would hide it.
scope.set_acquire_mode("SAMPLE")
scope.set_fastframe_state(False)
scope.set_sample_rate(SAMPLE_RATE_HZ)
scope.write("HORizontal:POSition 30")
# Free-run rather than single-sequence, so the trace keeps updating.
scope.write("ACQuire:STOPAfter RUNSTop")
scope.write("ACQuire:STATE RUN")
def stop_inspection(scope) -> None:
"""Halt the free-running acquisition.
The next scan reconfigures the scope from scratch, so this only needs to
stop the sweep — it does not try to restore the acquisition profile.
"""
scope.write("ACQuire:STATE STOP")
core/scope_sras.py
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"""Oscilloscope SCPI policy for SRAS acquisition.
All the Tektronix-specific instrument setup the scan depends on, in one
Qt-free place: per-channel display/coupling config, trigger programming,
the background average, and per-row FastFrame transfer.
"""
from __future__ import annotations
import logging
import time
from dataclasses import dataclass
logger = logging.getLogger(__name__)
SAMPLE_RATE_HZ = 6.25e9 # 6.25 GS/s → 160 ps/sample
TRIG_LEVEL_V = 0.500
BACKGROUND_AVERAGES = 1024
BACKGROUND_TIMEOUT_S = 60.0
@dataclass(frozen=True)
class ChannelProfile:
"""Display/input configuration for one scope channel."""
label: str
scale_v_div: float
position_div: float
termination_ohm: int
coupling: str
bandwidth_hz: float
# Standard SRAS front-end configuration.
SRAS_CHANNELS = {
1: ChannelProfile("RF Acoustic Packet", 0.07, 0.0, 50, "DC", 250e6),
2: ChannelProfile("Trigger Signal", 0.5, -2.72, 1_000_000, "DC", 20e6),
3: ChannelProfile("Max Vel Gate", 1.0, -2.72, 1_000_000, "DC", 20e6),
4: ChannelProfile("Bias - B", 0.1, -2.72, 1_000_000, "DC", 20e6),
}
def configure_channels(scope, profiles=None) -> None:
"""Apply the standard SRAS channel configuration."""
profiles = profiles if profiles is not None else SRAS_CHANNELS
for ch, p in profiles.items():
scope.write(f"SELect:CH{ch} ON")
scope.set_channel_label_name(ch, p.label)
scope.set_channel_scale(ch, p.scale_v_div)
scope.set_channel_position(ch, p.position_div)
scope.set_channel_termination(ch, p.termination_ohm)
scope.set_channel_coupling(ch, p.coupling)
scope.set_channel_bandwidth(ch, p.bandwidth_hz)
def configure_acquisition(scope) -> int:
"""Program the edge trigger and timebase; returns samples per frame.
Edge trigger on the rising edge of CH2 (laser pulse). FastFrame stays
off here so the background capture runs as a single record.
"""
scope.write("TRIGger:A:TYPe EDGE")
scope.set_trigger_source(2)
scope.set_trigger_slope("RISE")
scope.set_trigger_level(2, TRIG_LEVEL_V)
scope.set_trigger_mode("NORMAL") # wait for trigger (don't auto-sweep)
scope.set_acquire_mode("SAMPLE")
scope.set_fastframe_state(False)
# Pin the transfer format instead of inheriting front-panel state — the
# file header hardcodes bytes_per_sample=1, and a scope left on 2 bytes
# would corrupt every frame written.
scope.set_data_encoding("RIBinary")
scope.set_data_width(1)
scope.set_sample_rate(SAMPLE_RATE_HZ)
scope.write("HORizontal:POSition 30") # 10 % trigger offset
time.sleep(0.3) # let the timebase settle before reading back
return scope.get_record_length()
def read_preambles(scope, channels) -> list[str]:
"""Snapshot WFMOutpre per channel (captures YMULT/YOFF/YZERO)."""
preambles = []
for ch in channels:
scope.set_data_source(ch)
preambles.append(scope.query_wfmoutpre())
return preambles
def capture_background(scope, should_abort=lambda: False,
on_status=lambda msg: None) -> bytes:
"""Capture one CH1 waveform averaged over BACKGROUND_AVERAGES shots.
The scope auto-stops after the sequence; poll ACQuire:STATE until it
does rather than assuming a duration.
"""
on_status(f"Capturing background waveform ({BACKGROUND_AVERAGES}-average) …")
scope.set_acquire_mode("AVERAGE")
scope.write(f"ACQuire:NUMAVg {BACKGROUND_AVERAGES}")
scope.write("ACQuire:STOPAfter SEQuence")
scope.set_data_source(1)
scope.write("ACQuire:STATE RUN")
deadline = time.time() + BACKGROUND_TIMEOUT_S
while time.time() < deadline:
if should_abort():
break
if scope.query("ACQuire:STATE?").strip() == "0":
break
time.sleep(0.25)
else:
scope.write("ACQuire:STATE STOP")
on_status("Warning: background average timed out; stopping early.")
time.sleep(0.1)
return scope.transfer_curve()
def configure_scan_trigger(scope) -> None:
"""Switch to the scan-time logic-AND trigger (CH2 HIGH AND CH3 HIGH).
CH3 is the BBD202 TRIGOUT_MAXV gate, so frames only accumulate while the
stage is at full scan velocity.
"""
scope.write("ACQuire:STOPAfter RUNSTop")
scope.set_acquire_mode("SAMPLE")
scope.set_fastframe_state(True)
scope.write("TRIGger:A:TYPe LOGIc")
scope.write("TRIGger:A:LOGIc:FUNCtion AND")
scope.set_trigger_level(2, TRIG_LEVEL_V)
scope.set_trigger_level(3, TRIG_LEVEL_V)
scope.write("TRIGger:A:LOGICPattern:CH2 HIGH")
scope.write("TRIGger:A:LOGICPattern:CH3 HIGH")
time.sleep(0.2)
def arm_row(scope) -> None:
"""Start acquisition for one scan row."""
scope.write("ACQuire:STATE RUN")
time.sleep(0.05)
def finish_row(scope) -> None:
"""Wait for trailing frames, then stop acquisition."""
time.sleep(0.2)
scope.write("ACQuire:STATE STOP")
def transfer_channel(scope, ch: int) -> list[bytes]:
"""Fetch one channel's FastFrame block as raw int8 frames."""
scope.set_data_source(ch)
return scope.transfer_fastframe(parse=False)
core/sras_analysis.py
+296
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"""SRAS analysis: scope calibration, image reducers, and the SAW
matched-filter pipeline. Qt-free; operates on the per-angle arrays
returned by core.sras_format.SrasFile.load_angle().
Channel semantics (fixed by the acquisition app):
CH1 — RF Acoustic Packet: FFT → peak frequency
CH3 — Bias A (DC): waveform mean
CH4 — Bias B (DC): waveform mean — also the RF valid-pixel mask source
"""
from __future__ import annotations
import os
import re
from concurrent.futures import ThreadPoolExecutor
from dataclasses import dataclass
import numpy as np
from scipy.signal import butter, hilbert, sosfiltfilt
# Channel indices into the on-disk channel axis (order fixed by SCAN_CHANNELS)
CH1_IDX, CH3_IDX, CH4_IDX = 0, 1, 2
# Fallback scope calibration for preambles missing YMULT/YOFF/YZERO:
# 50 mV/div, 8 div full-scale, int8 ADC, position = -2.72 div
FALLBACK_YMULT_MV = 1.5625 # mV per ADC count
FALLBACK_YOFF_ADC = -87.04 # ADC count that represents 0 V
def parse_preamble(preamble: str) -> dict[str, float]:
"""Extract YMULT, YOFF, YZERO from a Tektronix WFMOutpre string."""
result = {}
for key in ("YMULT", "YOFF", "YZERO"):
m = re.search(rf'\b{key}\s+([-+]?\d*\.?\d+(?:[Ee][+-]?\d+)?)', preamble)
if m:
result[key] = float(m.group(1))
return result
@dataclass
class ChannelCalibration:
"""Per-channel ADC↔mV conversion, parsed from the file's preambles."""
ymult_mv: list[float]
yoff_adc: list[float]
yzero_mv: list[float]
@classmethod
def from_preambles(cls, preambles: list[str]) -> "ChannelCalibration":
cal = cls([], [], [])
for p in preambles:
vals = parse_preamble(p)
# YMULT/YZERO from the scope are in V; stored here in mV
cal.ymult_mv.append(vals.get("YMULT", FALLBACK_YMULT_MV / 1000) * 1000)
cal.yoff_adc.append(vals.get("YOFF", FALLBACK_YOFF_ADC))
cal.yzero_mv.append(vals.get("YZERO", 0.0) * 1000)
return cal
def adc_to_mv(self, adc, ch: int):
return (adc - self.yoff_adc[ch]) * self.ymult_mv[ch] + self.yzero_mv[ch]
def mv_to_adc(self, mv, ch: int):
return (mv - self.yzero_mv[ch]) / self.ymult_mv[ch] + self.yoff_adc[ch]
def power_spectrum(waveform: np.ndarray) -> np.ndarray:
"""FFT power with the DC bin suppressed."""
power = np.abs(np.fft.rfft(waveform)) ** 2
power[..., 0] = 0.0
return power
# ---------------------------------------------------------------------------
# Image reducers — all take the (n_rows, n_ch, n_frames, spf) angle view
# ---------------------------------------------------------------------------
def compute_dc_image(angle_view: np.ndarray, ch_idx: int) -> np.ndarray:
"""Mean of each waveform → (n_rows, n_frames) float32.
Computed directly on the int8 view — no float32 copy of the block.
"""
return angle_view[:, ch_idx].mean(axis=-1, dtype=np.float32)
def _valid_ch1_waveforms(angle_view: np.ndarray, calib: ChannelCalibration,
dc_threshold_mv: float,
background: np.ndarray | None,
) -> tuple[np.ndarray, np.ndarray]:
"""CH4-DC mask + float32 CH1 waveforms for only the pixels that pass.
Materializes float32 for the valid pixels alone (fancy-index on the int8
view first), so a mostly-masked angle costs almost nothing.
"""
dc4_mv = calib.adc_to_mv(compute_dc_image(angle_view, CH4_IDX), CH4_IDX)
valid = dc4_mv >= dc_threshold_mv
if not valid.any():
return valid, np.empty((0, angle_view.shape[-1]), dtype=np.float32)
waves = angle_view[:, CH1_IDX][valid].astype(np.float32) # (n_valid, spf)
if background is not None:
waves -= background
return valid, waves
def compute_rf_image(angle_view: np.ndarray, calib: ChannelCalibration,
freq_axis_mhz: np.ndarray,
dc_threshold_mv: float,
background: np.ndarray | None = None,
gate_start_ns: float | None = None,
gate_end_ns: float | None = None,
time_axis_ns: np.ndarray | None = None) -> np.ndarray:
"""FFT of each CH1 waveform; pixel = peak frequency in MHz.
Pixels whose CH4 DC mean (in mV) is below dc_threshold_mv are 0 and the
FFT is skipped for them. Optional time gate zeroes samples outside
[gate_start_ns, gate_end_ns] before the FFT.
"""
valid, waves = _valid_ch1_waveforms(angle_view, calib, dc_threshold_mv, background)
img = np.zeros(valid.shape, dtype=np.float32)
if len(waves):
if (gate_start_ns is not None or gate_end_ns is not None) and time_axis_ns is not None:
keep = np.ones(len(time_axis_ns), dtype=bool)
if gate_start_ns is not None:
keep &= time_axis_ns >= gate_start_ns
if gate_end_ns is not None:
keep &= time_axis_ns <= gate_end_ns
waves[:, ~keep] = 0.0
peak_bins = np.argmax(power_spectrum(waves), axis=-1)
img[valid] = freq_axis_mhz[peak_bins]
return img
def compute_saw_image(angle_view: np.ndarray, calib: ChannelCalibration,
dc_threshold_mv: float,
pipeline: "SawPipeline", mode: str,
background: np.ndarray | None = None) -> np.ndarray:
"""Matched-filter pipeline over every valid pixel.
mode : "amplitude" → MF envelope peak in the SAW window
"tof" → arrival time (ns) of that peak
Only the requested scalar is kept per pixel — the per-shot intermediate
arrays are dropped inside the worker instead of being accumulated.
"""
valid, waves = _valid_ch1_waveforms(angle_view, calib, dc_threshold_mv, background)
img = np.zeros(valid.shape, dtype=np.float32)
if len(waves):
key = "peak_amplitude" if mode == "amplitude" else "peak_time_ns"
def _scalar(w):
return pipeline.process_shot_metrics(w)[key]
n_workers = min(os.cpu_count() or 4, len(waves))
with ThreadPoolExecutor(max_workers=n_workers) as executor:
img[valid] = np.fromiter(executor.map(_scalar, waves),
dtype=np.float32, count=len(waves))
return img
# ---------------------------------------------------------------------------
# SAW signal processing pipeline
# ---------------------------------------------------------------------------
class SawPipeline:
"""EMI-cleaning and SAW extraction pipeline.
Stages (each independently bypassable):
1. EMI gate — cosine-taper the first `emi_gate_ns` ns to suppress the
laser-firing burst at t≈0; leaves the SAW packet alone.
2. Bandpass — 6th-order Butterworth zero-phase (sosfiltfilt).
3. Matched filter — FFT cross-correlation with a Hann-windowed template
built from the average of N clean shots.
4. Analytic — Hilbert transform of MF output → amplitude envelope.
"""
def __init__(self, sample_rate_hz: float,
emi_gate_ns: float = 50.0,
bp_lo_mhz: float = 85.0,
bp_hi_mhz: float = 200.0,
saw_window_ns: tuple[float, float] = (80.0, 350.0)):
self.sample_rate_hz = float(sample_rate_hz)
self.emi_gate_ns = float(emi_gate_ns)
self.bp_lo_mhz = float(bp_lo_mhz)
self.bp_hi_mhz = float(bp_hi_mhz)
self.saw_window_ns = (float(saw_window_ns[0]), float(saw_window_ns[1]))
self.template: np.ndarray | None = None
self._template_fft: dict[int, np.ndarray] = {} # nfft → rfft(template)
self._emi_gate_samples = max(1, int(round(
self.emi_gate_ns * 1e-9 * self.sample_rate_hz)))
nyq = self.sample_rate_hz / 2.0
lo = np.clip(self.bp_lo_mhz * 1e6 / nyq, 1e-6, 0.999)
hi = np.clip(self.bp_hi_mhz * 1e6 / nyq, lo + 1e-6, 0.9999)
# 6th-order Butterworth → 12th-order bandpass; ~120 dB/decade rolloff
self._sos = butter(6, [lo, hi], btype='bandpass', output='sos')
def gate_emi(self, signal: np.ndarray) -> np.ndarray:
"""Cosine-taper (raised cosine 0→1) the first emi_gate samples.
The taper rolls up smoothly from zero so the abrupt EMI burst is
suppressed without introducing a step discontinuity at the gate edge.
"""
n = min(self._emi_gate_samples, len(signal))
out = signal.copy()
out[:n] *= 0.5 * (1.0 - np.cos(np.pi * np.arange(n) / n))
return out
def bandpass(self, signal: np.ndarray) -> np.ndarray:
"""Zero-phase IIR Butterworth bandpass (sosfiltfilt), float32 in/out."""
return sosfiltfilt(self._sos, signal).astype(np.float32, copy=False)
def build_template(self, waveforms: np.ndarray) -> None:
"""Average N shots (EMI-gated + bandpassed), Hann-windowed to the
declared SAW window, to form the matched-filter template."""
processed = np.stack([
self.bandpass(self.gate_emi(np.asarray(w, dtype=np.float32)))
for w in waveforms
])
avg = processed.mean(axis=0)
n = len(avg)
t_ns = np.arange(n) / self.sample_rate_hz * 1e9
i0 = max(0, int(np.searchsorted(t_ns, self.saw_window_ns[0])))
i1 = min(n, int(np.searchsorted(t_ns, self.saw_window_ns[1])))
windowed = np.zeros(n, dtype=np.float32)
if i1 > i0:
windowed[i0:i1] = avg[i0:i1] * np.hanning(i1 - i0)
self.template = windowed
self._template_fft.clear()
def matched_filter(self, signal: np.ndarray) -> tuple[np.ndarray, np.ndarray]:
"""FFT cross-correlation with the template → (mf_output, envelope)."""
if self.template is None:
raise RuntimeError("No template — call build_template() first")
n = len(signal)
nfft = 1 << (n + len(self.template) - 1).bit_length()
T = self._template_fft.get(nfft)
if T is None:
T = np.conj(np.fft.rfft(self.template, nfft))
self._template_fft[nfft] = T
S = np.fft.rfft(signal, nfft)
mf = np.fft.irfft(S * T, nfft)[:n]
env = np.abs(hilbert(mf))
return mf.astype(np.float32, copy=False), env.astype(np.float32, copy=False)
def process_shot(self, signal: np.ndarray) -> dict:
"""EMI gate → bandpass → matched filter on one shot; returns every
stage plus metrics (for diagnostics displays)."""
raw = np.asarray(signal, dtype=np.float32)
gated = self.gate_emi(raw)
filtered = self.bandpass(gated)
if self.template is not None:
mf_out, env = self.matched_filter(filtered)
else:
mf_out = filtered.copy()
env = np.abs(hilbert(filtered)).astype(np.float32)
metrics = self._envelope_metrics(env, filtered)
return {
"raw": raw,
"gated": gated,
"filtered": filtered,
"mf_output": mf_out,
"envelope": env,
"sample_rate_hz": self.sample_rate_hz,
**metrics,
}
def process_shot_metrics(self, signal: np.ndarray) -> dict:
"""Like process_shot but returns only the scalar metrics — used for
whole-image sweeps where retaining per-shot arrays would multiply
memory by the pixel count."""
filtered = self.bandpass(self.gate_emi(np.asarray(signal, dtype=np.float32)))
if self.template is not None:
_, env = self.matched_filter(filtered)
else:
env = np.abs(hilbert(filtered))
return self._envelope_metrics(env, filtered)
def _envelope_metrics(self, env: np.ndarray, filtered: np.ndarray) -> dict:
sr = self.sample_rate_hz
t_ns = np.arange(len(env)) / sr * 1e9
s0, s1 = self.saw_window_ns
roi = (t_ns >= s0) & (t_ns <= s1)
if roi.any():
peak_sample = int(np.where(roi)[0][np.argmax(env[roi])])
else:
peak_sample = int(np.argmax(env))
peak_amplitude = float(env[peak_sample])
peak_time_ns = float(peak_sample / sr * 1e9)
# SNR: peak / RMS of the noise floor inside the gated EMI region
noise_seg = filtered[:self._emi_gate_samples]
noise_rms = float(np.sqrt(np.mean(noise_seg ** 2))) if len(noise_seg) else 1.0
return {
"peak_amplitude": peak_amplitude,
"peak_sample": peak_sample,
"peak_time_ns": peak_time_ns,
"snr": peak_amplitude / noise_rms if noise_rms > 0 else 0.0,
}
core/sras_format.py
+368
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"""SRAS binary scan-file format (v6 and v10) — the single implementation.
Full byte-level spec: scan_format.md. Summary:
header >4sBHfffffffIdBB magic ver n_angles xs_nom ys_nom xd_nom yd_nom
row_spacing velocity laser_freq spf sample_rate
bytes_per_sample n_channels
angle table n_angles × >f
geometry table n_angles × >ffIH (x_start x_delta n_frames n_rows)
row tables (ragged) per angle: n_rows × >f (y positions)
preambles n_channels × (>H length + utf-8 WFMOutpre string)
background block >I length + raw int8 CH1 average
waveform data angle-major, row-minor, channel-inner:
for each angle, for each row, for each channel,
n_frames × samples_per_frame × bytes_per_sample
Incomplete files are valid: the data block is one contiguous append-only
stream, so the readable prefix defines a single frontier past which nothing
has been written yet (see ``SrasFile.angle_status``).
Version 10 is the SAW quality check (core.saw_check): byte layout identical
to v6, but every angle declares exactly one row — the row-wise middle of the
ROI. The version byte is the whole difference, and it exists so a reader can
tell a one-row-per-angle check from a full scan that was aborted after its
first row. ``create_scan_file`` enforces the one-row rule at write time.
"""
from __future__ import annotations
import mmap
import struct
from dataclasses import dataclass, field
from pathlib import Path
from typing import BinaryIO
import numpy as np
from core.scan_geometry import AngleGeometry, ScanPlan
MAGIC = b"SRAS"
VERSION = 6
# One row per angle, taken from the middle of the ROI — see core.saw_check.
VERSION_SAW_CHECK = 10
SUPPORTED_VERSIONS = (VERSION, VERSION_SAW_CHECK)
HDR_FMT = ">4sBHfffffffIdBB"
HDR_SIZE = struct.calcsize(HDR_FMT) # 49 bytes
GEOM_FMT = ">ffIH"
GEOM_SIZE = struct.calcsize(GEOM_FMT) # 14 bytes
# Oscilloscope channels recorded, in on-disk order.
SCAN_CHANNELS = [1, 3, 4]
STATUS_OK = "OK"
STATUS_TRUNCATED = "TRUNCATED"
STATUS_MISSING = "MISSING"
@dataclass
class ScanHeader:
"""The fixed v6 global header (everything but magic/version)."""
n_angles: int
x_start_nominal: float
y_start_nominal: float
x_delta_nominal: float
y_delta_nominal: float
row_spacing: float
velocity: float
laser_freq: float
samples_per_frame: int
sample_rate: float
bytes_per_sample: int
n_channels: int
@dataclass
class AngleStatus:
"""How much of one angle's declared data is actually on disk."""
index: int
angle_deg: float
n_rows: int # declared
row_bytes: int
data_offset: int
n_rows_available: int
status: str # STATUS_OK / STATUS_TRUNCATED / STATUS_MISSING
@property
def complete(self) -> bool:
return self.status == STATUS_OK
def create_scan_file(path: Path, plan: ScanPlan, samples_per_frame: int,
sample_rate: float, preambles: list[str],
background_waveform: bytes,
version: int = VERSION) -> BinaryIO:
"""Create a new .sras file and write the header + tables.
``version`` selects which kind of file this is — VERSION for a full scan,
VERSION_SAW_CHECK for a middle-row quality check. The layout is the same
either way; the one-row-per-angle rule that gives v10 its meaning is
checked here, since nothing downstream can recover from a v10 file that
breaks it.
Returns an open binary file positioned at the start of the data block;
the caller appends waveform rows and must close it (try/finally).
"""
if version not in SUPPORTED_VERSIONS:
raise ValueError(
f"Cannot write SRAS format version {version} "
f"(supported: {', '.join(str(v) for v in SUPPORTED_VERSIONS)})"
)
if version == VERSION_SAW_CHECK:
bad = [f"{pa.angle_deg:.1f}° has {pa.n_rows}"
for pa in plan.per_angle if pa.n_rows != 1]
if bad:
raise ValueError(
"A v10 SAW-check file holds exactly one row per angle, but "
+ ", ".join(bad) + " — build the plan with "
"core.saw_check.middle_row_plan()."
)
path.parent.mkdir(parents=True, exist_ok=True)
f = open(path, "wb")
f.write(struct.pack(
HDR_FMT, MAGIC, version,
plan.n_angles,
plan.x_start_nominal, plan.y_start_nominal,
plan.x_delta_nominal, plan.y_delta_nominal,
plan.row_spacing,
plan.velocity_mm_s, plan.laser_freq_hz,
samples_per_frame,
sample_rate,
1, # bytes_per_sample: int8 from scope default
len(SCAN_CHANNELS),
))
f.write(struct.pack(f">{plan.n_angles}f", *plan.angles))
for pa in plan.per_angle:
f.write(struct.pack(GEOM_FMT, pa.x_start, pa.x_delta, pa.n_frames, pa.n_rows))
for pa in plan.per_angle:
f.write(struct.pack(f">{pa.n_rows}f", *pa.y_positions))
for p in preambles:
enc = p.encode("utf-8")
f.write(struct.pack(">H", len(enc)))
f.write(enc)
f.write(struct.pack(">I", len(background_waveform)))
f.write(background_waveform)
return f
@dataclass
class SrasFile:
"""Parsed .sras file (v6 or v10): header, tables, and lazy (memmap) access.
Parsing reads only the header/tables — never the waveform block — so
opening a multi-GB file is cheap. ``load_angle``/``load_row`` return
read-only numpy views backed by a shared mmap; no data is copied until
the caller computes on it.
"""
path: Path
version: int = field(init=False)
header: ScanHeader = field(init=False)
per_angle: list[AngleGeometry] = field(init=False)
preambles: list[str] = field(init=False)
preambles_raw: list[bytes] = field(init=False)
background: bytes = field(init=False)
data_start_offset: int = field(init=False)
file_size: int = field(init=False)
def __post_init__(self):
self.path = Path(self.path)
self._mmap: mmap.mmap | None = None
self._parse()
def _parse(self):
self.file_size = self.path.stat().st_size
with open(self.path, "rb") as f:
raw = f.read(HDR_SIZE)
if len(raw) < HDR_SIZE:
raise ValueError(f"{self.path.name}: file too short to contain a valid header")
(magic, version, n_angles, x_start_nominal, y_start_nominal,
x_delta_nominal, y_delta_nominal, row_spacing, velocity, laser_freq,
samples_per_frame, sample_rate, bytes_per_sample,
n_channels) = struct.unpack(HDR_FMT, raw)
if magic != MAGIC:
raise ValueError(f"{self.path.name}: not a valid SRAS file (bad magic)")
if version not in SUPPORTED_VERSIONS:
raise ValueError(
f"{self.path.name}: unsupported SRAS format version {version} "
f"(supported: {', '.join(str(v) for v in SUPPORTED_VERSIONS)})"
)
self.version = version
self.header = ScanHeader(
n_angles=n_angles,
x_start_nominal=x_start_nominal, y_start_nominal=y_start_nominal,
x_delta_nominal=x_delta_nominal, y_delta_nominal=y_delta_nominal,
row_spacing=row_spacing, velocity=velocity, laser_freq=laser_freq,
samples_per_frame=samples_per_frame, sample_rate=sample_rate,
bytes_per_sample=bytes_per_sample, n_channels=n_channels,
)
angles = struct.unpack(f">{n_angles}f", f.read(4 * n_angles))
self.per_angle = []
for a in angles:
x_start, x_delta, n_frames, n_rows = struct.unpack(GEOM_FMT, f.read(GEOM_SIZE))
self.per_angle.append(AngleGeometry(
angle_deg=a, x_start=x_start, x_delta=x_delta,
n_frames=n_frames, n_rows=n_rows,
))
for pa in self.per_angle:
pa.y_positions = list(struct.unpack(f">{pa.n_rows}f", f.read(4 * pa.n_rows)))
self.preambles_raw = []
for _ in range(n_channels):
(plen,) = struct.unpack(">H", f.read(2))
self.preambles_raw.append(f.read(plen))
self.preambles = [p.decode("utf-8", errors="replace") for p in self.preambles_raw]
(n_bg,) = struct.unpack(">I", f.read(4))
self.background = f.read(n_bg)
self.data_start_offset = f.tell()
@property
def is_saw_check(self) -> bool:
"""True for a v10 middle-row SAW quality check rather than a scan."""
return self.version == VERSION_SAW_CHECK
# ── Frontier / truncation analysis ───────────────────────────────────────
def row_bytes(self, angle_idx: int) -> int:
pa = self.per_angle[angle_idx]
return (self.header.n_channels * pa.n_frames
* self.header.samples_per_frame * self.header.bytes_per_sample)
def angle_status(self) -> list[AngleStatus]:
"""Walk declared per-row byte counts against the actual file size.
Because the data is one contiguous append-only stream, once an angle
is found short every later angle is necessarily absent too — there is
a single frontier past which nothing has been written yet.
"""
statuses = []
cursor = self.data_start_offset
frontier_seen = False
for ai, pa in enumerate(self.per_angle):
row_bytes = self.row_bytes(ai)
data_offset = cursor
if frontier_seen:
n_rows_available = 0
status = STATUS_MISSING
else:
declared_bytes = row_bytes * pa.n_rows
if row_bytes > 0 and cursor + declared_bytes <= self.file_size:
n_rows_available = pa.n_rows
status = STATUS_OK
cursor += declared_bytes
else:
remaining = max(0, self.file_size - cursor)
n_rows_available = remaining // row_bytes if row_bytes > 0 else 0
status = STATUS_MISSING if n_rows_available == 0 else STATUS_TRUNCATED
frontier_seen = True
statuses.append(AngleStatus(
index=ai, angle_deg=pa.angle_deg, n_rows=pa.n_rows,
row_bytes=row_bytes, data_offset=data_offset,
n_rows_available=n_rows_available, status=status,
))
return statuses
def angle_data_offset(self, angle_idx: int) -> int:
offset = self.data_start_offset
for ai in range(angle_idx):
offset += self.row_bytes(ai) * self.per_angle[ai].n_rows
return offset
# ── Lazy data access ─────────────────────────────────────────────────────
def _ensure_mmap(self) -> mmap.mmap:
if self._mmap is None:
# The mapping stays valid after the file object is closed, so
# don't hold the descriptor open for the (long) life of a viewer
# session.
with open(self.path, "rb") as f:
self._mmap = mmap.mmap(f.fileno(), 0, access=mmap.ACCESS_READ)
return self._mmap
def _dtype(self) -> np.dtype:
return np.dtype(np.int16 if self.header.bytes_per_sample == 2 else np.int8)
def load_angle(self, angle_idx: int, n_rows: int | None = None) -> np.ndarray:
"""Read-only view of one angle's data block, shape
(n_rows, n_channels, n_frames, samples_per_frame).
``n_rows`` limits the view to the rows actually on disk (pass
``AngleStatus.n_rows_available`` for truncated files); default is the
declared row count.
"""
pa = self.per_angle[angle_idx]
h = self.header
if n_rows is None:
n_rows = pa.n_rows
start = self.angle_data_offset(angle_idx)
count = n_rows * h.n_channels * pa.n_frames * h.samples_per_frame
arr = np.frombuffer(self._ensure_mmap(), dtype=self._dtype(),
count=count, offset=start)
arr = arr.reshape(n_rows, h.n_channels, pa.n_frames, h.samples_per_frame)
arr.flags.writeable = False
return arr
def load_row(self, angle_idx: int, row: int, channel_idx: int) -> np.ndarray:
"""Read-only view of one row/channel, shape (n_frames, samples_per_frame)."""
pa = self.per_angle[angle_idx]
h = self.header
ch_bytes = pa.n_frames * h.samples_per_frame * h.bytes_per_sample
start = (self.angle_data_offset(angle_idx) + row * self.row_bytes(angle_idx)
+ channel_idx * ch_bytes)
arr = np.frombuffer(self._ensure_mmap(), dtype=self._dtype(),
count=pa.n_frames * h.samples_per_frame, offset=start)
arr = arr.reshape(pa.n_frames, h.samples_per_frame)
arr.flags.writeable = False
return arr
def close(self):
"""Release this file's hold on the mapping.
Views handed out earlier stay valid — they keep the mapping alive
until they are garbage-collected, at which point the OS frees it.
"""
if self._mmap is not None:
try:
self._mmap.close()
except BufferError:
pass # live numpy views still reference the buffer
self._mmap = None
def __enter__(self):
return self
def __exit__(self, exc_type, exc_val, exc_tb):
self.close()
# ── Axes helpers (viewer conveniences, derived from header fields) ───────
def pixel_pitch_x_mm(self) -> float:
"""Distance between adjacent frames along X."""
return self.header.velocity / self.header.laser_freq
def x_axis_mm(self, angle_idx: int) -> np.ndarray:
pa = self.per_angle[angle_idx]
return pa.x_start + np.arange(pa.n_frames) * self.pixel_pitch_x_mm()
def time_axis_ns(self) -> np.ndarray:
h = self.header
return np.arange(h.samples_per_frame) / h.sample_rate * 1e9
def freq_axis_mhz(self, nfft: int) -> np.ndarray:
return np.fft.rfftfreq(nfft, d=1.0 / self.header.sample_rate) / 1e6
def plan_from_header(sras: SrasFile) -> ScanPlan:
"""Reconstruct the ScanPlan a file was written with (for resume)."""
h = sras.header
return ScanPlan(
x_start_nominal=h.x_start_nominal, y_start_nominal=h.y_start_nominal,
x_delta_nominal=h.x_delta_nominal, y_delta_nominal=h.y_delta_nominal,
row_spacing=h.row_spacing,
velocity_mm_s=h.velocity, laser_freq_hz=h.laser_freq,
per_angle=list(sras.per_angle),
)
docs/genesis_verification.md
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# Genesis laser — hardware verification checklist
`hardware/genesis_core.py` was extracted from `tools/genesis_laser_gui.py`,
but the extraction changed behavior in ways only the bench can adjudicate.
Until every row below is resolved, **both files stay in the repo unchanged**:
`genesis_laser_gui.py` is the reference implementation, `genesis_core.py`
(+ `tools/genesis_laser_control.py`) is the intended successor.
Run these with the Genesis laser connected, interlock chain accessible, and
a front-panel/manual reference for current and temperature readouts.
| # | Divergence | Bench test | Resolution |
|---|---|---|---|
| 1 | **ADS7828 command byte.** Reference passes raw command bytes (`0x84`, `0xe4`, `0x94` — `genesis_laser_gui.py:73-77`); core synthesizes `0x80 \| (ch<<4) \| 0x0c` → `0x8C` for ch0 (`genesis_core.py:413`), different PD1/PD0 power-down bits. | Read the same ADC channel through both implementations; compare against the front-panel current readout. Also check for settling differences right after power-up. | Keep whichever matches the panel; fix the other. |
| 2 | **LDD enable polarity.** Reference `get_ldd_enable()` returns `not bool(value & 0x01)` ("Inverted logic", `genesis_laser_gui.py:602-612`); core returns the un-inverted bit (`genesis_core.py:585-599`). Same register, opposite answers. | With emission verifiably OFF (keyswitch off), read LDD status via both. Exactly one will say "disabled". | Adopt the polarity that matches reality; document the register semantics inline. |
| 3 | **Shutter: manual or bit-controlled?** Reference docs say "this laser has a MANUAL shutter" and `emergency_stop()` deliberately leaves it alone; core `set_shutter()` toggles a PCA9555 bit and `emergency_stop()`/`enter_safe_state()` rely on it. | Toggle `set_shutter()` from core with the beam blocked; observe whether anything physical actuates. | If the bit is inert, remove `set_shutter` and fix the safe-state functions; if real, correct the `tools/` docs. |
| 4 | **ADC filtering dropped.** Reference reads 3× and takes median (`i2c_read_discard_high_low`, `genesis_laser_gui.py:341-364`) or retries until two reads agree; core does single unfiltered reads. | Log ~100 consecutive current readings through core; if the spread is more than display noise, filtering was load-bearing. | Port the median-of-3 helper into `genesis_core.I2CProtocol`. |
| 5 | **Scaling dropped.** Reference converts to Amps/Watts (`AMPS_FULLSCALE * ADC_TO_VOLTS`); core returns raw 0–4095 counts. | Compare a scaled reading against the front panel. | Port the scaling constants + conversion into core. |
| 6 | **Temperatures + power monitoring dropped.** `get_main_temp` / `get_etalon_temp` / `get_shg_temp` / `get_power_actual` exist only in the reference. | Confirm each channel's reading is sane vs. front panel. | Port the four getters into core. |
| 7 | **`pre_flight_check()` dropped.** Reference validates remote-enable + keyswitch + interlock before emission. | n/a — code review + one interlock-open test. | Port into core; call it from `genesis_laser_control.py` before enabling. |
When all rows are resolved: port the verified behavior into
`genesis_core.py`, update `tools/genesis_laser_control.py`, delete
`tools/genesis_laser_gui.py`, and remove this checklist plus the warning
header in `genesis_core.py`.
genesis_worker.py
-193
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@@ -1,193 +0,0 @@
"""
Genesis Laser Worker Thread
Manages Genesis laser connection in a separate thread to keep the UI responsive.
Provides async querying and status monitoring via Qt signals.
"""
from PyQt6 import QtCore
from hardware.genesis_core import SerialComm, I2CProtocol, I2CDevices, LaserControl
import queue
import time
from typing import Optional
class GenesisCommand:
"""Represents a genesis laser command"""
def __init__(self, cmd_type: str, **kwargs):
self.cmd_type = cmd_type
self.params = kwargs
class GenesisWorker(QtCore.QObject):
"""
Worker object for handling Genesis laser control in a separate thread.
Signals:
connected: Emitted when laser connects successfully
disconnected: Emitted when laser disconnects
connection_failed: Emitted when connection fails (error_msg: str)
laser_info_updated: Emitted with laser status
query_completed: Emitted when a query operation completes (result: dict)
error_occurred: Emitted when an error occurs (error_msg: str)
"""
# Signals
connected = QtCore.pyqtSignal()
disconnected = QtCore.pyqtSignal()
connection_failed = QtCore.pyqtSignal(str)
laser_info_updated = QtCore.pyqtSignal(dict) # Status information
query_completed = QtCore.pyqtSignal(dict) # Query result
error_occurred = QtCore.pyqtSignal(str) # Error message
def __init__(self, port: str = "/dev/ttyUSB0", baudrate: int = 9600):
super().__init__()
self.serial_comm = SerialComm()
self.i2c_protocol = I2CProtocol(self.serial_comm)
self.i2c_devices = I2CDevices(self.i2c_protocol)
self.laser_control = LaserControl(self.i2c_devices)
self.port = port
self.baudrate = baudrate
self.is_connected = False
self.command_queue = queue.Queue()
self.running = True
# Last known laser state
self.last_laser_state = {}
# Update interval for status polling
self.last_status_update_time = 0
self.status_update_interval = 1.0 # seconds
@QtCore.pyqtSlot()
def run(self):
"""Main worker loop - processes commands from queue"""
print(f"Genesis laser worker thread started - connecting to {self.port}")
# Try to connect on startup
if self.connect():
self.connected.emit()
else:
error_msg = f"Failed to connect to Genesis laser on {self.port}"
print(error_msg)
self.connection_failed.emit(error_msg)
while self.running:
try:
# Check for commands with timeout to allow periodic status updates
try:
cmd = self.command_queue.get(timeout=0.05) # 50ms timeout
self.process_command(cmd)
except queue.Empty:
pass
# Periodically update status if connected
if self.is_connected:
current_time = time.time()
if current_time - self.last_status_update_time >= self.status_update_interval:
self.update_laser_status()
self.last_status_update_time = current_time
except Exception as e:
print(f"Error in genesis worker loop: {e}")
self.error_occurred.emit(str(e))
# Cleanup on exit
self.disconnect()
print("Genesis laser worker thread stopped")
def connect(self) -> bool:
"""Establish connection to the laser"""
try:
if self.serial_comm.connect(self.port, self.baudrate):
self.is_connected = True
print(f"Connected to Genesis laser on {self.port}")
return True
else:
print(f"Failed to open serial port {self.port}")
return False
except Exception as e:
print(f"Connection error: {e}")
return False
def disconnect(self):
"""Disconnect from the laser"""
if self.is_connected:
self.serial_comm.disconnect()
self.is_connected = False
self.disconnected.emit()
print("Disconnected from Genesis laser")
def process_command(self, cmd: GenesisCommand):
"""Process a command from the queue"""
if not self.is_connected:
self.error_occurred.emit("Laser not connected")
return
try:
if cmd.cmd_type == "query_all":
result = self.query_all_status()
self.query_completed.emit(result)
elif cmd.cmd_type == "query_current":
result = {"current": self.laser_control.get_current_actual()}
self.query_completed.emit(result)
elif cmd.cmd_type == "query_interlock":
result = {"interlock": self.laser_control.get_interlock_status()}
self.query_completed.emit(result)
elif cmd.cmd_type == "set_current":
value = cmd.params.get("value", 0)
success = self.laser_control.set_current(int(value))
self.query_completed.emit({"success": success})
elif cmd.cmd_type == "set_shutter":
state = cmd.params.get("state", False)
success = self.laser_control.set_shutter(state)
self.query_completed.emit({"success": success})
else:
self.error_occurred.emit(f"Unknown command: {cmd.cmd_type}")
except Exception as e:
self.error_occurred.emit(f"Command execution error: {e}")
def update_laser_status(self):
"""Query and emit current laser status"""
if not self.is_connected:
return
try:
status = {
"connected": True,
"current_actual": self.laser_control.get_current_actual(),
"interlock_status": self.laser_control.get_interlock_status(),
"ldd_enable_status": self.laser_control.get_ldd_enable_status(),
"psglue_in_status": self.laser_control.get_psglue_in_status(),
"psglue_out_status": self.laser_control.get_psglue_out_status(),
"head_dio_status": self.laser_control.get_head_dio_status(),
}
# Only emit if something changed
if status != self.last_laser_state:
self.last_laser_state = status
self.laser_info_updated.emit(status)
except Exception as e:
print(f"Error updating laser status: {e}")
def query_all_status(self) -> dict:
"""Query all laser status information"""
return {
"connected": True,
"current_actual": self.laser_control.get_current_actual(),
"interlock_status": self.laser_control.get_interlock_status(),
"ldd_enable_status": self.laser_control.get_ldd_enable_status(),
"psglue_in_status": self.laser_control.get_psglue_in_status(),
"psglue_out_status": self.laser_control.get_psglue_out_status(),
"head_dio_status": self.laser_control.get_head_dio_status(),
}
def queue_command(self, cmd: GenesisCommand):
"""Queue a command for execution"""
self.command_queue.put(cmd)
def stop(self):
"""Stop the worker thread"""
self.running = False
gui/__init__.py
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"""Shared PyQt6 layer: adapters and widgets used by more than one app."""
gui/inspect_bridge.py
+113
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"""Qt bridge over the headless AngleInspector.
Inspection is command-driven rather than one long run: the operator clicks an
angle, waits for the stage to park, looks at the scope, clicks again. That is
exactly the shape QueueWorker exists for — it blocks on the queue between
commands instead of polling, so an inspection window left open costs nothing.
Every stage move and rotation blocks for seconds, so all of it runs on this
worker's thread; the window only ever enqueues and reacts to signals.
"""
from __future__ import annotations
import traceback
from PyQt6.QtCore import pyqtSignal
from core.angle_inspect import AngleInspector, InspectCallbacks
from gui.qt_workers import QueueWorker
class QtAngleInspector(QueueWorker):
"""Runs an AngleInspector on its own QThread and republishes its events."""
ready = pyqtSignal(object) # InspectionPoint — start() succeeded
start_failed = pyqtSignal(str)
point_changed = pyqtSignal(object) # InspectionPoint
status_msg = pyqtSignal(str)
busy_changed = pyqtSignal(bool) # True while a move is in flight
stopped = pyqtSignal()
def __init__(self, stage, scope, rotator, plan, on_inspect_active=None):
super().__init__()
self._on_inspect_active = on_inspect_active
callbacks = InspectCallbacks(
on_status=self.status_msg.emit,
on_point=self.point_changed.emit,
on_busy=self.busy_changed.emit,
)
self._inspector = AngleInspector(stage, scope, rotator, plan,
callbacks=callbacks)
self._handlers = {
"start": self._do_start,
"goto": self._do_goto,
"new_point": self._do_new_point,
"stop": self._do_stop,
}
# ── Introspection (safe from the GUI thread: reads the plan, not the rig) ──
def angle_labels(self) -> list[str]:
return self._inspector.angle_labels()
@property
def n_angles(self) -> int:
return self._inspector.n_angles
# ── Command submission (GUI thread) ───────────────────────────────────────
def request_start(self):
self._enqueue("start")
def request_goto(self, angle_idx: int):
self._enqueue("goto", angle_idx=angle_idx)
def request_new_point(self):
self._enqueue("new_point")
def request_stop(self):
self._enqueue("stop")
# ── Handlers (worker thread) ──────────────────────────────────────────────
def _do_start(self):
if self._on_inspect_active is not None:
self._on_inspect_active(True)
try:
point = self._inspector.start()
except Exception as exc:
traceback.print_exc()
if self._on_inspect_active is not None:
self._on_inspect_active(False)
self.start_failed.emit(str(exc))
return
self.ready.emit(point)
def _do_goto(self, angle_idx: int):
self._inspector.goto_angle(angle_idx)
def _do_new_point(self):
self._inspector.new_point()
def _do_stop(self):
try:
self._inspector.stop()
finally:
if self._on_inspect_active is not None:
self._on_inspect_active(False)
self.stopped.emit()
def _on_stop(self):
"""Worker loop exiting — make sure the rig is left in a safe state.
Covers the case where the window is closed without a clean stop
command reaching the queue.
"""
try:
self._inspector.stop()
except Exception:
traceback.print_exc()
finally:
if self._on_inspect_active is not None:
self._on_inspect_active(False)
gui/qt_t3r.py
+55
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"""Qt adapter over the (Qt-free) T3RDriver.
The driver fires its callbacks on the reader thread. This adapter turns
each one into a Qt signal emitted from that thread; because the adapter
lives on the GUI thread, Qt queues the delivery and slots run on the GUI
thread — which is what widget code requires.
Command methods are forwarded to the driver, so panels can hold the adapter
alone and use it exactly like the old QObject driver.
"""
from __future__ import annotations
from PyQt6.QtCore import QObject, pyqtSignal
from hardware.t3r_driver import T3RDriver
class QtT3RAdapter(QObject):
port_opened = pyqtSignal()
handshake_ok = pyqtSignal(int, int, int) # proto_ver, fw_ver, num_channels
disconnected = pyqtSignal(str) # reason ("" = user-initiated)
info_updated = pyqtSignal(int, object) # ch, proto.Info
drv_status_updated = pyqtSignal(int, object)
position_updated = pyqtSignal(int, int)
motion_done = pyqtSignal(int, int)
stopped = pyqtSignal(int, int)
fault_occurred = pyqtSignal(int, int)
ack_received = pyqtSignal(int, int)
frame_received = pyqtSignal(int, bytes)
_EVENTS = ("port_opened", "handshake_ok", "disconnected", "info_updated",
"drv_status_updated", "position_updated", "motion_done",
"stopped", "fault_occurred", "ack_received", "frame_received")
def __init__(self, driver: T3RDriver | None = None, parent=None):
super().__init__(parent)
self.driver = driver if driver is not None else T3RDriver()
for name in self._EVENTS:
getattr(self.driver, name).connect(getattr(self, name).emit)
# Class attributes (constants) the panels read off the driver
CHANNEL_NAMES = T3RDriver.CHANNEL_NAMES
GR_AXIS_CH = T3RDriver.GR_AXIS_CH
@property
def is_open(self) -> bool:
return self.driver.is_open
def __getattr__(self, name):
# Only reached for attributes this QObject doesn't define, i.e. the
# driver's command API (open/close/move/jog/enable/...).
if name.startswith("_"):
raise AttributeError(name)
return getattr(object.__getattribute__(self, "driver"), name)
gui/qt_workers.py
+118
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"""Shared Qt worker base for hardware that must be driven off the GUI thread.
Every device worker in this project was the same shape: a command queue, a
`while running: get(timeout=…)` loop, an if/elif dispatch, and a standard
connected/disconnected/failed signal trio. The timeout-poll versions woke
10–20 times a second forever, even with nothing to do; this base blocks on
the queue instead and wakes only when there is work.
"""
from __future__ import annotations
import queue
from PyQt6.QtCore import QObject, pyqtSignal, pyqtSlot
_STOP = object()
class QueueWorker(QObject):
"""Base for a device worker living on its own QThread.
Subclasses register handlers in ``self._handlers`` (command name →
callable) and call ``self._enqueue(name, **kwargs)`` from the GUI thread.
Override ``_on_stop`` to release hardware when the loop exits.
"""
connected = pyqtSignal()
disconnected = pyqtSignal()
connection_failed = pyqtSignal(str)
error_occurred = pyqtSignal(str)
def __init__(self):
super().__init__()
self._cmd_q: queue.Queue = queue.Queue()
self._handlers: dict[str, callable] = {}
self._running = False
self.is_connected = False
# ── Command submission (GUI thread) ───────────────────────────────────────
def _enqueue(self, cmd_type: str, **kwargs):
self._cmd_q.put((cmd_type, kwargs))
def stop_worker(self):
self._cmd_q.put(_STOP)
# ── Worker loop ───────────────────────────────────────────────────────────
@pyqtSlot()
def run(self):
self._running = True
while self._running:
item = self._cmd_q.get() # blocks — no idle wake-ups
if item is _STOP:
break
cmd_type, kwargs = item
handler = self._handlers.get(cmd_type)
if handler is None:
self.error_occurred.emit(f"Unknown command: {cmd_type}")
continue
try:
handler(**kwargs)
except Exception as exc:
self.error_occurred.emit(str(exc))
self._running = False
self._on_stop()
def _on_stop(self):
"""Release hardware when the loop exits. Override as needed."""
class PollingQueueWorker(QueueWorker):
"""QueueWorker that also polls the device on an interval.
The poll is self-rescheduling: the next one is queued only after the
previous finishes, so a device slower than the interval can never
accumulate a backlog of stale poll commands (which is exactly what the
old free-running QTimer did to the Helios laser).
"""
POLL_CMD = "_poll"
def __init__(self, poll_interval_s: float = 1.0):
super().__init__()
self._poll_interval_s = poll_interval_s
self._polling = False
self._handlers[self.POLL_CMD] = self._poll_and_reschedule
def start_polling(self):
if not self._polling:
self._polling = True
self._enqueue(self.POLL_CMD)
def stop_polling(self):
self._polling = False
def _poll_and_reschedule(self):
if not self._polling or not self.is_connected:
self._polling = False
return
try:
self._poll_once()
finally:
if self._polling and self.is_connected:
self._schedule_next_poll()
def _schedule_next_poll(self):
# A timer thread rather than a sleep here, so the worker stays
# responsive to commands during the interval.
import threading
t = threading.Timer(self._poll_interval_s,
lambda: self._enqueue(self.POLL_CMD))
t.daemon = True
t.start()
self._poll_timer = t
def _poll_once(self):
"""Read device state and emit updates. Implemented by subclasses."""
gui/scan_bridge.py
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"""Qt bridge over the headless ScanEngine.
Exposes exactly the signal surface the old in-GUI ScanWorker had, so window
code connects to it unchanged, and adapts prompts/progress to Qt. The
engine itself stays Qt-free and reusable by any other front end.
"""
from __future__ import annotations
import threading
import traceback
from PyQt6.QtCore import QObject, pyqtSignal, pyqtSlot
from core.scan_engine import ScanAborted, ScanCallbacks, ScanEngine
class QtScanController(QObject):
"""Runs a ScanEngine on the caller's QThread and republishes its events.
Move this to a QThread and connect `started` → `run`, exactly like the
previous ScanWorker.
"""
started = pyqtSignal()
completed = pyqtSignal()
dc_bias_updated = pyqtSignal(int, object) # row index, per-frame DC means
failed = pyqtSignal(str)
row_started = pyqtSignal(int, int, int, int) # row, n_rows, angle_idx, n_angles
row_done = pyqtSignal(int, int, int, int)
status_msg = pyqtSignal(str)
user_prompt = pyqtSignal(str, str) # title, message
paused_changed = pyqtSignal(bool) # True while paused at a row boundary
def __init__(self, stage, scope, rotator, plan, out_path,
resume=None, on_scan_active=None, burst_mode=False,
strict_rows=False):
super().__init__()
self._prompt_event = threading.Event()
self._on_scan_active = on_scan_active
callbacks = ScanCallbacks(
on_status=self.status_msg.emit,
on_started=self.started.emit,
on_row_started=self.row_started.emit,
on_row_done=self.row_done.emit,
on_dc_bias=self.dc_bias_updated.emit,
on_paused_changed=self.paused_changed.emit,
prompt=self._blocking_prompt,
)
self._engine = ScanEngine(stage, scope, rotator, plan, out_path,
resume=resume, callbacks=callbacks,
burst_mode=burst_mode,
strict_rows=strict_rows)
# ── Engine control (called from the GUI thread) ───────────────────────────
def abort(self):
self._engine.abort()
self._prompt_event.set() # release a scan parked on a prompt
def pause(self):
self._engine.pause()
def resume(self):
self._engine.resume()
def acknowledge_prompt(self):
"""Called from the GUI thread when the operator dismisses a prompt."""
self._prompt_event.set()
# ── Callback plumbing ─────────────────────────────────────────────────────
def _blocking_prompt(self, title: str, message: str):
"""Ask the GUI thread, then block the scan thread until answered.
Polls rather than waiting forever so an abort during a prompt takes
effect immediately instead of deadlocking the scan thread.
"""
self._prompt_event.clear()
self.user_prompt.emit(title, message)
while not self._prompt_event.wait(0.2):
if self._engine.aborted:
return
@pyqtSlot()
def run(self):
if self._on_scan_active is not None:
self._on_scan_active(True)
try:
self._engine.run()
self.completed.emit()
except ScanAborted as exc:
self.failed.emit(str(exc))
except Exception as exc:
traceback.print_exc()
self.failed.emit(str(exc))
finally:
if self._on_scan_active is not None:
self._on_scan_active(False)
gui/widgets.py
+187
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"""Widgets shared by the main app and the per-device test benches.
Each of these was hand-rolled several times across the apps, with slightly
different behaviour every time (only one log console bounded its buffer,
only one port picker sorted by device type).
"""
from __future__ import annotations
from PyQt6.QtCore import Qt, pyqtSignal
from PyQt6.QtGui import QFont
from PyQt6.QtWidgets import (
QComboBox, QGroupBox, QHBoxLayout, QLabel, QPlainTextEdit, QPushButton,
QVBoxLayout, QWidget,
)
from hardware.serial_util import scored_ports
def set_toggle(btn, checked: bool, text: str, enabled: bool = True):
"""Update a checkable button without re-triggering its toggled signal."""
btn.blockSignals(True)
btn.setChecked(checked)
btn.setText(text)
btn.setEnabled(enabled)
btn.blockSignals(False)
class PortSelector(QWidget):
"""Serial port combo + refresh button, likeliest device first."""
def __init__(self, parent=None):
super().__init__(parent)
row = QHBoxLayout(self)
row.setContentsMargins(0, 0, 0, 0)
self.combo = QComboBox()
self.combo.setMinimumWidth(220)
refresh = QPushButton("⟳")
refresh.setFixedWidth(30)
refresh.setToolTip("Rescan serial ports")
refresh.clicked.connect(self.refresh)
row.addWidget(self.combo, stretch=1)
row.addWidget(refresh)
self.refresh()
def refresh(self):
"""Repopulate the list, preserving the current selection if present."""
current = self.current_port()
self.combo.clear()
for device, label in scored_ports():
self.combo.addItem(label, device)
if self.combo.count() == 0:
self.combo.addItem("(no serial ports found)", None)
elif current:
idx = self.combo.findData(current)
if idx >= 0:
self.combo.setCurrentIndex(idx)
def current_port(self) -> str | None:
return self.combo.currentData()
def set_port(self, device: str):
idx = self.combo.findData(device)
if idx >= 0:
self.combo.setCurrentIndex(idx)
class ConnectionBar(QGroupBox):
"""Port picker + connect toggle + status label.
Emits connect_requested(port) / disconnect_requested(); the owner drives
the state back through on_connected/on_disconnected/on_failed so the
button can never disagree with the hardware.
"""
connect_requested = pyqtSignal(str)
disconnect_requested = pyqtSignal()
def __init__(self, title: str = "Connection", parent=None):
super().__init__(title, parent)
layout = QVBoxLayout(self)
self.port_selector = PortSelector()
layout.addWidget(self.port_selector)
row = QHBoxLayout()
self.toggle = QPushButton("Connect")
self.toggle.setCheckable(True)
self.toggle.toggled.connect(self._on_toggled)
self.status = QLabel("Disconnected")
self.status.setStyleSheet("font-weight: bold;")
row.addWidget(self.toggle)
row.addWidget(self.status, stretch=1)
layout.addLayout(row)
def _on_toggled(self, checked: bool):
if checked:
port = self.port_selector.current_port()
if not port:
set_toggle(self.toggle, False, "Connect")
self.status.setText("No port selected")
return
self.toggle.setText("Connecting…")
self.toggle.setEnabled(False)
self.connect_requested.emit(port)
else:
self.disconnect_requested.emit()
def on_connected(self, detail: str = "Connected"):
set_toggle(self.toggle, True, "Disconnect")
self.status.setText(detail)
self.status.setStyleSheet("font-weight: bold; color: green;")
def on_disconnected(self, detail: str = "Disconnected"):
set_toggle(self.toggle, False, "Connect")
self.status.setText(detail)
self.status.setStyleSheet("font-weight: bold;")
def on_failed(self, message: str):
set_toggle(self.toggle, False, "Connect")
self.status.setText(f"Failed: {message}")
self.status.setStyleSheet("font-weight: bold; color: red;")
class LogConsole(QWidget):
"""Bounded, monospace, auto-scrolling log view with a Clear button.
The block cap is the point: unbounded QTextEdit logs grew for the whole
session in every app that hand-rolled one.
"""
KINDS = {"tx": "→", "rx": "←", "info": "●", "err": "!"}
def __init__(self, max_blocks: int = 2000, parent=None):
super().__init__(parent)
layout = QVBoxLayout(self)
layout.setContentsMargins(0, 0, 0, 0)
self.view = QPlainTextEdit()
self.view.setReadOnly(True)
self.view.setMaximumBlockCount(max_blocks)
font = QFont("Menlo")
font.setStyleHint(QFont.StyleHint.Monospace)
font.setPointSize(11)
self.view.setFont(font)
layout.addWidget(self.view)
row = QHBoxLayout()
row.addStretch(1)
clear = QPushButton("Clear")
clear.clicked.connect(self.view.clear)
row.addWidget(clear)
layout.addLayout(row)
def log(self, message: str, kind: str = "info"):
self.view.appendPlainText(f"{self.KINDS.get(kind, '●')} {message}")
self.view.verticalScrollBar().setValue(
self.view.verticalScrollBar().maximum())
class StatusGrid(QWidget):
"""Label/value rows with consistent ok/warn/error colouring."""
_COLORS = {"ok": "green", "warn": "#b8860b", "error": "red", "": ""}
def __init__(self, fields: list[str], parent=None):
super().__init__(parent)
layout = QVBoxLayout(self)
layout.setContentsMargins(0, 0, 0, 0)
self._values: dict[str, QLabel] = {}
for name in fields:
row = QHBoxLayout()
label = QLabel(f"{name}:")
value = QLabel("—")
value.setAlignment(Qt.AlignmentFlag.AlignRight
| Qt.AlignmentFlag.AlignVCenter)
row.addWidget(label)
row.addWidget(value, stretch=1)
layout.addLayout(row)
self._values[name] = value
def set(self, name: str, text: str, state: str = ""):
label = self._values.get(name)
if label is None:
return
label.setText(text)
color = self._COLORS.get(state, "")
label.setStyleSheet(f"color: {color};" if color else "")
hardware/__init__.py
+6 -7
View File
@@ -1,7 +1,6 @@
"""Hardware driver modules for ScanEngine-3""" """Hardware driver modules for ScanEngine-3.
from .pybbd202 import ThorlabsServoDriver, TriggerBitsServo, AXIS_X, AXIS_Y, CONTROLLER
from .t3r_driver import T3RDriver Import drivers by module (e.g. ``from hardware.t3r_driver import T3RDriver``);
from .uc480_camera import * nothing is re-exported here so that importing one driver never drags in
from .tektronix_base import * another driver's SDK (the uEye camera stack in particular).
from .coherent_hops_laser import * """
from .genesis_core import *
hardware/coherent_hops_laser.py
-45
View File
@@ -1,45 +0,0 @@
"""
Coherent HOPS Laser Driver - Stub Module
This is a temporary stub to allow testing camera integration.
"""
class CoherentHOPSLaser:
"""Stub class for Coherent HOPS Laser"""
pass
class DummyLaser:
"""Dummy laser for testing without hardware"""
def connect(self):
"""Simulate connection"""
pass
def disconnect(self):
"""Simulate disconnection"""
pass
def get_hardware_id(self):
"""Return simulated hardware ID"""
return "SIM-12345"
def get_laser_model(self):
"""Return simulated model"""
return "Genesis Simulator"
def get_interlock_status(self):
"""Return simulated interlock status"""
return "OK"
def get_key_switch_status(self):
"""Return simulated key switch status"""
return "ON"
def get_temperature_main(self):
"""Return simulated main temperature"""
return 25.5
def get_temperature_eta(self):
"""Return simulated ETA temperature"""
return 26.3
hardware/genesis_core.py
+10 -1
View File
@@ -2,6 +2,16 @@
Genesis SLM MX 532 Laser Core Hardware Control Module Genesis SLM MX 532 Laser Core Hardware Control Module
====================================================== ======================================================
.. warning::
QUARANTINED — do not modify semantics or dedupe against
``tools/genesis_laser_gui.py`` until the bench checklist in
``docs/genesis_verification.md`` has been run. This module was
extracted from that GUI but diverges from it in ways only hardware can
adjudicate: ADS7828 command byte (0x84 vs 0x8C), LDD enable polarity
(inverted vs not), shutter semantics (manual vs bit-controlled),
dropped median-of-3 ADC filtering, dropped Amps/Watts scaling, dropped
temperature reads and pre-flight check.
This module provides low-level hardware control for the Genesis SLM MX 532 laser This module provides low-level hardware control for the Genesis SLM MX 532 laser
using NXP I2C-over-serial protocol. It contains reusable classes for serial using NXP I2C-over-serial protocol. It contains reusable classes for serial
communication, I2C protocol handling, device control, and laser operations. communication, I2C protocol handling, device control, and laser operations.
@@ -34,7 +44,6 @@ from typing import Optional, List
from enum import IntEnum from enum import IntEnum
import serial import serial
from serial.tools import list_ports
# ============================================================================ # ============================================================================
hardware/helios_laser.py
+71 -208
View File
@@ -3,12 +3,13 @@ Helios Laser System Driver
Basic implementation for controlling the Helios pulsed laser. Basic implementation for controlling the Helios pulsed laser.
""" """
import serial
import time import time
import logging import logging
from typing import Optional, List from typing import Optional, List
from enum import Enum from enum import Enum
from hardware.serial_util import open_8n1
logger = logging.getLogger(__name__) logger = logging.getLogger(__name__)
@@ -28,13 +29,7 @@ class HeliosLaser:
""" """
def __init__(self, port: str = None, timeout: float = 1.0): def __init__(self, port: str = None, timeout: float = 1.0):
""" """Initialize Helios laser driver."""
Initialize Helios laser driver.
Args:
port: Serial port (e.g., '/dev/ttyUSB0' or 'COM5')
timeout: Serial timeout in seconds
"""
self.port = port self.port = port
self.timeout = timeout self.timeout = timeout
self.serial = None self.serial = None
@@ -42,21 +37,12 @@ class HeliosLaser:
@staticmethod @staticmethod
def list_available_ports() -> List[str]: def list_available_ports() -> List[str]:
"""List available serial ports""" """List available serial ports, likeliest devices first."""
import serial.tools.list_ports from hardware.serial_util import list_port_devices
ports = serial.tools.list_ports.comports() return list_port_devices()
return [port.device for port in ports]
def connect(self, port: str = None) -> bool: def connect(self, port: str = None) -> bool:
""" """Connect to the Helios laser."""
Connect to the Helios laser.
Args:
port: Serial port (uses stored port if None)
Returns:
True if connection successful
"""
if port: if port:
self.port = port self.port = port
@@ -65,14 +51,7 @@ class HeliosLaser:
return False return False
try: try:
self.serial = serial.Serial( self.serial = open_8n1(self.port, baudrate=9600, timeout=self.timeout)
port=self.port,
baudrate=9600,
bytesize=serial.EIGHTBITS,
parity=serial.PARITY_NONE,
stopbits=serial.STOPBITS_ONE,
timeout=self.timeout
)
time.sleep(0.1) # Allow time for connection to stabilize time.sleep(0.1) # Allow time for connection to stabilize
self.is_connected = True self.is_connected = True
logger.info(f"Connected to Helios laser on {self.port}") logger.info(f"Connected to Helios laser on {self.port}")
@@ -98,15 +77,7 @@ class HeliosLaser:
self.serial = None self.serial = None
def _send_command(self, command: str) -> bool: def _send_command(self, command: str) -> bool:
""" """Send a command to the laser."""
Send a command to the laser.
Args:
command: ASCII command string (without CR)
Returns:
True if sent successfully
"""
if not self.is_connected or not self.serial: if not self.is_connected or not self.serial:
logger.error("Not connected to laser") logger.error("Not connected to laser")
return False return False
@@ -122,37 +93,36 @@ class HeliosLaser:
return False return False
def _query(self, command: str) -> Optional[str]: def _query(self, command: str) -> Optional[str]:
""" """Send a query and return the value from its response.
Send a query and read response.
Args: Reads until the CR terminator rather than sleeping a fixed interval:
command: ASCII query command (without CR or ?) the device usually answers in a few ms, so the old unconditional
0.05 + 0.2 s cost ~250 ms per query and made an 8-query status poll
Returns: take ~2 s — longer than the 1 s interval that scheduled it.
Response value string or None if error
""" """
try: try:
# Clear any pending data in the buffer # Clear any stale bytes so a previous timed-out reply can't be
# mistaken for this command's response.
self.serial.reset_input_buffer() self.serial.reset_input_buffer()
time.sleep(0.05)
if not self._send_command(command): if not self._send_command(command):
return None return None
time.sleep(0.2) # Give device time to respond
response = self.serial.read_until(b'\r').decode('ascii', errors='replace').strip() response = self.serial.read_until(b'\r').decode('ascii', errors='replace').strip()
if not response:
logger.warning(f"Query '{command}' timed out after {self.timeout}s")
return None
logger.debug(f"Query '{command}' response: {response}") logger.debug(f"Query '{command}' response: {response}")
# Helios format: "COMMAND = VALUE UNIT" # Helios format: "COMMAND = VALUE UNIT" — take just the value
# Extract just the value part
if '=' in response: if '=' in response:
parts = response.split('=') parts = response.split('=')
if len(parts) >= 2: if len(parts) >= 2:
value_part = parts[1].strip() value_part = parts[1].strip()
# Remove unit suffix if present (e.g., "ns", "mA", "mW") # Strip the unit suffix if present (e.g. "ns", "mA", "mW")
value = value_part.split()[0] fields = value_part.split()
return value if fields:
return fields[0]
return response return response
@@ -160,16 +130,19 @@ class HeliosLaser:
logger.error(f"Failed to read response for '{command}': {e}") logger.error(f"Failed to read response for '{command}': {e}")
return None return None
def _query_int(self, command: str) -> Optional[int]:
"""Query a value that should parse as an int; None if absent/unparseable."""
raw = self._query(command)
if raw is None:
return None
try:
return int(raw)
except ValueError:
logger.error(f"Query '{command}' returned non-integer {raw!r}")
return None
def set_frequency_hz(self, frequency: int) -> bool: def set_frequency_hz(self, frequency: int) -> bool:
""" """Set laser pulse frequency in Hz."""
Set laser pulse frequency in Hz.
Args:
frequency: Frequency in Hz (16700 - 125000)
Returns:
True if successful
"""
if not (16700 <= frequency <= 125000): if not (16700 <= frequency <= 125000):
logger.error(f"Frequency {frequency} Hz out of range (16700-125000)") logger.error(f"Frequency {frequency} Hz out of range (16700-125000)")
return False return False
@@ -186,15 +159,7 @@ class HeliosLaser:
return self._send_command(command) return self._send_command(command)
def set_current_ma(self, current: int) -> bool: def set_current_ma(self, current: int) -> bool:
""" """Set pump diode current in mA."""
Set pump diode current in mA.
Args:
current: Current in mA (0 - 2000 for this model)
Returns:
True if successful
"""
if not (0 <= current <= 2000): if not (0 <= current <= 2000):
logger.error(f"Current {current} mA out of range (0-2000)") logger.error(f"Current {current} mA out of range (0-2000)")
return False return False
@@ -203,28 +168,12 @@ class HeliosLaser:
return self._send_command(command) return self._send_command(command)
def set_pulse_mode(self, mode: PulseMode) -> bool: def set_pulse_mode(self, mode: PulseMode) -> bool:
""" """Set pulse mode."""
Set pulse mode.
Args:
mode: PulseMode enumeration value
Returns:
True if successful
"""
command = f"LDG {mode.value}" command = f"LDG {mode.value}"
return self._send_command(command) return self._send_command(command)
def set_laser_enable(self, enable: bool) -> bool: def set_laser_enable(self, enable: bool) -> bool:
""" """Enable or disable laser emission."""
Enable or disable laser emission.
Args:
enable: True to enable, False to disable
Returns:
True if successful
"""
command = f"LDO {1 if enable else 0}" command = f"LDO {1 if enable else 0}"
success = self._send_command(command) success = self._send_command(command)
@@ -235,60 +184,24 @@ class HeliosLaser:
return success return success
def is_laser_enabled(self) -> bool: def is_laser_enabled(self) -> bool:
""" """True if laser emission is currently enabled."""
Check if laser is currently enabled. return self._query_int("LDO") == 1
Returns:
True if laser is enabled
"""
response = self._query("LDO")
if response:
try:
return int(response) == 1
except ValueError:
logger.error(f"Invalid response for LDO: {response}")
return False
def get_frequency_hz(self) -> Optional[int]: def get_frequency_hz(self) -> Optional[int]:
""" """Current laser frequency in Hz, or None on error."""
Get current laser frequency in Hz. period_ns = self._query_int("LDF")
if not period_ns:
Returns: return None
Frequency in Hz or None if error return int(1e9 / period_ns)
"""
response = self._query("LDF")
if response:
try:
period_ns = int(response)
return int(1e9 / period_ns)
except (ValueError, ZeroDivisionError):
logger.error(f"Invalid response for LDF: {response}")
return None
def get_current_ma(self) -> Optional[int]: def get_current_ma(self) -> Optional[int]:
""" """Current pump diode current in mA, or None on error."""
Get current pump diode current in mA. return self._query_int("LDS")
Returns:
Current in mA or None if error
"""
response = self._query("LDS")
if response:
try:
return int(response)
except ValueError:
logger.error(f"Invalid response for LDS: {response}")
return None
def _query_millicelsius(self, command: str) -> Optional[float]: def _query_millicelsius(self, command: str) -> Optional[float]:
"""Query a temperature register (returns milli-°C) and convert to °C.""" """Query a temperature register (milli-°C) and convert to °C."""
response = self._query(command) value = self._query_int(command)
if response: return None if value is None else value / 1000.0
try:
return int(response) / 1000.0
except ValueError:
logger.error(f"Invalid response for {command}: {response}")
return None
def get_diode_temp_c(self) -> Optional[float]: def get_diode_temp_c(self) -> Optional[float]:
"""Diode temperature in °C (LTA, 5000–50000 milli-°C).""" """Diode temperature in °C (LTA, 5000–50000 milli-°C)."""
@@ -303,46 +216,22 @@ class HeliosLaser:
return self._query_millicelsius("EOA") return self._query_millicelsius("EOA")
def get_controller_serial(self) -> Optional[str]: def get_controller_serial(self) -> Optional[str]:
""" """Controller serial number, or None on error."""
Get controller serial number.
Returns:
Serial number string or None if error
"""
return self._query("CSR") return self._query("CSR")
def get_head_serial(self) -> Optional[str]: def get_head_serial(self) -> Optional[str]:
""" """Laser head serial number, or None on error."""
Get laser head serial number.
Returns:
Serial number string or None if error
"""
return self._query("HSR") return self._query("HSR")
def get_status_registers(self) -> tuple: def get_status_registers(self) -> tuple:
"""Query the LER, LCE and CCE status registers.
Each is a bitmask (sum of flags); non-zero means active faults,
cleared with reset_faults(). Returns (ler, lce, cce), any of which
is None if that register could not be read.
""" """
Query LER, LCE, and CCE status registers. return (self._query_int("LER"), self._query_int("LCE"),
self._query_int("CCE"))
Each register is a bitmask (sum of flags). Non-zero values indicate
active faults. Reset with reset_faults().
Returns:
Tuple of (ler, lce, cce) as ints, or None for each on error.
"""
def _read_reg(cmd):
resp = self._query(cmd)
if resp is not None:
try:
return int(resp)
except ValueError:
logger.error(f"Invalid response for {cmd}: {resp}")
return None
ler = _read_reg("LER")
lce = _read_reg("LCE")
cce = _read_reg("CCE")
return (ler, lce, cce)
def reset_faults(self) -> bool: def reset_faults(self) -> bool:
""" """
@@ -364,38 +253,19 @@ class HeliosLaser:
return ok return ok
def get_remote_enable(self) -> Optional[bool]: def get_remote_enable(self) -> Optional[bool]:
""" """Remote enable state (LRE — utility connector pin 8); None on error."""
Query the remote enable state (LRE - activates utility connector pin 8). value = self._query_int("LRE")
return None if value is None else value == 1
Returns:
True if remote enable is active, False if not, None on error
"""
response = self._query("LRE")
if response is not None:
try:
return int(response) == 1
except ValueError:
logger.error(f"Invalid response for LRE: {response}")
return None
def send_raw_command(self, command: str) -> Optional[str]: def send_raw_command(self, command: str) -> Optional[str]:
""" """Send a raw command and return the unparsed response (diagnostics)."""
Send a raw command string and return the raw response.
Useful for diagnostics. Sends *command* + CR, waits briefly,
then reads whatever the device returns (up to the first CR or timeout).
Returns:
Raw response string (decoded, stripped) or None on error.
"""
if not self.is_connected or not self.serial: if not self.is_connected or not self.serial:
logger.error("Not connected to laser") logger.error("Not connected to laser")
return None return None
try: try:
self.serial.reset_input_buffer() self.serial.reset_input_buffer()
time.sleep(0.05) if not self._send_command(command):
self.serial.write((command + '\r').encode('ascii')) return None
time.sleep(0.3)
raw = self.serial.read_until(b'\r') raw = self.serial.read_until(b'\r')
if not raw: if not raw:
raw = self.serial.read(self.serial.in_waiting) raw = self.serial.read(self.serial.in_waiting)
@@ -405,18 +275,11 @@ class HeliosLaser:
return None return None
def set_remote_enable(self, enable: bool) -> bool: def set_remote_enable(self, enable: bool) -> bool:
""" """Set the remote enable state (LRE - utility connector pin 8)."""
Set the remote enable state (LRE - utility connector pin 8).
Args:
enable: True to activate remote enable, False to deactivate
Returns:
True if successful
"""
command = f"LRE {1 if enable else 0}" command = f"LRE {1 if enable else 0}"
return self._send_command(command) return self._send_command(command)
def __del__(self): # No __del__: it used to call disconnect(), which disables the laser and
"""Destructor - ensure cleanup""" # writes to the serial port from the garbage collector at an
self.disconnect() # unpredictable time (including interpreter shutdown, when the port may
# already be torn down). Callers close the driver explicitly.
hardware/pybbd202/__init__.py
-2
View File
@@ -1,9 +1,7 @@
"""pybbd202 - Thorlabs BBD202 servo stage driver (pyserial-based)""" """pybbd202 - Thorlabs BBD202 servo stage driver (pyserial-based)"""
from .bbd20x import ThorlabsServoDriver from .bbd20x import ThorlabsServoDriver
from .apt_constants import TriggerBitsServo, StatusBits
# Axis address constants # Axis address constants
AXIS_X = 0x21 AXIS_X = 0x21
AXIS_Y = 0x22 AXIS_Y = 0x22
CONTROLLER = 0x11
hardware/pybbd202/apt_constants.py
+15 -10
View File
@@ -32,16 +32,6 @@ class StatusBits(IntFlag):
MOT_SB_COMMUTATIONERROR | MOT_SB_OVERLOAD | MOT_SB_COMMUTATIONERROR | MOT_SB_OVERLOAD |
MOT_SB_ERROR | MOT_SB_INSTRERROR) MOT_SB_ERROR | MOT_SB_INSTRERROR)
class TriggerBitsStepper(IntFlag):
TRIGIN_ENABLE = 0x01,
TRIGOUT_ENABLE = 0x02,
TRIGOUT_MODEFOLLOW = 0x04,
TRIGOUT_MODEMOVEEND = 0x08,
TRIG_RELMOVE = 0x10,
TRIG_ABSMOVE = 0x20,
TRIG_HOMEMOVE = 0x40,
TRIGOUT_NOTRIGIN = 0x80
class TriggerBitsServo(IntFlag): class TriggerBitsServo(IntFlag):
TRIGIN_HIGH = 0x01 TRIGIN_HIGH = 0x01
TRIGIN_RELMOVE = 0x02 TRIGIN_RELMOVE = 0x02
@@ -55,5 +45,20 @@ class TriggerBitsServo(IntFlag):
TRIGOUT_MAXV = TRIGOUT_HIGH | TRIGOUT_MAXVELOCITY TRIGOUT_MAXV = TRIGOUT_HIGH | TRIGOUT_MAXVELOCITY
# Gate off: no trigger-out function selected, so the pin idles inactive.
#
# Treat this as unverified until it has been checked on the rig. §7.6 of
# docs/hardware/BBD203_Communications_Protocol.md documents `mode` as an
# enumeration capping at 0x11, which flatly contradicts the bitmask this
# driver actually sends (TRIGOUT_MAXV = 0x90, known working), so the doc
# cannot settle what makes the pin idle low. Under the bitmask reading 0x00
# clears everything and the pin sits low. If instead TRIGOUT_HIGH is an
# active-high *polarity* bit, clearing it means active-low and the pin idles
# HIGH — which in burst mode floods the acquisition with flyback frames.
# ScanEngine's gate-off preflight catches that; if it trips, change this to
# TriggerBitsServo.TRIGOUT_HIGH.
TRIGOUT_GATE_OFF = TriggerBitsServo(0)
hardware/pybbd202/apt_messages.py
+1 -3
View File
@@ -4,7 +4,6 @@
Version 1 Version 1
''' '''
import struct import struct
from .apt_constants import StatusBits as sb
class APTProtocol(): class APTProtocol():
ADDRESSES = { 'HOST_PC': 0x01, 'CONTROLLER': 0x11, ADDRESSES = { 'HOST_PC': 0x01, 'CONTROLLER': 0x11,
@@ -281,8 +280,7 @@ class APTProtocol():
raise ValueError(f"No data fields have been defined for {msg_spec['name']}!") raise ValueError(f"No data fields have been defined for {msg_spec['name']}!")
unpacked_payload = struct.unpack(fmt_string, payload) unpacked_payload = struct.unpack(fmt_string, payload)
data = {field: value for field, value in zip(data_fields, data = dict(zip(data_fields, unpacked_payload, strict=True))
unpacked_payload)}
data['destination'] = dest data['destination'] = dest
data['source'] = src data['source'] = src
hardware/pybbd202/bbd20x.py
+88 -92
View File
@@ -7,17 +7,23 @@
import time import time
from threading import Thread, Event from threading import Thread, Event
from queue import Queue, Empty from queue import Queue, Empty
from .apt_constants import StatusBits, TriggerBitsServo from .apt_constants import StatusBits, TriggerBitsServo, TRIGOUT_GATE_OFF
from .apt_messages import APTProtocol from .apt_messages import APTProtocol
from .serial_comms import SerialSnooper from .serial_comms import SerialSnooper
# APT bay addresses for the two stage axes
AXIS_X_ADDR = 0x21
AXIS_Y_ADDR = 0x22
class ThorlabsServoDriver(): class ThorlabsServoDriver():
# These are specific to the MLS203-1 # These are specific to the MLS203-1
# change for a different application # change for a different application
counts_per_mm = 20000 counts_per_mm = 20000
accel_scaling = 13.744 accel_scaling = 13.744
velocity_scaling = 134217.73 velocity_scaling = 134217.73
TRAVEL_MM = (110.0, 75.0) # usable travel per channel (X, Y)
def __init__(self): def __init__(self):
self.am_connected = False self.am_connected = False
@@ -83,10 +89,27 @@ class ThorlabsServoDriver():
pass pass
if not self.bays_present: if not self.bays_present:
print(" [WARN] No bays detected!") # Fail loudly: reporting success with no bays made connecting to
# the wrong port look like it worked, and every later command
# then silently went nowhere.
self.disconnect()
raise RuntimeError(
f"No BBD202 bays responded on {port}. Check the port, the "
f"controller power, and that no other process holds the device."
)
self.am_connected = True self.am_connected = True
@staticmethod
def _channel_for(axis):
"""Map an APT axis address to this driver's 0-based channel index."""
if axis == AXIS_X_ADDR:
return 0
if axis == AXIS_Y_ADDR:
return 1
raise ValueError(f"Unknown axis address 0x{axis:02x} "
f"(expected 0x{AXIS_X_ADDR:02x} or 0x{AXIS_Y_ADDR:02x})")
# ── Worker threads ─────────────────────────────────────────── # ── Worker threads ───────────────────────────────────────────
def _tx_worker(self): def _tx_worker(self):
@@ -223,15 +246,18 @@ class ThorlabsServoDriver():
APTProtocol.build_message(0x0002, destination=addr, APTProtocol.build_message(0x0002, destination=addr,
source=0x01)) source=0x01))
time.sleep(0.2) # let TX worker flush them out time.sleep(0.2) # let TX worker flush them out
# Stop all worker loops, then wait for threads to exit # Stop all worker loops, then wait for threads to exit. Joins
# are bounded: disconnect() runs from closeEvent, and a wedged
# reader must not hang application shutdown.
self.am_listening = False self.am_listening = False
self.serial_snoop.stop() self.serial_snoop.stop()
self._rx_thread.join() for thread in (self._rx_thread, self._tx_thread, self._poll_thread,
self._tx_thread.join() self.serial_snoop):
self._poll_thread.join() if thread is not None:
self.serial_snoop.join() thread.join(timeout=2.0)
# Close port only after all threads are done # Close port only after all threads are done
self.serial_snoop.close() self.serial_snoop.close()
self.am_connected = False
# ── State update handlers ──────────────────────────────────── # ── State update handlers ────────────────────────────────────
@@ -288,25 +314,6 @@ class ThorlabsServoDriver():
self.am_moving[ch] = False self.am_moving[ch] = False
return return
def _update0x0212(self, msg):
'''
_update0x0212 - internal function that listens for CHANENABLESTATE
messages.
'''
if msg['source'] == 0x21:
ch = 0
elif msg['source'] == 0x22:
ch = 1
else:
raise ValueError("Wherever this message came from, it's WRONG!")
if msg['enable_state'] == 0x01:
self.am_enabled[ch] = True # enabled
elif msg['enable_state'] == 0x02:
self.am_enabled[ch] = False # disabled
else:
raise ValueError("Am I a joke to you? WTF did this even come from?!")
# ── Axis control ───────────────────────────────────────────── # ── Axis control ─────────────────────────────────────────────
def enable_axis(self, axis): def enable_axis(self, axis):
@@ -324,13 +331,8 @@ class ThorlabsServoDriver():
toggle_enabled_state(axis) - enables the axis if disabled. disables toggle_enabled_state(axis) - enables the axis if disabled. disables
if enabled. not much more to it. if enabled. not much more to it.
''' '''
if axis == 0x21: ch = self._channel_for(axis)
ch = 0 # Read the cached state and invert it
elif axis == 0x22:
ch = 1
else:
raise ValueError("I don't know that axis!")
# get the old state and flip it like a sample
new_state = not self.am_enabled[ch] new_state = not self.am_enabled[ch]
self.send_message(0x0210, chan_ident=1, self.send_message(0x0210, chan_ident=1,
enable_state=0x01 if new_state else 0x02, enable_state=0x01 if new_state else 0x02,
@@ -342,12 +344,7 @@ class ThorlabsServoDriver():
power up. Default timeout is 60s, but 20-30s is fine as well if power up. Default timeout is 60s, but 20-30s is fine as well if
you're in that much of a hurry. you're in that much of a hurry.
''' '''
if axis == 0x21: self._channel_for(axis) # validate the axis address
ch = 0
elif axis == 0x22:
ch = 1
else:
raise ValueError("I don't know that axis!")
self.send_and_wait(0x0443, timeout=timeout, retries=0, chan_ident=1, self.send_and_wait(0x0443, timeout=timeout, retries=0, chan_ident=1,
destination=axis, source=0x01) destination=axis, source=0x01)
@@ -359,11 +356,11 @@ class ThorlabsServoDriver():
moves the specified axis a specified distance in mm. moves the specified axis a specified distance in mm.
Timeout defaults to ten seconds. Timeout defaults to ten seconds.
''' '''
# sanity check travel = self.TRAVEL_MM[self._channel_for(axis)]
if axis == 0x21 and abs(distance_in_mm) > 110.0: if abs(distance_in_mm) > travel:
raise ValueError("You can't move farther than the stage is long.") raise ValueError(
elif axis == 0x22 and abs(distance_in_mm) > 75.0: f"Relative move of {distance_in_mm:.3f} mm exceeds the "
raise ValueError("You can't move farther than the stage is wide.") f"{travel:g} mm travel of this axis.")
_distance_in_encoder = int(round(distance_in_mm * self.counts_per_mm)) _distance_in_encoder = int(round(distance_in_mm * self.counts_per_mm))
self.send_and_wait(0x0448, timeout=timeout, chan_ident=1, self.send_and_wait(0x0448, timeout=timeout, chan_ident=1,
@@ -377,10 +374,12 @@ class ThorlabsServoDriver():
moves the specified axis to an absolute position in mm. moves the specified axis to an absolute position in mm.
Timeout defaults to ten seconds. Timeout defaults to ten seconds.
''' '''
if axis == 0x21 and (position_in_mm < 0.0 or position_in_mm > 110.0): ch = self._channel_for(axis)
raise ValueError("Position out of range for X axis (0-110 mm).") travel = self.TRAVEL_MM[ch]
elif axis == 0x22 and (position_in_mm < 0.0 or position_in_mm > 75.0): if not 0.0 <= position_in_mm <= travel:
raise ValueError("Position out of range for Y axis (0-75 mm).") raise ValueError(
f"Position {position_in_mm:.3f} mm is out of range for the "
f"{'XY'[ch]} axis (0-{travel:g} mm).")
_position_in_encoder = int(round(position_in_mm * self.counts_per_mm)) _position_in_encoder = int(round(position_in_mm * self.counts_per_mm))
self.send_and_wait(0x0453, timeout=timeout, chan_ident=1, self.send_and_wait(0x0453, timeout=timeout, chan_ident=1,
@@ -396,12 +395,7 @@ class ThorlabsServoDriver():
for the specified axis. Returns a dict with keys: for the specified axis. Returns a dict with keys:
min_velocity (mm/s), acceleration (mm/s2), max_velocity (mm/s) min_velocity (mm/s), acceleration (mm/s2), max_velocity (mm/s)
''' '''
if axis == 0x21: ch = self._channel_for(axis)
ch = 0
elif axis == 0x22:
ch = 1
else:
raise ValueError("I don't know that axis!")
result = self.send_and_wait(0x0414, timeout=timeout, chan_ident=1, result = self.send_and_wait(0x0414, timeout=timeout, chan_ident=1,
zero_this=0x00, destination=axis, zero_this=0x00, destination=axis,
@@ -424,12 +418,7 @@ class ThorlabsServoDriver():
Values are in mm/s and mm/s2 respectively. Any parameter Values are in mm/s and mm/s2 respectively. Any parameter
left as None keeps its current value. left as None keeps its current value.
''' '''
if axis == 0x21: ch = self._channel_for(axis)
ch = 0
elif axis == 0x22:
ch = 1
else:
raise ValueError("I don't know that axis!")
# Only query current params if we need to fill in a missing value # Only query current params if we need to fill in a missing value
if max_velocity is None or acceleration is None: if max_velocity is None or acceleration is None:
@@ -473,38 +462,45 @@ class ThorlabsServoDriver():
destination=axis, source=0x01) destination=axis, source=0x01)
return TriggerBitsServo(result['mode']) return TriggerBitsServo(result['mode'])
def set_trigger_trigin_high(self, axis):
'''Set trigger input to logic high.'''
self.set_trigger(axis, TriggerBitsServo.TRIGIN_HIGH)
def set_trigger_trigin_relmove(self, axis):
'''Set trigger input to initiate a relative move.'''
self.set_trigger(axis, TriggerBitsServo.TRIGIN_RELMOVE)
def set_trigger_trigin_absmove(self, axis):
'''Set trigger input to initiate an absolute move.'''
self.set_trigger(axis, TriggerBitsServo.TRIGIN_ABSMOVE)
def set_trigger_trigin_homemove(self, axis):
'''Set trigger input to initiate a home move.'''
self.set_trigger(axis, TriggerBitsServo.TRIGIN_HOMEMOVE)
def set_trigger_trigout_high(self, axis):
'''Set trigger output to logic high.'''
self.set_trigger(axis, TriggerBitsServo.TRIGOUT_HIGH)
def set_trigger_trigout_inmotion(self, axis):
'''Set trigger output high while axis is in motion.'''
self.set_trigger(axis, TriggerBitsServo.TRIGOUT_INMOTION)
def set_trigger_trigout_motioncomplete(self, axis):
'''Set trigger output to pulse when motion completes.'''
self.set_trigger(axis, TriggerBitsServo.TRIGOUT_MOTIONCOMPLETE)
def set_trigger_trigout_maxvelocity(self, axis):
'''Set trigger output to pulse at max velocity.'''
self.set_trigger(axis, TriggerBitsServo.TRIGOUT_MAXVELOCITY)
def set_trigger_trigout_maxv(self, axis): def set_trigger_trigout_maxv(self, axis):
'''Set trigger output high + pulse at max velocity (TRIGOUT_MAXV).''' '''Set trigger output high + pulse at max velocity (TRIGOUT_MAXV).'''
self.set_trigger(axis, TriggerBitsServo.TRIGOUT_MAXV) self.set_trigger(axis, TriggerBitsServo.TRIGOUT_MAXV)
def set_trigger_gate_off(self, axis):
'''Drive the trigger output inactive, so no pulses reach the gate.'''
self.set_trigger(axis, TRIGOUT_GATE_OFF)
def arm_scan_gate(self, axis, armed, verify=True):
'''
arm_scan_gate(axis, armed): Arms or drops the max-velocity trigger
output the oscilloscope AND-gate uses.
Burst acquisition runs one scope acquisition across many rows, so
the gate must be armed only for the acquiring pass and dropped for
the flyback — otherwise the return move hits max velocity and
injects frames between rows.
'''
mode = TriggerBitsServo.TRIGOUT_MAXV if armed else TRIGOUT_GATE_OFF
if verify:
self.set_trigger_verified(axis, mode)
else:
self.set_trigger(axis, mode)
def set_trigger_verified(self, axis, mode, timeout=5.0, retries=2):
'''
set_trigger_verified(axis, mode): Sets the trigger mode and reads
it back to confirm it landed.
set_trigger is fire-and-forget over the shared TX queue. Burst
acquisition toggles the gate between every row, and a dropped
change there silently fills the acquisition with flyback frames —
so confirm rather than assume.
'''
for _ in range(retries + 1):
self.set_trigger(axis, mode)
if int(self.get_trigger(axis, timeout=timeout)) == int(mode):
return
raise RuntimeError(
f"Axis 0x{axis:02X} did not accept trigger mode 0x{int(mode):02X} "
f"after {retries + 1} attempts"
)
hardware/serial_util.py
+44
View File
@@ -0,0 +1,44 @@
"""Shared serial-port helpers: 8N1 open and scored port enumeration.
Qt-free — GUI code adapts the (device, label) list into its own widgets.
"""
from __future__ import annotations
import serial
from serial.tools import list_ports
# Substrings that suggest a USB-serial adapter we actually talk to
# (ESP32-based T3R, CP210x/CH340 dongles, CDC-ACM devices); matching ports
# sort first in pickers.
DEVICE_HINTS = ("esp32", "jtag", "espressif", "usb serial", "cp210", "ch340", "cdc")
def open_8n1(port: str, baudrate: int, timeout: float,
write_timeout: float | None = None) -> serial.Serial:
"""Open a serial port with the 8N1 framing every device here uses."""
return serial.Serial(
port=port,
baudrate=baudrate,
bytesize=serial.EIGHTBITS,
parity=serial.PARITY_NONE,
stopbits=serial.STOPBITS_ONE,
timeout=timeout,
write_timeout=write_timeout,
)
def scored_ports() -> list[tuple[str, str]]:
"""Enumerate serial ports as (device, human label), likeliest-first."""
ports = list(list_ports.comports())
def score(p):
text = f"{p.description} {p.manufacturer or ''} {p.product or ''}".lower()
return -sum(h in text for h in DEVICE_HINTS)
ports.sort(key=score)
return [(p.device, f"{p.device} — {p.description or p.device}") for p in ports]
def list_port_devices() -> list[str]:
"""Plain device-path list, likeliest-first."""
return [dev for dev, _ in scored_ports()]
hardware/t3r_driver.py
+119 -63
View File
@@ -1,8 +1,12 @@
"""T3R Stepper Controller driver for ScanEngine-3. """T3R Stepper Controller driver for ScanEngine-3.
Qt-based driver that owns the serial connection and an internal reader QThread. Owns the serial connection and an internal reader thread. Events are
All events arrive as Qt signals; all commands are fire-and-forget writes. delivered as plain-Python callbacks (see ``Signal``); commands are
Create in the main (GUI) thread; no additional thread management required. fire-and-forget writes. No Qt — GUIs wrap this with gui.qt_t3r.QtT3RAdapter,
which re-emits every event as a queued Qt signal on the GUI thread.
Callbacks run on the reader thread. Keep them short, and never touch Qt
widgets from one directly.
Gear train (stage rotation via GR-axis, ch3): Gear train (stage rotation via GR-axis, ch3):
Motor → 10T pinion → 30T idler → 125T index gear (stage) Motor → 10T pinion → 30T idler → 125T index gear (stage)
@@ -11,23 +15,53 @@ Gear train (stage rotation via GR-axis, ch3):
from __future__ import annotations from __future__ import annotations
import logging
import threading import threading
import serial
from PyQt6.QtCore import QObject, QThread, QTimer, pyqtSignal
from . import t3r_protocol as proto from . import t3r_protocol as proto
from .serial_util import open_8n1
logger = logging.getLogger(__name__)
class _T3RReader(QThread): class Signal:
"""Blocking read loop — runs on its own QThread.""" """Minimal observer slot: ``connect(fn)`` then ``emit(*args)``.
frame = pyqtSignal(int, bytes) # (cmd, payload) for each valid frame Mirrors the pyqtSignal API used by the existing panels so the same call
finished_reason = pyqtSignal(str) # "" = clean stop, else I/O error string sites work against either this driver or a Qt adapter over it. A raising
subscriber is logged and skipped so one bad listener cannot kill the
reader thread.
"""
def __init__(self, ser: serial.Serial): __slots__ = ("_subs", "_name")
super().__init__()
def __init__(self, name: str = ""):
self._subs: list = []
self._name = name
def connect(self, fn) -> None:
self._subs.append(fn)
def disconnect(self, fn) -> None:
if fn in self._subs:
self._subs.remove(fn)
def emit(self, *args) -> None:
for fn in list(self._subs):
try:
fn(*args)
except Exception:
logger.exception("T3R %s subscriber failed", self._name)
class _Reader(threading.Thread):
"""Blocking read loop — decodes frames and hands them to `on_frame`."""
def __init__(self, ser, on_frame, on_finished):
super().__init__(daemon=True, name="T3RReader")
self._ser = ser self._ser = ser
self._on_frame = on_frame
self._on_finished = on_finished
self._running = True self._running = True
self._parser = proto.FrameParser() self._parser = proto.FrameParser()
@@ -44,20 +78,20 @@ class _T3RReader(QThread):
break break
if data: if data:
for cmd, payload in self._parser.feed(data): for cmd, payload in self._parser.feed(data):
self.frame.emit(cmd, payload) self._on_frame(cmd, payload)
self.finished_reason.emit(reason) self._on_finished(reason)
class T3RDriver(QObject): class T3RDriver:
"""Qt-based driver for the T3R four-channel stepper controller. """Driver for the T3R four-channel stepper controller.
Usage:: Usage::
driver = T3RDriver() driver = T3RDriver()
driver.handshake_ok.connect(lambda pv, fw, nc: print("connected")) driver.handshake_ok.connect(lambda pv, fw, nc: ...)
driver.info_updated.connect(on_info) driver.open("/dev/ttyUSB0")
driver.connect("/dev/ttyUSB0")
driver.move(0, steps=3200, velocity=8000, accel=4000) driver.move(0, steps=3200, velocity=8000, accel=4000)
driver.wait_motion_done(0, timeout=30.0)
""" """
CHANNEL_NAMES = ["T-axis (focus)", "Axis 1", "Axis 2", "GR-axis"] CHANNEL_NAMES = ["T-axis (focus)", "Axis 1", "Axis 2", "GR-axis"]
@@ -68,32 +102,33 @@ class T3RDriver(QObject):
GEAR_TEETH_MOTOR = 10 GEAR_TEETH_MOTOR = 10
GEAR_TEETH_STAGE = 125 # idler is 30T but does not change ratio GEAR_TEETH_STAGE = 125 # idler is 30T but does not change ratio
# ── Signals ─────────────────────────────────────────────────────────────── POLL_INTERVAL_S = 0.25
port_opened = pyqtSignal() # serial port open; PING sent def __init__(self):
handshake_ok = pyqtSignal(int, int, int) # proto_ver, fw_ver, num_channels self._ser = None
disconnected = pyqtSignal(str) # reason ("" = user-initiated) self._reader: _Reader | None = None
info_updated = pyqtSignal(int, object) # ch, proto.Info
drv_status_updated = pyqtSignal(int, object) # ch, proto.DrvStatus
position_updated = pyqtSignal(int, int) # ch, position (microsteps)
motion_done = pyqtSignal(int, int) # ch, final_position
stopped = pyqtSignal(int, int) # ch, final_position
fault_occurred = pyqtSignal(int, int) # ch, fault_mask
ack_received = pyqtSignal(int, int) # req_cmd, status (0=OK)
frame_received = pyqtSignal(int, bytes) # raw (cmd, payload) for log
def __init__(self, parent=None):
super().__init__(parent)
self._ser: serial.Serial | None = None
self._reader: _T3RReader | None = None
self._write_lock = threading.Lock() self._write_lock = threading.Lock()
self._tearing_down = False self._tearing_down = False
self._is_open = False self._is_open = False
self._poll_timer = QTimer(self) self._poll_stop = threading.Event()
self._poll_timer.setInterval(250) self._poll_thread: threading.Thread | None = None
self._poll_timer.timeout.connect(self._poll)
# Per-channel motion-completion events, so a caller can block on a
# move finishing instead of guessing its duration.
self._motion_events = [threading.Event() for _ in range(proto.NUM_CHANNELS)]
self.port_opened = Signal("port_opened") # ()
self.handshake_ok = Signal("handshake_ok") # proto_ver, fw_ver, n_ch
self.disconnected = Signal("disconnected") # reason ("" = user)
self.info_updated = Signal("info_updated") # ch, proto.Info
self.drv_status_updated = Signal("drv_status_updated") # ch, proto.DrvStatus
self.position_updated = Signal("position_updated") # ch, position
self.motion_done = Signal("motion_done") # ch, final_position
self.stopped = Signal("stopped") # ch, final_position
self.fault_occurred = Signal("fault_occurred") # ch, fault_mask
self.ack_received = Signal("ack_received") # req_cmd, status
self.frame_received = Signal("frame_received") # raw cmd, payload
# ── Connection ──────────────────────────────────────────────────────────── # ── Connection ────────────────────────────────────────────────────────────
@@ -101,26 +136,24 @@ class T3RDriver(QObject):
def is_open(self) -> bool: def is_open(self) -> bool:
return self._is_open return self._is_open
def connect(self, port: str, baud: int = 115200) -> None: def open(self, port: str, baud: int = 115200) -> None:
"""Open the serial port and start the reader. Emits port_opened on success.""" """Open the serial port and start the reader; emits port_opened."""
if self._is_open: if self._is_open:
self.disconnect() self.close()
try: try:
self._ser = serial.Serial(port, baudrate=baud, timeout=0.05) self._ser = open_8n1(port, baudrate=baud, timeout=0.05)
except Exception as exc: except Exception as exc:
raise RuntimeError(f"Cannot open {port}: {exc}") from exc raise RuntimeError(f"Cannot open {port}: {exc}") from exc
self._tearing_down = False self._tearing_down = False
self._is_open = True self._is_open = True
self._reader = _T3RReader(self._ser) self._reader = _Reader(self._ser, self._on_frame, self._on_reader_finished)
self._reader.frame.connect(self._on_frame)
self._reader.finished_reason.connect(self._on_reader_finished)
self._reader.start() self._reader.start()
self.port_opened.emit() self.port_opened.emit()
self.send_frame(proto.ping()) # handshake; polling starts on PONG self.send_frame(proto.ping()) # handshake; polling starts on PONG
def disconnect(self) -> None: def close(self) -> None:
"""Close port and stop polling.""" """Close the port and stop polling."""
self._teardown("") self._teardown("")
def _on_reader_finished(self, reason: str): def _on_reader_finished(self, reason: str):
@@ -131,16 +164,21 @@ class T3RDriver(QObject):
if self._tearing_down or not self._is_open: if self._tearing_down or not self._is_open:
return return
self._tearing_down = True self._tearing_down = True
self._poll_timer.stop() self.stop_polling()
self._is_open = False self._is_open = False
# Release anyone blocked in wait_motion_done so a disconnect during a
# move raises there instead of hanging until the timeout.
for ev in self._motion_events:
ev.set()
reader, self._reader = self._reader, None reader, self._reader = self._reader, None
ser, self._ser = self._ser, None ser, self._ser = self._ser, None
if reader is not None: if reader is not None:
reader.stop() reader.stop()
if QThread.currentThread() is not reader: if threading.current_thread() is not reader:
reader.wait(1000) reader.join(1.0)
if ser is not None: if ser is not None:
try: try:
ser.close() ser.close()
@@ -186,6 +224,7 @@ class T3RDriver(QObject):
self.send_frame(proto.set_current(ch, run_ma, hold_ma, ihold_delay)) self.send_frame(proto.set_current(ch, run_ma, hold_ma, ihold_delay))
def move(self, ch: int, steps: int, velocity: int, accel: int): def move(self, ch: int, steps: int, velocity: int, accel: int):
self._motion_events[ch].clear()
self.send_frame(proto.move(ch, steps, velocity, accel)) self.send_frame(proto.move(ch, steps, velocity, accel))
def jog(self, ch: int, velocity: int, accel: int): def jog(self, ch: int, velocity: int, accel: int):
@@ -215,30 +254,44 @@ class T3RDriver(QObject):
# ── Rotation helpers ────────────────────────────────────────────────────── # ── Rotation helpers ──────────────────────────────────────────────────────
def steps_for_angle(self, angle_deg: float, microsteps: int) -> int: def steps_for_angle(self, angle_deg: float, microsteps: int) -> int:
"""Compute GR-axis microsteps needed to rotate the stage by angle_deg.""" """GR-axis microsteps needed to rotate the stage by angle_deg."""
gear_ratio = self.GEAR_TEETH_STAGE / self.GEAR_TEETH_MOTOR gear_ratio = self.GEAR_TEETH_STAGE / self.GEAR_TEETH_MOTOR
steps_per_stage_rev = self.MOTOR_FULL_STEPS_PER_REV * microsteps * gear_ratio steps_per_stage_rev = self.MOTOR_FULL_STEPS_PER_REV * microsteps * gear_ratio
return round(steps_per_stage_rev * angle_deg / 360.0) return round(steps_per_stage_rev * angle_deg / 360.0)
def rotate_stage(self, angle_deg: float, microsteps: int, def rotate_stage(self, angle_deg: float, microsteps: int,
velocity: int = 8000, accel: int = 4000): velocity: int = 8000, accel: int = 4000):
"""Move GR-axis by the number of steps that rotate the stage by angle_deg.""" """Move GR-axis by the steps that rotate the stage by angle_deg."""
steps = self.steps_for_angle(angle_deg, microsteps) self.move(self.GR_AXIS_CH, self.steps_for_angle(angle_deg, microsteps),
self.move(self.GR_AXIS_CH, steps, velocity, accel) velocity, accel)
def wait_motion_done(self, ch: int, timeout: float) -> bool:
"""Block until the channel reports MOTION_DONE. False on timeout.
Cleared by ``move()``, set by the MOTION_DONE event and by teardown,
so a disconnect mid-move unblocks immediately.
"""
return self._motion_events[ch].wait(timeout)
# ── Polling ─────────────────────────────────────────────────────────────── # ── Polling ───────────────────────────────────────────────────────────────
def start_polling(self): def start_polling(self):
self._poll_timer.start() if self._poll_thread is not None and self._poll_thread.is_alive():
return
self._poll_stop.clear()
self._poll_thread = threading.Thread(target=self._poll_loop, daemon=True,
name="T3RPoll")
self._poll_thread.start()
def stop_polling(self): def stop_polling(self):
self._poll_timer.stop() self._poll_stop.set()
def _poll(self): def _poll_loop(self):
if not self._is_open: while not self._poll_stop.wait(self.POLL_INTERVAL_S):
return if not self._is_open:
for ch in range(proto.NUM_CHANNELS): break
self.send_frame(proto.get_info(ch)) for ch in range(proto.NUM_CHANNELS):
self.send_frame(proto.get_info(ch))
# ── Frame dispatcher ────────────────────────────────────────────────────── # ── Frame dispatcher ──────────────────────────────────────────────────────
@@ -274,14 +327,17 @@ class T3RDriver(QObject):
elif cmd == proto.EVT_MOTION_DONE: elif cmd == proto.EVT_MOTION_DONE:
ev = proto.decode_event_position(payload) ev = proto.decode_event_position(payload)
if ev and 0 <= ev.ch < proto.NUM_CHANNELS: if ev and 0 <= ev.ch < proto.NUM_CHANNELS:
self._motion_events[ev.ch].set()
self.motion_done.emit(ev.ch, ev.position) self.motion_done.emit(ev.ch, ev.position)
elif cmd == proto.EVT_STOPPED: elif cmd == proto.EVT_STOPPED:
ev = proto.decode_event_position(payload) ev = proto.decode_event_position(payload)
if ev and 0 <= ev.ch < proto.NUM_CHANNELS: if ev and 0 <= ev.ch < proto.NUM_CHANNELS:
self._motion_events[ev.ch].set()
self.stopped.emit(ev.ch, ev.position) self.stopped.emit(ev.ch, ev.position)
elif cmd == proto.EVT_FAULT: elif cmd == proto.EVT_FAULT:
ev = proto.decode_fault(payload) ev = proto.decode_fault(payload)
if ev and 0 <= ev.ch < proto.NUM_CHANNELS: if ev and 0 <= ev.ch < proto.NUM_CHANNELS:
self._motion_events[ev.ch].set()
self.fault_occurred.emit(ev.ch, ev.position) self.fault_occurred.emit(ev.ch, ev.position)
hardware/t3r_protocol.py
-22
View File
@@ -193,14 +193,6 @@ def set_position(ch: int, position: int) -> bytes:
return build_frame(CMD_SET_POSITION, struct.pack("<Bi", ch, position)) return build_frame(CMD_SET_POSITION, struct.pack("<Bi", ch, position))
def read_reg(ch: int, reg: int) -> bytes:
return build_frame(CMD_READ_REG, struct.pack("<BB", ch, reg))
def write_reg(ch: int, reg: int, value: int) -> bytes:
return build_frame(CMD_WRITE_REG, struct.pack("<BBI", ch, reg, value))
# --------------------------------------------------------------------------- # ---------------------------------------------------------------------------
# Response / event decoders. Each returns a dataclass (or None on bad length). # Response / event decoders. Each returns a dataclass (or None on bad length).
# --------------------------------------------------------------------------- # ---------------------------------------------------------------------------
@@ -261,13 +253,6 @@ class Position:
position: int position: int
@dataclass
class Reg:
ch: int
reg: int
value: int
def decode_pong(p: bytes): def decode_pong(p: bytes):
if len(p) < 4: if len(p) < 4:
return None return None
@@ -304,13 +289,6 @@ def decode_position(p: bytes):
return Position(ch, pos) return Position(ch, pos)
def decode_reg(p: bytes):
if len(p) < 6:
return None
ch, reg, value = struct.unpack_from("<BBI", p, 0)
return Reg(ch, reg, value)
def decode_event_position(p: bytes): def decode_event_position(p: bytes):
"""MOTION_DONE / STOPPED share the (ch, position) layout.""" """MOTION_DONE / STOPPED share the (ch, position) layout."""
return decode_position(p) return decode_position(p)
hardware/tektronix_base.py
+117 -1125
View File
File diff suppressed because it is too large Load Diff
hardware/uc480_camera.py
+15 -126
View File
@@ -14,7 +14,6 @@ from PyQt6.QtCore import QThread, pyqtSignal, QObject
from PyQt6.QtGui import QImage from PyQt6.QtGui import QImage
import logging import logging
import threading import threading
from contextlib import contextmanager
from typing import List, Optional, Tuple from typing import List, Optional, Tuple
logger = logging.getLogger(__name__) logger = logging.getLogger(__name__)
@@ -92,12 +91,7 @@ class UC480Camera(QObject):
error_occurred = pyqtSignal(str) # Emitted when an error occurs error_occurred = pyqtSignal(str) # Emitted when an error occurs
def __init__(self, camera_id: int = 1): def __init__(self, camera_id: int = 1):
""" """Initialize the uC480 camera driver."""
Initialize the uC480 camera driver.
Args:
camera_id: Camera ID (1-based; use is_GetCameraList to find IDs)
"""
super().__init__() super().__init__()
self.camera_id = camera_id self.camera_id = camera_id
@@ -132,12 +126,7 @@ class UC480Camera(QObject):
self._settings_lock = threading.Lock() self._settings_lock = threading.Lock()
def initialize(self) -> bool: def initialize(self) -> bool:
""" """Initialize the camera and allocate memory."""
Initialize the camera and allocate memory.
Returns:
True if successful, False otherwise
"""
try: try:
# Initialize camera. After is_ExitCamera the UI124x series # Initialize camera. After is_ExitCamera the UI124x series
# resets and re-enumerates on USB (firmware reload), so retry # resets and re-enumerates on USB (firmware reload), so retry
@@ -265,12 +254,7 @@ class UC480Camera(QObject):
logger.error(f"is_ExitCamera failed: {ret} — camera handle may still be held by daemon") logger.error(f"is_ExitCamera failed: {ret} — camera handle may still be held by daemon")
def start_capture(self) -> bool: def start_capture(self) -> bool:
""" """Start continuous video capture."""
Start continuous video capture.
Returns:
True if successful, False otherwise
"""
if not self.is_initialized: if not self.is_initialized:
logger.error("Camera not initialized") logger.error("Camera not initialized")
return False return False
@@ -312,12 +296,7 @@ class UC480Camera(QObject):
return ret == ueye.IS_SUCCESS return ret == ueye.IS_SUCCESS
def stop_capture(self) -> bool: def stop_capture(self) -> bool:
""" """Stop continuous video capture."""
Stop continuous video capture.
Returns:
True if successful, False otherwise
"""
if not self.is_capturing: if not self.is_capturing:
return True return True
@@ -331,36 +310,8 @@ class UC480Camera(QObject):
logger.info("Video capture stopped") logger.info("Video capture stopped")
return True return True
@contextmanager
def _capture_paused(self):
"""
Context manager that temporarily stops live video while a camera
parameter is being changed, then restarts it. Many IDS cameras
return IS_CANT_COMMUNICATE_WITH_DRIVER (17) or IS_NO_SUCCESS (-1)
when gain/exposure commands are issued during active capture.
"""
with self._settings_lock:
was_capturing = self.is_capturing
if was_capturing:
ueye.is_StopLiveVideo(self.h_cam, ueye.IS_WAIT)
self.is_capturing = False
try:
yield
finally:
if was_capturing:
ret = ueye.is_CaptureVideo(self.h_cam, ueye.IS_DONT_WAIT)
if ret == ueye.IS_SUCCESS:
self.is_capturing = True
else:
logger.error(f"Failed to restart capture after settings change: {ret}")
def get_frame(self) -> Optional[QImage]: def get_frame(self) -> Optional[QImage]:
""" """Capture a single frame from the camera."""
Capture a single frame from the camera.
Returns:
QImage if successful, None otherwise
"""
if not self.is_initialized: if not self.is_initialized:
logger.error("Camera not initialized") logger.error("Camera not initialized")
return None return None
@@ -401,15 +352,7 @@ class UC480Camera(QObject):
return None return None
def set_exposure(self, exposure_ms: float) -> bool: def set_exposure(self, exposure_ms: float) -> bool:
""" """Set camera exposure time."""
Set camera exposure time.
Args:
exposure_ms: Exposure time in milliseconds
Returns:
True if successful, False otherwise
"""
if not self.is_initialized: if not self.is_initialized:
return False return False
@@ -429,12 +372,7 @@ class UC480Camera(QObject):
return False return False
def get_exposure(self) -> Optional[float]: def get_exposure(self) -> Optional[float]:
""" """Get current exposure time."""
Get current exposure time.
Returns:
Exposure time in milliseconds, or None if failed
"""
if not self.is_initialized: if not self.is_initialized:
return None return None
@@ -452,12 +390,7 @@ class UC480Camera(QObject):
return None return None
def get_pixel_clock_range(self) -> Optional[Tuple[int, int, int]]: def get_pixel_clock_range(self) -> Optional[Tuple[int, int, int]]:
""" """Query the sensor's supported pixel clock range."""
Query the sensor's supported pixel clock range.
Returns:
(min_mhz, max_mhz, increment_mhz), or None if the query failed
"""
if not self.is_initialized: if not self.is_initialized:
return None return None
@@ -476,15 +409,7 @@ class UC480Camera(QObject):
return None return None
def set_pixel_clock(self, pixel_clock_mhz: int) -> bool: def set_pixel_clock(self, pixel_clock_mhz: int) -> bool:
""" """Set camera pixel clock."""
Set camera pixel clock.
Args:
pixel_clock_mhz: Pixel clock in MHz
Returns:
True if successful, False otherwise
"""
if not self.is_initialized: if not self.is_initialized:
return False return False
@@ -535,34 +460,8 @@ class UC480Camera(QObject):
logger.error(f"Failed to set framerate: {ret}") logger.error(f"Failed to set framerate: {ret}")
return False return False
def get_framerate(self) -> Optional[float]:
"""
Get current framerate.
Returns:
Framerate in fps, or None if failed
"""
if not self.is_initialized:
return None
fps = ueye.c_double()
ret = ueye.is_GetFramesPerSecond(self.h_cam, fps)
if ret == ueye.IS_SUCCESS:
return fps.value
else:
return None
def set_gain(self, master_gain: int) -> bool: def set_gain(self, master_gain: int) -> bool:
""" """Set camera master gain."""
Set camera master gain.
Args:
master_gain: Gain value (0-100)
Returns:
True if successful, False otherwise
"""
if not self.is_initialized: if not self.is_initialized:
return False return False
@@ -583,9 +482,9 @@ class UC480Camera(QObject):
return True return True
elif ret == ueye.IS_CANT_COMMUNICATE_WITH_DRIVER: elif ret == ueye.IS_CANT_COMMUNICATE_WITH_DRIVER:
logger.error( logger.error(
f"Hardware gain not supported by this camera model " "Hardware gain not supported by this camera model "
f"(IS_CANT_COMMUNICATE_WITH_DRIVER). " "(IS_CANT_COMMUNICATE_WITH_DRIVER). "
f"Consider using gain boost instead." "Consider using gain boost instead."
) )
return False return False
else: else:
@@ -593,12 +492,7 @@ class UC480Camera(QObject):
return False return False
def get_sensor_info(self) -> dict: def get_sensor_info(self) -> dict:
""" """Get camera sensor information."""
Get camera sensor information.
Returns:
Dictionary with sensor information
"""
if not self.is_initialized: if not self.is_initialized:
return {} return {}
@@ -624,12 +518,7 @@ class CameraStreamThread(QThread):
error_occurred = pyqtSignal(str) error_occurred = pyqtSignal(str)
def __init__(self, camera: UC480Camera): def __init__(self, camera: UC480Camera):
""" """Initialize the camera stream thread."""
Initialize the camera stream thread.
Args:
camera: UC480Camera instance
"""
super().__init__() super().__init__()
self.camera = camera self.camera = camera
self.running = False self.running = False
helios_diagnostic.py
-217
View File
@@ -1,217 +0,0 @@
#!/usr/bin/env python3
"""
Helios Laser Serial Communication Diagnostic Tool
Helps troubleshoot communication issues with the Helios laser.
"""
import serial
import time
import sys
def test_port(port, baudrate=9600):
"""Test basic communication on a serial port."""
print(f"\n{'='*60}")
print(f"Testing {port} at {baudrate} baud")
print(f"{'='*60}")
try:
ser = serial.Serial(
port=port,
baudrate=baudrate,
bytesize=serial.EIGHTBITS,
parity=serial.PARITY_NONE,
stopbits=serial.STOPBITS_ONE,
timeout=1.0
)
print(f"✓ Port opened successfully")
time.sleep(0.1)
# Try to query the controller serial number
print("\nSending: 'SN?'")
ser.write(b'SN?\r')
time.sleep(0.5)
response = ser.readline().decode('ascii', errors='replace').strip()
print(f"Response: '{response}'")
if response:
print(f"✓ Got response: {response}")
return True, response
else:
print(f"✗ No response received")
# Try head serial number
print("\nSending: 'HSN?'")
ser.write(b'HSN?\r')
time.sleep(0.5)
response = ser.readline().decode('ascii', errors='replace').strip()
print(f"Response: '{response}'")
if response:
print(f"✓ Got response: {response}")
ser.close()
return True, response
else:
print(f"✗ No response received")
# Try laser enable status
print("\nSending: 'LE?'")
ser.write(b'LE?\r')
time.sleep(0.5)
response = ser.readline().decode('ascii', errors='replace').strip()
print(f"Response: '{response}'")
if response:
print(f"✓ Got response: {response}")
ser.close()
return True, response
else:
print(f"✗ No response received")
ser.close()
return False, "No response to any query"
except Exception as e:
print(f"✗ Error: {e}")
return False, str(e)
def test_raw_communication(port, baudrate=9600):
"""Test raw serial communication and display hex."""
print(f"\n{'='*60}")
print(f"Raw Communication Test: {port} at {baudrate} baud")
print(f"{'='*60}")
try:
ser = serial.Serial(
port=port,
baudrate=baudrate,
bytesize=serial.EIGHTBITS,
parity=serial.PARITY_NONE,
stopbits=serial.STOPBITS_ONE,
timeout=2.0
)
print(f"✓ Port opened successfully")
time.sleep(0.2)
# Send a simple query
command = b'SN?\r'
print(f"\nSending command (hex): {command.hex()}")
print(f"Sending command (ascii): {command}")
ser.write(command)
time.sleep(0.5)
# Read response byte by byte
response = b''
while True:
byte = ser.read(1)
if not byte:
break
response += byte
if byte == b'\n' or byte == b'\r':
break
print(f"\nRaw response (hex): {response.hex()}")
print(f"Raw response (ascii): {response}")
print(f"Response length: {len(response)} bytes")
# Check for common issues
if not response:
print("✗ No response - device may not be responding or wrong baud rate")
elif response == b'\r' or response == b'\n':
print("⚠ Only got line terminator - device may be echoing but not responding to command")
else:
print("✓ Got a response!")
ser.close()
return True
except Exception as e:
print(f"✗ Error: {e}")
return False
def test_echo(port, baudrate=9600):
"""Test if the device echoes commands back."""
print(f"\n{'='*60}")
print(f"Echo Test: {port} at {baudrate} baud")
print(f"{'='*60}")
try:
ser = serial.Serial(
port=port,
baudrate=baudrate,
bytesize=serial.EIGHTBITS,
parity=serial.PARITY_NONE,
stopbits=serial.STOPBITS_ONE,
timeout=1.0
)
# Send a test character
test_char = b'T'
print(f"Sending test character: {test_char}")
ser.write(test_char)
time.sleep(0.1)
echo = ser.read(1)
if echo == test_char:
print(f"✓ Device echoes input")
elif echo:
print(f"⚠ Device sent something but not the same: {echo}")
else:
print(f"✗ No echo")
ser.close()
return True
except Exception as e:
print(f"✗ Error: {e}")
return False
def main():
"""Run diagnostic tests."""
port = "/dev/ttyUSB2"
if len(sys.argv) > 1:
port = sys.argv[1]
print(f"\n{'#'*60}")
print(f"# Helios Laser Serial Diagnostic Tool")
print(f"# Testing port: {port}")
print(f"{'#'*60}")
# Test standard baud rate
success, response = test_port(port, 9600)
if not success:
print("\n" + "="*60)
print("Standard baud rate (9600) failed. Trying alternatives...")
print("="*60)
# Try other common baud rates
for baudrate in [115200, 19200, 4800, 2400]:
success, response = test_port(port, baudrate)
if success:
print(f"\n✓ SUCCESS! Device responds at {baudrate} baud")
break
else:
print(f"\n✓ SUCCESS! Device responds at 9600 baud")
# Run additional diagnostics
print("\n")
test_raw_communication(port, 9600)
print("\n")
test_echo(port, 9600)
print(f"\n{'#'*60}")
print("# Diagnostic Tests Complete")
print(f"{'#'*60}\n")
if __name__ == "__main__":
main()
helios_terminal.py
-71
View File
@@ -1,71 +0,0 @@
#!/usr/bin/env python3
"""
Simple serial terminal for manual Helios laser testing.
Allows sending raw commands and viewing responses.
"""
import serial
import sys
from threading import Thread
import time
def read_from_port(ser):
"""Read data from serial port and display it."""
while True:
try:
if ser.in_waiting:
data = ser.read(ser.in_waiting)
print(f"\n[RX] {data.decode('ascii', errors='replace')}", end='')
sys.stdout.flush()
except:
break
time.sleep(0.01)
def main():
"""Run interactive serial terminal."""
port = "/dev/ttyUSB2"
if len(sys.argv) > 1:
port = sys.argv[1]
try:
ser = serial.Serial(
port=port,
baudrate=9600,
bytesize=serial.EIGHTBITS,
parity=serial.PARITY_NONE,
stopbits=serial.STOPBITS_ONE,
timeout=0.1
)
print(f"Connected to {port} at 9600 baud")
print("Type commands and press Enter. Type 'quit' to exit.\n")
# Start reader thread
reader_thread = Thread(target=read_from_port, args=(ser,), daemon=True)
reader_thread.start()
while True:
try:
user_input = input("[TX] ")
if user_input.lower() == 'quit':
break
# Send command with carriage return
command = user_input + '\r'
ser.write(command.encode('ascii'))
time.sleep(0.1)
except KeyboardInterrupt:
break
except Exception as e:
print(f"Error: {e}")
ser.close()
print("\nDisconnected")
except Exception as e:
print(f"Failed to open {port}: {e}")
sys.exit(1)
if __name__ == "__main__":
main()
helios_test_app.py
+88 -68
View File
@@ -6,15 +6,13 @@ Simple PyQt6 GUI for testing and controlling the Helios laser.
import sys import sys
import logging import logging
from typing import Optional
from enum import Enum
from PyQt6.QtWidgets import ( from PyQt6.QtWidgets import (
QApplication, QMainWindow, QWidget, QVBoxLayout, QHBoxLayout, QApplication, QMainWindow, QWidget, QVBoxLayout, QHBoxLayout,
QGroupBox, QLabel, QLineEdit, QPushButton, QComboBox, QSpinBox, QGroupBox, QLabel, QLineEdit, QPushButton, QComboBox, QSpinBox,
QStatusBar, QMessageBox, QTabWidget, QTextEdit QMessageBox, QTabWidget, QTextEdit
) )
from PyQt6.QtCore import Qt, QThread, pyqtSignal, QObject from PyQt6.QtCore import QThread, pyqtSignal, pyqtSlot, QObject
from PyQt6.QtGui import QFont from PyQt6.QtGui import QFont
from hardware.helios_laser import HeliosLaser, PulseMode from hardware.helios_laser import HeliosLaser, PulseMode
@@ -142,6 +140,20 @@ class LaserWorker(QObject):
super().__init__() super().__init__()
self.laser = laser self.laser = laser
@pyqtSlot(str, object)
def invoke(self, method_name: str, args: tuple):
"""Run one of this worker's methods on the worker thread.
Reached through a queued signal connection, so the serial I/O (and
its blocking reads) stays off the GUI thread. Calling the methods
directly, as this app used to, executes them in the caller's thread
and freezes the UI for the duration.
"""
try:
getattr(self, method_name)(*args)
except Exception as exc:
self.operation_complete.emit(False, str(exc))
def set_frequency(self, freq: int): def set_frequency(self, freq: int):
try: try:
success = self.laser.set_frequency_hz(freq) success = self.laser.set_frequency_hz(freq)
@@ -199,15 +211,13 @@ class LaserWorker(QObject):
self.operation_complete.emit(False, str(e)) self.operation_complete.emit(False, str(e))
def query_power(self): def query_power(self):
try: # HeliosLaser has no power query: the driver README advertises
power = self.laser.get_power_mw() # get_power_mw(), but no such method exists and the protocol
if power is not None: # mnemonic for an output-power read is not documented anywhere in
self.power_updated.emit(power) # this repo. This used to raise AttributeError into a popup.
self.operation_complete.emit(True, f"Power: {power:.2f} mW") # See KNOWN_ISSUES.md — needs the command from the Helios manual.
else: self.operation_complete.emit(
self.operation_complete.emit(False, "Failed to query power") False, "Power query is not implemented (no known protocol command)")
except Exception as e:
self.operation_complete.emit(False, str(e))
def query_enabled(self): def query_enabled(self):
try: try:
@@ -291,6 +301,9 @@ class LaserWorker(QObject):
class HeliosTestApp(QMainWindow): class HeliosTestApp(QMainWindow):
"""Main application window for Helios laser testing.""" """Main application window for Helios laser testing."""
# Dispatches a worker method name + args across the thread boundary.
worker_call = pyqtSignal(str, object)
def __init__(self): def __init__(self):
super().__init__() super().__init__()
self.laser = HeliosLaser() self.laser = HeliosLaser()
@@ -588,6 +601,10 @@ class HeliosTestApp(QMainWindow):
power_layout = QHBoxLayout() power_layout = QHBoxLayout()
btn_get_power = QPushButton("Query Power") btn_get_power = QPushButton("Query Power")
btn_get_power.setEnabled(False)
btn_get_power.setToolTip(
"Not implemented: no documented Helios protocol command for "
"output power (see KNOWN_ISSUES.md).")
btn_get_power.clicked.connect(self.on_query_power) btn_get_power.clicked.connect(self.on_query_power)
power_layout.addWidget(btn_get_power) power_layout.addWidget(btn_get_power)
@@ -699,6 +716,9 @@ class HeliosTestApp(QMainWindow):
self.worker = LaserWorker(self.laser) self.worker = LaserWorker(self.laser)
self.worker_thread = QThread() self.worker_thread = QThread()
self.worker.moveToThread(self.worker_thread) self.worker.moveToThread(self.worker_thread)
# Queued (cross-thread) connection: the worker's methods run on
# the worker thread, not on whichever thread emits.
self.worker_call.connect(self.worker.invoke)
self.worker.operation_complete.connect(self.on_operation_complete) self.worker.operation_complete.connect(self.on_operation_complete)
self.worker.frequency_updated.connect(self.on_frequency_updated) self.worker.frequency_updated.connect(self.on_frequency_updated)
self.worker.current_updated.connect(self.on_current_updated) self.worker.current_updated.connect(self.on_current_updated)
@@ -715,11 +735,27 @@ class HeliosTestApp(QMainWindow):
else: else:
QMessageBox.critical(self, "Connection Error", f"Failed to connect to {port}") QMessageBox.critical(self, "Connection Error", f"Failed to connect to {port}")
def _require_connection(self) -> bool:
"""Warn and return False when no laser is connected."""
if self.laser.is_connected and self.worker is not None:
return True
QMessageBox.warning(self, "Error", "Not connected to laser")
return False
def _call_worker(self, method_name: str, *args):
"""Run a worker method on the worker thread via a queued signal."""
if self.worker is not None:
self.worker_call.emit(method_name, args)
def disconnect_laser(self): def disconnect_laser(self):
"""Disconnect from the laser.""" """Disconnect from the laser."""
if self.worker_thread: if self.worker_thread:
self.worker_thread.quit() self.worker_thread.quit()
self.worker_thread.wait() self.worker_thread.wait(2000)
# Drop both references: a reconnect used to leak the previous
# QThread, worker, and all nine signal connections.
self.worker = None
self.worker_thread = None
self.laser.disconnect() self.laser.disconnect()
self.lbl_status.setText("Status: Disconnected") self.lbl_status.setText("Status: Disconnected")
@@ -731,137 +767,121 @@ class HeliosTestApp(QMainWindow):
def on_set_frequency(self): def on_set_frequency(self):
"""Set the laser frequency.""" """Set the laser frequency."""
if not self.laser.is_connected: if not self._require_connection():
QMessageBox.warning(self, "Error", "Not connected to laser")
return return
freq = self.spin_frequency.value() freq = self.spin_frequency.value()
self.worker.set_frequency(freq) self._call_worker("set_frequency", freq)
def on_query_frequency(self): def on_query_frequency(self):
"""Query the laser frequency.""" """Query the laser frequency."""
if not self.laser.is_connected: if not self._require_connection():
QMessageBox.warning(self, "Error", "Not connected to laser")
return return
self.worker.query_frequency() self._call_worker("query_frequency")
def on_set_current(self): def on_set_current(self):
"""Set the laser current.""" """Set the laser current."""
if not self.laser.is_connected: if not self._require_connection():
QMessageBox.warning(self, "Error", "Not connected to laser")
return return
current = self.spin_current.value() current = self.spin_current.value()
self.worker.set_current(current) self._call_worker("set_current", current)
def on_query_current(self): def on_query_current(self):
"""Query the laser current.""" """Query the laser current."""
if not self.laser.is_connected: if not self._require_connection():
QMessageBox.warning(self, "Error", "Not connected to laser")
return return
self.worker.query_current() self._call_worker("query_current")
def on_set_mode(self): def on_set_mode(self):
"""Set the laser pulse mode.""" """Set the laser pulse mode."""
if not self.laser.is_connected: if not self._require_connection():
QMessageBox.warning(self, "Error", "Not connected to laser")
return return
mode = self.combo_mode.currentData() mode = self.combo_mode.currentData()
self.worker.set_pulse_mode(mode) self._call_worker("set_pulse_mode", mode)
def on_enable_laser(self): def on_enable_laser(self):
"""Enable the laser.""" """Enable the laser."""
if not self.laser.is_connected: if not self._require_connection():
QMessageBox.warning(self, "Error", "Not connected to laser")
return return
self.worker.set_laser_enable(True) self._call_worker("set_laser_enable", True)
def on_disable_laser(self): def on_disable_laser(self):
"""Disable the laser.""" """Disable the laser."""
if not self.laser.is_connected: if not self._require_connection():
QMessageBox.warning(self, "Error", "Not connected to laser")
return return
self.worker.set_laser_enable(False) self._call_worker("set_laser_enable", False)
def on_query_enabled(self): def on_query_enabled(self):
"""Query if laser is enabled.""" """Query if laser is enabled."""
if not self.laser.is_connected: if not self._require_connection():
QMessageBox.warning(self, "Error", "Not connected to laser")
return return
self.worker.query_enabled() self._call_worker("query_enabled")
def on_query_power(self): def on_query_power(self):
"""Query the laser output power.""" """Query the laser output power."""
if not self.laser.is_connected: if not self._require_connection():
QMessageBox.warning(self, "Error", "Not connected to laser")
return return
self.worker.query_power() self._call_worker("query_power")
def on_query_all(self): def on_query_all(self):
"""Query all laser parameters.""" """Query all laser parameters."""
if not self.laser.is_connected: if not self._require_connection():
QMessageBox.warning(self, "Error", "Not connected to laser")
return return
self.worker.query_serials() self._call_worker("query_serials")
self.worker.query_frequency() self._call_worker("query_frequency")
self.worker.query_current() self._call_worker("query_current")
self.worker.query_power() self._call_worker("query_power")
self.worker.query_enabled() self._call_worker("query_enabled")
self.worker.query_status_registers() self._call_worker("query_status_registers")
self.worker.query_remote_enable() self._call_worker("query_remote_enable")
def on_query_status(self): def on_query_status(self):
"""Query LER/LCE/CCE status registers.""" """Query LER/LCE/CCE status registers."""
if not self.laser.is_connected: if not self._require_connection():
QMessageBox.warning(self, "Error", "Not connected to laser")
return return
self.worker.query_status_registers() self._call_worker("query_status_registers")
def on_reset_faults(self): def on_reset_faults(self):
"""Send the fault reset sequence.""" """Send the fault reset sequence."""
if not self.laser.is_connected: if not self._require_connection():
QMessageBox.warning(self, "Error", "Not connected to laser")
return return
self.worker.do_reset_faults() self._call_worker("do_reset_faults")
def on_query_remote_enable(self): def on_query_remote_enable(self):
"""Query the remote enable (LRE) state.""" """Query the remote enable (LRE) state."""
if not self.laser.is_connected: if not self._require_connection():
QMessageBox.warning(self, "Error", "Not connected to laser")
return return
self.worker.query_remote_enable() self._call_worker("query_remote_enable")
def on_set_remote_enable(self, enable: bool): def on_set_remote_enable(self, enable: bool):
"""Set the remote enable (LRE) state.""" """Set the remote enable (LRE) state."""
if not self.laser.is_connected: if not self._require_connection():
QMessageBox.warning(self, "Error", "Not connected to laser")
return return
self.worker.set_remote_enable(enable) self._call_worker("set_remote_enable", enable)
def on_ler_reset(self): def on_ler_reset(self):
"""Send LER 0 only.""" """Send LER 0 only."""
if not self.laser.is_connected: if not self._require_connection():
QMessageBox.warning(self, "Error", "Not connected to laser")
return return
self.worker.do_ler_reset() self._call_worker("do_ler_reset")
def on_send_raw(self): def on_send_raw(self):
"""Send the raw command from the terminal input.""" """Send the raw command from the terminal input."""
if not self.laser.is_connected: if not self._require_connection():
QMessageBox.warning(self, "Error", "Not connected to laser")
return return
cmd = self.le_raw_cmd.text().strip() cmd = self.le_raw_cmd.text().strip()
if not cmd: if not cmd:
return return
self.worker.send_raw(cmd) self._call_worker("send_raw", cmd)
def on_raw_response(self, cmd: str, response: str): def on_raw_response(self, cmd: str, response: str):
"""Display raw TX/RX pair in the terminal log.""" """Display raw TX/RX pair in the terminal log."""
motion_worker.py
-395
View File
@@ -1,395 +0,0 @@
"""
Motion Controller Worker Thread
Handles all motion control operations in a separate thread to keep the UI responsive.
Provides async command queueing and position updates via Qt signals.
"""
from PyQt6 import QtCore
from hardware.pybbd202 import ThorlabsServoDriver, AXIS_X, AXIS_Y
import queue
import time
from typing import Optional, Dict, Any
class MotionCommand:
"""Represents a motion command"""
def __init__(self, cmd_type: str, **kwargs):
self.cmd_type = cmd_type
self.params = kwargs
class MotionWorker(QtCore.QObject):
"""
Worker object for handling motion control in a separate thread.
Signals:
connected: Emitted when controller connects successfully
disconnected: Emitted when controller disconnects
connection_failed: Emitted when connection fails (error_msg: str)
position_updated: Emitted when position changes (x: float, y: float)
homed_status: Emitted with home status (x_homed: bool, y_homed: bool)
move_completed: Emitted when a move completes (axis: str)
error_occurred: Emitted when an error occurs (error_msg: str)
"""
# Signals
connected = QtCore.pyqtSignal()
disconnected = QtCore.pyqtSignal()
connection_failed = QtCore.pyqtSignal(str)
position_updated = QtCore.pyqtSignal(float, float) # x, y in mm
homed_status = QtCore.pyqtSignal(bool, bool) # x_homed, y_homed
motion_status = QtCore.pyqtSignal(bool, bool) # x_moving, y_moving
move_completed = QtCore.pyqtSignal(str) # axis name
error_occurred = QtCore.pyqtSignal(str) # error message
def __init__(self):
super().__init__()
self.controller: Optional[ThorlabsServoDriver] = None
self.is_connected = False
self.command_queue = queue.Queue()
self.running = True
# Default parameters
self.jog_speed = 20.0 # mm/s
self.acceleration = 50.0 # mm/s^2
self.step_size = 1.0 # mm
# Position tracking
self.last_x = None
self.last_y = None
# Status tracking
self.last_x_homed = None
self.last_y_homed = None
self.last_x_moving = None
self.last_y_moving = None
# Position update throttling
self.last_position_update_time = 0
self.position_update_interval = 0.2 # seconds between position reads
# Flag to pause polling during scanning (scan worker handles its own position queries)
self.scanning_active = False
@QtCore.pyqtSlot()
def run(self):
"""Main worker loop - processes commands from queue"""
print("Motion worker thread started")
while self.running:
try:
# Check for commands with timeout to allow periodic position updates
try:
cmd = self.command_queue.get(timeout=0.05) # 50ms timeout
self.process_command(cmd)
except queue.Empty:
pass
# Periodically update position and status if connected
# Skip updates during scanning - scan worker handles its own position queries
if self.is_connected and self.controller and not self.scanning_active:
self.update_position()
self.update_home_status()
self.update_motion_status()
except Exception as e:
print(f"Error in motion worker loop: {e}")
self.error_occurred.emit(str(e))
# Cleanup on exit
if self.controller:
try:
self.controller.disconnect()
except:
pass
print("Motion worker thread stopped")
def process_command(self, cmd: MotionCommand):
"""Process a motion command"""
try:
if cmd.cmd_type == 'connect':
self.do_connect()
elif cmd.cmd_type == 'disconnect':
self.do_disconnect()
elif cmd.cmd_type == 'jog':
self.do_jog(cmd.params['axis'], cmd.params['direction'])
elif cmd.cmd_type == 'home':
self.do_home(cmd.params['axis'])
elif cmd.cmd_type == 'set_velocity':
self.do_set_velocity(cmd.params['speed'], cmd.params['accel'])
elif cmd.cmd_type == 'set_step_size':
self.step_size = cmd.params['step_size']
elif cmd.cmd_type == 'set_axis_enable':
self.do_set_axis_enable(cmd.params['axis'], cmd.params['enabled'])
elif cmd.cmd_type == 'stop':
self.running = False
except Exception as e:
print(f"Error processing command {cmd.cmd_type}: {e}")
self.error_occurred.emit(f"Command '{cmd.cmd_type}' failed: {str(e)}")
def do_connect(self):
"""Connect to the motion controller"""
try:
self.controller = ThorlabsServoDriver()
self.controller.connect()
# Enable channels
self.controller.enable_axis(AXIS_X)
self.controller.enable_axis(AXIS_Y)
# Start polling to populate cached state (positions, homed, moving, errors)
self.controller.start_polling(interval=0.2)
# Wait for first polling cycle to populate status
time.sleep(0.3)
# Set initial velocity parameters
for dest in [AXIS_X, AXIS_Y]:
self.controller.set_velocity_params(
dest,
max_velocity=self.jog_speed,
acceleration=self.acceleration
)
self.is_connected = True
# Force initial updates (they will be emitted because last values are None)
self.update_position()
self.update_home_status()
self.update_motion_status()
self.connected.emit()
print("Motion controller connected successfully")
except Exception as e:
print(f"Failed to connect to motion controller: {e}")
self.connection_failed.emit(str(e))
def do_disconnect(self):
"""Disconnect from the motion controller"""
if self.controller:
try:
self.controller.disconnect()
print("Motion controller disconnected")
except Exception as e:
print(f"Error during disconnect: {e}")
self.controller = None
self.is_connected = False
self.disconnected.emit()
def do_jog(self, axis: str, direction: int):
"""Execute a jog move"""
if not self.is_connected or not self.controller:
return
try:
dest = AXIS_X if axis == 'x' else AXIS_Y
# Calculate relative distance
distance = self.step_size * direction
# Execute the move (blocking, with short timeout for continuous jogging)
self.controller.move_axis_relative(dest, distance, timeout=0.5)
# Update position
self.update_position()
self.move_completed.emit(axis)
except TimeoutError:
# Timeout is expected during continuous jog - don't report as error
pass
except Exception as e:
print(f"Jog error: {e}")
self.error_occurred.emit(f"Jog failed: {str(e)}")
def do_home(self, axis: str):
"""Home an axis"""
if not self.is_connected or not self.controller:
return
try:
dest = AXIS_X if axis == 'x' else AXIS_Y
print(f"Homing {axis.upper()} axis...")
self.controller.home_axis(dest, timeout=60.0)
# Update position and status after homing
self.update_position()
self.update_home_status()
print(f"{axis.upper()} axis homed successfully")
except TimeoutError:
print(f"Home timeout: {axis.upper()} axis")
self.error_occurred.emit(f"Homing {axis.upper()} timed out")
except Exception as e:
print(f"Home error: {e}")
self.error_occurred.emit(f"Homing {axis.upper()} failed: {str(e)}")
def do_set_velocity(self, speed: float, accel: float):
"""Set velocity parameters"""
if not self.is_connected or not self.controller:
self.jog_speed = speed
self.acceleration = accel
return
try:
self.jog_speed = speed
self.acceleration = accel
for dest in [AXIS_X, AXIS_Y]:
self.controller.set_velocity_params(
dest,
max_velocity=self.jog_speed,
acceleration=self.acceleration
)
except Exception as e:
print(f"Set velocity error: {e}")
def do_set_axis_enable(self, axis: str, enabled: bool):
"""Enable or disable an axis for manual movement"""
if not self.is_connected or not self.controller:
return
try:
dest = AXIS_X if axis == 'x' else AXIS_Y
if enabled:
self.controller.enable_axis(dest)
else:
self.controller.disable_axis(dest)
state_str = "enabled" if enabled else "disabled"
print(f"{axis.upper()} axis {state_str}")
except Exception as e:
print(f"Set axis enable error: {e}")
self.error_occurred.emit(f"Failed to {'enable' if enabled else 'disable'} {axis.upper()} axis: {str(e)}")
def update_position(self):
"""Update current position and emit signal if changed"""
if not self.is_connected or not self.controller:
return
# Throttle position reads to avoid excessive signal emission
current_time = time.time()
if current_time - self.last_position_update_time < self.position_update_interval:
return
self.last_position_update_time = current_time
try:
# Read cached positions (populated by polling worker)
x_pos = self.controller.positions[0]
y_pos = self.controller.positions[1]
# Always emit on first update, or if position changed significantly (> 0.001mm)
if (self.last_x is None or self.last_y is None or
abs(x_pos - self.last_x) > 0.001 or abs(y_pos - self.last_y) > 0.001):
self.last_x = x_pos
self.last_y = y_pos
print(f"Position update: X={x_pos:.3f}mm, Y={y_pos:.3f}mm")
self.position_updated.emit(x_pos, y_pos)
except Exception as e:
print(f"Error updating position: {e}")
import traceback
traceback.print_exc()
def update_home_status(self):
"""Update home status and emit signal if changed"""
if not self.is_connected or not self.controller:
return
try:
x_homed = self.controller.am_homed[0]
y_homed = self.controller.am_homed[1]
# Only emit if status changed
if x_homed != self.last_x_homed or y_homed != self.last_y_homed:
self.last_x_homed = x_homed
self.last_y_homed = y_homed
self.homed_status.emit(x_homed, y_homed)
except Exception as e:
print(f"Error updating home status: {e}")
import traceback
traceback.print_exc()
def update_motion_status(self):
"""Update motion status and emit signal if changed.
The new driver's polling worker keeps am_moving[], am_error[]
up to date automatically via status update messages.
"""
if not self.is_connected or not self.controller:
return
try:
# Check for any error conditions
if self.controller.am_error[0]:
self.error_occurred.emit("X-axis error detected")
if self.controller.am_error[1]:
self.error_occurred.emit("Y-axis error detected")
# Read cached motion status (updated by polling worker)
x_moving = self.controller.am_moving[0]
y_moving = self.controller.am_moving[1]
# Only emit if status changed
if x_moving != self.last_x_moving or y_moving != self.last_y_moving:
self.last_x_moving = x_moving
self.last_y_moving = y_moving
self.motion_status.emit(x_moving, y_moving)
except Exception as e:
print(f"Error updating motion status: {e}")
import traceback
traceback.print_exc()
# Slot methods for queuing commands
@QtCore.pyqtSlot()
def queue_connect(self):
"""Queue a connect command"""
self.command_queue.put(MotionCommand('connect'))
@QtCore.pyqtSlot()
def queue_disconnect(self):
"""Queue a disconnect command"""
self.command_queue.put(MotionCommand('disconnect'))
@QtCore.pyqtSlot(str, int)
def queue_jog(self, axis: str, direction: int):
"""Queue a jog command"""
self.command_queue.put(MotionCommand('jog', axis=axis, direction=direction))
@QtCore.pyqtSlot(str)
def queue_home(self, axis: str):
"""Queue a home command"""
self.command_queue.put(MotionCommand('home', axis=axis))
@QtCore.pyqtSlot(float, float)
def queue_set_velocity(self, speed: float, accel: float):
"""Queue a set velocity command"""
self.command_queue.put(MotionCommand('set_velocity', speed=speed, accel=accel))
@QtCore.pyqtSlot(float)
def queue_set_step_size(self, step_size: float):
"""Queue a set step size command"""
self.command_queue.put(MotionCommand('set_step_size', step_size=step_size))
@QtCore.pyqtSlot(str, bool)
def queue_set_axis_enable(self, axis: str, enabled: bool):
"""Queue a command to enable or disable an axis"""
self.command_queue.put(MotionCommand('set_axis_enable', axis=axis, enabled=enabled))
@QtCore.pyqtSlot()
def stop(self):
"""Stop the worker thread"""
# Set running to False immediately so the main loop can exit
# even if it's blocked waiting for a response from the controller
self.running = False
# Also queue a stop command to ensure the command_queue.get() returns
self.command_queue.put(MotionCommand('stop'))
ruff.toml
+19
View File
@@ -0,0 +1,19 @@
target-version = "py311"
line-length = 120
[lint]
# F: pyflakes (unused imports/variables, undefined names)
# E7/E9: comparison and runtime-error prone constructs
# B: bugbear (mutable defaults, useless expressions)
select = ["F", "E7", "E9", "B"]
ignore = [
"E731", # lambda assignment — used deliberately for short Qt slot glue
"E741", # ambiguous single-letter names — used in math-heavy geometry code
"E702", # `w = QLabel(); w.setFont(f)` on one line — the widget-layout idiom here
]
[lint.per-file-ignores]
# Deliberate package re-exports
"hardware/pybbd202/__init__.py" = ["F401"]
# Quarantined pending hardware verification (docs/genesis_verification.md)
"tools/genesis_laser_gui.py" = ["B007"]
saw_check_viewer.py
Executable
+674
View File
@@ -0,0 +1,674 @@
#!/usr/bin/env python3
"""
SAW Check Viewer — every angle's frequency on one graph.
Opens a v10 middle-row SAW check (written by the main app's "SAW Quality
Check") and plots the peak SAW frequency along each angle's row, all angles
on the same axes. ``core.saw_check`` explains why that answers an alignment
question: every angle's middle row crosses the same ROI centre, so the angles
all measure the same material and a spread between them belongs to the rig.
Two readings share the window:
* the main graph — frequency along the row, one curve per angle. Curves
that lie on top of each other and run flat are what a well-aligned rig
looks like; a curve offset from the rest indicts its angle, and a sloped
curve indicts the ROI (tilt or defocus across it, at that angle).
* the summary — each angle's median with ±1σ, plotted against angle, plus
the same numbers per angle in a table.
A full v6 scan opens too: the same middle row is pulled out of it, so a scan
can be re-examined with the check's own read-out after the fact.
"""
import sys
from pathlib import Path
import numpy as np
from PyQt6.QtCore import Qt, QThread, QTimer, pyqtSignal, QObject
from PyQt6.QtGui import QColor
from PyQt6.QtWidgets import (
QApplication, QCheckBox, QComboBox, QDoubleSpinBox, QFileDialog, QFrame,
QGroupBox, QHBoxLayout, QHeaderView, QLabel, QListWidget, QListWidgetItem,
QMainWindow, QMessageBox, QPushButton, QSizePolicy, QSpinBox, QSplitter,
QTabWidget, QTableWidget, QTableWidgetItem, QVBoxLayout, QWidget,
)
from matplotlib import colormaps
from matplotlib.backends.backend_qtagg import FigureCanvasQTAgg, NavigationToolbar2QT
from matplotlib.figure import Figure
sys.path.insert(0, str(Path(__file__).resolve().parent))
from core.saw_check import alignment_summary, frequency_traces
from core.sras_analysis import ChannelCalibration
from core.sras_format import SrasFile
RECOMPUTE_DEBOUNCE_MS = 250
# Angle curve colours, sampled across the sequence so the legend reads as the
# progression 0° → 180° rather than as an arbitrary set.
ANGLE_CMAP = "viridis"
VERDICT_STYLE = {
"good": ("#1b5e20", "#c8e6c9", "Alignment looks good"),
"marginal": ("#7a4f01", "#ffe0b2", "Alignment is marginal"),
"poor": ("#7f1d1d", "#ffcdd2", "Alignment needs attention"),
}
X_AXIS_MODES = [
("Offset from row centre", "offset"),
("Absolute stage X", "absolute"),
]
def angle_colors(n: int) -> list:
cmap = colormaps[ANGLE_CMAP]
if n <= 1:
return [cmap(0.5)]
return [cmap(i / (n - 1)) for i in range(n)]
def nan_moving_mean(y: np.ndarray, window: int) -> np.ndarray:
"""Moving mean over `window` frames that steps over masked pixels.
A plain convolution would let one NaN swallow a whole window, which on a
sparsely-masked row erases most of the trace; this divides by the number
of samples that actually contributed instead.
"""
if window <= 1:
return y
valid = np.isfinite(y)
kernel = np.ones(int(window))
num = np.convolve(np.where(valid, y, 0.0), kernel, mode="same")
den = np.convolve(valid.astype(float), kernel, mode="same")
return np.divide(num, den, out=np.full(num.shape, np.nan), where=den > 0)
class LoadedCheck:
"""A parsed check file plus the traces currently computed from it."""
def __init__(self, path: Path):
self.sras = SrasFile(path)
self.calib = ChannelCalibration.from_preambles(self.sras.preambles)
bg = np.frombuffer(self.sras.background, dtype=np.int8)
self.background = bg.astype(np.float32) if len(bg) else None
self.traces = []
self.summary = None
def describe(self) -> str:
h = self.sras.header
kind = ("v10 SAW check" if self.sras.is_saw_check
else f"v{self.sras.version} scan — middle row of each angle")
return (f"{self.sras.path.name}\n{kind}\n"
f"{h.n_angles} angle(s) · {h.samples_per_frame} samples/frame · "
f"{h.sample_rate / 1e9:.2f} GS/s")
def close(self):
self.sras.close()
class FnWorker(QObject):
"""Runs a callable on a QThread; emits its return value or the error."""
finished = pyqtSignal(object)
error = pyqtSignal(str)
def __init__(self, fn):
super().__init__()
self._fn = fn
def run(self):
try:
self.finished.emit(self._fn())
except Exception as exc:
self.error.emit(str(exc))
class TraceCanvas(FigureCanvasQTAgg):
"""Frequency along the row, one curve per angle, all on one axes."""
def __init__(self, parent=None):
fig = Figure(figsize=(8, 5), tight_layout=True)
self.ax = fig.add_subplot(111)
super().__init__(fig)
self.setParent(parent)
self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding)
self.clear("Open a SAW check file to begin.")
def clear(self, message: str):
self.ax.clear()
self.ax.text(0.5, 0.5, message, ha="center", va="center",
transform=self.ax.transAxes, color="#888888")
self.ax.set_xticks([])
self.ax.set_yticks([])
self.draw_idle()
def plot(self, traces, colors, visible, x_mode, scale, unit, y_label,
smoothing, show_median):
self.ax.clear()
shown = 0
for trace, color in zip(traces, colors, strict=True):
if not visible.get(trace.angle_idx, True):
continue
x = trace.offset_mm if x_mode == "offset" else trace.x_mm
y = nan_moving_mean(trace.freq_mhz, smoothing) * scale
self.ax.plot(x, y, color=color, linewidth=1.0,
label=f"{trace.angle_deg:+.1f}° "
f"med {trace.median_mhz * scale:.2f}")
shown += 1
if shown == 0:
self.clear("No angle selected.")
return
if show_median:
medians = [t.median_mhz for t in traces
if visible.get(t.angle_idx, True) and t.n_valid]
if medians:
self.ax.axhline(float(np.median(medians)) * scale, color="#555555",
linestyle="--", linewidth=1.0,
label="median of shown angles")
self.ax.set_xlabel("Offset from row centre (mm)" if x_mode == "offset"
else "Stage X (mm)")
self.ax.set_ylabel(y_label)
self.ax.grid(True, alpha=0.25)
self.ax.legend(fontsize=7, ncol=2, loc="best", framealpha=0.85)
self.draw_idle()
class SummaryCanvas(FigureCanvasQTAgg):
"""Each angle's median frequency, ±1σ, against the GR angle."""
def __init__(self, parent=None):
fig = Figure(figsize=(8, 2.6), tight_layout=True)
self.ax = fig.add_subplot(111)
super().__init__(fig)
self.setParent(parent)
self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding)
def plot(self, traces, colors, scale, unit):
self.ax.clear()
usable = [(t, c) for t, c in zip(traces, colors, strict=True) if t.n_valid]
if not usable:
self.ax.set_xticks([])
self.ax.set_yticks([])
self.draw_idle()
return
order = sorted(usable, key=lambda tc: tc[0].angle_deg)
angles = [t.angle_deg for t, _ in order]
medians = np.array([t.median_mhz for t, _ in order]) * scale
sigmas = np.array([0.0 if not np.isfinite(t.std_mhz) else t.std_mhz
for t, _ in order]) * scale
self.ax.plot(angles, medians, color="#999999", linewidth=1.0, zorder=1)
self.ax.errorbar(angles, medians, yerr=sigmas, fmt="none",
ecolor="#999999", capsize=3, zorder=2)
for (_, color), angle, median in zip(order, angles, medians, strict=True):
self.ax.plot([angle], [median], marker="o", markersize=6,
color=color, zorder=3)
self.ax.axhline(float(np.median(medians)), color="#555555",
linestyle="--", linewidth=1.0)
self.ax.set_xlabel("GR angle (deg)")
self.ax.set_ylabel(f"Median ({unit})")
self.ax.grid(True, alpha=0.25)
self.draw_idle()
class SawCheckWindow(QMainWindow):
"""Left: what to compute and what to show. Right: the graphs."""
TABLE_COLUMNS = ["Angle (°)", "Y (mm)", "Median", "σ", "Drift (/mm)", "Valid (%)"]
def __init__(self, initial_path: str | None = None):
super().__init__()
self.setWindowTitle("SAW Check Viewer")
self.resize(1280, 860)
self._check: LoadedCheck | None = None
self._colors: list = []
self._visible: dict[int, bool] = {}
self._compute_thread: QThread | None = None
self._compute_worker: FnWorker | None = None
self._pending_recompute = False
self._debounce = QTimer(self)
self._debounce.setSingleShot(True)
self._debounce.setInterval(RECOMPUTE_DEBOUNCE_MS)
self._debounce.timeout.connect(self._recompute)
self._build_ui()
if initial_path:
self._load(Path(initial_path))
# ── Layout ────────────────────────────────────────────────────────────────
def _build_ui(self):
splitter = QSplitter(Qt.Orientation.Horizontal, self)
splitter.addWidget(self._build_controls())
splitter.addWidget(self._build_plots())
splitter.setStretchFactor(0, 0)
splitter.setStretchFactor(1, 1)
splitter.setSizes([340, 940])
self.setCentralWidget(splitter)
def _build_controls(self) -> QWidget:
panel = QWidget(self)
layout = QVBoxLayout(panel)
# File
grp_file = QGroupBox("File")
fl = QVBoxLayout(grp_file)
self.btn_open = QPushButton("Open SAW Check…")
self.btn_open.clicked.connect(self._on_open)
fl.addWidget(self.btn_open)
self.lbl_file = QLabel("No file loaded.")
self.lbl_file.setWordWrap(True)
self.lbl_file.setStyleSheet("color: #666; font-size: 11px;")
fl.addWidget(self.lbl_file)
layout.addWidget(grp_file)
# Analysis — anything here changes the numbers, so it recomputes.
self.grp_analysis = QGroupBox("Analysis")
al = QVBoxLayout(self.grp_analysis)
thr_row = QHBoxLayout()
thr_row.addWidget(QLabel("CH4 DC threshold:"))
self.spin_threshold_mv = QDoubleSpinBox()
self.spin_threshold_mv.setRange(-500.0, 500.0)
self.spin_threshold_mv.setDecimals(1)
self.spin_threshold_mv.setSingleStep(5.0)
self.spin_threshold_mv.setSuffix(" mV")
self.spin_threshold_mv.setValue(50.0)
self.spin_threshold_mv.setToolTip(
"Pixels whose CH4 DC mean falls below this are dropped from the "
"trace — the detection beam was off the sample or out of focus there."
)
self.spin_threshold_mv.valueChanged.connect(self._queue_recompute)
thr_row.addWidget(self.spin_threshold_mv)
al.addLayout(thr_row)
self.chk_bg_sub = QCheckBox("Subtract background waveform")
self.chk_bg_sub.setChecked(True)
self.chk_bg_sub.toggled.connect(self._queue_recompute)
al.addWidget(self.chk_bg_sub)
self.chk_gate = QCheckBox("Time gate before FFT")
self.chk_gate.toggled.connect(self._on_gate_toggled)
al.addWidget(self.chk_gate)
gate_row = QHBoxLayout()
gate_row.addWidget(QLabel("Start:"))
self.spin_gate_start = QDoubleSpinBox()
self.spin_gate_start.setRange(0.0, 100000.0)
self.spin_gate_start.setDecimals(1)
self.spin_gate_start.setSingleStep(10.0)
self.spin_gate_start.setSuffix(" ns")
self.spin_gate_start.setValue(50.0)
self.spin_gate_start.setEnabled(False)
self.spin_gate_start.valueChanged.connect(self._queue_recompute)
gate_row.addWidget(self.spin_gate_start)
gate_row.addWidget(QLabel("End:"))
self.spin_gate_end = QDoubleSpinBox()
self.spin_gate_end.setRange(0.0, 100000.0)
self.spin_gate_end.setDecimals(1)
self.spin_gate_end.setSingleStep(10.0)
self.spin_gate_end.setSuffix(" ns")
self.spin_gate_end.setValue(200.0)
self.spin_gate_end.setEnabled(False)
self.spin_gate_end.valueChanged.connect(self._queue_recompute)
gate_row.addWidget(self.spin_gate_end)
al.addLayout(gate_row)
layout.addWidget(self.grp_analysis)
# Display — cheap, so these only redraw.
grp_display = QGroupBox("Display")
dl = QVBoxLayout(grp_display)
x_row = QHBoxLayout()
x_row.addWidget(QLabel("X axis:"))
self.combo_x = QComboBox()
for label, _ in X_AXIS_MODES:
self.combo_x.addItem(label)
self.combo_x.setToolTip(
"Every angle's row is centred on the same ROI centre, so offset "
"puts the angles over the same piece of sample; absolute shows "
"where each rotated bounding box actually sat on the stage."
)
self.combo_x.currentIndexChanged.connect(self._redraw)
x_row.addWidget(self.combo_x)
dl.addLayout(x_row)
y_row = QHBoxLayout()
y_row.addWidget(QLabel("Y axis:"))
self.combo_y = QComboBox()
self.combo_y.addItems(["Frequency (MHz)", "Velocity (m/s)"])
self.combo_y.currentIndexChanged.connect(self._on_y_mode_changed)
y_row.addWidget(self.combo_y)
dl.addLayout(y_row)
grat_row = QHBoxLayout()
grat_row.addWidget(QLabel("Grating:"))
self.spin_grating_um = QDoubleSpinBox()
self.spin_grating_um.setRange(0.1, 1000.0)
self.spin_grating_um.setDecimals(2)
self.spin_grating_um.setSingleStep(0.5)
self.spin_grating_um.setSuffix(" µm")
self.spin_grating_um.setValue(12.5)
self.spin_grating_um.setEnabled(False)
self.spin_grating_um.setToolTip("v (m/s) = freq (MHz) × grating (µm)")
self.spin_grating_um.valueChanged.connect(self._redraw)
grat_row.addWidget(self.spin_grating_um)
dl.addLayout(grat_row)
smooth_row = QHBoxLayout()
smooth_row.addWidget(QLabel("Smoothing:"))
self.spin_smoothing = QSpinBox()
self.spin_smoothing.setRange(1, 2001)
self.spin_smoothing.setSingleStep(10)
self.spin_smoothing.setSuffix(" frames")
self.spin_smoothing.setValue(1)
self.spin_smoothing.setToolTip(
"Moving average along the row, masked pixels skipped. Display "
"only — the table's statistics always use the unsmoothed trace."
)
self.spin_smoothing.valueChanged.connect(self._redraw)
smooth_row.addWidget(self.spin_smoothing)
dl.addLayout(smooth_row)
self.chk_median_line = QCheckBox("Show median of shown angles")
self.chk_median_line.setChecked(True)
self.chk_median_line.toggled.connect(self._redraw)
dl.addWidget(self.chk_median_line)
layout.addWidget(grp_display)
# Angles
grp_angles = QGroupBox("Angles")
gl = QVBoxLayout(grp_angles)
self.list_angles = QListWidget()
self.list_angles.setMaximumHeight(190)
self.list_angles.itemChanged.connect(self._on_angle_toggled)
gl.addWidget(self.list_angles)
btn_row = QHBoxLayout()
btn_all = QPushButton("All")
btn_all.clicked.connect(lambda: self._set_all_angles(True))
btn_none = QPushButton("None")
btn_none.clicked.connect(lambda: self._set_all_angles(False))
btn_row.addWidget(btn_all)
btn_row.addWidget(btn_none)
gl.addLayout(btn_row)
layout.addWidget(grp_angles)
# Verdict
self.lbl_verdict = QLabel("—")
self.lbl_verdict.setWordWrap(True)
self.lbl_verdict.setFrameShape(QFrame.Shape.StyledPanel)
self.lbl_verdict.setMinimumHeight(92)
self.lbl_verdict.setAlignment(Qt.AlignmentFlag.AlignTop)
layout.addWidget(self.lbl_verdict)
self.lbl_status = QLabel("")
self.lbl_status.setStyleSheet("color: #666; font-size: 11px;")
layout.addWidget(self.lbl_status)
layout.addStretch(1)
return panel
def _build_plots(self) -> QWidget:
splitter = QSplitter(Qt.Orientation.Vertical, self)
top = QWidget()
tl = QVBoxLayout(top)
tl.setContentsMargins(0, 0, 0, 0)
self.trace_canvas = TraceCanvas(top)
tl.addWidget(NavigationToolbar2QT(self.trace_canvas, top))
tl.addWidget(self.trace_canvas)
splitter.addWidget(top)
tabs = QTabWidget()
self.summary_canvas = SummaryCanvas(tabs)
tabs.addTab(self.summary_canvas, "Frequency vs angle")
self.table = QTableWidget(0, len(self.TABLE_COLUMNS))
self.table.setHorizontalHeaderLabels(self.TABLE_COLUMNS)
self.table.horizontalHeader().setSectionResizeMode(
QHeaderView.ResizeMode.Stretch)
self.table.setEditTriggers(QTableWidget.EditTrigger.NoEditTriggers)
tabs.addTab(self.table, "Per-angle statistics")
splitter.addWidget(tabs)
splitter.setStretchFactor(0, 3)
splitter.setStretchFactor(1, 1)
# Stretch factors alone leave the summary too short to fit its own
# axis label on first show; give it a real starting height.
splitter.setSizes([540, 300])
return splitter
# ── Loading ───────────────────────────────────────────────────────────────
def _on_open(self):
start = str(self._check.sras.path.parent) if self._check else ""
path, _ = QFileDialog.getOpenFileName(
self, "Open SAW Check File", start, "SRAS Files (*.sras)")
if path:
self._load(Path(path))
def _load(self, path: Path):
try:
check = LoadedCheck(path)
except Exception as exc:
QMessageBox.critical(self, "Cannot Open File",
f"Could not read {path.name}:\n\n{exc}")
return
if self._check is not None:
self._check.close()
self._check = check
self.setWindowTitle(f"SAW Check Viewer — {path.name}")
self.lbl_file.setText(check.describe())
if not check.sras.is_saw_check:
self.lbl_status.setText(
"Not a v10 check — reading the middle row of each angle "
"out of this scan instead.")
else:
self.lbl_status.setText("")
self._colors = angle_colors(check.sras.header.n_angles)
self._visible = {i: True for i in range(check.sras.header.n_angles)}
self._recompute()
# ── Compute ───────────────────────────────────────────────────────────────
def _queue_recompute(self):
if self._check is not None:
self._debounce.start()
def _on_gate_toggled(self, enabled: bool):
self.spin_gate_start.setEnabled(enabled)
self.spin_gate_end.setEnabled(enabled)
self._queue_recompute()
def _recompute(self):
if self._check is None:
return
if self._compute_thread is not None and self._compute_thread.isRunning():
# One worker owns the mmap at a time; fold this request into the
# one already in flight rather than racing it.
self._pending_recompute = True
return
check = self._check
gated = self.chk_gate.isChecked()
kwargs = dict(
dc_threshold_mv=self.spin_threshold_mv.value(),
background=check.background if self.chk_bg_sub.isChecked() else None,
gate_start_ns=self.spin_gate_start.value() if gated else None,
gate_end_ns=self.spin_gate_end.value() if gated else None,
calib=check.calib,
)
self.grp_analysis.setEnabled(False)
self.lbl_status.setText("Computing frequency traces …")
self._compute_thread = QThread(self)
self._compute_worker = FnWorker(
lambda: frequency_traces(check.sras, **kwargs))
self._compute_worker.moveToThread(self._compute_thread)
self._compute_thread.started.connect(self._compute_worker.run)
self._compute_worker.finished.connect(self._on_traces_ready)
self._compute_worker.error.connect(self._on_compute_error)
self._compute_thread.start()
def _finish_compute(self):
if self._compute_thread is not None:
self._compute_thread.quit()
self._compute_thread.wait(5000)
self._compute_thread = None
self._compute_worker = None
self.grp_analysis.setEnabled(True)
if self._pending_recompute:
self._pending_recompute = False
self._queue_recompute()
def _on_compute_error(self, message: str):
self._finish_compute()
self.lbl_status.setText("")
QMessageBox.critical(self, "Analysis Failed", message)
def _on_traces_ready(self, traces):
self._finish_compute()
if self._check is None:
return
self._check.traces = traces
self._check.summary = alignment_summary(traces)
self.lbl_status.setText(
f"{len(traces)} of {self._check.sras.header.n_angles} angle(s) "
f"produced a trace.")
self._rebuild_angle_list()
self._redraw()
# ── Display ───────────────────────────────────────────────────────────────
def _scale(self) -> tuple[float, str, str]:
"""Display factor, unit and axis label.
The file only ever holds a frequency; velocity is that frequency times
the grating period, applied at display time so switching units never
costs a recompute.
"""
if self.combo_y.currentIndex() == 1:
return self.spin_grating_um.value(), "m/s", "SAW velocity (m/s)"
return 1.0, "MHz", "Peak SAW frequency (MHz)"
def _on_y_mode_changed(self):
self.spin_grating_um.setEnabled(self.combo_y.currentIndex() == 1)
self._redraw()
def _rebuild_angle_list(self):
self.list_angles.blockSignals(True)
self.list_angles.clear()
for trace in self._check.traces:
item = QListWidgetItem(
f"{trace.angle_deg:+7.2f}° Y={trace.y_mm:.3f} mm")
item.setFlags(item.flags() | Qt.ItemFlag.ItemIsUserCheckable)
item.setCheckState(
Qt.CheckState.Checked if self._visible.get(trace.angle_idx, True)
else Qt.CheckState.Unchecked)
item.setData(Qt.ItemDataRole.UserRole, trace.angle_idx)
r, g, b, _ = self._colors[trace.angle_idx]
item.setForeground(QColor(int(r * 255), int(g * 255), int(b * 255)))
self.list_angles.addItem(item)
self.list_angles.blockSignals(False)
def _on_angle_toggled(self, item: QListWidgetItem):
self._visible[item.data(Qt.ItemDataRole.UserRole)] = (
item.checkState() == Qt.CheckState.Checked)
self._redraw()
def _set_all_angles(self, visible: bool):
self.list_angles.blockSignals(True)
for row in range(self.list_angles.count()):
item = self.list_angles.item(row)
item.setCheckState(Qt.CheckState.Checked if visible
else Qt.CheckState.Unchecked)
self._visible[item.data(Qt.ItemDataRole.UserRole)] = visible
self.list_angles.blockSignals(False)
self._redraw()
def _redraw(self):
if self._check is None or not self._check.traces:
self.trace_canvas.clear("No angle in this file has data on disk.")
return
traces = self._check.traces
colors = [self._colors[t.angle_idx] for t in traces]
scale, unit, y_label = self._scale()
self.trace_canvas.plot(
traces, colors, self._visible,
X_AXIS_MODES[self.combo_x.currentIndex()][1], scale, unit, y_label,
self.spin_smoothing.value(), self.chk_median_line.isChecked())
self.summary_canvas.plot(traces, colors, scale, unit)
self._fill_table(traces, scale, unit)
self._show_verdict(scale, unit)
def _fill_table(self, traces, scale: float, unit: str):
headers = list(self.TABLE_COLUMNS)
headers[2] = f"Median ({unit})"
headers[3] = f"σ ({unit})"
headers[4] = f"Drift ({unit}/mm)"
self.table.setHorizontalHeaderLabels(headers)
self.table.setRowCount(len(traces))
for row, trace in enumerate(traces):
values = [
f"{trace.angle_deg:+.2f}",
f"{trace.y_mm:.3f}",
f"{trace.median_mhz * scale:.3f}",
f"{trace.std_mhz * scale:.3f}",
f"{trace.drift_mhz_per_mm * scale:+.4f}",
f"{trace.valid_fraction * 100:.1f}",
]
for col, text in enumerate(values):
item = QTableWidgetItem(text)
item.setTextAlignment(Qt.AlignmentFlag.AlignRight
| Qt.AlignmentFlag.AlignVCenter)
if col == 0:
r, g, b, _ = self._colors[trace.angle_idx]
item.setForeground(QColor(int(r * 255), int(g * 255), int(b * 255)))
self.table.setItem(row, col, item)
def _show_verdict(self, scale: float, unit: str):
summary = self._check.summary
fg, bg, headline = VERDICT_STYLE[summary.level]
detail = summary.describe()
if scale != 1.0 and summary.n_angles:
detail += (f"\nIn {unit}: spread {summary.spread_mhz * scale:.3f} "
f"about {summary.median_mhz * scale:.1f}.")
self.lbl_verdict.setText(f"{headline}\n\n{detail}")
self.lbl_verdict.setStyleSheet(
f"color: {fg}; background: {bg}; padding: 8px; font-size: 11px;")
# ── Teardown ──────────────────────────────────────────────────────────────
def closeEvent(self, event):
self._debounce.stop()
if self._compute_thread is not None:
self._compute_thread.quit()
self._compute_thread.wait(5000)
if self._check is not None:
self._check.close()
super().closeEvent(event)
def main():
app = QApplication(sys.argv)
window = SawCheckWindow(sys.argv[1] if len(sys.argv) > 1 else None)
window.show()
sys.exit(app.exec())
if __name__ == "__main__":
main()
sc3-aui-main.ui
+41
View File
@@ -997,6 +997,46 @@
</property> </property>
</widget> </widget>
</item> </item>
<item>
<widget class="QCheckBox" name="burst_mode_check">
<property name="toolTip">
<string>Acquire as many whole rows per FastFrame acquisition as the scope can hold, and transfer each burst in one CURVe? transaction. The stage trigger output is gated off for the flyback between rows.</string>
</property>
<property name="text">
<string>Burst acquisition (multi-row FastFrame)</string>
</property>
</widget>
</item>
<item>
<widget class="QCheckBox" name="strict_rows_check">
<property name="toolTip">
<string>Stop the scan if a row does not acquire the expected number of frames, instead of zero-padding a short row or truncating a long one. Use for data runs where a silently squared-up row would be worse than a failed scan.</string>
</property>
<property name="text">
<string>Strict row packing (abort on frame-count mismatch)</string>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="saw_check_btn">
<property name="toolTip">
<string>Acquire one row per angle — the row-wise middle of the ROI — and save it as a v10 .sras SAW check. Costs one row-time per angle instead of a full scan, and every angle's row crosses the same ROI centre, so the per-angle frequencies can be compared in the SAW Check Viewer to judge the alignment.</string>
</property>
<property name="text">
<string>SAW Quality Check…</string>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="inspect_angles_btn">
<property name="toolTip">
<string>Rotate through the angles of the scan currently entered, parking at a random point in each so the SAW response can be checked on the oscilloscope before committing to the run.</string>
</property>
<property name="text">
<string>Inspect Angles…</string>
</property>
</widget>
</item>
<item> <item>
<widget class="QPushButton" name="start_scan_btn"> <widget class="QPushButton" name="start_scan_btn">
<property name="text"> <property name="text">
@@ -1056,6 +1096,7 @@
<tabstop>bbd_set_current_start_btn</tabstop> <tabstop>bbd_set_current_start_btn</tabstop>
<tabstop>bbd_set_delta_current_btn</tabstop> <tabstop>bbd_set_delta_current_btn</tabstop>
<tabstop>show_camera_toggle</tabstop> <tabstop>show_camera_toggle</tabstop>
<tabstop>saw_check_btn</tabstop>
<tabstop>start_scan_btn</tabstop> <tabstop>start_scan_btn</tabstop>
</tabstops> </tabstops>
<resources/> <resources/>
sc3-new.ui
-2635
View File
File diff suppressed because it is too large Load Diff
sc3_aui_app.py
+539 -1153
View File
File diff suppressed because it is too large Load Diff
scan_format.md
+101 -14
View File
@@ -1,8 +1,18 @@
# SRAS Scan Binary Format — Version 6 # SRAS Scan Binary Format — Versions 6 and 10
Each `.sras` file contains **one complete scan**: all GR rotation angles and all Each `.sras` file contains **one complete scan**: all GR rotation angles and all
Y rows. Files are named `{prefix}.sras`. Y rows. Files are named `{prefix}.sras`.
Two versions share this layout byte for byte — only the version field differs,
and with it what the file means:
| Version | Meaning | Rows per angle |
|---------|---------|----------------|
| 6 | A full scan. | Whatever the ROI needs. |
| 10 | A middle-row SAW quality check (`{prefix}-sawcheck.sras`). | Exactly 1. |
See [SAW Quality Check (v10)](#saw-quality-check-v10) below.
Starting in v6, each angle only scans the **bounding box of the nominal ROI Starting in v6, each angle only scans the **bounding box of the nominal ROI
rotated by that specific angle** — not the worst case across all angles — so rotated by that specific angle** — not the worst case across all angles — so
`x_start`, `x_delta` (and therefore `n_frames`, the points/row count) and `x_start`, `x_delta` (and therefore `n_frames`, the points/row count) and
@@ -34,7 +44,7 @@ All multi-byte integers and floats use **big-endian** byte order
| Offset | Size | Type | Field | Description | | Offset | Size | Type | Field | Description |
|--------|------|-----------|--------------------|--------------------------------------------------| |--------|------|-----------|--------------------|--------------------------------------------------|
| 0 | 4 | `4s` | `magic` | Always `SRAS` (0x53 0x52 0x41 0x53) | | 0 | 4 | `4s` | `magic` | Always `SRAS` (0x53 0x52 0x41 0x53) |
| 4 | 1 | `uint8` | `version` | Format version — `6` | | 4 | 1 | `uint8` | `version` | Format version — `6` (scan) or `10` (SAW check) |
| 5 | 2 | `uint16` | `n_angles` | Number of GR rotation angles | | 5 | 2 | `uint16` | `n_angles` | Number of GR rotation angles |
| 7 | 4 | `float32` | `x_start_nominal` | Nominal (pre-rotation) X scan start, mm | | 7 | 4 | `float32` | `x_start_nominal` | Nominal (pre-rotation) X scan start, mm |
| 11 | 4 | `float32` | `y_start_nominal` | Nominal (pre-rotation) Y scan start, mm | | 11 | 4 | `float32` | `y_start_nominal` | Nominal (pre-rotation) Y scan start, mm |
@@ -183,18 +193,94 @@ using that angle's `x_start` from the Per-Angle Geometry Table (not
--- ---
## Acquisition Settings (fixed by sc3_aui_app.py) ## Acquisition Settings (fixed by core/scope_sras.py)
| Parameter | Value | | Parameter | Value |
|-----------------------|------------------------------| |-----------------------|------------------------------------------|
| Oscilloscope trigger | CH2, rising edge, 1.24 V | | Setup trigger | CH2, rising edge, 0.500 V (`TRIG_LEVEL_V`) |
| Trigger offset | 0 % (trigger at left edge) | | Scan trigger | Logic AND, CH2 HIGH ∧ CH3 HIGH, 0.500 V |
| Sample rate | 6.25 GS/s (160 ps/sample) | | Horizontal position | 30 (`HORizontal:POSition`) |
| Channels recorded | CH1, CH3, CH4 | | Sample rate | 6.25 GS/s (160 ps/sample) |
| Stage X velocity | 100 mm/s | | Transfer format | `DATa:ENCdg RIBinary`, `DATa:WIDth 1` |
| Stage X acceleration | 1500 mm/s² | | Channels recorded | CH1, CH3, CH4 |
| Stage X trigger out | Logic-high at max velocity | | Stage X velocity | 100 mm/s |
| Acquisition mode | FastFrame, Normal trigger | | Stage X acceleration | 1500 mm/s² |
| Stage X trigger out | Logic-high at max velocity (`TRIGOUT_MAXV`) |
| Acquisition mode | FastFrame, Normal trigger |
None of these are stored in the file, so they do not affect byte layout — but
they do set where the acoustic packet lands inside each frame. Read them from
`core/scope_sras.py`; earlier revisions of this table drifted from the code.
---
## Acquisition Paths
Two acquisition strategies write **byte-identical** files; the choice is a
runtime flag (`ScanEngine(burst_mode=…)`, exposed as a checkbox in the app) and
is not recorded in the file.
| | Per-row (default) | Burst |
|---|---|---|
| FastFrame acquisitions | one per row | one per `floor(max_frames / n_frames)` rows |
| Curve transfers | one per channel per row | one per channel per burst |
| Stage X trigger out | armed for the whole scan | armed per acquiring pass, dropped for the flyback |
Burst mode runs a single acquisition across several rows, so the return move
must not trigger: the trigger output is dropped before each flyback and
re-armed for each acquiring pass. Row boundaries inside the burst come from
`ACQuire:NUMFRAMESACQuired?` sampled after each pass — the burst itself carries
no row markers. See `core/scope_burst.py`.
### Row packing
The format has no per-row length field, so a row that over- or under-triggers
cannot be written as it arrived — that would shift every later row. Two
policies are selectable (`ScanEngine(strict_rows=…)`, a checkbox in the app),
and the choice is not recorded in the file:
| | Pad (default) | Strict |
|---|---|---|
| Short row | zero-padded to `n_frames`, warned | scan stops |
| Long row | trailing frames dropped, warned | scan stops |
Pad keeps a scan running through an occasional mis-trigger, at the cost that
the affected row is indistinguishable from a good one afterwards — nothing in
the file records that it was padded. Strict is for data runs where that
ambiguity is worse than a failed scan: it aborts before writing the row, so
the file always ends on a whole-row boundary.
---
## SAW Quality Check (v10)
A full multi-angle scan takes hours, and a rig whose angles disagree produces
all of them before anyone finds out. The SAW quality check acquires **one row
per angle — the row-wise middle of the ROI** — and writes it as a v10 file.
The cost is one row-time per angle instead of `n_rows` of them.
Nothing about the byte layout changes. A v10 file is a v6 file in which every
angle's Per-Angle Geometry Table entry declares `n_rows = 1`, and its Row Table
holds that angle's single middle Y position. Every v6 reader that works from
the geometry table (rather than assuming a uniform shape) reads a v10 file
unchanged.
The version byte earns its keep because the two are otherwise
indistinguishable: **a v6 scan aborted after its first row is not a check**,
even though both hold one row per angle. A reader that guessed from the row
count would treat a failed scan as a deliberate measurement.
Why the middle row in particular: `core/scan_geometry.py` 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 therefore
measure the same material, and a spread in their SAW frequencies is a property
of the rig — which is what makes it an alignment check. `saw_check_viewer.py`
plots every angle's frequency on one graph for exactly that comparison.
Writers must honour the one-row rule; `core.sras_format.create_scan_file`
refuses a v10 write for any plan that breaks it. Producing the plan is
`core.saw_check.middle_row_plan(plan)`, and `n_rows // 2` is the middle-row
rule (the upper of the two central rows when the count is even).
--- ---
@@ -208,4 +294,5 @@ using that angle's `x_start` from the Per-Angle Geometry Table (not
| 4 | Added background waveform block (CH1, Helios ON / Genesis OFF) after the preamble blocks; stored as `uint32` sample count followed by raw `int8` ADC bytes. | | 4 | Added background waveform block (CH1, Helios ON / Genesis OFF) after the preamble blocks; stored as `uint32` sample count followed by raw `int8` ADC bytes. |
| 5 | (skipped) | | 5 | (skipped) |
| 6 | Each angle now scans only the bounding box of the nominal ROI rotated by that angle instead of the AABB-expanded worst case across all angles. Header no longer carries a single global `x_start`/`x_delta`/`n_rows` — replaced with `*_nominal` reference fields plus a new Per-Angle Geometry Table (`x_start`, `x_delta`, `n_frames`, `n_rows` per angle) and a ragged Row Table / Waveform Data block sized per angle. **Not compatible with v4 readers** (e.g. `sras_viewer.py`, which has not yet been updated for v6). | | 6 | Each angle now scans only the bounding box of the nominal ROI rotated by that angle instead of the AABB-expanded worst case across all angles. Header no longer carries a single global `x_start`/`x_delta`/`n_rows` — replaced with `*_nominal` reference fields plus a new Per-Angle Geometry Table (`x_start`, `x_delta`, `n_frames`, `n_rows` per angle) and a ragged Row Table / Waveform Data block sized per angle. **Not compatible with v4 readers** (e.g. `sras_viewer.py`, which has not yet been updated for v6). |
| 7–9 | (skipped) |
| 10 | Middle-row SAW quality check. Byte layout identical to v6, with every angle declaring exactly one row — the row-wise middle of the ROI. A v6 reader that derives its shape from the Per-Angle Geometry Table reads these unchanged; the version byte exists so a check is not confused with a scan aborted after its first row. Written by the main app's *SAW Quality Check*, read by `saw_check_viewer.py`. |
scanning/__init__.py
-3
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@@ -1,3 +0,0 @@
"""Scan planning and modeling modules"""
from .sc3_scan_model import SC3ScanModel
from .stage_scan_plan_generator import *
scanning/sc3_scan_model.py
-638
View File
@@ -1,638 +0,0 @@
"""
Scan Model Class.
Holds the scan configuration, and computes the
required start and end points for various specified angles.
Python implementation of SC3ScanModel.cs
"""
import math
from decimal import Decimal, InvalidOperation
from typing import List, Optional
import csv
class SC3ScanModel:
"""
Scan Model for generating scan paths and rotated scans.
Manages scan configuration and computes scan coordinates at various angles.
"""
def __init__(self):
# Private variables
self._x_origin: Decimal = Decimal('0.0')
self._y_origin: Decimal = Decimal('0.0')
self._x_delta: Decimal = Decimal('0.0')
self._y_delta: Decimal = Decimal('0.0')
self._row_spacing: Decimal = Decimal('0.0')
self._laser_frequency: Decimal = Decimal('2000.0') # Default: 2000 Hz
self._scan_velocity: Decimal = Decimal('100.0') # Default: 100 mm/s
self._scan_acceleration: Decimal = Decimal('0.0')
self._scan_angles: int = 0
self._points_required: int = 0
self._rows_required: int = 0
self._points_per_line: int = 0
# Optical axis centerline in stage coordinates
# Stage: MLS203-1
self._optical_x_origin: Decimal = Decimal('55.0')
self._optical_y_origin: Decimal = Decimal('37.5')
# Data storage
self._scan_coordinates: List[List[Decimal]] = []
self._scan_velocities: List[List[Decimal]] = []
self._scan_accelerations: List[List[Decimal]] = []
self._rotated_coordinates: List[List[List[Decimal]]] = []
# Constants
self._deg2rad: float = math.pi / 180.0
# Properties
@property
def x_origin(self) -> Decimal:
"""X coordinate of scan origin (mm)"""
return self._x_origin
@x_origin.setter
def x_origin(self, value: Decimal):
try:
self._x_origin = Decimal(str(value))
except (ValueError, InvalidOperation) as e:
raise ValueError(f"Invalid x_origin value: {value}") from e
@property
def y_origin(self) -> Decimal:
"""Y coordinate of scan origin (mm)"""
return self._y_origin
@y_origin.setter
def y_origin(self, value: Decimal):
try:
self._y_origin = Decimal(str(value))
except (ValueError, InvalidOperation) as e:
raise ValueError(f"Invalid y_origin value: {value}") from e
@property
def x_delta(self) -> Decimal:
"""Total X distance to scan (mm)"""
return self._x_delta
@x_delta.setter
def x_delta(self, value: Decimal):
try:
val = Decimal(str(value))
if val < 0:
raise ValueError("x_delta must be non-negative")
self._x_delta = val
self.calculate_points_per_line()
self.calculate_points_required()
except (ValueError, InvalidOperation) as e:
raise ValueError(f"Invalid x_delta value: {value}") from e
@property
def y_delta(self) -> Decimal:
"""Total Y distance to scan (mm)"""
return self._y_delta
@y_delta.setter
def y_delta(self, value: Decimal):
try:
val = Decimal(str(value))
if val < 0:
raise ValueError("y_delta must be non-negative")
self._y_delta = val
self.calculate_rows_required()
self.calculate_points_required()
except (ValueError, InvalidOperation) as e:
raise ValueError(f"Invalid y_delta value: {value}") from e
@property
def row_spacing(self) -> Decimal:
"""Spacing between scan rows (mm)"""
return self._row_spacing
@row_spacing.setter
def row_spacing(self, value: Decimal):
try:
val = Decimal(str(value))
if val < 0:
raise ValueError("row_spacing must be non-negative")
self._row_spacing = val
self.calculate_rows_required()
self.calculate_points_required()
except (ValueError, InvalidOperation) as e:
raise ValueError(f"Invalid row_spacing value: {value}") from e
@property
def laser_frequency(self) -> Decimal:
"""Laser pulse frequency (Hz)"""
return self._laser_frequency
@laser_frequency.setter
def laser_frequency(self, value: Decimal):
try:
val = Decimal(str(value))
if val <= 0:
raise ValueError("laser_frequency must be positive")
self._laser_frequency = val
self.calculate_points_per_line()
self.calculate_points_required()
except (ValueError, InvalidOperation) as e:
raise ValueError(f"Invalid laser_frequency value: {value}") from e
@property
def scan_velocity(self) -> Decimal:
"""Scan velocity (mm/s)"""
return self._scan_velocity
@scan_velocity.setter
def scan_velocity(self, value: Decimal):
try:
val = Decimal(str(value))
if val <= 0:
raise ValueError("scan_velocity must be positive")
self._scan_velocity = val
self.calculate_points_per_line()
self.calculate_points_required()
except (ValueError, InvalidOperation) as e:
raise ValueError(f"Invalid scan_velocity value: {value}") from e
@property
def scan_acceleration(self) -> Decimal:
"""Scan acceleration (mm/s²)"""
return self._scan_acceleration
@scan_acceleration.setter
def scan_acceleration(self, value: Decimal):
try:
val = Decimal(str(value))
if val < 0:
raise ValueError("scan_acceleration must be non-negative")
self._scan_acceleration = val
except (ValueError, InvalidOperation) as e:
raise ValueError(f"Invalid scan_acceleration value: {value}") from e
@property
def scan_angles(self) -> int:
"""Number of scan angles to compute"""
return self._scan_angles
@scan_angles.setter
def scan_angles(self, value: int):
if value < 0:
raise ValueError("scan_angles must be non-negative")
self._scan_angles = value
# Only compute rotated scans if we have base scan coordinates
if self._scan_coordinates:
self.compute_rotated_scans()
@property
def points_required(self) -> int:
"""Total number of points required for a single angle scan (computed)"""
return self._points_required
@property
def rows_required(self) -> int:
"""Number of rows required for the scan (computed)"""
return self._rows_required
@property
def points_per_line(self) -> int:
"""Number of points per scan line (computed)"""
return self._points_per_line
@property
def scan_coordinates(self) -> List[List[Decimal]]:
"""List of scan coordinates [x_start, y_start, x_end, y_end] in mm"""
return self._scan_coordinates
@property
def scan_velocities(self) -> List[List[Decimal]]:
"""List of velocity vectors [vx, vy] in mm/s for each angle"""
return self._scan_velocities
@property
def scan_accelerations(self) -> List[List[Decimal]]:
"""List of acceleration vectors [ax, ay] in mm/s² for each angle"""
return self._scan_accelerations
@property
def rotated_coordinates(self) -> List[List[List[Decimal]]]:
"""List of rotated scan coordinates for each angle in mm"""
return self._rotated_coordinates
@property
def optical_x_origin(self) -> Decimal:
"""X coordinate of optical axis origin in mm (read-only, MLS203-1 stage)"""
return self._optical_x_origin
@property
def optical_y_origin(self) -> Decimal:
"""Y coordinate of optical axis origin in mm (read-only, MLS203-1 stage)"""
return self._optical_y_origin
# Calculation Methods
def calculate_points_per_line(self):
"""
Calculates the number of data points per scan line based on
x_delta, scan_velocity, and laser_frequency.
Formula: points = (distance / velocity) * frequency
"""
if self._scan_velocity != 0:
self._points_per_line = int(
(self._x_delta / self._scan_velocity) * self._laser_frequency
)
def calculate_points_required(self):
"""
Calculates the total number of data points for a complete single-angle scan.
Also triggers computation of the zero-angle scan coordinates.
Formula: total_points = points_per_line * rows_required
"""
if self._rows_required != 0:
self._points_required = self._points_per_line * self._rows_required
self.compute_zero_scan()
def calculate_rows_required(self):
"""
Calculates the number of scan rows needed based on y_delta and row_spacing.
Formula: rows = ceil(y_delta / row_spacing)
"""
if self._row_spacing == 0:
self._rows_required = 0
else:
self._rows_required = int(math.ceil(self._y_delta / self._row_spacing))
def compute_zero_scan(self):
"""
Computes the zero-angle (reference) scan coordinates.
Each coordinate is [x_start, y_start, x_end, y_end].
"""
# Ignore the zero-row case
if self._rows_required == 0:
return
y_offset = Decimal('0.0')
self._scan_coordinates.clear()
for row in range(self._rows_required + 1):
# Calculate x/y origin/delta for each needed row
y_offset = Decimal(row) * self._row_spacing
coords = [
self._x_origin, # x_start
self._y_origin + y_offset, # y_start
self._x_origin + self._x_delta, # x_end
self._y_origin + y_offset # y_end (same as y_start for horizontal scan)
]
self._scan_coordinates.append(coords)
def _rotate_point(self, x: Decimal, y: Decimal, cosine: Decimal, sine: Decimal) -> tuple:
"""
Rotate a point around the optical axis origin.
Args:
x, y: Point coordinates to rotate
cosine, sine: Precomputed cos and sin of rotation angle
Returns:
Tuple of (rotated_x, rotated_y)
"""
# Rotation transformation:
# Xr = (X - Xo)*cos(a) + (Y - Yo)*sin(a) + Xo
# Yr = -(X - Xo)*sin(a) + (Y - Yo)*cos(a) + Yo
x_rot = ((x - self._optical_x_origin) * cosine +
(y - self._optical_y_origin) * sine +
self._optical_x_origin)
y_rot = (-(x - self._optical_x_origin) * sine +
(y - self._optical_y_origin) * cosine +
self._optical_y_origin)
return (x_rot, y_rot)
def _compute_rotated_aoi_bbox(self, angle_rad: float) -> tuple:
"""
Compute the bounding box of the rotated area of interest.
Rotates the four corners of the AoI rectangle and finds the
min/max extents to create a bounding box.
Args:
angle_rad: Rotation angle in radians
Returns:
Tuple of (min_x, min_y, max_x, max_y) as Decimals
"""
cosine = Decimal(str(math.cos(angle_rad)))
sine = Decimal(str(math.sin(angle_rad)))
# Define the four corners of the AoI rectangle
corners = [
(self._x_origin, self._y_origin),
(self._x_origin + self._x_delta, self._y_origin),
(self._x_origin + self._x_delta, self._y_origin + self._y_delta),
(self._x_origin, self._y_origin + self._y_delta)
]
# Rotate all corners
rotated_corners = []
for x, y in corners:
x_rot, y_rot = self._rotate_point(x, y, cosine, sine)
rotated_corners.append((x_rot, y_rot))
# Find bounding box extents
x_coords = [corner[0] for corner in rotated_corners]
y_coords = [corner[1] for corner in rotated_corners]
return (min(x_coords), min(y_coords), max(x_coords), max(y_coords))
def compute_rotated_scans(self):
"""
Computes rotated scan coordinates by rotating the area of interest (AoI)
and generating horizontal (+x direction) scans through the bounding box
of the rotated AoI.
The rotation covers 0 to 180 degrees with spacing determined by scan_angles.
For each angle:
1. Rotate the AoI rectangle around the optical axis origin
2. Compute the bounding box of the rotated rectangle
3. Generate horizontal scan lines through the bounding box
"""
if self._rows_required == 0:
return
# Compute spacing between scans
if self._scan_angles == 0:
angle_spacing = 180
else:
angle_spacing = 180 / self._scan_angles
self._rotated_coordinates.clear()
# Iterate through each required angle from 0 to 180 degrees
i = 0
while i < 180:
current_angle_radians = i * (math.pi / 180.0)
# Get bounding box of rotated AoI
min_x, min_y, max_x, max_y = self._compute_rotated_aoi_bbox(current_angle_radians)
# Calculate the y extent of the bounding box
y_extent = max_y - min_y
# Determine number of rows needed for this bounding box
if self._row_spacing == 0:
num_rows = 0
else:
num_rows = int(math.ceil(y_extent / self._row_spacing))
temp_list = []
# Generate horizontal scan lines through the bounding box
for row in range(num_rows + 1):
y_offset = Decimal(row) * self._row_spacing
y_pos = min_y + y_offset
# Create horizontal scan line at this y position
scan_line = [
min_x, # x_start
y_pos, # y_start
max_x, # x_end
y_pos # y_end (same as y_start for horizontal scan)
]
temp_list.append(scan_line)
self._rotated_coordinates.append(temp_list)
i += int(round(angle_spacing))
def compute_kinematics(self, offset: int = 0):
"""
Computes velocity and acceleration component vectors for each scan angle.
For each angle, decomposes the scalar velocity and acceleration into
X and Y components based on the scan direction angle.
Args:
offset: Angle offset in degrees (default: 0)
"""
if self._scan_angles == 0:
scan_increment = 180
else:
scan_increment = 180 // self._scan_angles
self._scan_velocities.clear()
self._scan_accelerations.clear()
for i in range(self._scan_angles):
deg_angle = scan_increment * i + offset
angle_rad = deg_angle * self._deg2rad
# Compute velocity components: V = V_mag * [cos(θ), sin(θ)]
velocities = [
Decimal(str(math.cos(angle_rad))) * self._scan_velocity,
Decimal(str(math.sin(angle_rad))) * self._scan_velocity
]
# Compute acceleration components: A = A_mag * [cos(θ), sin(θ)]
accels = [
Decimal(str(math.cos(angle_rad))) * self._scan_acceleration,
Decimal(str(math.sin(angle_rad))) * self._scan_acceleration
]
self._scan_velocities.append(velocities)
self._scan_accelerations.append(accels)
# Export Methods
def export_zero_scan_csv(self, filename: Optional[str] = None) -> str:
"""
Export the zero-angle scan coordinates to a CSV file.
Args:
filename: Output filename. If None, generates from row count.
Returns:
The filename that was written
Raises:
ValueError: If no scan coordinates have been computed
IOError: If file cannot be written
"""
if not self._scan_coordinates:
raise ValueError("No scan coordinates available. Configure scan parameters first.")
if filename is None:
filename = f"scantest-{self._rows_required}rows.csv"
try:
with open(filename, 'w', newline='') as f:
writer = csv.writer(f)
for coords in self._scan_coordinates:
writer.writerow([str(c) for c in coords])
except IOError as e:
raise IOError(f"Failed to write file {filename}: {e}") from e
return filename
def export_rotated_scan_csv(self, angle_index: int, filename: Optional[str] = None) -> str:
"""
Export a specific rotated scan to CSV.
Args:
angle_index: Index of the angle to export (0-based)
filename: Output filename. If None, generates from angle and row count.
Returns:
The filename that was written
Raises:
ValueError: If angle_index is invalid or no rotated coordinates exist
IOError: If file cannot be written
"""
if not self._rotated_coordinates:
raise ValueError("No rotated coordinates available. Set scan_angles first.")
if angle_index < 0 or angle_index >= len(self._rotated_coordinates):
raise ValueError(
f"Invalid angle_index {angle_index}. Must be 0-{len(self._rotated_coordinates)-1}"
)
if filename is None:
angle_deg = angle_index * (180 // self._scan_angles if self._scan_angles > 0 else 180)
filename = f"scantest-{angle_deg:03d}deg-{self._rows_required}rows.csv"
try:
with open(filename, 'w', newline='') as f:
writer = csv.writer(f)
for coords in self._rotated_coordinates[angle_index]:
writer.writerow([str(c) for c in coords])
except IOError as e:
raise IOError(f"Failed to write file {filename}: {e}") from e
return filename
def export_all_rotated_scans_csv(self, output_dir: str = ".") -> List[str]:
"""
Export all rotated scans to separate CSV files.
Args:
output_dir: Directory to write files to (default: current directory)
Returns:
List of filenames that were written
Raises:
ValueError: If no rotated coordinates exist
IOError: If files cannot be written
"""
if not self._rotated_coordinates:
raise ValueError("No rotated coordinates available. Set scan_angles first.")
import os
filenames = []
for angle_index in range(len(self._rotated_coordinates)):
angle_deg = angle_index * (180 // self._scan_angles if self._scan_angles > 0 else 180)
filename = f"scantest-{angle_deg:03d}deg-{self._rows_required}rows.csv"
filepath = os.path.join(output_dir, filename)
try:
with open(filepath, 'w', newline='') as f:
writer = csv.writer(f)
for coords in self._rotated_coordinates[angle_index]:
writer.writerow([str(c) for c in coords])
filenames.append(filepath)
except IOError as e:
raise IOError(f"Failed to write file {filepath}: {e}") from e
return filenames
def export_kinematics_csv(self, filename: Optional[str] = None) -> str:
"""
Export velocity and acceleration data to CSV.
Format: vx, vy, ax, ay for each angle.
Args:
filename: Output filename. If None, generates from row count.
Returns:
The filename that was written
Raises:
ValueError: If no kinematics data has been computed
IOError: If file cannot be written
"""
if not self._scan_velocities or not self._scan_accelerations:
raise ValueError("No kinematics data available. Call compute_kinematics() first.")
if filename is None:
filename = f"kinematics-{self._rows_required}rows.csv"
try:
with open(filename, 'w', newline='') as f:
writer = csv.writer(f)
# Optional: write header
writer.writerow(['vx', 'vy', 'ax', 'ay'])
for i in range(len(self._scan_velocities)):
row = [
str(self._scan_velocities[i][0]),
str(self._scan_velocities[i][1]),
str(self._scan_accelerations[i][0]),
str(self._scan_accelerations[i][1])
]
writer.writerow(row)
except IOError as e:
raise IOError(f"Failed to write file {filename}: {e}") from e
return filename
# Utility Methods
def get_angle_list(self) -> List[int]:
"""
Get the list of scan angles in degrees.
Returns:
List of angles in degrees for the configured scan_angles
"""
if self._scan_angles == 0:
return []
scan_increment = 180 // self._scan_angles
return [scan_increment * i for i in range(self._scan_angles)]
def get_scan_info(self) -> dict:
"""
Get a dictionary with current scan configuration and computed values.
Returns:
Dictionary containing scan parameters and computed values
"""
return {
'x_origin': float(self._x_origin),
'y_origin': float(self._y_origin),
'x_delta': float(self._x_delta),
'y_delta': float(self._y_delta),
'row_spacing': float(self._row_spacing),
'laser_frequency': float(self._laser_frequency),
'scan_velocity': float(self._scan_velocity),
'scan_acceleration': float(self._scan_acceleration),
'scan_angles': self._scan_angles,
'points_per_line': self._points_per_line,
'rows_required': self._rows_required,
'points_required': self._points_required,
'optical_x_origin': float(self._optical_x_origin),
'optical_y_origin': float(self._optical_y_origin),
'num_scan_coordinates': len(self._scan_coordinates),
'num_rotated_angles': len(self._rotated_coordinates),
'angle_list': self.get_angle_list(),
}
def __repr__(self) -> str:
"""String representation of the scan model."""
return (
f"SC3ScanModel("
f"origin=({self._x_origin},{self._y_origin}), "
f"delta=({self._x_delta},{self._y_delta}), "
f"rows={self._rows_required}, "
f"angles={self._scan_angles})"
)
scanning/stage_scan_plan_generator.py
-117
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@@ -1,117 +0,0 @@
"""
This module contains a StageScanPlanGenerator class that generates scanning plans
for microscope stages. The scans are generated in a single direction based on provided
start and end coordinates, as well as spacing between scan lines.
"""
import numpy as np
from typing import List, Tuple, Optional
class StageScanPlanGenerator:
"""
A class to generate scanning plans for microscope stages.
Attributes:
start_coords (Tuple[float, float]): Starting X and Y coordinates.
end_coords (Tuple[float, float]): Ending X and Y coordinates.
spacing (float): Spacing between scan lines in the perpendicular direction.
"""
def __init__(self, start_x: float, start_y: float,
end_x: float, end_y: float, spacing: float):
"""
Initialize the StageScanPlanGenerator with scan parameters.
Args:
start_x (float): Starting X coordinate.
start_y (float): Starting Y coordinate.
end_x (float): Ending X coordinate.
end_y (float): Ending Y coordinate.
spacing (float): Spacing between scan lines in the perpendicular direction.
"""
self.start_coords = (start_x, start_y)
self.end_coords = (end_x, end_y)
self.spacing = spacing
def _calculate_scan_direction(self) -> Tuple[float, float]:
"""
Calculate the direction vector of the scan.
Returns:
Tuple[float, float]: Normalized direction vector (dx, dy).
"""
dx = self.end_coords[0] - self.start_coords[0]
dy = self.end_coords[1] - self.start_coords[1]
length = np.sqrt(dx**2 + dy**2)
if length == 0:
raise ValueError("Start and end coordinates cannot be the same")
return dx / length, dy / length
def _calculate_perpendicular_direction(self) -> Tuple[float, float]:
"""
Calculate a perpendicular direction vector to the scan direction.
Returns:
Tuple[float, float]: Perpendicular vector (px, py).
"""
dx, dy = self._calculate_scan_direction()
# Rotate (dx, dy) by 90 degrees to get perpendicular vector
px = -dy
py = dx
return px, py
def generate_scan_plan(self) -> List[Tuple[Tuple[float, float], Tuple[float, float]]]:
"""
Generate a scan plan with waypoints for the microscope stage.
Returns:
List[Tuple[Tuple[float, float], Tuple[float, float]]]:
A list of (start_point, end_point) tuples for each scan line.
"""
dx, dy = self._calculate_scan_direction()
px, py = self._calculate_perpendicular_direction()
# Calculate the total length in the perpendicular direction
start_x, start_y = self.start_coords
end_x, end_y = self.end_coords
min_coord_perp = min(start_x * px + start_y * py, end_x * px + end_y * py)
max_coord_perp = max(start_x * px + start_y * py, end_x * px + end_y * py)
# Generate scan lines
waypoints = []
current_pos_perp = min_coord_perp
while current_pos_perp <= max_coord_perp:
# Calculate start and end points for this scan line
perp_offset = current_pos_perp - (start_x * px + start_y * py)
line_start_x = start_x + perp_offset * dx
line_start_y = start_y + perp_offset * dy
line_end_x = line_start_x + dx * abs(self.end_coords[0] - self.start_coords[0])
line_end_y = line_start_y + dy * abs(self.end_coords[1] - self.start_coords[1])
waypoints.append(((line_start_x, line_start_y), (line_end_x, line_end_y)))
current_pos_perp += self.spacing
return waypoints
# Example usage:
if __name__ == "__main__":
# Create a scan plan generator
generator = StageScanPlanGenerator(
start_x=0.0, start_y=0.0,
end_x=10.0, end_y=10.0,
spacing=2.5
)
# Generate the scan plan
scan_plan = generator.generate_scan_plan()
# Print the scan plan
print("Scan Plan:")
for i, (start, end) in enumerate(scan_plan):
print(f"Line {i+1}: Start at {start}, End at {end}")
sras_scan_manager.py
+43 -99
View File
@@ -9,25 +9,24 @@ n_rows) and waveform data block. This tool lists those per-angle sub-scans
and lets you export a subset to a new .sras file, or delete a subset from and lets you export a subset to a new .sras file, or delete a subset from
the file in place — both operations rewrite the angle/geometry/row tables the file in place — both operations rewrite the angle/geometry/row tables
and stream-copy only the selected angles' waveform data, producing a file and stream-copy only the selected angles' waveform data, producing a file
that is itself a valid v6 .sras readable by sras_viewer.py-style tools that is itself a valid .sras readable by sras_viewer.py-style tools
(once updated for v6) or sc3_aui_app.py. (once updated for v6) or sc3_aui_app.py.
Only format version 6 is supported. Format versions 6 (full scan) and 10 (middle-row SAW check) are supported.
A subset keeps the version of the file it came from — a v10 check exports as
a v10 check, since dropping angles from one leaves it one row per angle.
""" """
import argparse import argparse
import struct import struct
import sys import sys
from dataclasses import dataclass, field from dataclasses import dataclass
from datetime import datetime from datetime import datetime
from pathlib import Path from pathlib import Path
BLOB_MAGIC = b"SRAS" sys.path.insert(0, str(Path(__file__).resolve().parent))
BLOB_VERSION = 6
HDR_FMT = ">4sBHfffffffIdBB" from core.sras_format import GEOM_FMT, HDR_FMT, MAGIC, VERSION_SAW_CHECK, SrasFile
HDR_SIZE = struct.calcsize(HDR_FMT) # 49 bytes
GEOM_FMT = ">ffIH"
GEOM_SIZE = struct.calcsize(GEOM_FMT) # 14 bytes
@dataclass @dataclass
@@ -51,101 +50,45 @@ class AngleEntry:
class SrasScanFile: class SrasScanFile:
"""Parsed view of a v6 .sras file's header/tables plus per-angle data offsets.""" """Parsed view of a .sras file's header/tables plus per-angle data offsets."""
def __init__(self, path: Path): def __init__(self, path: Path):
self.path = Path(path) self.path = Path(path)
self._parse() self._parse()
def _parse(self): def _parse(self):
file_size = self.path.stat().st_size sras = SrasFile(self.path)
with open(self.path, "rb") as f: h = sras.header
raw = f.read(HDR_SIZE) self.version = sras.version
if len(raw) < HDR_SIZE: self.x_start_nominal = h.x_start_nominal
raise ValueError(f"{self.path.name}: file too short for a valid header") self.y_start_nominal = h.y_start_nominal
(magic, version, n_angles, x_start_nom, y_start_nom, x_delta_nom, self.x_delta_nominal = h.x_delta_nominal
y_delta_nom, row_spacing, velocity, laser_freq, samples_per_frame, self.y_delta_nominal = h.y_delta_nominal
sample_rate, bytes_per_sample, n_channels) = struct.unpack(HDR_FMT, raw) self.row_spacing_mm = h.row_spacing
self.velocity_mm_s = h.velocity
self.laser_freq_hz = h.laser_freq
self.samples_per_frame = h.samples_per_frame
self.sample_rate_hz = h.sample_rate
self.bytes_per_sample = h.bytes_per_sample
self.n_channels = h.n_channels
self.preambles_raw = sras.preambles_raw
self.background_raw = sras.background
self.data_start_offset = sras.data_start_offset
self.file_size = sras.file_size
if magic != BLOB_MAGIC: self.angles = [
raise ValueError(f"{self.path.name}: bad magic {magic!r}, not a .sras file") AngleEntry(
if version != BLOB_VERSION: index=st.index, angle_deg=st.angle_deg,
raise ValueError( x_start=pa.x_start, x_delta=pa.x_delta,
f"{self.path.name}: unsupported format version {version} " n_frames=pa.n_frames, n_rows_declared=pa.n_rows,
f"(this tool only supports v{BLOB_VERSION})") y_positions=pa.y_positions, row_bytes=st.row_bytes,
data_offset=st.data_offset,
self.x_start_nominal = x_start_nom n_rows_available=st.n_rows_available,
self.y_start_nominal = y_start_nom data_size_available=st.n_rows_available * st.row_bytes,
self.x_delta_nominal = x_delta_nom complete=st.complete,
self.y_delta_nominal = y_delta_nom
self.row_spacing_mm = row_spacing
self.velocity_mm_s = velocity
self.laser_freq_hz = laser_freq
self.samples_per_frame = samples_per_frame
self.sample_rate_hz = sample_rate
self.bytes_per_sample = bytes_per_sample
self.n_channels = n_channels
angles = list(struct.unpack(f">{n_angles}f", f.read(4 * n_angles)))
geoms = []
for _ in range(n_angles):
x_start, x_delta, n_frames, n_rows = struct.unpack(GEOM_FMT, f.read(GEOM_SIZE))
geoms.append((x_start, x_delta, n_frames, n_rows))
row_tables = []
for (_, _, _, n_rows) in geoms:
row_tables.append(list(struct.unpack(f">{n_rows}f", f.read(4 * n_rows))))
preambles_raw = []
for _ in range(n_channels):
(plen,) = struct.unpack(">H", f.read(2))
preambles_raw.append(f.read(plen))
self.preambles_raw = preambles_raw
(n_bg,) = struct.unpack(">I", f.read(4))
self.background_raw = f.read(n_bg)
data_start_offset = f.tell()
# Build angle entries and compute what's actually present on disk,
# in case the file was closed early (aborted scan) — see scan_format.md's
# "Incomplete files" note. Waveform data is angle-major/row-minor with a
# fixed per-row byte count within an angle, so we walk cumulative offsets.
self.angles = []
cursor = data_start_offset
truncated_seen = False
for i, (angle, (x_start, x_delta, n_frames, n_rows)) in enumerate(zip(angles, geoms)):
row_bytes = n_channels * n_frames * samples_per_frame * bytes_per_sample
entry = AngleEntry(
index=i, angle_deg=angle, x_start=x_start, x_delta=x_delta,
n_frames=n_frames, n_rows_declared=n_rows,
y_positions=row_tables[i], row_bytes=row_bytes,
data_offset=cursor,
) )
if truncated_seen: for pa, st in zip(sras.per_angle, sras.angle_status(), strict=True)
entry.n_rows_available = 0 ]
entry.data_size_available = 0
entry.complete = False
else:
declared_bytes = row_bytes * n_rows
if row_bytes > 0 and cursor + declared_bytes <= file_size:
entry.n_rows_available = n_rows
entry.data_size_available = declared_bytes
entry.complete = True
cursor += declared_bytes
else:
remaining = max(0, file_size - cursor)
n_complete = remaining // row_bytes if row_bytes > 0 else 0
entry.n_rows_available = n_complete
entry.data_size_available = n_complete * row_bytes
entry.complete = (n_complete == n_rows)
cursor += entry.data_size_available
truncated_seen = True
self.angles.append(entry)
self.data_start_offset = data_start_offset
self.file_size = file_size
def get(self, index: int) -> AngleEntry: def get(self, index: int) -> AngleEntry:
return self.angles[index] return self.angles[index]
@@ -156,7 +99,7 @@ class SrasScanFile:
# --------------------------------------------------------------------------- # ---------------------------------------------------------------------------
def _write_subset(sf: SrasScanFile, indices: list, dst_path: Path) -> list: def _write_subset(sf: SrasScanFile, indices: list, dst_path: Path) -> list:
"""Write a new v6 .sras file containing only the given angle indices """Write a new .sras file containing only the given angle indices
(in the given order). Returns a list of warning strings (e.g. for (in the given order). Returns a list of warning strings (e.g. for
angles that were truncated on disk and thus exported with fewer rows angles that were truncated on disk and thus exported with fewer rows
than declared). than declared).
@@ -165,7 +108,7 @@ def _write_subset(sf: SrasScanFile, indices: list, dst_path: Path) -> list:
selected = [sf.get(i) for i in indices] selected = [sf.get(i) for i in indices]
header = struct.pack( header = struct.pack(
HDR_FMT, BLOB_MAGIC, BLOB_VERSION, len(selected), HDR_FMT, MAGIC, sf.version, len(selected),
sf.x_start_nominal, sf.y_start_nominal, sf.x_start_nominal, sf.y_start_nominal,
sf.x_delta_nominal, sf.y_delta_nominal, sf.x_delta_nominal, sf.y_delta_nominal,
sf.row_spacing_mm, sf.velocity_mm_s, sf.laser_freq_hz, sf.row_spacing_mm, sf.velocity_mm_s, sf.laser_freq_hz,
@@ -281,7 +224,8 @@ def parse_index_spec(spec: str, max_index: int) -> list:
def print_summary(sf: SrasScanFile, selected: set): def print_summary(sf: SrasScanFile, selected: set):
print() print()
print(f"File: {sf.path} (v{BLOB_VERSION}, {_human_size(sf.file_size)})") kind = " SAW check" if sf.version == VERSION_SAW_CHECK else ""
print(f"File: {sf.path} (v{sf.version}{kind}, {_human_size(sf.file_size)})")
print(f"Nominal ROI: x_start={sf.x_start_nominal:.4f} x_delta={sf.x_delta_nominal:.4f} " print(f"Nominal ROI: x_start={sf.x_start_nominal:.4f} x_delta={sf.x_delta_nominal:.4f} "
f"y_start={sf.y_start_nominal:.4f} y_delta={sf.y_delta_nominal:.4f} mm " f"y_start={sf.y_start_nominal:.4f} y_delta={sf.y_delta_nominal:.4f} mm "
f"row_spacing={sf.row_spacing_mm:.4f} mm") f"row_spacing={sf.row_spacing_mm:.4f} mm")
sras_viewer.py
+513 -938
View File
File diff suppressed because it is too large Load Diff
sras_viewer_requirements.txt
+1
View File
@@ -1,3 +1,4 @@
PyQt6==6.10.2 PyQt6==6.10.2
numpy==2.4.1 numpy==2.4.1
matplotlib==3.10.8 matplotlib==3.10.8
scipy==1.16.3
t3r_control_panel.py
+14 -21
View File
@@ -19,7 +19,7 @@ Usage::
from __future__ import annotations from __future__ import annotations
from PyQt6.QtCore import Qt, QTimer from PyQt6.QtCore import Qt
from PyQt6.QtGui import QFont from PyQt6.QtGui import QFont
from PyQt6.QtWidgets import ( from PyQt6.QtWidgets import (
QCheckBox, QComboBox, QDialog, QDoubleSpinBox, QFrame, QGridLayout, QCheckBox, QComboBox, QDialog, QDoubleSpinBox, QFrame, QGridLayout,
@@ -27,9 +27,10 @@ from PyQt6.QtWidgets import (
QSpinBox, QSplitter, QVBoxLayout, QWidget, QSpinBox, QSplitter, QVBoxLayout, QWidget,
) )
from hardware.t3r_driver import T3RDriver from gui.qt_t3r import QtT3RAdapter
from hardware.serial_util import scored_ports
from hardware.t3r_driver import T3RDriver # class constants (gear train, channel names)
import hardware.t3r_protocol as proto import hardware.t3r_protocol as proto
import serial.tools.list_ports
# ── Utilities ───────────────────────────────────────────────────────────────── # ── Utilities ─────────────────────────────────────────────────────────────────
@@ -62,7 +63,7 @@ def _spin(lo: int, hi: int, val: int) -> QSpinBox:
class ChannelPanel(QGroupBox): class ChannelPanel(QGroupBox):
"""Controls and live readouts for one T3R axis.""" """Controls and live readouts for one T3R axis."""
def __init__(self, ch: int, driver: T3RDriver): def __init__(self, ch: int, driver: QtT3RAdapter):
label = f"Axis {ch} — {T3RDriver.CHANNEL_NAMES[ch]}" label = f"Axis {ch} — {T3RDriver.CHANNEL_NAMES[ch]}"
super().__init__(label) super().__init__(label)
self.ch = ch self.ch = ch
@@ -278,7 +279,7 @@ class ChannelPanel(QGroupBox):
class GroupPanel(QGroupBox): class GroupPanel(QGroupBox):
"""Ganged motion — selected axes step in lockstep.""" """Ganged motion — selected axes step in lockstep."""
def __init__(self, driver: T3RDriver, log_fn): def __init__(self, driver: QtT3RAdapter, log_fn):
super().__init__("Ganged / synchronised motion — selected axes move in lockstep") super().__init__("Ganged / synchronised motion — selected axes move in lockstep")
self._driver = driver self._driver = driver
self._log = log_fn self._log = log_fn
@@ -389,7 +390,7 @@ class RotationPanel(QGroupBox):
Ratio = 125/10 = 12.5 Ratio = 125/10 = 12.5
""" """
def __init__(self, driver: T3RDriver): def __init__(self, driver: QtT3RAdapter):
super().__init__( super().__init__(
f"Stage Rotation (GR-axis ch{T3RDriver.GR_AXIS_CH}) — " f"Stage Rotation (GR-axis ch{T3RDriver.GR_AXIS_CH}) — "
f"gear: {T3RDriver.GEAR_TEETH_MOTOR}T motor → 30T idler → " f"gear: {T3RDriver.GEAR_TEETH_MOTOR}T motor → 30T idler → "
@@ -481,12 +482,12 @@ class RotationPanel(QGroupBox):
class T3RControlPanel(QDialog): class T3RControlPanel(QDialog):
"""User-hidable T3R control window. """User-hidable T3R control window.
Pass a T3RDriver instance. The panel connects to its signals and forwards Pass a QtT3RAdapter instance. The panel connects to its signals and forwards
commands via its API. Connection management (port open/close) is handled commands via its API. Connection management (port open/close) is handled
inside the panel itself. inside the panel itself.
""" """
def __init__(self, driver: T3RDriver, parent=None): def __init__(self, driver: QtT3RAdapter, parent=None):
super().__init__(parent) super().__init__(parent)
self.setWindowTitle("T3R Stepper Controller") self.setWindowTitle("T3R Stepper Controller")
self.setWindowFlags( self.setWindowFlags(
@@ -613,16 +614,8 @@ class T3RControlPanel(QDialog):
def _refresh_ports(self): def _refresh_ports(self):
current = self.port_combo.currentText() current = self.port_combo.currentText()
self.port_combo.clear() self.port_combo.clear()
ports = list(serial.tools.list_ports.comports()) for device, label in scored_ports():
self.port_combo.addItem(label, device)
def score(p):
text = f"{p.description} {p.manufacturer or ''} {p.product or ''}".lower()
hints = ("esp32", "jtag", "espressif", "usb serial", "cp210", "ch340", "cdc")
return -sum(h in text for h in hints)
ports.sort(key=score)
for p in ports:
self.port_combo.addItem(f"{p.device} — {p.description or p.device}", p.device)
if self.port_combo.count() == 0: if self.port_combo.count() == 0:
self.port_combo.addItem("(no serial ports found)", None) self.port_combo.addItem("(no serial ports found)", None)
elif current: elif current:
@@ -632,14 +625,14 @@ class T3RControlPanel(QDialog):
def _toggle_connect(self): def _toggle_connect(self):
if self._driver.is_open: if self._driver.is_open:
self._driver.disconnect() self._driver.close()
return return
port = self.port_combo.currentData() port = self.port_combo.currentData()
if not port: if not port:
self._log("No serial port selected", "err") self._log("No serial port selected", "err")
return return
try: try:
self._driver.connect(port) self._driver.open(port)
except Exception as exc: except Exception as exc:
self._log(f"Connect failed: {exc}", "err") self._log(f"Connect failed: {exc}", "err")
self.conn_lbl.setText("connect failed") self.conn_lbl.setText("connect failed")
@@ -650,7 +643,7 @@ class T3RControlPanel(QDialog):
self.conn_lbl.setText("opening…") self.conn_lbl.setText("opening…")
self.connect_btn.setText("Disconnect") self.connect_btn.setText("Disconnect")
self.port_combo.setEnabled(False) self.port_combo.setEnabled(False)
self._log(f"Port opened, sending PING…", "evt") self._log("Port opened, sending PING…", "evt")
def _on_handshake_ok(self, proto_ver: int, fw_ver: int, num_ch: int): def _on_handshake_ok(self, proto_ver: int, fw_ver: int, num_ch: int):
self.conn_lbl.setText("connected") self.conn_lbl.setText("connected")
tests/conftest.py
+41
View File
@@ -0,0 +1,41 @@
"""Shared test setup: repo-root imports, headless Qt, pyueye stub.
The IDS uEye SDK (pyueye + libueye) only exists on the Linux rig. On any
other machine we stub the module before hardware.uc480_camera is imported;
everything in uc480_camera references `ueye.*` at call time, not import
time, so an attribute-permissive dummy is sufficient for constructing
windows and importing modules.
"""
import os
import sys
import types
from pathlib import Path
ROOT = Path(__file__).resolve().parent.parent
if str(ROOT) not in sys.path:
sys.path.insert(0, str(ROOT))
os.environ.setdefault("QT_QPA_PLATFORM", "offscreen")
try:
import pyueye # noqa: F401
except ImportError:
class _UeyeStub:
"""Permissive attribute sink standing in for pyueye.ueye."""
IS_SUCCESS = 0
def __getattr__(self, name):
return _UeyeStub()
def __call__(self, *args, **kwargs):
return _UeyeStub()
def __or__(self, other):
return 0
def __ror__(self, other):
return 0
_pyueye = types.ModuleType("pyueye")
_pyueye.ueye = _UeyeStub()
sys.modules["pyueye"] = _pyueye
tests/fakes.py
+268
View File
@@ -0,0 +1,268 @@
"""Recording fake hardware for headless ScanEngine tests.
Each fake records an ordered call trace, so a test can assert the exact
command sequence the engine issues — the property that matters when the
real rig isn't available.
The stage and scope are wired together the way the rig is: an X move at scan
velocity with the trigger gate armed feeds frames into a running acquisition,
at the real 20 kHz / 100 mm/s rate. Per-row and burst acquisition therefore
get their frame counts from the same model, which is what makes a
byte-identity comparison between the two paths meaningful — and it means a
gate the engine forgets to drop shows up as extra frames instead of passing
silently.
"""
from __future__ import annotations
from core.scan_engine import (
AXIS_X, LASER_FREQ_HZ, SCAN_RAMP_BUFFER_MM, SCAN_RAMP_MM,
SCAN_VELOCITY_MM_S,
)
RAMP_TOTAL_MM = SCAN_RAMP_MM + SCAN_RAMP_BUFFER_MM
class Trace:
"""Ordered record of hardware calls, shared by all fakes in one test."""
def __init__(self):
self.calls: list[tuple] = []
def record(self, *entry):
self.calls.append(entry)
def names(self) -> list[str]:
return [c[0] for c in self.calls]
def of(self, name: str) -> list[tuple]:
return [c for c in self.calls if c[0] == name]
def count(self, name: str) -> int:
return len(self.of(name))
class FakeStage:
"""Stands in for ThorlabsServoDriver."""
def __init__(self, trace: Trace, homed=(True, True), enabled=(True, True),
scope=None):
self._t = trace
self.am_homed = list(homed)
self.am_enabled = list(enabled)
self.positions = [0.0, 0.0]
self._scope = scope
self.gate_armed = False
def attach_scope(self, scope):
"""Route gated motion into `scope`, as the TRIGOUT pin does on the rig."""
self._scope = scope
def enable_axis(self, axis):
self._t.record("enable_axis", axis)
self.am_enabled[0 if axis == AXIS_X else 1] = True
def home_axis(self, axis, timeout=0.0):
self._t.record("home_axis", axis)
self.am_homed[0 if axis == AXIS_X else 1] = True
def set_velocity_params(self, axis, max_velocity=None, acceleration=None):
self._t.record("set_velocity_params", axis, max_velocity, acceleration)
def set_trigger_trigout_maxv(self, axis):
self._t.record("set_trigger_trigout_maxv", axis)
if axis == AXIS_X:
self.gate_armed = True
def set_trigger_gate_off(self, axis):
self._t.record("set_trigger_gate_off", axis)
if axis == AXIS_X:
self.gate_armed = False
def arm_scan_gate(self, axis, armed, verify=True):
self._t.record("arm_scan_gate", axis, bool(armed))
if axis == AXIS_X:
self.gate_armed = bool(armed)
def move_axis_absolute(self, axis, pos, timeout=0.0):
idx = 0 if axis == AXIS_X else 1
prev = self.positions[idx]
self._t.record("move_axis_absolute", axis, round(pos, 6))
self.positions[idx] = pos
# The gate is high only at max velocity, i.e. over the move minus its
# two ramps — direction-agnostic, so a flyback the engine failed to
# gate off produces frames instead of quietly producing none.
if axis == AXIS_X and self.gate_armed and self._scope is not None:
at_speed_mm = abs(pos - prev) - 2 * RAMP_TOTAL_MM
if at_speed_mm > 0:
self._scope.acquire_frames(
round(at_speed_mm * LASER_FREQ_HZ / SCAN_VELOCITY_MM_S))
class FakeScope:
"""Stands in for TektronixOscilloscopeBase.
Returns deterministic frame bytes so the written file can be compared
against an expected byte pattern.
"""
def __init__(self, trace: Trace, samples_per_frame=8, max_frames=4096):
self._t = trace
self.samples_per_frame = samples_per_frame
self.max_frames = max_frames
self._acq_polls = 0
self._running = False
self._acquired = 0
# Per-channel running frame index. Frame content is a function of
# (channel, index) alone, so the same total frame sequence yields the
# same bytes however it is chopped into transfers.
self._next_frame: dict[int, int] = {}
# -- driven by FakeStage ------------------------------------------------
def acquire_frames(self, n):
if self._running:
self._acquired += n
# -- writes / queries ---------------------------------------------------
def write(self, cmd):
self._t.record("write", cmd)
if cmd == "ACQuire:STATE RUN":
self._running = True
self._acquired = 0
elif cmd == "ACQuire:STATE STOP":
self._running = False
def query(self, cmd):
self._t.record("query", cmd)
if cmd == "ACQuire:STATE?":
self._acq_polls += 1
# STOPAfter SEQuence self-stops when the sequence completes, so
# reporting "stopped" and staying armed would be inconsistent.
self._running = False
return "0" # background average finished
if cmd == "ACQuire:NUMFRAMESACQuired?":
return str(self._acquired)
return ""
# -- typed setters used by core.scope_sras ------------------------------
def set_trigger_source(self, ch):
self._t.record("set_trigger_source", ch)
def set_trigger_slope(self, slope):
self._t.record("set_trigger_slope", slope)
def set_trigger_level(self, ch, level):
self._t.record("set_trigger_level", ch, level)
def set_trigger_mode(self, mode):
self._t.record("set_trigger_mode", mode)
def set_acquire_mode(self, mode):
self._t.record("set_acquire_mode", mode)
def set_fastframe_state(self, on):
self._t.record("set_fastframe_state", on)
def set_fastframe_count(self, n):
self._t.record("set_fastframe_count", n)
def get_fastframe_state(self):
return 1
def get_fastframe_max_frames(self):
self._t.record("get_fastframe_max_frames")
return self.max_frames
def set_sample_rate(self, sr):
self._t.record("set_sample_rate", sr)
def get_record_length(self):
return self.samples_per_frame
def set_data_source(self, ch):
self._t.record("set_data_source", ch)
self._source = ch
def set_data_encoding(self, encoding):
self._t.record("set_data_encoding", encoding)
def set_data_width(self, width):
self._t.record("set_data_width", width)
def query_wfmoutpre(self):
return f"WFMOUTPRE:CH{self._source};YMULT 1.5625E-3;YOFF -87.04;YZERO 0.0"
def transfer_curve(self):
self._t.record("transfer_curve")
return bytes(range(self.samples_per_frame))
def _frames(self, ch, count):
spf = self.samples_per_frame
start = self._next_frame.get(ch, 0)
self._next_frame[ch] = start + count
return [bytes((ch * 31 + g + s) % 256 for s in range(spf))
for g in range(start, start + count)]
def transfer_fastframe(self, parse=True, byte_count=1, signed=True,
byte_order='MSB'):
self._t.record("transfer_fastframe", self._source)
return self._frames(self._source, self._acquired)
def transfer_fastframe_bulk(self, frame_count, samples_per_frame,
bytes_per_sample=1):
self._t.record("transfer_fastframe_bulk", self._source, frame_count)
return bytearray(b"".join(self._frames(self._source, frame_count)))
# channel config (only used by configure_channels)
def set_channel_label_name(self, ch, name):
self._t.record("set_channel_label_name", ch, name)
def set_channel_scale(self, ch, v):
self._t.record("set_channel_scale", ch, v)
def set_channel_position(self, ch, v):
self._t.record("set_channel_position", ch, v)
def set_channel_termination(self, ch, v):
self._t.record("set_channel_termination", ch, v)
def set_channel_coupling(self, ch, v):
self._t.record("set_channel_coupling", ch, v)
def set_channel_bandwidth(self, ch, v):
self._t.record("set_channel_bandwidth", ch, v)
class FakeT3R:
"""Stands in for the (Qt-free) T3RDriver, for RotationAxis."""
GR_AXIS_CH = 3
MOTOR_FULL_STEPS_PER_REV = 200
GEAR_TEETH_MOTOR = 10
GEAR_TEETH_STAGE = 125
def __init__(self, trace: Trace, is_open=True, motion_completes=True):
self._t = trace
self.is_open = is_open
self._motion_completes = motion_completes
def set_microstep(self, ch, micro):
self._t.record("t3r_set_microstep", ch, micro)
def set_current(self, ch, run_ma, hold_ma, ihold):
self._t.record("t3r_set_current", ch, run_ma, hold_ma, ihold)
def enable(self, ch):
self._t.record("t3r_enable", ch)
def steps_for_angle(self, angle_deg, microsteps):
ratio = self.GEAR_TEETH_STAGE / self.GEAR_TEETH_MOTOR
return round(self.MOTOR_FULL_STEPS_PER_REV * microsteps * ratio
* angle_deg / 360.0)
def rotate_stage(self, angle_deg, microsteps, velocity, accel):
self._t.record("t3r_rotate", round(angle_deg, 6))
def wait_motion_done(self, ch, timeout):
self._t.record("t3r_wait_motion_done", ch)
return self._motion_completes
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{
"header": {
"version": 6,
"n_angles": 2,
"x_start_nominal": 1.0,
"y_start_nominal": 1.0,
"x_delta_nominal": 0.019999999552965164,
"y_delta_nominal": 0.019999999552965164,
"row_spacing": 0.009999999776482582,
"velocity": 100.0,
"laser_freq": 20000.0,
"samples_per_frame": 8,
"sample_rate": 6250000000.0,
"bytes_per_sample": 1,
"n_channels": 3,
"angles": [
0.0,
-180.0
],
"per_angle": [
{
"angle": 0.0,
"x_start": 1.0,
"x_delta": 0.019999999552965164,
"n_frames": 4,
"n_rows": 3,
"y_positions": [
1.0,
1.0099999904632568,
1.0199999809265137
]
},
{
"angle": -180.0,
"x_start": 1.0,
"x_delta": 0.019999999552965164,
"n_frames": 4,
"n_rows": 3,
"y_positions": [
1.0,
1.0099999904632568,
1.0199999809265137
]
}
],
"data_start_offset": 265
},
"statuses": {
"complete.sras": [
{
"index": 0,
"angle_deg": 0.0,
"n_rows": 3,
"row_bytes": 96,
"data_offset": 265,
"n_rows_available": 3,
"status": "OK"
},
{
"index": 1,
"angle_deg": -180.0,
"n_rows": 3,
"row_bytes": 96,
"data_offset": 553,
"n_rows_available": 3,
"status": "OK"
}
],
"trunc_midrow_a1.sras": [
{
"index": 0,
"angle_deg": 0.0,
"n_rows": 3,
"row_bytes": 96,
"data_offset": 265,
"n_rows_available": 3,
"status": "OK"
},
{
"index": 1,
"angle_deg": -180.0,
"n_rows": 3,
"row_bytes": 96,
"data_offset": 553,
"n_rows_available": 1,
"status": "TRUNCATED"
}
],
"trunc_rowboundary_a1.sras": [
{
"index": 0,
"angle_deg": 0.0,
"n_rows": 3,
"row_bytes": 96,
"data_offset": 265,
"n_rows_available": 3,
"status": "OK"
},
{
"index": 1,
"angle_deg": -180.0,
"n_rows": 3,
"row_bytes": 96,
"data_offset": 553,
"n_rows_available": 2,
"status": "TRUNCATED"
}
],
"trunc_angleboundary.sras": [
{
"index": 0,
"angle_deg": 0.0,
"n_rows": 3,
"row_bytes": 96,
"data_offset": 265,
"n_rows_available": 3,
"status": "OK"
},
{
"index": 1,
"angle_deg": -180.0,
"n_rows": 3,
"row_bytes": 96,
"data_offset": 553,
"n_rows_available": 0,
"status": "MISSING"
}
],
"trunc_midrow_a0.sras": [
{
"index": 0,
"angle_deg": 0.0,
"n_rows": 3,
"row_bytes": 96,
"data_offset": 265,
"n_rows_available": 1,
"status": "TRUNCATED"
},
{
"index": 1,
"angle_deg": -180.0,
"n_rows": 3,
"row_bytes": 96,
"data_offset": 265,
"n_rows_available": 0,
"status": "MISSING"
}
],
"header_only.sras": [
{
"index": 0,
"angle_deg": 0.0,
"n_rows": 3,
"row_bytes": 96,
"data_offset": 265,
"n_rows_available": 0,
"status": "MISSING"
},
{
"index": 1,
"angle_deg": -180.0,
"n_rows": 3,
"row_bytes": 96,
"data_offset": 265,
"n_rows_available": 0,
"status": "MISSING"
}
]
}
}
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tests/golden_util.py
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"""Shared constants for the golden .sras fixtures.
These mirror the values tests/gen_goldens.py used when the fixtures were
generated against the pre-refactor code (commit d185676); they must never
change, or the byte-identical comparisons stop meaning anything.
"""
SPF = 8
SAMPLE_RATE = 6.25e9
CHANNELS = [1, 3, 4]
PREAMBLES = [f"WFMOUTPRE:CH{ch};SYNTHETIC;PT_FMT Y;XINCR 1.6E-10" for ch in CHANNELS]
BACKGROUND = bytes(range(SPF))
# build_plan inputs for the fixture geometry: 2 angles × 3 rows × 4 frames
TINY_PLAN_ARGS = dict(x_start=1.0, y_start=1.0, x_delta=0.02, y_delta=0.02,
num_angles=2, row_spacing=0.01)
LASER_FREQ_HZ = 20000.0
VELOCITY_MM_S = 100.0
def synthetic_frame(ai, ri, ci, fi):
return bytes((ai * 7 + ri * 5 + ci * 3 + fi + s) % 256 for s in range(SPF))
tests/test_angle_inspect.py
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"""Pre-scan angle inspection, driven entirely by fake hardware.
The feature's defining constraint is that it reads nothing back from the
scope — the operator looks at the instrument. These tests pin that, the scope
state the app is responsible for putting the instrument into, and the motion
sequence across angles.
"""
import random
import pytest
from core.angle_inspect import AngleInspector, InspectCallbacks
from core.rotation import RotationAxis, RotationSettings
from core.scan_engine import AXIS_X, AXIS_Y
from core.scan_geometry import build_plan
from core.scope_inspect import (
BIAS_CHANNELS, BIAS_POSITION_DIV, BIAS_SCALE_V_DIV, BIAS_WINDOW_V,
INSPECT_TRIG_LEVEL_V, inspect_channel_profiles,
)
from core.scope_sras import SRAS_CHANNELS
from fakes import FakeScope, FakeStage, FakeT3R, Trace
SPF = 8
def make_plan(num_angles=3):
return build_plan(40.0, 30.0, 2.0, 1.0, num_angles, 0.25,
laser_freq_hz=20000.0, velocity_mm_s=100.0)
def build(num_angles=3, seed=1234, callbacks=None, rotator_open=True):
trace = Trace()
scope = FakeScope(trace, samples_per_frame=SPF)
stage = FakeStage(trace, scope=scope)
t3r = FakeT3R(trace, is_open=rotator_open)
rotator = RotationAxis(t3r, RotationSettings())
plan = make_plan(num_angles)
insp = AngleInspector(stage, scope, rotator, plan,
callbacks=callbacks or InspectCallbacks(),
rng=random.Random(seed))
return insp, trace, plan
def writes(trace):
return [c[1] for c in trace.of("write")]
# ── The defining constraint ──────────────────────────────────────────────────
def test_inspection_never_reads_a_waveform_back():
"""The operator reads the scope; the app must not pull data off it.
If this fails, someone has added a transfer path to a feature whose whole
premise is that there isn't one.
"""
insp, trace, plan = build()
insp.start()
for i in range(plan.n_angles):
insp.goto_angle(i)
insp.new_point()
insp.stop()
forbidden = {"transfer_fastframe", "transfer_fastframe_bulk",
"transfer_curve", "set_data_source", "query_wfmoutpre"}
assert forbidden.isdisjoint(set(trace.names()))
assert "CURVe?" not in writes(trace)
# ── Scope configuration ──────────────────────────────────────────────────────
def test_start_sets_an_edge_trigger_on_ch2_above_the_scan_level():
insp, trace, _ = build()
insp.start()
assert "TRIGger:A:TYPe EDGE" in writes(trace)
assert trace.of("set_trigger_source")[-1][1] == 2
assert trace.of("set_trigger_slope")[-1][1] == "RISE"
ch, level = trace.of("set_trigger_level")[-1][1:3]
assert (ch, level) == (2, INSPECT_TRIG_LEVEL_V)
assert INSPECT_TRIG_LEVEL_V >= 2.0
def test_start_disables_fastframe_averaging_and_the_logic_trigger():
"""Everything the scan needs and inspection must not inherit."""
insp, trace, _ = build()
insp.start()
assert trace.of("set_fastframe_state")[-1][1] is False
assert trace.of("set_acquire_mode")[-1][1] == "SAMPLE"
w = writes(trace)
assert not any("LOGIc" in cmd or "LOGICPattern" in cmd for cmd in w)
def test_start_leaves_the_acquisition_free_running():
"""The display has to keep updating while the operator looks at it."""
insp, trace, _ = build()
insp.start()
w = writes(trace)
assert "ACQuire:STOPAfter RUNSTop" in w
assert w.index("ACQuire:STOPAfter RUNSTop") < w.index("ACQuire:STATE RUN")
assert "ACQuire:STATE STOP" not in w
def test_bias_channels_are_directly_comparable():
"""CH3/CH4 must share scale and position or the eye comparison is a lie."""
profiles = inspect_channel_profiles()
a, b = (profiles[ch] for ch in BIAS_CHANNELS)
assert a.scale_v_div == b.scale_v_div
assert a.position_div == b.position_div
# Same front end as the scan records — only the display changes.
for ch in BIAS_CHANNELS:
assert profiles[ch].termination_ohm == SRAS_CHANNELS[ch].termination_ohm
assert profiles[ch].coupling == SRAS_CHANNELS[ch].coupling
assert profiles[ch].bandwidth_hz == SRAS_CHANNELS[ch].bandwidth_hz
@pytest.mark.parametrize("n_divisions", [8, 10])
def test_bias_window_shows_zero_to_700mv_with_headroom(n_divisions):
"""0–700 mV must fit on screen, above ground, on either graticule size.
Ground sits BIAS_POSITION_DIV divisions below centre, so the visible
window runs from (-N/2 - pos)*scale to (+N/2 - pos)*scale.
"""
half = n_divisions / 2
bottom = (-half - BIAS_POSITION_DIV) * BIAS_SCALE_V_DIV
top = (half - BIAS_POSITION_DIV) * BIAS_SCALE_V_DIV
assert bottom < 0.0, "no room below ground for undershoot"
assert top > BIAS_WINDOW_V, "700 mV is clipped or sitting on the top edge"
# The point of moving the trace down: most of the screen is above ground.
assert abs(bottom) < top
def test_ch1_keeps_the_acquisition_front_end():
"""What you see at a point is what a scan would record there."""
assert inspect_channel_profiles()[1] == SRAS_CHANNELS[1]
# ── Stage and rotation ───────────────────────────────────────────────────────
def test_start_parks_on_the_first_angle():
insp, _, plan = build()
point = insp.start()
assert point.angle_idx == 0
assert point.angle_deg == plan.per_angle[0].angle_deg
assert insp.current_point == point
def test_the_gate_is_off_for_the_whole_inspection():
"""Nothing here is gated, and an armed output keeps driving the line."""
insp, trace, _ = build()
insp.start()
insp.goto_angle(2)
insp.new_point()
assert trace.count("set_trigger_gate_off") >= 1
assert trace.count("set_trigger_trigout_maxv") == 0
assert [c[2] for c in trace.of("arm_scan_gate") if c[2]] == []
def test_points_land_on_the_scan_grid():
"""A point the scan would never sample tells you nothing about the scan."""
insp, _, plan = build()
insp.start()
for i in range(plan.n_angles):
pa = plan.per_angle[i]
for _ in range(5):
pt = insp.new_point() if insp.angle_idx == i else insp.goto_angle(i)
assert pt.angle_idx == i
assert pt.y_mm in pa.y_positions
assert pa.x_start <= pt.x_mm <= pa.x_start + pa.x_delta
def test_goto_angle_rotates_then_moves():
insp, trace, plan = build()
insp.start()
trace.calls.clear()
insp.goto_angle(2)
# t3r_rotate carries the delta, so assert the resulting absolute angle.
assert trace.count("t3r_rotate") == 1, "expected exactly one rotation"
assert insp._rotator.current_deg == pytest.approx(plan.per_angle[2].angle_deg)
moves = trace.of("move_axis_absolute")
assert [m[1] for m in moves] == [AXIS_Y, AXIS_X], "Y then X, as the scan does"
def test_new_point_re_rolls_without_rotating():
"""Distinguishing a bad spot from a bad angle depends on not rotating."""
insp, trace, _ = build()
insp.start()
insp.goto_angle(1)
trace.calls.clear()
first = insp.current_point
second = insp.new_point()
assert second.angle_idx == first.angle_idx == 1
assert (second.x_mm, second.y_mm) != (first.x_mm, first.y_mm)
assert trace.count("t3r_rotate") == 0, "new_point must not rotate"
assert [m[1] for m in trace.of("move_axis_absolute")] == [AXIS_Y, AXIS_X]
def test_next_and_prev_wrap_around():
insp, _, plan = build(num_angles=3)
insp.start()
assert insp.next_angle().angle_idx == 1
assert insp.next_angle().angle_idx == 2
assert insp.next_angle().angle_idx == 0, "should wrap forward"
assert insp.prev_angle().angle_idx == plan.n_angles - 1, "should wrap back"
def test_angle_labels_cover_every_angle():
insp, _, plan = build(num_angles=9)
labels = insp.angle_labels()
assert len(labels) == 9
assert labels[0].startswith("Angle 1/9")
# ── Guards ───────────────────────────────────────────────────────────────────
def test_multi_angle_inspection_requires_the_rotator():
insp, _, _ = build(num_angles=3, rotator_open=False)
with pytest.raises(RuntimeError, match="T3R rotation stage"):
insp.start()
def test_single_angle_inspection_works_without_the_rotator():
insp, _, _ = build(num_angles=1, rotator_open=False)
point = insp.start()
assert point.angle_idx == 0
def test_navigation_before_start_is_rejected():
insp, _, _ = build()
with pytest.raises(RuntimeError, match="not been started"):
insp.goto_angle(1)
with pytest.raises(RuntimeError, match="not been started"):
insp.new_point()
def test_out_of_range_angle_is_rejected():
insp, _, _ = build(num_angles=3)
insp.start()
with pytest.raises(IndexError):
insp.goto_angle(3)
def test_stop_halts_the_sweep_and_sends_the_rotator_home():
insp, trace, _ = build()
insp.start()
insp.goto_angle(2)
trace.calls.clear()
insp.stop()
assert "ACQuire:STATE STOP" in writes(trace)
assert trace.count("t3r_rotate") == 1, "GR not sent home"
assert insp._rotator.current_deg == pytest.approx(0.0)
def test_stop_is_idempotent():
insp, trace, _ = build()
insp.start()
insp.stop()
trace.calls.clear()
insp.stop() # must not re-issue anything or raise
assert trace.calls == []
def test_busy_callback_brackets_every_move():
"""The window disables its controls on this, so it has to pair up."""
events = []
insp, _, _ = build(callbacks=InspectCallbacks(on_busy=events.append))
insp.start()
insp.goto_angle(1)
insp.new_point()
insp.stop()
assert events, "no busy events emitted"
assert events[0] is True and events[-1] is False
depth = 0
for e in events:
depth += 1 if e else -1
assert depth in (0, 1), f"unbalanced busy events: {events}"
assert depth == 0
tests/test_config.py
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"""core.config: round-trip, tolerance, and the helios_port regression.
The old dict-based writer rebuilt the JSON from only the main window's
fields, silently discarding helios_port every time a port was edited.
ScanDefaults.save() always writes every field.
"""
import json
from core.config import ScanDefaults
def test_roundtrip(tmp_path):
p = tmp_path / "defaults.json"
d = ScanDefaults(t3r_port="/dev/ttyACM3", helios_port="/dev/ttyUSB9")
d.save(p)
loaded = ScanDefaults.load(p)
assert loaded == d
def test_missing_file_creates_defaults(tmp_path):
p = tmp_path / "defaults.json"
d = ScanDefaults.load(p)
assert d == ScanDefaults()
assert p.exists()
def test_corrupt_file_falls_back(tmp_path):
p = tmp_path / "defaults.json"
p.write_text("{not json")
assert ScanDefaults.load(p) == ScanDefaults()
def test_unknown_keys_ignored(tmp_path):
p = tmp_path / "defaults.json"
p.write_text(json.dumps({"t3r_port": "/dev/ttyACM7", "laser_freq_hz": 20000.0}))
d = ScanDefaults.load(p)
assert d.t3r_port == "/dev/ttyACM7"
assert d.helios_port == ScanDefaults().helios_port
def test_helios_port_survives_partial_update(tmp_path):
"""Regression: editing main-window ports must not clobber helios_port."""
p = tmp_path / "defaults.json"
ScanDefaults(helios_port="/dev/ttyUSB7").save(p)
d = ScanDefaults.load(p)
d.t3r_port = "/dev/ttyACM1" # what _persist_defaults does
d.save(p)
assert ScanDefaults.load(p).helios_port == "/dev/ttyUSB7"
tests/test_qt_workers.py
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"""gui.qt_workers: the shared queue/poll worker base."""
import threading
import time
import pytest
from PyQt6.QtCore import QThread
from PyQt6.QtWidgets import QApplication
from gui.qt_workers import PollingQueueWorker, QueueWorker
@pytest.fixture(scope="module")
def qapp():
yield QApplication.instance() or QApplication([])
class _Recorder(QueueWorker):
def __init__(self):
super().__init__()
self.seen = []
self.stopped = threading.Event()
self._handlers.update({
"note": self._note,
"boom": self._boom,
})
def _note(self, value):
self.seen.append(value)
def _boom(self):
raise RuntimeError("handler failed")
def _on_stop(self):
self.stopped.set()
def _run_until(worker, predicate, timeout=5.0):
"""Run the worker loop on a plain thread until predicate() is true.
Pumps the Qt event loop while waiting: signals emitted from the worker
thread are delivered as queued events on this (main) thread.
"""
app = QApplication.instance()
t = threading.Thread(target=worker.run, daemon=True)
t.start()
deadline = time.monotonic() + timeout
while not predicate() and time.monotonic() < deadline:
app.processEvents()
time.sleep(0.01)
app.processEvents()
return t
def test_commands_dispatch_in_order(qapp):
w = _Recorder()
for i in range(5):
w._enqueue("note", value=i)
t = _run_until(w, lambda: len(w.seen) == 5)
w.stop_worker()
t.join(timeout=5)
assert w.seen == [0, 1, 2, 3, 4]
assert w.stopped.is_set()
def test_handler_exception_is_reported_not_fatal(qapp):
w = _Recorder()
errors = []
w.error_occurred.connect(errors.append)
w._enqueue("boom")
w._enqueue("note", value="after")
t = _run_until(w, lambda: w.seen == ["after"])
w.stop_worker()
t.join(timeout=5)
assert w.seen == ["after"], "loop died on a failing handler"
assert errors and "handler failed" in errors[0]
def test_unknown_command_reported(qapp):
w = _Recorder()
errors = []
w.error_occurred.connect(errors.append)
w._enqueue("nope")
t = _run_until(w, lambda: bool(errors))
w.stop_worker()
t.join(timeout=5)
assert errors and "Unknown command" in errors[0]
def test_idle_worker_does_not_spin(qapp):
"""The loop must block on the queue, not poll it on a timeout."""
w = _Recorder()
t = threading.Thread(target=w.run, daemon=True)
t.start()
time.sleep(0.3) # idle
cpu_before = time.process_time()
time.sleep(0.5) # still idle
cpu_used = time.process_time() - cpu_before
w.stop_worker()
t.join(timeout=5)
# A 10–20 Hz timeout-poll loop burns measurable CPU here; blocking uses ~0.
assert cpu_used < 0.05, f"idle worker used {cpu_used:.3f}s CPU"
class _Poller(PollingQueueWorker):
def __init__(self):
super().__init__(poll_interval_s=0.02)
self.polls = 0
self.in_flight = 0
self.overlaps = 0
self.is_connected = True
def _poll_once(self):
self.in_flight += 1
if self.in_flight > 1:
self.overlaps += 1
time.sleep(0.05) # deliberately slower than the poll interval
self.polls += 1
self.in_flight -= 1
def test_polling_never_overlaps_or_backs_up(qapp):
"""A device slower than the interval must not accumulate stale polls."""
w = _Poller()
t = threading.Thread(target=w.run, daemon=True)
t.start()
w.start_polling()
time.sleep(0.6)
w.stop_polling()
time.sleep(0.15)
queued = w._cmd_q.qsize()
w.stop_worker()
t.join(timeout=5)
assert w.polls >= 3, "polling did not run"
assert w.overlaps == 0, "polls overlapped"
# Self-rescheduling means at most one poll is ever pending.
assert queued <= 1, f"{queued} stale polls queued up"
def test_stop_polling_halts_the_cycle(qapp):
w = _Poller()
t = threading.Thread(target=w.run, daemon=True)
t.start()
w.start_polling()
time.sleep(0.2)
w.stop_polling()
time.sleep(0.2)
settled = w.polls
time.sleep(0.2)
w.stop_worker()
t.join(timeout=5)
assert w.polls == settled, "polling continued after stop_polling()"
def test_worker_runs_on_its_qthread(qapp):
"""Sanity check the intended usage: run() executes on the QThread."""
w = _Recorder()
thread = QThread()
w.moveToThread(thread)
thread.started.connect(w.run)
ids = []
w._handlers["note"] = lambda value: ids.append(threading.get_ident())
thread.start()
w._enqueue("note", value=None)
deadline = time.monotonic() + 5
while not ids and time.monotonic() < deadline:
qapp.processEvents()
time.sleep(0.01)
w.stop_worker()
thread.quit()
assert thread.wait(5000)
assert ids and ids[0] != threading.get_ident()
tests/test_saw_check.py
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"""Middle-row SAW quality check: plan reduction, the v10 file, and the read-out.
The acquisition half runs on the same fake rig as the scan tests; the
analysis half runs on a synthetic v10 file whose CH1 is a pure sine at a
known FFT bin, so the frequency a trace reports is a number the test knows
in advance rather than one it copies from the implementation.
"""
import math
import numpy as np
import pytest
from core.rotation import RotationAxis, RotationSettings
from core.saw_check import (
SPREAD_GOOD_PCT, alignment_summary, frequency_traces, middle_row_index,
middle_row_plan,
)
from core.scan_engine import ScanCallbacks, ScanEngine
from core.scan_geometry import ScanGeometryError, build_plan
from core.sras_format import (
SCAN_CHANNELS, VERSION, VERSION_SAW_CHECK, SrasFile, create_scan_file,
)
from fakes import FakeScope, FakeStage, FakeT3R, Trace
SAMPLE_RATE = 6.25e9
SPF = 256
LASER_FREQ_HZ = 20000.0
VELOCITY_MM_S = 100.0
PREAMBLES = [f"WFMOUTPRE:CH{ch};YMULT 1.5625E-3;YOFF -87.04;YZERO 0.0"
for ch in SCAN_CHANNELS]
# adc_to_mv with those constants maps 0 → +136 mV and -120 → -51 mV, so a
# frame of zeros passes a 50 mV CH4 gate and a frame of -120 does not.
DC_THRESHOLD_MV = 50.0
CH4_PASS = bytes(SPF)
CH4_FAIL = bytes([256 - 120]) * SPF
def full_plan(num_angles=3, y_delta=0.05):
"""A small ROI, well inside the stage limits, with several rows per angle."""
return build_plan(40.0, 30.0, 0.02, y_delta, num_angles, 0.01,
laser_freq_hz=LASER_FREQ_HZ, velocity_mm_s=VELOCITY_MM_S)
def bin_mhz(k: int) -> float:
return k * SAMPLE_RATE / SPF / 1e6
def sine_frame(k: int) -> bytes:
"""One frame holding a pure sine at FFT bin `k`."""
n = np.arange(SPF)
return np.round(100 * np.sin(2 * math.pi * k * n / SPF)).astype(np.int8).tobytes()
def write_check(path, bins, n_masked_frames=0, plan=None):
"""A synthetic v10 file: angle `i`'s CH1 is a sine at FFT bin `bins[i]`."""
plan = plan if plan is not None else middle_row_plan(full_plan(len(bins)))
f = create_scan_file(path, plan, SPF, SAMPLE_RATE, PREAMBLES, bytes(SPF),
version=VERSION_SAW_CHECK)
try:
for ai, pa in enumerate(plan.per_angle):
wave = sine_frame(bins[ai])
for ch in SCAN_CHANNELS:
for fi in range(pa.n_frames):
if ch == 1:
f.write(wave)
elif ch == 3:
f.write(bytes(SPF))
else:
f.write(CH4_FAIL if fi < n_masked_frames else CH4_PASS)
finally:
f.close()
return plan
# ── Plan reduction ───────────────────────────────────────────────────────────
def test_middle_row_plan_keeps_one_middle_row_per_angle():
plan = full_plan(num_angles=3)
check = middle_row_plan(plan)
assert check.n_angles == plan.n_angles
assert [pa.n_rows for pa in check.per_angle] == [1] * plan.n_angles
for original, reduced in zip(plan.per_angle, check.per_angle, strict=True):
mid = original.n_rows // 2
assert reduced.y_positions == [original.y_positions[mid]]
# The row is scanned exactly as the full scan would have scanned it.
assert reduced.angle_deg == original.angle_deg
assert reduced.x_start == original.x_start
assert reduced.x_delta == original.x_delta
assert reduced.n_frames == original.n_frames
def test_middle_row_plan_does_not_mutate_its_input():
plan = full_plan(num_angles=3)
before = [(pa.n_rows, list(pa.y_positions)) for pa in plan.per_angle]
middle_row_plan(plan)
assert [(pa.n_rows, pa.y_positions) for pa in plan.per_angle] == before
def test_every_angles_middle_row_crosses_the_roi_centre():
"""The premise the whole comparison rests on: one shared point on the sample."""
plan = full_plan(num_angles=5)
check = middle_row_plan(plan)
cx = plan.x_start_nominal + plan.x_delta_nominal / 2
cy = plan.y_start_nominal + plan.y_delta_nominal / 2
for pa in check.per_angle:
assert pa.x_start + pa.x_delta / 2 == pytest.approx(cx, abs=1e-6)
# Within one row spacing — the middle row is a grid point, not exact.
assert abs(pa.y_positions[0] - cy) <= plan.row_spacing
def test_middle_row_index_rule():
assert [middle_row_index(n) for n in (1, 2, 3, 4, 6)] == [0, 1, 1, 2, 3]
def test_middle_row_plan_rejects_an_empty_plan():
plan = full_plan(num_angles=1)
plan.per_angle = []
with pytest.raises(ScanGeometryError, match="no angles"):
middle_row_plan(plan)
def test_middle_row_plan_rejects_an_angle_with_no_rows():
plan = full_plan(num_angles=1)
plan.per_angle[0].y_positions = []
with pytest.raises(ScanGeometryError, match="no middle row"):
middle_row_plan(plan)
# ── The v10 file ─────────────────────────────────────────────────────────────
def test_v10_write_read_roundtrip(tmp_path):
out = tmp_path / "check.sras"
plan = write_check(out, bins=(8, 8, 8))
sras = SrasFile(out)
assert sras.version == VERSION_SAW_CHECK
assert sras.is_saw_check
assert [s.status for s in sras.angle_status()] == ["OK"] * plan.n_angles
assert [pa.n_rows for pa in sras.per_angle] == [1] * plan.n_angles
sras.close()
def test_v10_rejects_a_multi_row_plan(tmp_path):
plan = full_plan(num_angles=2)
assert any(pa.n_rows > 1 for pa in plan.per_angle)
with pytest.raises(ValueError, match="exactly one row per angle"):
create_scan_file(tmp_path / "bad.sras", plan, SPF, SAMPLE_RATE,
PREAMBLES, bytes(SPF), version=VERSION_SAW_CHECK)
assert not (tmp_path / "bad.sras").exists()
def test_unknown_version_rejected_at_write(tmp_path):
with pytest.raises(ValueError, match="version 7"):
create_scan_file(tmp_path / "bad.sras", middle_row_plan(full_plan(1)),
SPF, SAMPLE_RATE, PREAMBLES, bytes(SPF), version=7)
def test_v6_file_is_not_a_saw_check():
sras = SrasFile("tests/golden/complete.sras")
assert sras.version == VERSION and not sras.is_saw_check
# ── Acquisition through the engine ───────────────────────────────────────────
def run_engine(tmp_path, num_angles=3):
trace = Trace()
scope = FakeScope(trace, samples_per_frame=SPF)
stage = FakeStage(trace, scope=scope)
rotator = RotationAxis(FakeT3R(trace), RotationSettings())
plan = full_plan(num_angles)
check = middle_row_plan(plan)
engine = ScanEngine(stage, scope, rotator, check, tmp_path / "check.sras",
callbacks=ScanCallbacks(),
file_version=VERSION_SAW_CHECK)
return engine.run(), plan, check, trace
def test_engine_writes_a_complete_v10_check(tmp_path):
result, plan, check, _ = run_engine(tmp_path)
assert not result.aborted
assert result.rows_written == check.n_angles # exactly one row per angle
assert result.angles_acquired == list(range(check.n_angles))
sras = SrasFile(result.path)
assert sras.is_saw_check
assert [s.status for s in sras.angle_status()] == ["OK"] * check.n_angles
assert [pa.y_positions for pa in sras.per_angle] == [
[pytest.approx(original.y_positions[original.n_rows // 2], abs=1e-4)]
for original in plan.per_angle
]
sras.close()
def test_engine_visits_each_middle_row_once(tmp_path):
_, _, check, trace = run_engine(tmp_path)
y_moves = [round(c[2], 4) for c in trace.of("move_axis_absolute")
if c[1] == 0x22]
assert y_moves == [round(pa.y_positions[0], 4) for pa in check.per_angle]
def test_engine_still_writes_v6_by_default(tmp_path):
trace = Trace()
scope = FakeScope(trace, samples_per_frame=SPF)
stage = FakeStage(trace, scope=scope)
rotator = RotationAxis(FakeT3R(trace), RotationSettings())
engine = ScanEngine(stage, scope, rotator, full_plan(1),
tmp_path / "scan.sras", callbacks=ScanCallbacks())
result = engine.run()
assert SrasFile(result.path).version == VERSION
# ── Analysis ─────────────────────────────────────────────────────────────────
def test_traces_report_the_injected_frequency(tmp_path):
out = tmp_path / "check.sras"
bins = (8, 9, 10)
write_check(out, bins=bins)
with SrasFile(out) as sras:
traces = frequency_traces(sras, dc_threshold_mv=DC_THRESHOLD_MV)
assert len(traces) == len(bins)
for trace, k in zip(traces, bins, strict=True):
assert np.allclose(trace.freq_mhz, bin_mhz(k))
assert trace.median_mhz == pytest.approx(bin_mhz(k))
assert trace.valid_fraction == 1.0
assert trace.drift_mhz_per_mm == pytest.approx(0.0, abs=1e-6)
def test_masked_pixels_become_nan_not_zero(tmp_path):
out = tmp_path / "check.sras"
write_check(out, bins=(8, 8, 8), n_masked_frames=2)
with SrasFile(out) as sras:
traces = frequency_traces(sras, dc_threshold_mv=DC_THRESHOLD_MV)
for trace in traces:
assert np.isnan(trace.freq_mhz[:2]).all()
assert np.isfinite(trace.freq_mhz[2:]).all()
# A masked pixel must not drag the median toward 0 MHz.
assert trace.median_mhz == pytest.approx(bin_mhz(8))
assert trace.valid_fraction < 1.0
def test_traces_are_centred_on_a_common_offset(tmp_path):
out = tmp_path / "check.sras"
write_check(out, bins=(8, 9, 10))
with SrasFile(out) as sras:
traces = frequency_traces(sras, dc_threshold_mv=DC_THRESHOLD_MV)
# Absolute X differs per angle (different bounding boxes); the offset the
# viewer plots against does not, which is what puts the curves together.
assert len({round(t.x_mm[0], 6) for t in traces}) > 1
for trace in traces:
assert trace.offset_mm[0] == pytest.approx(-trace.offset_mm[-1])
def test_angles_with_no_data_are_skipped(tmp_path):
out = tmp_path / "check.sras"
write_check(out, bins=(8, 8, 8))
full = out.read_bytes()
with SrasFile(out) as sras:
last_offset = sras.angle_data_offset(2)
out.write_bytes(full[:last_offset]) # angle 3 never acquired
with SrasFile(out) as sras:
traces = frequency_traces(sras, dc_threshold_mv=DC_THRESHOLD_MV)
assert [t.angle_idx for t in traces] == [0, 1]
def test_summary_flags_agreeing_angles_as_good(tmp_path):
out = tmp_path / "check.sras"
write_check(out, bins=(8, 8, 8))
with SrasFile(out) as sras:
summary = alignment_summary(
frequency_traces(sras, dc_threshold_mv=DC_THRESHOLD_MV))
assert summary.n_angles == 3
assert summary.median_mhz == pytest.approx(bin_mhz(8))
assert summary.spread_mhz == pytest.approx(0.0)
assert summary.spread_pct <= SPREAD_GOOD_PCT
assert summary.level == "good"
def test_summary_flags_disagreeing_angles(tmp_path):
out = tmp_path / "check.sras"
write_check(out, bins=(8, 9, 10))
with SrasFile(out) as sras:
traces = frequency_traces(sras, dc_threshold_mv=DC_THRESHOLD_MV)
summary = alignment_summary(traces)
assert summary.spread_mhz == pytest.approx(bin_mhz(10) - bin_mhz(8))
assert summary.level == "poor"
assert summary.worst_angle_deg == traces[0].angle_deg # lowest median
assert summary.best_angle_deg == traces[2].angle_deg # highest median
assert f"{summary.spread_mhz:.3f} MHz" in summary.describe()
def test_summary_calls_out_a_mostly_masked_row(tmp_path):
out = tmp_path / "check.sras"
plan = middle_row_plan(full_plan(3))
# Mask nearly every frame of every angle: the spread is meaningless then.
write_check(out, bins=(8, 8, 8), plan=plan,
n_masked_frames=max(pa.n_frames for pa in plan.per_angle) - 1)
with SrasFile(out) as sras:
summary = alignment_summary(
frequency_traces(sras, dc_threshold_mv=DC_THRESHOLD_MV))
assert summary.level == "poor"
assert "DC threshold" in summary.describe()
def test_summary_of_nothing_is_not_a_crash():
summary = alignment_summary([])
assert summary.n_angles == 0 and summary.level == "poor"
assert "No angle" in summary.describe()
def test_middle_row_of_a_full_v6_scan_is_readable():
"""The check's read-out applied to a finished scan, after the fact."""
with SrasFile("tests/golden/complete.sras") as sras:
traces = frequency_traces(sras, dc_threshold_mv=-1e6)
assert len(traces) == sras.header.n_angles
for trace, pa in zip(traces, sras.per_angle, strict=True):
assert trace.row_idx == pa.n_rows // 2
assert len(trace.freq_mhz) == pa.n_frames
tests/test_scan_engine.py
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"""Headless ScanEngine tests driven entirely by fake hardware.
These cover what can't be checked without the rig: the command sequence,
the written file layout, and abort/pause behaviour.
"""
import threading
import time
import pytest
from core.rotation import RotationAxis, RotationSettings
from core.scan_engine import (
AXIS_X, AXIS_Y, ScanAborted, ScanCallbacks, ScanEngine, ResumeState,
ResumeTarget,
)
from core.scan_geometry import ScanGeometryError, build_plan
from core.sras_format import SCAN_CHANNELS, SrasFile
from fakes import FakeScope, FakeStage, FakeT3R, Trace
SPF = 8
def make_plan(num_angles=1, y_delta=0.005):
# Small ROI well inside the stage limits: few rows, few frames per angle.
return build_plan(40.0, 30.0, 0.02, y_delta, num_angles, 0.01,
laser_freq_hz=20000.0, velocity_mm_s=100.0)
def build(tmp_path, num_angles=1, callbacks=None, resume=None, plan=None,
burst_mode=False, max_frames=4096, out_name="out.sras",
strict_rows=False, **kw):
trace = Trace()
scope = FakeScope(trace, samples_per_frame=SPF, max_frames=max_frames)
stage = FakeStage(trace, scope=scope)
t3r = FakeT3R(trace, **kw)
rotator = RotationAxis(t3r, RotationSettings())
plan = plan if plan is not None else make_plan(num_angles)
engine = ScanEngine(stage, scope, rotator, plan, tmp_path / out_name,
resume=resume,
callbacks=callbacks or ScanCallbacks(),
burst_mode=burst_mode, strict_rows=strict_rows)
return engine, trace, plan
def test_single_angle_scan_writes_readable_file(tmp_path):
engine, trace, plan = build(tmp_path)
result = engine.run()
assert not result.aborted
assert result.rows_written == plan.per_angle[0].n_rows
assert result.angles_acquired == [0]
sras = SrasFile(result.path)
assert sras.header.n_angles == 1
assert sras.header.samples_per_frame == SPF
assert sras.header.n_channels == len(SCAN_CHANNELS)
# File is complete: every declared row present on disk
assert [s.status for s in sras.angle_status()] == ["OK"]
assert len(sras.preambles) == 3
assert sras.background == bytes(range(SPF))
def test_command_sequence_order(tmp_path):
engine, trace, plan = build(tmp_path)
engine.run()
names = trace.names()
def first(name):
return names.index(name)
# Stage prepared, then scope configured, then rows executed
assert first("set_trigger_trigout_maxv") < first("set_sample_rate")
assert first("set_sample_rate") < first("transfer_fastframe")
# Velocity set for both axes before any scan move
assert trace.count("set_velocity_params") == 2
# Per row: Y positioned, then X pre-ramp, then X run
moves = trace.of("move_axis_absolute")
assert moves[0][1] == AXIS_Y
assert moves[1][1] == AXIS_X and moves[2][1] == AXIS_X
assert moves[1][2] < moves[2][2] # pre-ramp start < run-off end
# Data channels transferred (CH3 is synthesized, not read)
assert [c[1] for c in trace.of("transfer_fastframe")] == [1, 4]
def test_multi_angle_rotates_and_returns_home(tmp_path):
engine, trace, plan = build(tmp_path, num_angles=3)
engine.run()
rotations = [c[1] for c in trace.of("t3r_rotate")]
# Three angles at 0/-90/-180 → two moves out, then one back to 0
assert rotations == [-90.0, -90.0, 180.0]
# Every move waits for completion instead of sleeping a guess
assert trace.count("t3r_wait_motion_done") == len(rotations)
# GR configured once, before any rotation
assert trace.names().index("t3r_set_microstep") < trace.names().index("t3r_rotate")
sras = SrasFile(tmp_path / "out.sras")
assert [s.status for s in sras.angle_status()] == ["OK"] * 3
def test_fastframe_count_rearmed_per_angle(tmp_path):
engine, trace, plan = build(tmp_path, num_angles=3)
engine.run()
counts = [c[1] for c in trace.of("set_fastframe_count")]
assert counts == [pa.n_frames for pa in plan.per_angle]
def test_abort_before_start_raises_and_stops_early(tmp_path):
engine, trace, _ = build(tmp_path)
engine.abort()
with pytest.raises(ScanAborted):
engine.run()
assert trace.count("transfer_fastframe") == 0
def test_abort_during_prompt_unblocks(tmp_path):
"""A prompt that never returns must not deadlock an aborting scan."""
released = threading.Event()
def prompt(title, msg):
# Simulates the GUI bridge: waits until abort flips the flag.
while not engine.aborted:
if released.wait(0.01):
return
engine, trace, _ = build(tmp_path, callbacks=ScanCallbacks(prompt=prompt))
errors = []
def run():
try:
engine.run()
except ScanAborted:
errors.append("aborted")
t = threading.Thread(target=run, daemon=True)
t.start()
time.sleep(0.2) # let it reach the first prompt
engine.abort()
t.join(timeout=5)
assert not t.is_alive(), "engine deadlocked on a prompt during abort"
assert errors == ["aborted"]
def test_pause_and_resume_at_row_boundary(tmp_path):
states = []
engine, trace, plan = build(
tmp_path, num_angles=1,
callbacks=ScanCallbacks(on_paused_changed=states.append))
engine.pause()
done = threading.Event()
def run():
try:
engine.run()
except ScanAborted:
pass # only reachable via the failure escape hatch below
finally:
done.set()
t = threading.Thread(target=run, daemon=True)
t.start()
try:
# The engine's instrument-settling sleeps run before the first row,
# so poll for the pause rather than assuming a fixed delay.
deadline = time.monotonic() + 10.0
while not states and time.monotonic() < deadline:
time.sleep(0.05)
paused = bool(states)
assert paused and states[0] is True, "engine did not report the pause"
finally:
# Always release the scan thread; if the pause never arrived, abort
# too, so a failed assertion can't leave it parked forever.
if not states:
engine.abort()
engine.resume()
t.join(timeout=10)
assert done.is_set()
assert states[-1] is False
def test_dc_bias_callback_reports_per_frame_means(tmp_path):
rows = []
engine, trace, plan = build(
tmp_path, callbacks=ScanCallbacks(on_dc_bias=lambda r, m: rows.append((r, m))))
engine.run()
assert len(rows) == plan.per_angle[0].n_rows
row_idx, means = rows[0]
assert row_idx == 1
assert len(means) == plan.per_angle[0].n_frames
assert all(isinstance(v, float) for v in means)
def test_offstage_plan_rejected_before_touching_hardware(tmp_path):
trace = Trace()
scope = FakeScope(trace, samples_per_frame=SPF)
stage = FakeStage(trace, scope=scope)
# X range that runs off the 110 mm stage once ramps are added
plan = build_plan(80.0, 30.0, 40.0, 5.0, 1, 0.25,
laser_freq_hz=20000.0, velocity_mm_s=100.0)
engine = ScanEngine(stage, scope, None, plan, tmp_path / "bad.sras")
with pytest.raises(ScanGeometryError):
engine.run()
assert trace.calls == [], "hardware touched despite invalid geometry"
def test_multi_angle_without_rotator_raises(tmp_path):
trace = Trace()
engine = ScanEngine(FakeStage(trace), FakeScope(trace, samples_per_frame=SPF),
None, make_plan(3), tmp_path / "x.sras")
with pytest.raises(RuntimeError, match="T3R rotation stage"):
engine.run()
def test_missing_hardware_raises(tmp_path):
trace = Trace()
with pytest.raises(RuntimeError, match="BBD202"):
ScanEngine(None, FakeScope(trace), None, make_plan(),
tmp_path / "x.sras").run()
with pytest.raises(RuntimeError, match="Oscilloscope"):
ScanEngine(FakeStage(trace), None, None, make_plan(),
tmp_path / "x.sras").run()
def test_resume_seeks_to_angle_offset_and_skips_others(tmp_path):
# First produce a complete 3-angle file
engine, trace, plan = build(tmp_path, num_angles=3)
engine.run()
path = tmp_path / "out.sras"
original = path.read_bytes()
sras = SrasFile(path)
statuses = sras.angle_status()
target = statuses[1]
resume = ResumeState(
path=path,
targets=[ResumeTarget(target.index, target.data_offset,
target.n_rows, target.angle_deg)],
samples_per_frame=SPF,
)
engine2, trace2, _ = build(tmp_path, num_angles=3, resume=resume)
result = engine2.run()
assert result.angles_acquired == [1]
# Only the middle angle's rows were re-acquired
assert result.rows_written == plan.per_angle[1].n_rows
rewritten = path.read_bytes()
assert len(rewritten) == len(original)
# Angle 0's block is untouched; angle 1's changed (fresh frame data)
a1_start, a1_end = target.data_offset, target.data_offset + target.row_bytes * target.n_rows
assert rewritten[:a1_start] == original[:a1_start]
assert rewritten[a1_start:a1_end] != original[a1_start:a1_end]
assert rewritten[a1_end:] == original[a1_end:]
def test_resume_record_length_mismatch_rejected(tmp_path):
engine, trace, plan = build(tmp_path)
engine.run()
path = tmp_path / "out.sras"
resume = ResumeState(path=path,
targets=[ResumeTarget(0, 0, 1, 0.0)],
samples_per_frame=SPF + 1) # scope changed
engine2, _, _ = build(tmp_path, resume=resume)
with pytest.raises(RuntimeError, match="record length"):
engine2.run()
# ── Burst acquisition ────────────────────────────────────────────────────────
# 6 rows × 4 frames/row; max_frames=14 gives 14//4 = 3 rows per burst, so the
# angle needs two bursts and the second is not a whole burst wide.
BURST_PLAN = dict(y_delta=0.05)
BURST_MAX_FRAMES = 14
def test_burst_and_serial_produce_identical_files(tmp_path):
"""The whole point: burst mode must be a pure acquisition optimisation."""
plan = make_plan(**BURST_PLAN)
assert plan.per_angle[0].n_rows == 6 and plan.per_angle[0].n_frames == 4
serial, _, _ = build(tmp_path, plan=plan, out_name="serial.sras")
serial.run()
burst, _, _ = build(tmp_path, plan=plan, out_name="burst.sras",
burst_mode=True, max_frames=BURST_MAX_FRAMES)
burst.run()
assert (tmp_path / "burst.sras").read_bytes() == \
(tmp_path / "serial.sras").read_bytes()
def test_burst_multi_angle_file_is_complete(tmp_path):
plan = make_plan(num_angles=3, **BURST_PLAN)
engine, trace, _ = build(tmp_path, plan=plan, burst_mode=True,
max_frames=BURST_MAX_FRAMES)
result = engine.run()
assert result.rows_written == plan.total_rows
assert result.angles_acquired == [0, 1, 2]
sras = SrasFile(tmp_path / "out.sras")
assert [s.status for s in sras.angle_status()] == ["OK"] * 3
def test_burst_gates_the_flyback_and_runs_once_per_burst(tmp_path):
plan = make_plan(**BURST_PLAN)
engine, trace, _ = build(tmp_path, plan=plan, burst_mode=True,
max_frames=BURST_MAX_FRAMES)
engine.run()
# Two bursts (3 + 3 rows), two preflight acquisitions, one background.
runs = [c for c in trace.of("write") if c[1] == "ACQuire:STATE RUN"]
assert len(runs) == 5
# Every acquiring pass is bracketed by an arm/disarm, so the gate is low
# for each flyback. 6 rows + 1 preflight pass = 7 arms.
gate = [c[2] for c in trace.of("arm_scan_gate")]
assert gate.count(True) == 7
# No two arms without a disarm between them — that is what would let a
# flyback into the acquisition. (A repeated disarm is just defensive.)
for a, b in zip(gate, gate[1:], strict=False):
assert not (a and b), f"acquiring pass with no disarm before it: {gate}"
assert gate[-1] is False, "scan left the gate armed"
# One bulk transfer per data channel per burst, none per row.
assert [(c[1], c[2]) for c in trace.of("transfer_fastframe_bulk")] == [
(1, 12), (4, 12), (1, 12), (4, 12)]
assert trace.count("transfer_fastframe") == 0
def test_burst_preflight_rejects_a_leaky_gate(tmp_path):
plan = make_plan(**BURST_PLAN)
engine, trace, _ = build(tmp_path, plan=plan, burst_mode=True,
max_frames=BURST_MAX_FRAMES)
stage = engine._stage
# A gate that ignores the disable request — the failure mode the preflight
# exists to catch (TRIGOUT_GATE_OFF set to the wrong mode value).
def stuck_gate(axis, armed, verify=True):
trace.record("arm_scan_gate", axis, bool(armed))
stage.gate_armed = True
stage.arm_scan_gate = stuck_gate
with pytest.raises(RuntimeError, match="not idling low"):
engine.run()
def test_burst_preflight_rejects_a_dark_laser(tmp_path):
"""A gate that never fires would let a leak check pass vacuously."""
plan = make_plan(**BURST_PLAN)
engine, trace, _ = build(tmp_path, plan=plan, burst_mode=True,
max_frames=BURST_MAX_FRAMES)
engine._stage.attach_scope(None) # no pulses ever reach the scope
with pytest.raises(RuntimeError, match="no frames acquired"):
engine.run()
def _clip_one_row(engine, which_pass=2, lost=1):
"""Make one acquiring pass come up `lost` frames short.
`which_pass` counts acquiring passes from 1, so the default clips the
second data row (row 2) — far enough in that a mishandled short row shows
up as a shift in the rows after it.
"""
scope = engine._scope
real_acquire = scope.acquire_frames
passes = {"n": 0}
def clipped(n):
if scope._running:
passes["n"] += 1
if passes["n"] == which_pass:
n -= lost
real_acquire(n)
scope.acquire_frames = clipped
@pytest.mark.parametrize("burst_mode", [False, True])
def test_short_row_is_padded_to_declared_frame_count(tmp_path, burst_mode):
"""A clipped row must not shift every later row in the file.
v6 declares n_frames per row up front and has no per-row length, so an
under-triggered row has to be squared up. In burst mode this also proves
the splitter advances by what actually arrived, not by n_frames.
"""
warnings = []
plan = make_plan(**BURST_PLAN)
engine, trace, _ = build(
tmp_path, plan=plan, burst_mode=burst_mode,
max_frames=BURST_MAX_FRAMES,
callbacks=ScanCallbacks(on_status=warnings.append))
# The preflight is covered by its own tests; skipping it keeps the
# acquiring-pass count below identical in both modes.
engine._preflight_done = True
_clip_one_row(engine)
result = engine.run()
assert result.rows_written == 6
assert any("Row 2: 3 frames acquired, 4 expected" in w for w in warnings)
assert any("zero-padded" in w for w in warnings)
sras = SrasFile(tmp_path / "out.sras")
assert [s.status for s in sras.angle_status()] == ["OK"]
# The padding lands at the end of the short row, not in the next one.
assert bytes(sras.load_row(0, 1, 0)[-1]) == bytes(SPF)
assert bytes(sras.load_row(0, 2, 0)[0]) != bytes(SPF)
# ── Strict row packing ───────────────────────────────────────────────────────
@pytest.mark.parametrize("burst_mode", [False, True])
def test_strict_row_packing_aborts_on_a_short_row(tmp_path, burst_mode):
"""Strict mode fails the scan instead of silently squaring a row up.
The default padding keeps the file readable but makes a mis-triggered row
indistinguishable from a good one after the fact, since v6 records no
per-row frame count. Strict mode trades the salvaged rows for knowing.
"""
plan = make_plan(**BURST_PLAN)
engine, _, _ = build(tmp_path, plan=plan, burst_mode=burst_mode,
max_frames=BURST_MAX_FRAMES, strict_rows=True)
engine._preflight_done = True
_clip_one_row(engine)
with pytest.raises(RuntimeError, match="Row 2: 3 frames acquired, 4 expected"):
engine.run()
@pytest.mark.parametrize("burst_mode", [False, True])
def test_strict_row_packing_does_not_disturb_a_clean_scan(tmp_path, burst_mode):
"""Strict mode is inert when every row acquires what it declared."""
plan = make_plan(**BURST_PLAN)
engine, _, _ = build(tmp_path, plan=plan, burst_mode=burst_mode,
max_frames=BURST_MAX_FRAMES, strict_rows=True)
engine._preflight_done = True
result = engine.run()
assert result.rows_written == plan.total_rows
sras = SrasFile(tmp_path / "out.sras")
assert [s.status for s in sras.angle_status()] == ["OK"]
def test_strict_row_packing_writes_nothing_for_the_failed_row(tmp_path):
"""The abort must not leave a half-written row behind.
CH1 leads SCAN_CHANNELS, so the frame count is known before any of the
row's channels are written — the file should end on a whole-row boundary.
"""
plan = make_plan(**BURST_PLAN)
engine, _, _ = build(tmp_path, plan=plan, strict_rows=True)
engine._preflight_done = True
_clip_one_row(engine)
with pytest.raises(RuntimeError, match="Strict row packing"):
engine.run()
# Row 1 was written in full; row 2 aborted before writing anything, so
# the file ends exactly on a row boundary.
sras = SrasFile(tmp_path / "out.sras")
written = (tmp_path / "out.sras").stat().st_size - sras.data_start_offset
assert written == sras.row_bytes(0)
def test_engine_imports_without_qt():
"""The engine must be usable from a non-Qt front end."""
import subprocess
import sys
code = (
"import sys;"
"sys.modules['PyQt6'] = None;"
"import core.scan_engine, core.rotation, core.scope_sras,"
" core.scan_resume, core.sras_format, core.scan_geometry;"
"print('ok')"
)
out = subprocess.run([sys.executable, "-c", code], capture_output=True,
text=True, cwd=str(__import__('pathlib').Path(__file__).parent.parent))
assert out.returncode == 0, out.stderr
assert "ok" in out.stdout
tests/test_scan_geometry.py
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"""core.scan_geometry vs the pre-refactor golden geometry fixtures,
plus structural invariants and travel-limit validation."""
import json
import math
from pathlib import Path
import pytest
from core.scan_geometry import (
EtaEstimator, ScanGeometryError, StageLimits, build_plan, format_eta,
validate_plan,
)
GOLDEN = Path(__file__).parent / "golden"
@pytest.fixture(scope="module")
def geometry():
with open(GOLDEN / "geometry.json") as f:
return json.load(f)
def _plan_from_case(case, consts):
i = case["inputs"]
return build_plan(
float(i["XS"]), float(i["YS"]), float(i["XD"]), float(i["YD"]),
int(i["num_angles"]), float(i["row_spacing"]),
laser_freq_hz=consts["LASER_FREQ_HZ"],
velocity_mm_s=consts["SCAN_VELOCITY_MM_S"],
rotation_sign=consts["GR_ROTATION_SIGN"],
)
def test_all_golden_cases_match(geometry):
consts = geometry["constants"]
for label, case in geometry["cases"].items():
plan = _plan_from_case(case, consts)
exp = case["params"]
assert plan.x_start_nominal == exp["x_start_nominal"], label
assert plan.y_start_nominal == exp["y_start_nominal"], label
assert plan.x_delta_nominal == exp["x_delta_nominal"], label
assert plan.y_delta_nominal == exp["y_delta_nominal"], label
assert plan.row_spacing == exp["row_spacing"], label
assert plan.n_angles == exp["num_angles"], label
assert len(plan.per_angle) == len(exp["per_angle"]), label
for pa, e in zip(plan.per_angle, exp["per_angle"], strict=True):
assert pa.angle_deg == e["angle"], label
assert pa.x_start == e["x_start"], label
assert pa.x_delta == e["x_delta"], label
assert pa.n_frames == e["n_frames"], label
assert pa.n_rows == e["n_rows"], label
assert pa.y_positions == e["y_positions"], label
def test_golden_error_cases_raise(geometry):
consts = geometry["constants"]
for case in geometry["error_cases"].values():
with pytest.raises(ValueError):
_plan_from_case(case, consts)
def test_zero_degree_bbox_equals_nominal_roi():
plan = build_plan(10.0, 5.0, 20.0, 8.0, 1, 0.5,
laser_freq_hz=20000.0, velocity_mm_s=100.0)
pa = plan.per_angle[0]
assert pa.angle_deg == 0.0
assert math.isclose(pa.x_start, 10.0)
assert math.isclose(pa.x_delta, 20.0)
assert math.isclose(pa.y_positions[0], 5.0)
def test_rotated_bbox_contains_all_roi_corners():
plan = build_plan(30.0, 20.0, 24.0, 10.0, 7, 0.1,
laser_freq_hz=20000.0, velocity_mm_s=100.0)
cy = 20.0 + 5.0
corners = [(-12.0, -5.0), (12.0, -5.0), (-12.0, 5.0), (12.0, 5.0)]
for pa in plan.per_angle:
r = math.radians(pa.angle_deg)
half_w = pa.x_delta / 2.0
y_lo, y_hi = min(pa.y_positions), max(pa.y_positions)
for dx, dy in corners:
# ROI corner in the rotated frame
rx = dx * math.cos(r) - dy * math.sin(r)
ry = dx * math.sin(r) + dy * math.cos(r)
assert abs(rx) <= half_w + 1e-9, pa.angle_deg
# Row grid covers within one row-spacing at the edges
assert y_lo - 0.1 - 1e-9 <= cy + ry <= y_hi + 0.1 + 1e-9, pa.angle_deg
def test_plus_minus_theta_symmetry():
a = build_plan(10, 10, 20, 10, 5, 0.25, laser_freq_hz=20000.0,
velocity_mm_s=100.0, rotation_sign=1)
b = build_plan(10, 10, 20, 10, 5, 0.25, laser_freq_hz=20000.0,
velocity_mm_s=100.0, rotation_sign=-1)
for pa, pb in zip(a.per_angle, b.per_angle, strict=True):
assert pa.angle_deg == -pb.angle_deg
assert math.isclose(pa.x_delta, pb.x_delta)
assert pa.n_rows == pb.n_rows
assert pa.n_frames == pb.n_frames
def test_validate_plan_limit_violations():
limits = StageLimits()
ramp, buf = 100.0**2 / (2 * 1500.0), 1.0
ok = build_plan(20.0, 10.0, 40.0, 30.0, 3, 0.25,
laser_freq_hz=20000.0, velocity_mm_s=100.0)
validate_plan(ok, ramp, buf, limits) # must not raise
too_left = build_plan(2.0, 10.0, 40.0, 30.0, 1, 0.25,
laser_freq_hz=20000.0, velocity_mm_s=100.0)
with pytest.raises(ScanGeometryError, match="pre-ramp start"):
validate_plan(too_left, ramp, buf, limits)
too_right = build_plan(80.0, 10.0, 40.0, 30.0, 1, 0.25,
laser_freq_hz=20000.0, velocity_mm_s=100.0)
with pytest.raises(ScanGeometryError, match="run-off end"):
validate_plan(too_right, ramp, buf, limits)
too_low = build_plan(30.0, -5.0, 40.0, 30.0, 1, 0.25,
laser_freq_hz=20000.0, velocity_mm_s=100.0)
with pytest.raises(ScanGeometryError, match="Y axis minimum"):
validate_plan(too_low, ramp, buf, limits)
too_high = build_plan(30.0, 60.0, 40.0, 30.0, 1, 0.25,
laser_freq_hz=20000.0, velocity_mm_s=100.0)
with pytest.raises(ScanGeometryError, match="Y axis maximum"):
validate_plan(too_high, ramp, buf, limits)
def test_format_eta():
assert format_eta(-3) == "0s"
assert format_eta(42) == "42s"
assert format_eta(90) == "1m 30s"
assert format_eta(3720) == "1h 02m"
def test_eta_estimator_rolls_and_resets_on_angle_change():
eta = EtaEstimator(window=3)
assert eta.eta_secs(5) is None
t = 100.0
for dur in (2.0, 4.0, 6.0, 8.0):
eta.row_started(now=t)
eta.row_finished(angle_idx=1, now=t + dur)
t += dur
# window=3 keeps [4, 6, 8] → avg 6
assert eta.eta_secs(2) == pytest.approx(12.0)
# angle change wipes history
eta.row_started(now=t)
eta.row_finished(angle_idx=2, now=t + 10.0)
assert eta.eta_secs(3) == pytest.approx(30.0)
tests/test_scan_resume.py
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"""core.scan_resume: the frontier contiguity rule, over real fixture files."""
from pathlib import Path
from core.scan_resume import is_compatible, plan_resume
from core.sras_format import SrasFile
GOLDEN = Path(__file__).parent / "golden"
def _statuses(name):
return SrasFile(GOLDEN / name).angle_status()
def test_complete_file_frontier_is_past_the_end():
st = _statuses("complete.sras")
plan = plan_resume(st, selected={0})
assert plan.frontier_idx == len(st)
assert [t.angle_idx for t in plan.targets] == [0]
assert plan.auto_added == []
def test_selecting_past_frontier_backfills_the_gap():
# angle 0 complete, angle 1 truncated → frontier = 1
st = _statuses("trunc_rowboundary_a1.sras")
assert st[0].complete and not st[1].complete
plan = plan_resume(st, selected={1})
assert plan.frontier_idx == 1
assert [t.angle_idx for t in plan.targets] == [1]
assert plan.auto_added == []
def test_selection_before_frontier_is_untouched():
st = _statuses("trunc_rowboundary_a1.sras")
plan = plan_resume(st, selected={0})
assert [t.angle_idx for t in plan.targets] == [0]
assert plan.auto_added == []
def test_selecting_only_a_later_angle_pulls_in_the_frontier():
"""Data is one contiguous stream, so angle 1 can't be skipped to reach 2."""
st = _statuses("header_only.sras") # nothing written: frontier = 0
assert plan_resume(st, selected={0}).frontier_idx == 0
plan = plan_resume(st, selected={1})
assert [t.angle_idx for t in plan.targets] == [0, 1]
assert plan.auto_added == [0]
def test_targets_carry_offsets_and_rows():
st = _statuses("complete.sras")
plan = plan_resume(st, selected={0, 1})
for target, status in zip(plan.targets, st, strict=True):
assert target.data_offset == status.data_offset
assert target.n_rows == status.n_rows
assert target.angle_deg == status.angle_deg
assert plan.total_rows == sum(s.n_rows for s in st)
def test_to_state_carries_samples_per_frame():
sras = SrasFile(GOLDEN / "complete.sras")
state = plan_resume(sras.angle_status(), selected={0}).to_state(sras)
assert state.path == sras.path
assert state.samples_per_frame == sras.header.samples_per_frame
assert state.target_indices == {0}
def test_is_compatible_checks_acquisition_settings():
sras = SrasFile(GOLDEN / "complete.sras")
h = sras.header
ok = dict(velocity=h.velocity, laser_freq=h.laser_freq,
sample_rate=h.sample_rate, n_channels=h.n_channels)
assert is_compatible(sras, **ok)
assert not is_compatible(sras, **{**ok, "velocity": h.velocity + 1})
assert not is_compatible(sras, **{**ok, "laser_freq": h.laser_freq * 2})
assert not is_compatible(sras, **{**ok, "sample_rate": h.sample_rate * 2})
assert not is_compatible(sras, **{**ok, "n_channels": h.n_channels + 1})
tests/test_scope_burst.py
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"""Burst sizing and row-splitting, exercised without any instrument."""
import pytest
from core.scope_burst import (
frame_means_block, normalize_row, rows_per_burst, split_row_counts,
)
SPF = 8
# ── rows_per_burst ───────────────────────────────────────────────────────────
def test_rows_per_burst_rounds_down():
# 9.7 rows' worth of capacity is 9 rows: a partial row is unusable.
assert rows_per_burst(97, 10, SPF, rows_remaining=100) == 9
assert rows_per_burst(100, 10, SPF, rows_remaining=100) == 10
def test_rows_per_burst_clamped_by_rows_remaining():
assert rows_per_burst(1000, 10, SPF, rows_remaining=3) == 3
def test_rows_per_burst_clamped_by_memory_budget():
# Budget holds 4 rows of 10 frames × 8 samples; the scope would hold 100.
assert rows_per_burst(1000, 10, SPF, rows_remaining=100,
memory_budget=4 * 10 * SPF) == 4
def test_rows_per_burst_headroom_reserves_slack_per_row():
assert rows_per_burst(100, 10, SPF, rows_remaining=100, headroom=0) == 10
assert rows_per_burst(100, 10, SPF, rows_remaining=100, headroom=2) == 8
def test_rows_per_burst_never_returns_zero():
"""A row too big for any budget still goes, or the scan cannot progress."""
assert rows_per_burst(5, 10, SPF, rows_remaining=100) == 1
assert rows_per_burst(1000, 10, SPF, rows_remaining=100,
memory_budget=1) == 1
def test_rows_per_burst_rejects_degenerate_geometry():
with pytest.raises(ValueError):
rows_per_burst(100, 0, SPF, rows_remaining=1)
# ── split_row_counts ─────────────────────────────────────────────────────────
def test_split_row_counts_differences_the_cumulative_counter():
assert split_row_counts([4, 8, 12]) == [4, 4, 4]
assert split_row_counts([4, 7, 12]) == [4, 3, 5]
assert split_row_counts([]) == []
def test_split_row_counts_rejects_a_counter_that_went_backwards():
# Only happens if the acquisition restarted mid-burst, which would
# misattribute every later row.
with pytest.raises(RuntimeError, match="backwards"):
split_row_counts([8, 4])
# ── normalize_row ────────────────────────────────────────────────────────────
def test_normalize_row_passes_an_exact_row_through():
buf = bytes(range(4 * SPF))
assert bytes(normalize_row(buf, 0, 4, 4, SPF)) == buf
def test_normalize_row_pads_a_short_row():
buf = bytes(range(3 * SPF))
out = bytes(normalize_row(buf, 0, 3, 4, SPF))
assert len(out) == 4 * SPF
assert out[:3 * SPF] == buf
assert out[3 * SPF:] == bytes(SPF)
def test_normalize_row_truncates_a_long_row():
buf = bytes(range(6 * SPF))
out = bytes(normalize_row(buf, 0, 6, 4, SPF))
assert out == buf[:4 * SPF]
def test_normalize_row_reads_at_an_offset():
buf = bytes(range(8 * SPF))
out = bytes(normalize_row(buf, 2 * SPF, 4, 4, SPF))
assert out == buf[2 * SPF:6 * SPF]
def test_normalize_row_pads_a_buffer_that_ends_early():
"""Defensive: a truncated transfer must not shorten the row on disk."""
out = bytes(normalize_row(bytes(2 * SPF), 0, 4, 4, SPF))
assert len(out) == 4 * SPF
# ── frame_means_block ────────────────────────────────────────────────────────
def test_frame_means_block_is_per_frame():
buf = bytes([1] * SPF + [3] * SPF)
assert frame_means_block(buf, 0, 2, SPF) == [1.0, 3.0]
def test_frame_means_block_reads_signed_samples_at_an_offset():
buf = bytes([0] * SPF) + bytes([0xFF] * SPF) # 0xFF == -1 as int8
assert frame_means_block(buf, SPF, 1, SPF) == [-1.0]
tests/test_smoke_apps.py
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"""Offscreen smoke tests: every GUI app must construct without hardware.
These don't exercise behavior — they catch import errors, missing .ui
widgets, and constructor regressions during the refactor.
"""
import pytest
from PyQt6.QtWidgets import QApplication
@pytest.fixture(scope="session")
def qapp():
app = QApplication.instance() or QApplication([])
yield app
def _pump(qapp):
qapp.processEvents()
def test_sc3_aui_main_window(qapp):
import sc3_aui_app
win = sc3_aui_app.MainWindow()
_pump(qapp)
try:
assert win.x_start_edit.text()
assert win.windowTitle() == "Scanengine-3 AUI"
finally:
for worker, thread in (
(win._bbd_worker, win._bbd_thread),
(win._oscope_worker, win._oscope_thread),
(win._helios_worker, win._helios_thread),
):
worker.stop_worker()
thread.quit()
assert thread.wait(2000)
win._camera_win.deleteLater()
win.deleteLater()
_pump(qapp)
def test_sras_viewer_window(qapp):
import sras_viewer
win = sras_viewer.SrasViewerWindow()
_pump(qapp)
try:
assert win.windowTitle()
finally:
win.deleteLater()
_pump(qapp)
def test_saw_check_viewer_window(qapp):
import saw_check_viewer
win = saw_check_viewer.SawCheckWindow()
_pump(qapp)
try:
assert win.windowTitle()
finally:
win.deleteLater()
_pump(qapp)
def test_helios_test_app(qapp):
import helios_test_app
win = helios_test_app.HeliosTestApp()
_pump(qapp)
try:
assert win.windowTitle()
finally:
win.deleteLater()
_pump(qapp)
def test_bbd202_test_app(qapp):
import bbd202_test_app
win = bbd202_test_app.BBD202TestApp()
_pump(qapp)
try:
assert win.windowTitle()
finally:
win.close()
_pump(qapp)
def test_camera_test_app(qapp):
import camera_test_app
win = camera_test_app.CameraTestWindow()
_pump(qapp)
try:
assert win.windowTitle()
finally:
win.deleteLater()
_pump(qapp)
def test_t3r_control_panel(qapp):
from hardware.t3r_driver import T3RDriver
from t3r_control_panel import T3RControlPanel
driver = T3RDriver()
panel = T3RControlPanel(driver)
_pump(qapp)
try:
assert panel.windowTitle()
finally:
panel.deleteLater()
_pump(qapp)
def test_sras_scan_manager_importable():
import sras_scan_manager # noqa: F401
tests/test_sras_analysis.py
+142
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"""core.sras_analysis + the viewer's LoadedScan/compute path, run headlessly
over the golden fixtures."""
from pathlib import Path
import numpy as np
import pytest
from core.sras_analysis import (
CH1_IDX, CH4_IDX, ChannelCalibration, FALLBACK_YMULT_MV,
SawPipeline, compute_dc_image, compute_rf_image, power_spectrum,
)
GOLDEN = Path(__file__).parent / "golden"
def _loaded_scan(name="complete.sras"):
# Imported lazily: sras_viewer pulls in PyQt6/matplotlib.
from sras_viewer import LoadedScan
return LoadedScan(str(GOLDEN / name))
def test_loaded_scan_basics():
scan = _loaded_scan()
assert scan.rows_available == [3, 3]
assert scan.background is not None and len(scan.background) == 8
assert len(scan.calib.ymult_mv) == 3
view = scan.angle_view(0)
assert view.shape == (3, 3, 4, 8)
scan.close()
def test_loaded_scan_truncated_rows():
scan = _loaded_scan("trunc_rowboundary_a1.sras")
assert scan.rows_available == [3, 2]
assert scan.angle_view(1).shape[0] == 2
scan = _loaded_scan("header_only.sras")
assert scan.rows_available == [0, 0]
assert scan.angle_view(0).shape[0] == 0
def test_compute_dc_image_matches_manual():
scan = _loaded_scan()
view = scan.angle_view(0)
img = compute_dc_image(view, CH4_IDX)
manual = view[:, CH4_IDX].astype(np.float64).mean(axis=-1)
assert img.shape == (3, 4)
assert img.dtype == np.float32
np.testing.assert_allclose(img, manual, rtol=1e-6)
def test_compute_rf_image_mask_and_values():
scan = _loaded_scan()
view = scan.angle_view(0)
sras = scan.sras
f_mhz = sras.freq_axis_mhz(sras.header.samples_per_frame)
# Threshold below everything: all pixels valid, values from the freq axis
img_all = compute_rf_image(view, scan.calib, f_mhz, dc_threshold_mv=-1e9)
assert img_all.shape == (3, 4)
assert set(np.unique(img_all)).issubset(set(f_mhz))
# Threshold above everything: fully masked, zero image, no FFT work
img_none = compute_rf_image(view, scan.calib, f_mhz, dc_threshold_mv=1e9)
assert not img_none.any()
def test_compute_rf_image_gate_zeroes_samples():
scan = _loaded_scan()
view = scan.angle_view(0)
sras = scan.sras
f_mhz = sras.freq_axis_mhz(sras.header.samples_per_frame)
t_ns = sras.time_axis_ns()
img = compute_rf_image(view, scan.calib, f_mhz, dc_threshold_mv=-1e9,
gate_start_ns=float(t_ns[2]), gate_end_ns=float(t_ns[5]),
time_axis_ns=t_ns)
assert img.shape == (3, 4)
def test_calibration_roundtrip_and_fallback():
cal = ChannelCalibration.from_preambles(["", "", ""])
assert cal.ymult_mv == [FALLBACK_YMULT_MV] * 3
assert cal.mv_to_adc(cal.adc_to_mv(42.0, 0), 0) == pytest.approx(42.0)
cal2 = ChannelCalibration.from_preambles(
["YMULT 1.0E-3;YOFF -10.0;YZERO 2.0E-3"])
assert cal2.ymult_mv[0] == pytest.approx(1.0)
assert cal2.yoff_adc[0] == pytest.approx(-10.0)
assert cal2.yzero_mv[0] == pytest.approx(2.0)
def test_power_spectrum_dc_suppressed():
x = np.ones(64, dtype=np.float32) * 5.0
p = power_spectrum(x)
assert p[0] == 0.0
assert not p[1:].any()
def test_saw_pipeline_finds_injected_packet():
sr = 6.25e9
n = 1250
t = np.arange(n) / sr
rng = np.random.default_rng(42)
def make_shot(delay_ns=200.0):
sig = rng.normal(0, 0.05, n).astype(np.float32)
packet = np.exp(-((t * 1e9 - delay_ns) / 25.0) ** 2) \
* np.sin(2 * np.pi * 140e6 * t)
return sig + 3.0 * packet.astype(np.float32)
pipe = SawPipeline(sr, emi_gate_ns=50.0, bp_lo_mhz=85.0, bp_hi_mhz=200.0,
saw_window_ns=(80.0, 350.0))
pipe.build_template(np.stack([make_shot() for _ in range(10)]))
assert pipe.template is not None
metrics = pipe.process_shot_metrics(make_shot())
assert metrics["peak_time_ns"] == pytest.approx(200.0, abs=15.0)
assert metrics["snr"] > 3.0
# process_shot returns the same metrics plus the stage arrays
full = pipe.process_shot(make_shot())
for key in ("raw", "gated", "filtered", "mf_output", "envelope"):
assert isinstance(full[key], np.ndarray)
def test_compute_saw_image_scalars_only():
# Synthetic angle view: golden frames (8 samples) are too short for the
# 6th-order zero-phase bandpass; real records are >1000 samples.
from core.sras_analysis import compute_saw_image
rng = np.random.default_rng(1)
view = rng.integers(-40, 40, size=(3, 3, 4, 512), dtype=np.int8)
view[:, CH4_IDX] = 100 # every pixel passes the DC mask
calib = ChannelCalibration.from_preambles(["", "", ""])
pipe = SawPipeline(6.25e9, saw_window_ns=(10.0, 70.0))
pipe.build_template(view[0, CH1_IDX, :4].astype(np.float32))
img = compute_saw_image(view, calib, -1e9, pipe, "amplitude")
assert img.shape == (3, 4)
assert img.dtype == np.float32
assert (img > 0).all()
tof = compute_saw_image(view, calib, -1e9, pipe, "tof")
assert tof.shape == (3, 4)
tests/test_sras_format.py
+137
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"""core.sras_format vs the pre-refactor golden fixtures.
The goldens were produced by the original sc3_aui_app implementation; the
extracted module must reproduce them byte-for-byte (writer) and
field-for-field (parser + frontier walk).
"""
import json
from dataclasses import asdict
from pathlib import Path
import numpy as np
import pytest
from core.scan_geometry import build_plan
from core.sras_format import SrasFile, create_scan_file
from golden_util import (
BACKGROUND, CHANNELS, LASER_FREQ_HZ, PREAMBLES, SAMPLE_RATE, SPF,
TINY_PLAN_ARGS, VELOCITY_MM_S, synthetic_frame,
)
GOLDEN = Path(__file__).parent / "golden"
@pytest.fixture(scope="module")
def expected():
with open(GOLDEN / "sras_expected.json") as f:
return json.load(f)
def _tiny_plan():
return build_plan(**TINY_PLAN_ARGS, laser_freq_hz=LASER_FREQ_HZ,
velocity_mm_s=VELOCITY_MM_S)
def _write_complete(path):
plan = _tiny_plan()
f = create_scan_file(path, plan, SPF, SAMPLE_RATE, PREAMBLES, BACKGROUND)
try:
for ai, pa in enumerate(plan.per_angle):
for ri in range(pa.n_rows):
for ci in range(len(CHANNELS)):
for fi in range(pa.n_frames):
f.write(synthetic_frame(ai, ri, ci, fi))
finally:
f.close()
def test_writer_byte_identical_to_golden(tmp_path):
out = tmp_path / "rewrite.sras"
_write_complete(out)
assert out.read_bytes() == (GOLDEN / "complete.sras").read_bytes()
def test_header_matches_golden(expected):
sras = SrasFile(GOLDEN / "complete.sras")
h = expected["header"]
assert asdict(sras.header) == {
"n_angles": h["n_angles"],
"x_start_nominal": h["x_start_nominal"], "y_start_nominal": h["y_start_nominal"],
"x_delta_nominal": h["x_delta_nominal"], "y_delta_nominal": h["y_delta_nominal"],
"row_spacing": h["row_spacing"], "velocity": h["velocity"],
"laser_freq": h["laser_freq"],
"samples_per_frame": h["samples_per_frame"], "sample_rate": h["sample_rate"],
"bytes_per_sample": h["bytes_per_sample"], "n_channels": h["n_channels"],
}
assert sras.data_start_offset == h["data_start_offset"]
assert [pa.angle_deg for pa in sras.per_angle] == h["angles"]
for pa, exp in zip(sras.per_angle, h["per_angle"], strict=True):
assert pa.angle_deg == exp["angle"]
assert pa.x_start == exp["x_start"]
assert pa.x_delta == exp["x_delta"]
assert pa.n_frames == exp["n_frames"]
assert pa.n_rows == exp["n_rows"]
assert pa.y_positions == exp["y_positions"]
def test_frontier_all_truncation_variants(expected):
for name, exp_statuses in expected["statuses"].items():
statuses = SrasFile(GOLDEN / name).angle_status()
assert [asdict(s) for s in statuses] == exp_statuses, f"mismatch for {name}"
def test_preambles_and_background_roundtrip():
sras = SrasFile(GOLDEN / "complete.sras")
assert sras.preambles == PREAMBLES
assert sras.background == BACKGROUND
def test_load_angle_memmap_equals_eager():
with SrasFile(GOLDEN / "complete.sras") as sras:
raw = (GOLDEN / "complete.sras").read_bytes()
for ai, pa in enumerate(sras.per_angle):
view = sras.load_angle(ai)
h = sras.header
assert view.shape == (pa.n_rows, h.n_channels, pa.n_frames, h.samples_per_frame)
start = sras.angle_data_offset(ai)
eager = np.frombuffer(
raw, dtype=np.int8, offset=start, count=view.size
).reshape(view.shape)
assert np.array_equal(view, eager)
assert not view.flags.writeable
def test_load_row_matches_synthetic_pattern():
with SrasFile(GOLDEN / "complete.sras") as sras:
for ai in range(2):
for ri in range(3):
for ci in range(3):
row = sras.load_row(ai, ri, ci)
expected_bytes = b"".join(
synthetic_frame(ai, ri, ci, fi)
for fi in range(sras.per_angle[ai].n_frames)
)
assert row.tobytes() == expected_bytes
def test_truncated_load_angle_partial_rows():
sras = SrasFile(GOLDEN / "trunc_rowboundary_a1.sras")
st = sras.angle_status()[1]
assert st.status == "TRUNCATED" and st.n_rows_available == 2
view = sras.load_angle(1, n_rows=st.n_rows_available)
assert view.shape[0] == 2
sras.close()
def test_bad_magic_and_version_rejected(tmp_path):
bad = tmp_path / "bad.sras"
bad.write_bytes(b"XXXX" + bytes(60))
with pytest.raises(ValueError, match="bad magic"):
SrasFile(bad)
data = bytearray((GOLDEN / "complete.sras").read_bytes())
data[4] = 5 # version byte
v5 = tmp_path / "v5.sras"
v5.write_bytes(bytes(data))
with pytest.raises(ValueError, match="version 5"):
SrasFile(v5)
tools/genesis_laser_control.py
+3 -10
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@@ -31,26 +31,19 @@ Date: 2026-01-24
""" """
import sys import sys
import time
import struct
from datetime import datetime
from typing import Optional, List, Tuple
from enum import IntEnum
import serial
from serial.tools import list_ports from serial.tools import list_ports
from PyQt6.QtWidgets import ( from PyQt6.QtWidgets import (
QApplication, QMainWindow, QWidget, QVBoxLayout, QHBoxLayout, QApplication, QMainWindow, QWidget, QVBoxLayout, QHBoxLayout,
QTabWidget, QLabel, QSlider, QPushButton, QSpinBox, QCheckBox, QTabWidget, QLabel, QSlider, QPushButton, QSpinBox, QCheckBox,
QComboBox, QTextEdit, QLineEdit, QGroupBox, QGridLayout, QComboBox, QTextEdit, QLineEdit, QGroupBox, QGridLayout,
QMessageBox, QStatusBar, QProgressBar QMessageBox, QStatusBar
) )
from PyQt6.QtCore import Qt, QTimer, pyqtSignal, QSettings from PyQt6.QtCore import Qt, QTimer, QSettings
from PyQt6.QtGui import QFont, QPalette, QColor from PyQt6.QtGui import QFont
# Import core hardware control classes # Import core hardware control classes
from hardware.genesis_core import ( from hardware.genesis_core import (
I2CAddress, PCA9555Register, ControlBitmask,
SerialComm, I2CProtocol, I2CDevices, LaserControl SerialComm, I2CProtocol, I2CDevices, LaserControl
) )
tools/genesis_laser_gui.py
-1
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@@ -39,7 +39,6 @@ from PyQt6.QtWidgets import (
QLineEdit, QTextEdit, QCheckBox, QMessageBox, QGroupBox, QGridLayout QLineEdit, QTextEdit, QCheckBox, QMessageBox, QGroupBox, QGridLayout
) )
from PyQt6.QtCore import QObject, pyqtSignal, QTimer, Qt from PyQt6.QtCore import QObject, pyqtSignal, QTimer, Qt
from PyQt6.QtGui import QPalette, QColor
# ============================================================================ # ============================================================================
# CONSTANTS # CONSTANTS
ui_mainwindow.py
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