Three independent fixes:
- sub_tomo_scan(): in 360-degree tomo_type-1 mode, every sub-tomogram used
to sweep the full 0-360 range, so each one's own fine grid contained
angle pairs exactly 180deg apart -- redundant tomographic information.
Sub-tomograms now each cover a 180deg span, split into low/high halves
by subtomo_number % 4 with a bit-reversal-of-4 phase table, so adjacent
pairs (1,2)/(3,4)/(5,6)/(7,8), either quartet, and all 8 combined each
independently form a complete, evenly-spaced 360deg tomogram at
successively finer spacing. Total projection count for a given
tomo_angle_stepsize is now identical between 180 and 360 mode (same N,
no longer doubled). Updated the 4 other consumers of the old N/step
formula (zero-deg reference gating, _tomo_type1_actual_grid, the
parameter wizard, the PDF report) to match. 180-degree mode is
unchanged. Live-verified against the running flomni sim: real motor
motion traces the expected boustrophedon path with no duplicate or
180deg-apart angles.
- Sample storage: added an owner field, packed into the same EPICS DESC
field as the sample name ("name | owner", via new sample_desc_codec.py)
since there's no separate PV for it. Wired through
FlomniSampleStorage, the CLI (flomni_modify_storage_non_interactive,
ftransfer_modify_storage), the two transfer routines that forward a
raw DESC value across a gripper move (now unpacked/repacked so owner
survives the move instead of being dropped or double-packed), and
SampleStorageWidget. Scoped to flomni only this session; OMNY's
storage/transfer mixin is unchanged.
- ConsoleButtonsWidget's ABORT button used to send SIGINT then, 500ms
later, a stop_devices() broadcast to ALL devices with no stop_id --
an un-suppressed error from that broadcast landing on a queue-tracked
instruction could kill the scan worker thread outright, requiring a
full BEC restart. Replaced with: queue.request_scan_abortion() (safe
no-op if idle, but registers a stop_id so expected errors are
suppressed), then SIGINT, then a direct, immediate Galil hard stop via
new GalilController.hard_abort_and_restore_positioning_mode() -- the
same method ftransfer_abort() now delegates to, so the CLI and GUI
paths can't drift apart again. SIGINT is sent before the hard stop:
live testing showed that if the hard stop's mntprgs-clearing side
effect lands first, a same-session polling loop can mistake it for
normal completion and fall through into ensure_gripper_up(), which
must not happen mid-transfer -- sending SIGINT first (near-instant)
gives that loop's own KeyboardInterrupt handler a head start before
the hard stop's own multi-step sequence completes. The button is
labeled per beamline (e.g. "Flomni Motion Stop") and disabled rather
than silently inert when no hard-stop device is configured/enabled.
Scoped to flomni only this session (OMNY/LamNI wiring deferred).
Live-verified against the running sim, including the exact
stop-lands-mid-queued-instruction scenario that previously crashed
the scan worker.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
TOMO_QUEUE_COMMAND_JOBS_PLAN.md and TOMO_QUEUE_TESTING.md were written
while command jobs (Step 2) were still in progress; update both now
that it's implemented and sim-tested (16/16 e2e tests passing,
including the 6 new command-job ones - see TOMO_QUEUE_TESTING.md
section 4D for what each covers), and record the Redis test-state
contamination gotcha found while testing it.
Also fixes the harness-script path references in SIMULATED_ENDSTATIONS.md
and the two scripts' own docstrings, stale after tests/e2e and
tests/sim_*_harness.py moved to omny_e2e_tests/ (in the previous
commit) - kept out of tests/ specifically so gitea's CI, which runs
pytest against ./csaxs_bec/tests/ unconditionally, doesn't sweep up
tests that need a live sim + Redis.
Covers add-time validation (unknown action, disallowed device,
out-of-range/wrong-type params, unknown kwarg - each rejected without
landing in the queue), the execution-time allow-list re-check as the
real safety boundary, the tomo_queue_actions global var matching the
live registry, tomo_queue_show()/the webpage generator surviving a
command job, legacy kind-less jobs still running as tomograms
alongside a real command-job device move, and the non-idempotent
resume prompt (distinct from the executor's own start-confirmation
prompt).
Also fixes flomni_sim: it only snapshotted/restored whatever was
already in the tomo_queue/tomo_progress global vars, so a stale entry
left behind by an earlier crashed run or manual debugging session
against the same shared sim Redis would contaminate every test that
assumed it started from an empty queue. Now resets both to empty at
setup, in addition to snapshotting/restoring around the test.
Type-tags queue jobs with a "kind" field (back-compat: missing kind
defaults to "tomo"), and adds "command" jobs that reconfigure the
beamline (currently: absolute moves on an allow-listed device, plus an
optimize_idgap stub) between tomograms instead of running a scan.
Command jobs are added via tomo_queue_add_command() against a curated
named-action registry (_TOMO_QUEUE_ACTIONS) - not arbitrary code - so
every queued action is auditable and safe to persist across a kernel
restart. Validation is two-layer: schema checks at add time, and each
action re-checks its own arguments against live hardware at execution
time, which is the actual safety boundary. Crash-resume for a command
job re-runs the whole step sequence from the top if every step is
idempotent, or prompts the operator otherwise.
flomni_webpage_generator.py is guarded against command jobs, which
have no "params" key.
See AI_docs/TOMO_QUEUE_COMMAND_JOBS_PLAN.md for the full design.
