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>
Select a single tomo job (command jobs have no params, so they're
excluded) in the queue dialog and click "Load into editor" to enter
edit mode on the params panel populated from that job's saved
snapshot instead of the live backend. Reuses the existing edit-mode
machinery (_enter_edit_mode_with(), factored out of enter_edit_mode())
so the operator reviews/tweaks and then uses the normal Submit or "Add
to queue" paths -- no new write path, nothing touches live params or
the queue itself just by loading. If an edit is already in progress,
confirms before discarding it. The button is disabled outside a
single-tomo-job selection and during sort mode, and re-evaluated on
selection change and on every table refresh.
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>
Qt's own vertical header (1-based) sat to the left of the dialog's own
0-based "#" column (which matches the CLI's indices -- tomo_queue_show(),
tomo_queue_delete(), tomo_queue_move()) -- two differently-based
indices next to each other read as confusing/wrong. Hides Qt's
gutter, keeping only the one that actually means something.
Also shows a tomo job's active at_each_angle_hook in the Details
column (e.g. "hook: name" or "hook: name (not registered)", checked
against the published tomo_at_each_angle_hooks list) -- previously
Details was always blank for tomo jobs, so a hook-driven queued job
looked identical to a plain one without expanding the row tooltip.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
flomnigui_show_progress()'s center label now includes a "Hook: name"
line when at_each_angle_hook is set, same condition/wording as
tomo_parameters()'s CLI note -- an operator watching the progress GUI
during an unattended queue run can tell a hook is active without
switching to a CLI session.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Adds _describe_active_hook() (flags a name that isn't currently
registered, e.g. after unregister_at_each_angle_hook() while
at_each_angle_hook still references it -- confirmed this is expected:
unregistering only removes it from the runtime dict, the property
itself is untouched) and _active_hook_source() (inspect.getsource(),
None if unavailable). Wired into:
- tomo_parameters()'s printed hook line, now flags "NOT registered"
- the end-of-scan scilog entry (name in the printed/scilog text,
source code appended to the scilog text only, not the console)
- write_pdf_report() (name as a report line, source appended to both
the PDF file and the scilog entry it sends)
So a hook-driven measurement's actual behavior is part of the
permanent record, not just inferable from a name that might not even
resolve anymore. Sim-verified all six states (unset, registered,
unregistered) for both helpers.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Previously the tomo_acquire_at_angle()-vs-tomo_scan_projection()
reminder only printed when tomo_parameters() happened to be called
afterward -- easy to miss if you just flip
single_point_instead_of_fermat_scan directly. Its setter now prints
the same note immediately when the value transitions False->True.
Gated on the transition (checked via the property's own getter before
the write) so restoring an already-True value across consecutive
queued jobs doesn't reprint it every time -- sim-verified: silent on
False->False, True->True (repeat), and True->False; prints exactly
once per False->True flip.
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>
Adds a wrapped, styled warning label under "Random shift max" in the
params panel, shown whenever "Single-point scan" is checked and hidden
otherwise -- same reminder tomo_parameters() now prints on the CLI
side: use tomo_acquire_at_angle(angle), not tomo_scan_projection(angle),
when single-point mode is on. Toggled from the existing
_on_single_point_changed() handler, so it updates on both a live edit
and every params-panel refresh (the widget's checkbox state already
drives this handler either way).
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
tomo_scan_projection() always runs a Fermat scan and tomo_acquire_at_angle()
always runs a single-point acquisition -- they aren't interchangeable, and
calling tomo_scan_projection() directly while single_point_instead_of_fermat_scan
is on triggers an interactive confirmation prompt that would hang an
unattended queue run. tomo_parameters() now prints a reminder of which one
to call (including inside a custom at_each_angle hook) whenever single-point
mode is enabled, surfacing this proactively instead of only at the point of
the runtime prompt.
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>
TQ_PARAM_DISPLAY (the queue job detail table) and _CURRENT_PARAM_KEYS
(the live 'Current measurement' section) are both hardcoded mirrors of
which tomo params to render -- at_each_angle_hook wasn't in either, so
a hook-driven job wouldn't crash the page but also wouldn't show that
anything non-standard was running. Adds at_each_angle_hook to
_CURRENT_PARAM_KEYS (Python side, gates inclusion in the JSON payload
on the value actually being set) and a conditional row in
buildParamRows() (JS side, only rendered when the value is present --
deliberately left out of TQ_PARAM_DISPLAY so a normal job doesn't grow
a "-" row nobody needs). Sim-validated: current_params includes
at_each_angle_hook when set and omits it when not.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
A new "At-each-angle hook" combo box in the params panel, built from
the live tomo_at_each_angle_hooks global var (no hardcoded mirror of
registered names). Rebuilt on every populate (i.e. every 2s poll while
not editing, and on entering edit mode), so hooks registered/
unregistered from the CLI while the dialog is open show up
automatically. The currently-set hook is always shown even if it
isn't in the published list (e.g. registered in a different or
since-restarted session), labeled accordingly, so it's never silently
hidden. Special-cased in _populate_fields()/_read_fields() like
tomo_type -- the generic QComboBox handling assumes integer data,
which doesn't fit a hook name string or None. This also makes the
manual params["at_each_angle_hook"] pass-through in
add_edited_to_queue() (added when there was no widget for this field)
redundant; removed, since _read_fields() now supplies it directly
from the dropdown.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Adds tomo_at_each_angle_hooks (a plain list of names), republished on
every register_at_each_angle_hook()/unregister_at_each_angle_hook()
call and reset to empty in __init__ (hooks are session-only, so a
stale list from a prior session must not linger). Same reasoning as
tomo_queue_actions for the command-job registry: a GUI (or any other
client) can build a dropdown from this directly, no hardcoded mirror.
Sim-validated: register/unregister updates the published list
correctly and the webpage generator's current_params payload picks up
an active hook.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Notes what was actually exercised against the live sim (registration/
list/unregister, per-job param snapshot including the reset-to-None
case, the hook firing during a real tomo_queue_execute() run, and the
unregistered-hook incomplete/resume path) and the scan_repeat retry
bug found and fixed along the way.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Found by testing the new at_each_angle_hook feature against the live
sim: _tomo_scan_at_angle is wrapped in @scan_repeat(max_repeats=10,
default=True), which retries *any* exception, including a FlomniError
raised for an unregistered hook -- a condition that will never
succeed by retrying. The operator saw 10 silent retries before a
generic "TooManyScanRestarts", with the actual, actionable error
message buried in __cause__ instead of reaching
tomo_queue_execute()'s printed failure message. Adds an exc_handler
that skips the retry for any FlomniError (a definite, non-transient
failure by convention throughout this file), letting the real message
surface immediately. General fix, not narrowly scoped to hooks --
every other FlomniError this method could raise gets the same benefit.
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>
TomoParamsWidget/TomoQueueDialog mirror flomni.py's snapshotted-param
list by hand (QUEUE_PARAM_NAMES/DEFAULTS) and it hadn't picked up the
new at_each_angle_hook parameter. Left as-is, a GUI-added job's params
dict would have no at_each_angle_hook key at all, so the executor's
per-job setattr loop would never touch it -- silently leaving whatever
hook the *previous* queued job had active in place for a job that
never asked for one. Adds the key to QUEUE_PARAM_NAMES/DEFAULTS (fixes
"Add current params to queue", which reads live global vars) and has
add_edited_to_queue() explicitly pass the live value through (there's
no editable widget for it yet, so it can't come from the form fields).
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Flomni._at_each_angle() already had an escape hatch for custom
per-projection behaviour (a flomni_at_each_angle function checked via
builtins), but it's invisible to the tomo queue -- not a snapshotted
parameter, so a queued job had no way to select it. Adds a
session-only registry (register_at_each_angle_hook/unregister/list)
populated from the IPython session, plus a new snapshotted
at_each_angle_hook parameter so a tomo-queue job can carry its own
hook selection through add/execute/resume like any other tomo param.
Curated means the queue only ever stores a hook *name*, never code --
_at_each_angle() raises a clear error rather than silently falling
back to default behaviour if a job's named hook isn't registered in
the session running the queue (hooks don't survive a kernel restart).
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Updates plan section 6.4 and the GUI test checklist (item 5, new test
step 23a) for narrowing sort-mode/tomo_queue_move() reordering to
pending-only, with running and incomplete both acting as a floor.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Sort mode and tomo_queue_move() let a pending job be dragged/moved
visually ahead of an incomplete one. Harmless to actual run order --
tomo_queue_execute()'s pick-next loop always resumes the first
running/incomplete job it finds regardless of list position -- but
confusing to read, since list order looked like run order and wasn't.
Narrows the GUI's _MOVABLE_STATUSES to ("pending",) and the CLI's
floor check to the highest index among all running/incomplete jobs,
not just the running one. Found while testing the reorder feature
against a real interrupted scan.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
feye_out() unconditionally moved dev.fttrx1 out of the way, raising
an unhandled DeviceConfigError on any session (e.g. sim) where that
device isn't configured, after already having closed the shutter and
moved other optics. Now checks "fttrx1" in dev first (same pattern
already used for rtx elsewhere in this file) and, if absent, asks via
OMNYTools.yesno() whether to continue without moving it instead of
crashing.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Updates plan section 6.1 (marks the two-write-paths rule as actually
implemented now) and the GUI test checklist (section 1 item 8, and
flags section 3 item 4 as needing re-testing since its old passing
result was against the since-replaced soft-warn Submit behaviour).
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Previously the only way to queue a new tomo parameter set was to
Submit it live first (writing the running scan's global vars) or use
the separate queue dialog's "Add current params to queue", which
snapshots the live vars and silently ignores any unsubmitted edit --
so there was no way to prepare a new parameter set in the GUI while a
scan was running without perturbing it.
Edit mode now shows an "Add to queue" button that packages the
current (possibly unsubmitted) form fields as a new pending tomo job,
writing only tomo_queue -- never the live param vars -- so it's always
allowed. Submit becomes a real hard block while the beamline is busy
instead of a Yes/Cancel confirmation, now that there's somewhere else
to put an in-progress edit (TOMO_QUEUE_COMMAND_JOBS_PLAN.md section
6.1's two-write-paths rule, finally enforced as written).
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
tomo_scan() called bec.messaging.scilog directly with no guard, so a
session without scilog enabled raised RuntimeError from inside
tomo_queue_execute() -- marking the job "incomplete" and pausing the
whole queue over a logging side effect unrelated to whether the
tomogram succeeded. Adds _scilog_write(), mirroring the enabled-check
already used for the PDF report entry, and routes the three unguarded
call sites (tomo_scan, scilog_last_ptycho_scans, the alignment-scan
entry) through it.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Updates plan section 6.7 and the GUI test checklist (section 1 item 7,
new test step 27) for the Label/Details stretch columns and the
dropped Added-at column.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
All 9 columns previously shared equal Stretch width, squeezing the two
free-text columns (Label, command-step Details) down to the same width
as short fixed-content ones like Type or Exp (s). Short columns now
auto-fit their content; Label and Details stretch to fill what's left
and left-align instead of centering. Also drops the Added-at column --
that value is still available via the row tooltip added earlier.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Previously start() did nothing at all when the BEC account didn't
match the system user (e.g. a dev/sim session run under a different
account) -- now it starts a status page on a separate fallback port
(default 8081) for local debugging, while still skipping everything
that assumes the active account is the "real" one for this host: the
cross-session singleton lock, remote upload, and session.htpasswd
changes. Not yet tested against a live/sim session.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Updates the command-jobs plan (status line, section 6.4's
implementation note, new section 6.7, commit breakdown) and the GUI
test checklist (section 1's what-was-built list, a new section 6a
with test steps 19-26, and the corrected known-limitations entry) to
reflect tomo_queue_move and the sort-mode/tooltip GUI work. Neither
has been validated against a live session yet.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Adds a checkable "Sort queue..." mode: other queue-mutating buttons
disable, the table goes single-select, and Move up/down swap the
selected row with an adjacent one -- but only between two
pending/incomplete rows, so a running or done neighbour blocks the
swap (gets the running-job floor and done-row pinning from
TOMO_QUEUE_COMMAND_JOBS_PLAN.md sections 6.3/6.4 without drag-and-drop
math). Also gives every row a full-detail tooltip (label, status,
steps/params, added-at) so hovering surfaces what the Label/Details
columns truncate at typical dialog widths.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Lets a queued job be moved to a new position via the CLI, refusing to
touch a running/done job and refusing any move that would displace the
currently running job (a hard floor, per the mid-run-reorder design in
AI_docs/TOMO_QUEUE_COMMAND_JOBS_PLAN.md section 6.4).
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
TOMO_QUEUE_GUI_TESTING.md is the manual verification plan for the new
command-job builder: baseline regression checks, the builder itself,
the status-keyed delete/clear guards, and an end-to-end mixed-queue
run, plus this iteration's known gaps (no mid-run reorder, one device
per move step, no live limit validation). Nobody has clicked through
the actual widget against a live session yet - it's built and
smoke-tested at the logic level only, not GUI-validated.
Section 8 covers continuing this work after leaving the current coding
session: a Claude Project with AI_docs/ attached as project knowledge
is for planning/discussion, a Claude Code session attached to this
repo is what's actually needed to keep editing tomo_params.py - and a
ready-to-paste prompt for starting that next session.
Also updates TOMO_QUEUE_COMMAND_JOBS_PLAN.md's status line: Step 3 has
a first iteration built, not the "not started" it said before.
First iteration of Step 3 (TOMO_QUEUE_COMMAND_JOBS_PLAN.md section 6)
on top of the existing TomoParamsWidget/TomoQueueDialog baseline:
- CommandJobBuilderDialog: a structured step-by-step form (action
dropdown, per-action fields) built entirely from the live
tomo_queue_actions global var, so it tracks flomni.py's action
registry and device allow-list with no hardcoded mirror. Produces a
job dict identical to what tomo_queue_add_command() writes.
- TomoQueueDialog's queue table gained a "Details" column and renders
command jobs (CMD + step summary + idempotency marker) the same way
flomni.tomo_queue_show() does.
- "Add current params to queue" now stamps kind="tomo" and a fresh id
on the job, matching the CLI's own self-describing format.
- Delete/clear now refuse when a "running" job is involved instead of
silently allowing it (plan section 6.3).
Mid-run drag-reorder of queue jobs (plan section 6.4), multi-device
single move steps, and live device-limit validation are deliberately
not in this iteration - see TOMO_QUEUE_GUI_TESTING.md.
Generalizes the patterns and gotchas learned building the flOMNI
tomo-queue e2e suite (main-thread-only live-update machinery, the
builtins/reload import-order bootstrap, neutralizing real side
effects, the demo-config trap in pytest_bec_e2e's shipped fixtures,
the omny_e2e_tests/ folder convention, and the Redis
cross-test-contamination fixture bug) into a standalone reference for
adding e2e coverage to any plugin in this repo, not just flomni.
Intended to be added to a Claude Project alongside this repo so a
coding assistant finds it and follows these patterns instead of
re-deriving them from scratch.
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.
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.
Sections A-C of TOMO_QUEUE_TESTING.md's checklist, run against a live sim
session: params-restored-per-job, legacy queue migration, empty/all-done
no-ops, start_index semantics, exception/SIGKILL crash-resume, resume-
before-fresh ordering, and concurrent queue edits from a second client.
All 10 tests pass together with no cross-test interference.
The flomni_sim fixture and _bootstrap.py factor out what it takes to
construct a live Flomni against the sim (builtins/reload bootstrap,
side-effect neutralization, RT-feedback/fsamx setup) for reuse by both
in-process tests and the SIGKILL-based subprocess tests.
Also adds the AI_docs/ handoff docs (testing checklist results, command-
jobs plan with the action-registry decisions) that this work updated.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
The constant lists live scan properties snapshotted/restored by the tomo
queue, not queue state itself -- the old name was misleading. Confirmed
with Mirko. Updates the matching comment in tomo_params.py, which mirrors
this tuple as QUEUE_PARAM_NAMES (unchanged name, own mirror constant).
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
XrayEyeAlign.gui is a property delegating to lamni.xeyegui and has no
setter. Mock lamni.xeyegui in the update_frame tests; drop the redundant
alignment_images reset, which __init__ already handles.
Drop test_save_frame (method no longer exists). Rewrite test_update_frame
against dev.fsh/dev.cam_xeye instead of the removed LamNI.alignment module.
Patch the module-level umv in test_tomo_rotate rather than builtins.
LamNI.__init__ calls set_client(), which unconditionally accessed
client.gui. This broke test_x_ray_eye_align.py under ClientMock, which
has no gui attribute. Use getattr with a None default; behaviour on a
real BEC client is unchanged.
- Enable DAP fit parameter forwarding (self.gui.set_dap_params_forwarding),
never called before -- without it the dap_params_update signal was never
connected, so no fit data could ever reach fit_params_x/y regardless of
how long anything waited. Disabled again once the fit is read (or on
abort, via the existing KeyboardInterrupt cleanup in lamni.py).
- Replace the fixed 5s sleep before reading the DAP fit with
_wait_for_dap_fit(), which polls fit_params_x/y for the real converged
shape (up to 30s) instead of guessing a duration.
- Fix write_output()'s offset reference: was using one of the 8 angle
points as its own zero-reference (first via an off-by-one at k=1, then
at k=2), which forces that point's offset to exactly 0 by construction
and biases the fit. Now references alignment_values[0] (the FZP centre,
the only angle-independent point in the procedure), matching both
FlOMNI's own reference point and the original SPEC macro
(l_xrayeyealign.mac) exactly, including the asymmetric x/y sign
convention.
- pixel_calibration is now a property reading the cam_xeye device's
pixel_calibration user parameter, matching FlOMNI's camera-sourced
calibration, with the old hardcoded constant kept only as a fallback
(PIXEL_CALIBRATION_DEFAULT) -- by design, to match FlOMNI's own pattern.
- lamni_optics_mixin.py: lfzp_in() and loptics_out() now print before/after
re-establishing interferometer feedback, previously silent.
- device_configs: add the missing userParameter.pixel_calibration to
cam_xeye in ptycho_lamni.yaml and simulated_omny/simulated_lamni.yaml
(present on the FlOMNI side already; this is what the pixel_calibration
property above actually reads at runtime).
