register_at_each_angle_hook() stores a function object by reference, so
editing a hook's def and forgetting to re-register left the old version
running silently -- easy to miss mid-beamtime. Detect it via
func.__globals__ (a redefined top-level def, or a reloaded module,
mutates the same namespace dict in place) and auto-adopt the new
definition with a printed note instead of failing or staying stale.
Centralizes the shared lookup/error logic (previously duplicated in
lamni.py and flomni.py) into TomoQueueMixin._resolve_at_each_angle_hook().
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
The tool is called BEC_ptycho_align now, not SPEC_ptycho_align.m as
the previous docs/comments said -- fixes the references introduced in
the previous commit (12b2538) in lamni.py's docstrings/print message
and the user docs.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Replaces the awkward documented workaround (configure a full tomo_type
1 setup with 96 projections, then launch just sub_tomo_scan(1, 0)) with
a dedicated command, ported from flomni's tomo_alignment_scan(): adjust
tomo_parameters() (FOV/step/counting time), then call
lamni.tomo_alignment_scan() directly -- no tomo_type/sub-tomogram
bookkeeping involved, matching flomni's clean two-step workflow.
Runs 12 points evenly spaced across the full 360 degrees (lamni has no
180-degree symmetry the way flomni does, so unlike flomni's 5-point/
180-degree scan, this covers the full circle -- point count matches
what the old workaround's docs defaulted to, endpoint=False since
360==0 degrees). Aborts if x-ray-eye alignment hasn't been done yet
(tomo_fit_xray_eye unset), mirroring flomni's equivalent guard.
write_alignment_scan_numbers() writes the same 4-line scan-number/
angle/offset log flomni's version does, to
~/data/raw/logs/ptychotomoalign_scannum.txt for SPEC_ptycho_align.m,
also printed at the console (flomni's own console-print equivalent is
dead/commented-out code; lamni's actually prints).
Scope note: flomni's version conditionally skips its eye-out/optics-in
transition when already in measurement condition with feedback
running, to avoid an unneeded interferometer reset -- lamni has no
equivalent helpers for that check, so this calls leye_out()
unconditionally instead. Left as a possible follow-up, not in scope
here.
Item 6 of csaxs_bec/bec_ipython_client/plugins/LamNI/AI_docs/
FLOMNI_LAMNI_FEATURE_GAPS_2026-07.md. Documented in
docs/user/ptychography/lamni.md's "Fine alignment" section.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Add both to the tomo-queue command reference in flomni.md and
lamni.md: tomo_queue_resume() as an alias for tomo_queue_execute(),
and tomo_queue_reacquire(job_index, projection_number) for reopening
a job (including an already-"done" one) at an earlier projection and
cascading later jobs to pending, mirroring the code added in the
previous commit.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Generalize TomoParamsWidget to lamni via a SETUP_PROFILES mechanism
(setup detection, per-setup field lists/order, a new Offsets section,
a setup-agnostic "Duplicate job" queue button), fixing two latent
TomoQueueDialog bugs that silently mishandled lamni jobs along the way.
While verifying the GUI's projection-count preview against the CLI,
found two real, pre-existing bugs in LamNI.sub_tomo_scan() unrelated
to the GUI itself: a duplicate closing angle every sub-tomogram
(360=0 degrees), and a phase offset computed from the raw stepsize
instead of the achievable one, breaking the equally-spaced-when-
combined guarantee for sub-tomogram pairs/quads/the full set. Both
fixed to mirror Flomni's existing, correct equivalents.
Also fills in lamni's user documentation with the queue/command-job/
at-each-angle-hook system, which it previously lacked entirely,
mirroring flomni.md's coverage.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
holler