Feat/update lamni to flomni standards run1 #258

2026-07-12T18:14:29+02:00

holler commented

2026-07-12 18:14:29 +02:00

No description provided.

holler added 13 commits 2026-07-12 18:14:29 +02:00

feat(LamNI): migrate X-ray eye alignment from LabView/EPICS to BEC GUI d9004bffa7

- Add x_ray_eye_align.py: GUI-based alignment procedure collecting sample
  centre at 8 angles (0-315 deg, full 360 deg rotation), submitting x/y
  offsets to XRayEye widget fit tab, reading sinusoidal fit parameters back
  via omny_xray_gui device signals
- Update gui_tools.py: modernise to current BEC widget API (single new()
  call with object_name, _is_deleted() existence checks, add_ring() progress
  bar API, start/eta time display); add lamnigui_show_xeyealign_fittab()
- Update alignment.py: add read_xray_eye_correction_from_gui(), remove
  obsolete GUI-procedure methods now in x_ray_eye_align.py, fix __init__
  (remove orphaned _reset_init_values() call)
- Update lamni.py: add set_client() call in __init__, add
  xrayeye_alignment_start(keep_shutter_open) and xrayeye_update_frame()
  matching FlOMNI naming convention, import XrayEyeAlignGUI
- Fix LamNIMoveToScanCenter: replace arg_input/arg_bundle_size device-bundle
  pattern with required_kwargs; float dict keys caused msgpack >= 1.0
  ValueError with strict_map_key=True
- Update all lamni_move_to_scan_center() call sites to keyword arguments
- Update docs/user/ptychography/lamni.md: document new commands, remove
  MATLAB/LabView references

documentation update flomni fzp 797fbf32bd

refactor 0061aa1d32

path corrections ed1a47ceed

refactor f2cff67800

fix test 680a7c5813

wip for tests dbad0d00b8

fix omny docs e5425318b0

fix typo 610bb6bac5

feat(lamni): persist tomo scan progress via BEC global var e3ff5ffd48

Replace the plain self.progress dict with a global-var-backed
_ProgressProxy (same shape and key as FlOMNI's), so progress survives
a client restart. Adds heartbeat + idle-time-gap detection in
_tomo_scan_at_angle, ETA computation in _print_progress, and
tomo_start_time/reset handling in tomo_scan(). Adds
tomo_progress_reset() and _format_duration() for parity.

gui_tools.py's progress display already read these fields; no GUI
change needed.

feat(lamni): persist alignment lookup-table corrections

corr_pos_x/corr_pos_y/corr_angle (+ _2 iteration) become
global-var-backed properties (lamni_corr_pos_x, lamni_corr_pos_y,
lamni_corr_angle, ..._2) instead of plain instance lists that reset
on every client restart. No default correction file exists for
LamNI, so reset_correction()/reset_correction_2() just clear to
empty.

feat(lamni): add frames_per_trigger (burst mode) support

LamNIFermatScan already inherits from AsyncFlyScanBase and already
accepts/passes through frames_per_trigger -- only the client-side
plumbing was missing. Adds a validated, global-var-backed
frames_per_trigger property, threads it into
tomo_scan_projection()'s lamni_fermat_scan() call, and exposes it in
tomo_parameters(). Also folds it into the idle-time cadence estimate
alongside stitch tile count.

feat(lamni): add crosshair and structured HDF5 output to X-ray eye alignment

Set the alignment crosshair at the FZP centre (step k=0, raw pixel
coords), hidden on normal completion and on Ctrl-C abort.

update_frame() now actually captures and stores each frame
(previously not stored at all); roi_pixel_data is now collected at
every submit. write_output() additionally writes a timestamped HDF5
file (alignment_values, alignment_images, roi_pixel_data,
alignment_fit) alongside the existing plain-text archival file.

fix(lamni): stop resetting correction state on every XrayEyeAlign instantiation

A fresh XrayEyeAlign is constructed on every call to both
xrayeye_alignment_start() and xrayeye_update_frame(); resetting
corr_pos_x/y/angle and tomo_fit_xray_eye in __init__ meant the
latter -- meant as a lightweight frame check -- silently wiped valid
persisted correction data every time. Reset moved to the start of
align() itself.

fix(lamni): use dev.fsh instead of dev.omnyfsh for the alignment shutter

The shared XRayEye widget monitors and controls dev.fsh; the
alignment script was opening/closing a different device, which
would desync the GUI's shutter toggle from the actual hardware
state.

fix(lamni): correct stale self.align reference in MagLamNI.rotate_slowly

self.align no longer exists as an attribute now that
LamNIAlignmentMixin is mixed directly into LamNI. Use
self.tomo_fovx_offset/self.tomo_fovy_offset directly.

feat(lamni): align gui_tools with flomni's current parity fixes 8b4018359c

- Add lamnigui_stop_gui(), matching flomnigui_stop_gui()
- lamnigui_show_xeyealign(): check/enable cam_xeye live mode on every
  call, not just when the xeyegui widget is first created -- matches
  flomnigui_show_xeyealign()
- lamnigui_idle(): refresh the splash text on every call rather than
  only at first creation -- matches flomnigui_idle()

check list, to remove later

CI for csaxs_bec / test (push) Failing after 1m24s

Details

48f1ebb95f

fix(lamni): correct X-ray eye alignment DAP forwarding, offset reference point, and pixel calibration

CI for csaxs_bec / test (push) Failing after 1m36s

Details

CI for csaxs_bec / test (pull_request) Failing after 1m23s

Details

b76593e4ff

- 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).

bec_bl_push-gitea added 1 commit 2026-07-12 18:23:37 +02:00

fix(lamni): tolerate clients without a gui attribute in set_client

CI for csaxs_bec / test (push) Failing after 1m25s

Details

CI for csaxs_bec / test (pull_request) Failing after 1m29s

Details

6d29e05087

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.

bec_bl_push-gitea added 1 commit 2026-07-12 18:33:20 +02:00

test(lamni): update x-ray eye align tests to post-EPICS interface

CI for csaxs_bec / test (push) Failing after 1m26s

Details

CI for csaxs_bec / test (pull_request) Failing after 1m24s

Details

69b89fcd85

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.

bec_bl_push-gitea added 1 commit 2026-07-12 18:38:51 +02:00

test(lamni): stub xeyegui instead of the read-only gui property

CI for csaxs_bec / test (pull_request) Successful in 1m31s

Details

Read the Docs Deploy Trigger / trigger-rtd-webhook (push) Successful in 2s

Details

CI for csaxs_bec / test (push) Successful in 1m32s

Details

3dbd9313ed

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.

holler merged commit 3dbd9313ed into main

2026-07-12 19:07:18 +02:00

holler deleted branch feat/update_lamni_to_flomni_standards

2026-07-12 19:07:18 +02:00

Sign in to join this conversation.

2 Participants

Notifications

Due Date

No due date set.

Dependencies

No dependencies set.

Reference: bec/csaxs_bec#258