Same gap as flomni.md (fixed previous commit): lamni.md had no mention of
stitching. Add the equivalent paragraph using lamni's own parameter names
(lamni_stitch_x/y, lamni_piezo_range_x/y) and cite tomo_scan_projection(),
which passes them straight through to scans.lamni_fermat_scan().
Also add an omny/AI_docs TODO note -- omny.md has the same gap and omny's
mechanism turns out to use identical parameter names to flomni's
(stitch_x/stitch_y/tomo_stitch_overlap), so the flomni.md paragraph should
carry over directly once written.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_0132KBoxsovfcMNRGJhS1Pbw
flomni.md had no mention of stitching at all. Add a paragraph explaining
the tiled-Fermat-scan mechanism (flomni.py:3521-3527) and tomo_stitch_overlap,
matching the existing zero_deg_reference_at_each_subtomo callout's style.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_0132KBoxsovfcMNRGJhS1Pbw
Add an intuitive spacing table (x spacing stays at step, y spacing
becomes step/fermat_asymmetry) with a worked example, derived from
measuring actual generated positions (area-per-point vs. point count,
averaged over 20 randomized draws per ratio) rather than just stating
the formula. Mirrored into the OMNY port TODO so the same relationship
gets documented there once ported.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Lx3KffiFyyDMKT8vvPENUW
Implements docs/plans/flomni-fermat-asymmetry.md as written: generate the
spiral against an inflated fovy half-width (length_axis2 * fermat_asymmetry),
then compress the accepted y-coordinate back down by the ratio before
storing -- keeps x spacing fixed at step, scales y spacing by the ratio,
preserves the requested FOV. Composes with the already-landed sub-step
randomization: the offset is subtracted at the raw (pre-compression) scale
on both axes, before the inflated-window check, so the offset's phase-shift
stays proportional to the local spacing on both axes.
Wired through the scan class (FlomniFermatScan), Flomni's global var +
queue/CLI plumbing (_TOMO_SCAN_PARAM_NAMES, scan_kwargs, tomo_parameters()
print/prompt, _set_default_tomo_params()), and the tomo_params Qt widget
(new field with a "?" help button, following the widget's existing
offsets-section help-button pattern).
Added tests verifying the inflate/compress math directly (against an
equivalent call with an inflated FOV and fermat_asymmetry=1.0, same seed)
rather than via an approximate spacing-ratio heuristic -- a first attempt
at the latter proved too noisy on a Fermat spiral to assert reliably.
Updated the flOMNI user docs and the OMNY port TODO (out of scope here,
explicitly excludes LamNI per the plan).
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Lx3KffiFyyDMKT8vvPENUW
The Example: line was left out of sync with the parameter table fix
in 5141854 - argument order didn't match, and burst_at_each_point was
missing. Now mirrors the code docstring's example.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Mode A (per-gate aggregate) and Mode B (continuous raw-sample) need
different PandA hardware layouts and can't run simultaneously, so
omny_panda is now two device config entries in ptycho_flomni.yaml:
omny_panda (legacy, kept commented as the restore reference) and
omny_panda_continuous (raw_stream_mode: true, enabled).
Also fixes on_complete for the continuous case. PCAP.CAPTURED can't be
used to detect end-of-acquisition on this layout: CLOCK1 drives
PCAP.gate/trig continuously, so the captured count never naturally
stops increasing while armed -- the previous settle-based wait would
have just run out its timeout. COUNTER1 (frame_counter) instead counts
completed exposures directly (triggered on the detector-trigger's
falling edge), so PandaBoxOMNY now waits for it to reach the exact
expected num_points * frames_per_trigger, mirroring the legacy
exact-count check instead of guessing when capture has "settled".
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TsfqLcPWspjJ6vedMyCxco
Adds an opt-in raw_stream_mode to omny_panda alongside the existing
per-gate averaged burst acquisition, so a burst window can instead be
captured as continuous raw samples plus a detector-gate bit and a
monotonic frame counter for completeness checking. Client-side
coalescing bounds the message rate to the BEC message bus regardless of
PandA's own network-frame batching, and completion uses a settle-based
check since an exact expected sample count isn't predictable for
continuous capture. Defaults to off, preserving today's behavior
exactly; hardware wiring/layout and the raw data schema are documented
under docs/developer/ pending PandA hardware access to configure and
validate against.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Reorders omny.md's parameter table to match the actual signature,
adds the previously undocumented readout_time parameter, and adds an
Examples block to OmnyFermatScan's docstring (mirroring the flomni fix).
Also rewords flomni.md's corridor_size default to read "3 um" for
consistency with omny, while noting it is auto-estimated when omitted.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FFeiCHv3qUxxssmP9Qzhom
Reorders parameters to match the actual signature, adds the
undocumented burst_at_each_point parameter, and corrects the
corridor_size default (None/auto-estimated, not a literal 3 um).
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FFeiCHv3qUxxssmP9Qzhom
Port the flomni doc addition to omny -- both setups share the identical
tomo_alignment_fit mechanism (OMNYAlignmentMixin.get_alignment_offset
mirrors Flomni's), so the same command-line offset nudge applies verbatim.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FFeiCHv3qUxxssmP9Qzhom
Add a snippet to the XrayEye alignment section showing how to patch the
constant x/y offset terms of tomo_alignment_fit directly on the command
line, for a quick few-micron correction (e.g. after moving foptz) without
recording a new fit.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FFeiCHv3qUxxssmP9Qzhom
find_rotation_center_smear_experimental() rotated 45->0 for its post-shift
verification sweep, needlessly re-treading ground the preceding full smear
sweep already covered and adding a long extra blocking move that could
starve the GUI heartbeat past _gui_call_with_retry's budget, surfacing as
RuntimeError: GUI is not alive. Sweep straight back to 0 instead, and widen
the retry budget (8x1.5s -> 25x2.0s) so update_frame() can ride out long
blocking moves on slower hardware.
Also tidy a stray comment-block artifact in ptycho_lamni.yaml and update
lamni.md docs for the current xrayeye_rotation_center_calibration_* API.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
- Remove the manual fit-parameter reload docs: fit params already load
automatically, and the fallback path pointed at the retired
~/Data10/specES1 layout.
- Fix stale slits/slit0wh references (slits takes no argument; the
gap monitor is now slit1).
- Stop writing the plain-text xrayeye_alignmentvalues archive in
write_output() -- it was only for external fitting scripts and now
collides with xrayeye_alignmentvalues being a directory used for the
per-run HDF5 archives.
Add docs/developer/lamni_smear_architecture.md covering the three-tier
device/ipython-client/GUI architecture this feature exercises: the
camera's two PreviewSignal channels (image vs smear_preview) and why
composite pushes needed their own channel, XRayEye.set_live_view_signal
and exactly when the caller must switch it back, the sweep algorithm
(non-blocking mv() + ScanReport.status polling + max-projection), and
the bw-generate-cli regeneration step required whenever a plugin
widget's USER_ACCESS changes (the cause of this session's confusing
AttributeError even after a full client/GUI restart).
Also expand the user-facing description in lamni.md with a note on the
live-updating composite display and a cross-reference to the new
developer page.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
rotation_center_calibration_start(sample_type="isolated") didn't match the
xrayeye_* naming convention used by the other X-ray eye entry points, and
the sample_type string enum was easy to forget (both the parameter name
and its accepted values). Split into two entry points instead:
lamni.xrayeye_rotation_center_calibration_isolated(keep_shutter_open=False)
lamni.xrayeye_rotation_center_calibration_extended(keep_shutter_open=False)
Both delegate to a shared _xrayeye_rotation_center_calibration() private
helper (single copy of the KeyboardInterrupt cleanup). Updated the user
docs to match; XrayEyeAlign.find_rotation_center()'s own sample_type
parameter is unchanged since it's internal shared implementation, not
what was being objected to.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
lsamx_center/lsamy_center have to be re-measured by hand for nearly every
new sample (the rotation stage is tilted on top of lsamx/lsamy, so the
effective axis position shifts with sample thickness/mounting). Add
XrayEyeAlign.find_rotation_center()/lamni.rotation_center_calibration_start()
to automate this using the existing X-ray eye GUI and lamni_move_to_scan_center
interferometer-feedback move:
- "isolated" sample: click particle centre at 0 and 180 deg, use the
midpoint (angle-tilt-independent) as the rotation axis position.
- "extended" sample: live 0->180->0 sweep for visual identification, single
click, then a verification sweep and an accept/iterate prompt.
Both write the result to lsamx/lsamy's "center" userParameter after
confirmation. Heavily verbose logging throughout since this is fundamentally
an interactive, hardware-in-the-loop procedure that can't be fully exercised
by automated tests.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Adds a worked example to both lamni.md and flomni.md showing a hook
loaded from a file that temporarily bumps tomo_countingtime and
tomo_shellstep every 5th projection within sub-tomogram 2 (tomo_type 1),
restoring both in a finally block -- demonstrating that a hook can
change any scan parameter, not just move devices like the existing
polarizer example. Notes that progress["subtomo"]/["subtomo_projection"]
work the same way for tomo_types 2/3, just with an open-ended
sub-tomogram count there instead of type 1's fixed 8.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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>
GUI test checklist: sections 6c/6d/6e (items 37-52) all passed
real-session testing, including the stale-"running" override fixing
an actual stuck job found live -- status line and section 1 items
updated. New section 6f (items 53-55) for the "Add current params to
queue" mid-edit warning, plus section 1 item 13.
Plan doc section 6.1: records the second live-vs-unsaved-edit
confusion (a second window, not just the panel's own button) and why
it's a warning, not a block, unlike Submit.
User manual: new paragraph distinguishing the params panel's "Add to
queue" from the queue window's "Add current params to queue", and
when the warning fires.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
User manual: notes that declining the fermat-scan confirmation now
fails the job instead of silently skipping a projection, plus how to
recover a job stuck at "running" (tomo_queue_delete has no status
guard; update_by_id to fix the status directly; the GUI's staleness
override).
AI_docs: plan section 3.4 records the second real incident (declined
confirmation silently returning) and its fix; section 6.3 records the
stale-"running" GUI guard fix. GUI test checklist gets section 6e
(test steps 48-52) and section 1 item 12, status line updated to flag
6c/6d/6e as not yet clicked through.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
User manual: new paragraph in the queueing section explaining the
button and that Submit/"Add to queue" still gate the actual write.
AI_docs: plan section 6.8 records the design (not a third write path,
confirm-before-discard, button-eligibility gating) and the
_enter_edit_mode_with() refactor; GUI test checklist gets section 6d
(test steps 42-47) and a new section 1 item 11, with the status line
updated to flag 6c/6d as not yet clicked through.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
User manual: notes that the hook (name + source, when registered)
appears in tomo_parameters(), the scilog entry, the PDF report, and
the progress-ring label, and clarifies that unregistering a hook does
not clear at_each_angle_hook -- confirmed expected behavior.
AI_docs test checklist: records that sections 3-6b passed real-session
testing (updating the stale "not yet clicked through" status), adds
section 6c (test steps 37-41) for the fixes found during that testing,
and updates section 1's summary (new item 10).
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Two additions to the at_each_angle hook writeup: registering a hook
stores the function object at that moment, not a live link to its
name, so editing the function later requires calling
register_at_each_angle_hook() again -- redefining it alone does
nothing. And tomo_scan_projection()/tomo_acquire_at_angle() are not
interchangeable (Fermat vs single-point); the example hook now calls
tomo_scan_projection() plainly (no more confusing _internal=True in
user-facing code) with a clear note on when to use the other one
instead, matching the new CLI/GUI warnings.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
User manual: explains the new "At-each-angle hook" dropdown and its
"None (default)"/"(not registered in this session)" states, plus that
an active hook shows on the status webpage.
AI_docs: updates section 3.4 (GUI widget added, webpage display
added, extended sim-validation note for the global-var publishing and
webpage payload) and the plan's top status line. GUI test checklist
gets a new section 6b (test steps 28-35: dropdown population/refresh,
Submit vs Add-to-queue behaviour, the "not registered" label, and the
webpage's queue-detail + Current-measurement rendering) and an updated
section 1 item 9 + top status line noting none of this is click-tested
yet.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Adds a "Custom behavior at each projection angle" subsection to the
Tomography section of the flOMNI user manual (docs/user/ptychography/flomni.md):
what a hook function looks like, a polarizer-modulation example, and
how to register/activate/deactivate/list/unregister one, with an
explicit warning about resetting at_each_angle_hook before queuing a
normal follow-up job. Also links it from the quick-start queueing
section. AI_docs/TOMO_QUEUE_COMMAND_JOBS_PLAN.md gets a new section
3.4 recording the design decision (session-only registry, not a
hardcoded one; a new _TOMO_SCAN_PARAM_NAMES entry, not a new job kind;
the GUI param-snapshot leak found and fixed while wiring this up; no
GUI widget yet).
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Adds a "Command jobs" reference section covering
tomo_queue_add_command(), the move/optimize_idgap action registry, the
mokev/idgap device allow-list, tomo_queue_show() output format, and
the idempotent-vs-prompt crash-resume behaviour, plus a pointer to it
from the quick-start queueing section.
Passing -1 stows the sample currently in the sample stage into a free
tray slot without mounting a replacement, matching the old control
system's sample_change(-1) behavior. Existing swap-path logic is
unchanged.
umvr_fsamy_tracked/umv_fsamy_tracked require feedback OFF but did not
enforce it. Add an _internal flag; for user/CLI calls, warn that feedback
must be off (active alignment may be lost), prompt (default yes), and
disable feedback on confirm. Internal callers pass _internal=True since
they already manage the feedback lifecycle (ftransfer_flomni_stage_out,
x_ray_eye_align height-centering and mvy jog).
zhang_y7