Fix/minor fixes lamni #278

2026-07-27T17:52:57+02:00

holler commented

2026-07-27 17:52:57 +02:00

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holler added 28 commits 2026-07-27 17:52:57 +02:00

docs+fix(LamNI): trim obsolete xrayeye doc section, drop archival text file

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2f07c3e251

- 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.

feat(LamNI): notify BEC client before long lsamrot reset-moves f736900a52

feedback_enable_with_reset() silently rotates lsamrot back to 0 as part
of the interferometer reset; when the stage is far from 0 this can take
a while with no feedback in the client session. A plain print() there
only reaches the device-server console, not the client, so use
connector.send_client_info() instead.

fix(LamNI): drop duplicate debug print in interferometer readback 40002b9a48

RtLamniReadbackSignal._socket_get() printed the same raw socket
response twice in a row with nothing modifying it in between --
leftover debug output, not by design.

feat(LamNI): make camera live-mode poll interval configurable 0fef9157d3

IDSCamera's live-mode loop had a hardcoded 0.2s sleep (nominal 5 Hz
cap) between frame grabs. Expose it as live_mode_poll_interval_s
(default 0.2, unchanged for existing cameras) and lower it for LamNI's
cam_xeye (0.02s) so exposure/acquisition time, not this artificial
sleep, becomes the real limit on smear-sweep capture rate.

feat(LamNI): show and prompt for sample name in the XRayEye GUI 866891398f

The shared XRayEye widget already supports a sample_name field, but
LamNI's x_ray_eye_align.py never set it (unlike FlOMNI's align(),
which does) -- so it was always blank. Add _sync_sample_name(): pushes
lamni.sample_name into the GUI everywhere align()/find_rotation_center*
run, and additionally prompts for it (Enter keeps the current value,
same as tomo_parameters()) at the rotation-center steps, since those
are often the first alignment action for a new sample.

fix(tomo_params): block submit/queue-add when Fermat scan is below minimum 574a1bdde8

The estimated Fermat-scan point count was only ever flagged with an
orange label -- Submit and Add-to-queue would both happily accept a
configuration that's guaranteed to abort when actually run. Enforce
the same minimum in _validate(), shared by both actions, so it's now a
hard block instead of a cosmetic warning.

fix(LamNI): stop double-printing the Xeye correction table 33c9c0e433

lamni_compute_additional_correction_xeye_mu() always printed its
result. write_alignment_scan_numbers() called it once per angle just
to grab the x-offset for the log file, which dumped all 12 corrections
up front -- immediately followed by the exact same values reprinted
one-by-one as tomo_alignment_scan() actually runs each angle. Add a
verbose flag (default True) and pass verbose=False from the lookahead
call.

feat(LamNI): add ring-progress display for tomo_alignment_scan() b5655fd6eb

tomo_alignment_scan() had no GUI feedback at all -- just console
prints -- unlike the real tomogram, which already drives a
RingProgressBar via lamnigui_show_progress(). Add the same kind of
single-ring display for the 12-angle alignment loop
(lamnigui_show_alignment_progress()/_lamnigui_update_alignment_progress()),
backed by its own alignment_scan_progress global var rather than
tomo_progress, so anything watching tomo_progress for the real
tomogram (heartbeat/idle-time tracking) never sees alignment-scan
writes mixed in.

feat(OMNY): upload tomo PDF report to the samples web folder cdc20457f1

Replaces the old, already-broken upload_last_pon.sh shell-out (and
assorted other dead/abandoned upload attempts left commented out in
flomni.py) with a direct HTTP upload: POSTs the just-written PDF,
base64-encoded, to omny-test.psi.ch/samples/upload.php with
filename="new.pdf" so the server assigns the number itself from its
own counter file -- the same counter newmeasurement.php
(TomoIDManager.register(), called via add_sample_database() just
before write_pdf_report()) already incremented and returned as
self.tomo_id. Runs in a background thread so a slow/unreachable host
never delays the calling tomo_scan(), and cross-checks the response
against the expected filename to flag a possible race with a
concurrent registration.

Added to TomoQueueMixin (OMNY_shared) rather than duplicated in both
LamNI and Flomni, following add_sample_database()'s existing pattern
of shared, setup-agnostic tomo-id/database logic.

fix(flomni): stop calling write_pdf_report() twice per scan start

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297b0dd7d3

tomo_scan()'s new-scan branch called write_pdf_report() once inside
the "real e-account" if-branch and again unconditionally right after,
so every scan start under a real account wrote the PDF, sent the
scilog entry, and (as of the previous commit) uploaded to the samples
folder twice. Keep only the unconditional call, matching LamNI's
equivalent structure.

feat(LamNI): invalidate X-ray-eye/fine alignment on a new rotation centre 9fc0770055

Re-running rotation-center calibration after X-ray-eye alignment (or
fine alignment) was already done left the stale fit/correction in
place, silently calibrated around the old center. Record
lamni_center_found_at and cascade-invalidate via the existing
reset_xray_eye_correction()/reset_correction() whenever a new center
is actually applied, in both find_rotation_center() and
find_rotation_center_smear_experimental().

feat(LamNI): warn (overridable) when alignment steps are stale or missing e911f8d5e3

Nothing previously enforced the intended sequence: rotation-center
calibration -> X-ray-eye alignment -> fine alignment scan -> real
tomogram. Add three soft gates -- xrayeye_alignment_start() (no center
found yet), tomo_alignment_scan() (X-ray-eye fit missing/invalidated,
softened from a hard abort), and tomo_scan() (no fine alignment
loaded) -- each printing a specific warning and prompting to continue,
via a new shared _confirm_sequence_override() helper. Not a hard
block: each method also gets force: bool = False to skip the check
entirely for cases that legitimately don't need it (e.g. a large FOV
that doesn't need fine alignment).

feat(OMNY): register test-account measurements against the test server b95c284de9

TomoIDManager.register() used to skip OMNY registration entirely for
any non-e-account (e.g. test accounts), always returning the tomo ID
0 fallback. Register against a new TEST_OMNY_URL (omny-test.psi.ch)
instead for those accounts, so testing still gets a real, incrementing
tomo ID matching the counter the samples-folder PDF upload reads from
on that same host -- accepting a mismatched eaccount in that test
database. FALLBACK_TOMO_ID is now reserved for genuine failures
(server unreachable), not merely a non-standard account name.

fix(OMNY): skip PDF upload without a real tomo_id, widen error logging fe47059f88

tomo_id == FALLBACK_TOMO_ID (0) means add_sample_database() never
actually registered a measurement server-side, so there's no reserved
"new.pdf" slot -- uploading anyway would silently claim whatever
number countersaver.txt currently holds, i.e. an unrelated real
measurement's slot. Skip with a clear message instead. Also widen the
truncated response text in the upload warning/log messages (120 -> 400
chars), which had cut off the file+line a real PHP error would show,
making a live parse-error response undiagnosable from the client log
alone (as happened while testing this).

feat(OMNY): add OMNYTools.printredbold() 64f5a57fa1

Mirrors the existing printgreenbold() -- needed for the tomo_scan()
unattended-queue warning (bold red instead of bold green).

fix(LamNI): don't block the tomo queue on the fine-alignment check 1159b018f0

tomo_queue_execute() runs queued scans unattended, potentially for
hours -- tomo_scan()'s fine-alignment prompt would block forever there
with nobody watching. Add interactive: bool = True; when False (queue
use), the check no longer prompts or aborts -- it prints a bold red
warning, waits 10s, and always proceeds.

Also remove the outer "bec.active_account != ''" short-circuit that
hard-coded tomo_id=0 for an empty account without even attempting
registration -- always call add_sample_database() now and let
TomoIDManager.register() (test-host registration, previous commit)
decide the right outcome instead of pre-empting it here.

fix(flomni): always attempt tomo_id registration, accept interactive kwarg d97692e090

Mirrors LamNI.tomo_scan()'s same fix: remove the outer
"bec.active_account != ''" short-circuit so an empty/test account still
goes through add_sample_database() -> TomoIDManager.register() (which
now handles test-host registration itself) instead of hard-coding
tomo_id=0. Also accept an unused interactive kwarg for signature
compatibility with LamNI.tomo_scan(), since tomo_queue_execute() (shared
between both setups) calls tomo_scan(interactive=False) uniformly.

fix(OMNY): call tomo_scan(interactive=False) from tomo_queue_execute()

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3422eedcc1

Wires the queue-safe fine-alignment warning (previous LamNI/Flomni
commits) into the actual queue dispatch path.

fix(OMNY): use requests instead of shelling out to wget for tomo ID

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eb61df1c93

TomoIDManager.register() called wget via subprocess with shell=True,
interpolating sample_name/eaccount/etc. unescaped into the command
string -- broke outright wherever wget isn't installed (as hit while
testing: "wget: command not found", silently falling back to tomo ID
0), and was a latent shell-injection risk. Use requests.get() with a
params dict instead: no external binary dependency, proper URL
encoding, and the same self-signed-cert/SSRF handling already used by
the samples PDF upload. Drops the now-unused OMNYToolsError class and
TMP_FILE/subprocess, which only existed to support the wget call.

fix(LamNI): use the real setup logo in the PDF report, fix column gaps f8ced692d3

Replace the ASCII-art header with the actual LamNI.png logo, embedded
via PDFWriter's underlying fpdf object (bec_lib's PDFWriter has no
public image API). Also fix the label/value formatting: values were
right-justified in a wide fixed field, leaving a big ragged gap after
short labels -- left-justify both instead for a clean, tight
"label: value" layout.

Also fixes a real bug found along the way: the scilog attachment
referenced "LamNI_logo.png", a file that has never existed (the actual
file is LamNI.png) -- the resulting FileNotFoundError was swallowed by
write_pdf_report()'s generic try/except, so the scilog message has
been silently failing to send every time. Now uses the one correct,
shared logo_path for both the PDF and the scilog attachment.

fix(flomni): use the real setup logo in the PDF report, fix column gaps

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97ea67b01a

Mirrors LamNI.write_pdf_report()'s same fix: replace the ASCII-art
header with the actual flOMNI.png logo (already correctly resolved
for the scilog attachment, just never used in the PDF itself),
embedded via PDFWriter's underlying fpdf object. Also left-justify
values instead of right-justifying them in a wide fixed field, to
remove the big ragged gap after short labels. Drops a leftover debug
print(logo_file).

refactor(OMNY): move omny_general_tools.py into OMNY_shared

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6954fbb7f4

OMNYTools, PtychoReconstructor, and TomoIDManager were sitting under
the omny plugin's own directory, but are imported by LamNI, FlOMNI,
and cSAXS too -- none of the three classes reference anything
OMNY-specific (device names are always passed in as parameters).
OMNY_shared already exists for exactly this kind of cross-setup code
(tomo_queue_mixin.py, web_common.py, webpage_generator_base.py), so
move it there and update all five import sites. Pure relocation, no
behavior change.

config(LamNI,flomni): add FZP diameter/zone-width/detector-distance params 8b3a65606c

Adds fzp_diameter (170 micron), fzp_outermost_zone_width (60 nm), and
detector_distance (-1, unknown for now) as userParameter entries on
loptx/foptx. LamNI's values match FlOMNI's already-documented active
FZP (per its "#170 micron, 60 nm" comment) -- confirmed with the user
that LamNI currently uses the same optic. Feeds the new PDF report
fields in the next commit.

fix(LamNI): lfzp_info() printed focal distance in meters labeled as mm e7df1209d1

focal_distance was computed in meters (consistent with the rest of the
function, e.g. beam_size's own internal *1000 conversions), but the
table row printed it directly as "X.XX mm" with no conversion -- off
by 1000x (e.g. showing "0.05 mm" instead of "51.34 mm"). FlOMNI's and
OMNY's equivalent ffzp_info()/ofzp_info() already convert correctly;
fix just the display here to match, without touching the
meters-based internal variable beam_size still depends on.

feat(LamNI,flomni): add FZP optics info to the PDF report 1b6b6a41a1

Adds FZP diameter, outermost zone width, focal distance,
focus-to-sample distance, and sample-to-detector distance to
write_pdf_report(). Diameter/zone-width/detector-distance come from
the userParameter entries just added to loptx/foptx; focal distance
is computed with the same formula lfzp_info()/ffzp_info() already use
(diameter * zone_width / wavelength); focus-to-sample distance reuses
their existing live z-stage-based calculation rather than storing a
separate value. Replaces this exact old SPEC workflow
(_tomo_other_parameters interactively asking for these same numbers
every time) with values read automatically from config + live
hardware.

Also fixes FlOMNI's "Current photon energy: To be implemented"
placeholder (never wired up) -- needed a real value for the new focal
distance calculation anyway, and dev.ccm_energy is the same device
ffzp_info() already reads.

fix(LamNI,flomni): FZP diameter/zone-width wrongly blanked to N/A 6c06b63ece

fzp_diameter_um/fzp_zone_width_nm were read inside the same try block
as the focal-distance calculation, which also needs energy_kev. When
the photon energy read fails (as it does in at least one simulated
session -- confirmed live: dev.ccm_energy unavailable), the exception
wiped out the diameter/zone-width display too, even though those come
from config (loptx/foptx userParameter) and were read just fine.
Split into two independent try blocks: diameter/zone-width no longer
depend on a working energy read, only the focal distance itself does.

feat(LamNI,flomni): add PSI logo to every PDF report page footer 79f257f072

Downloaded from https://intranet.psi.ch/themes/custom/design/logo.svg
(no gradients/filters/embedded fonts -- confirmed fpdf2 renders it
directly, no PNG conversion needed) and stored as psi_logo.svg in
OMNY_shared. Added TomoQueueMixin._add_psi_footer(), which overrides
the fpdf instance's footer() callback (PDFWriter/BECPDF live in
bec_lib, a separate repo with no public API for this) so the logo
repeats on every page -- unlike the header logo, which is drawn once
inline, a report can span multiple pages (e.g. a long
at_each_angle_hook source dump). Also drops the microseconds from the
existing "BEC, <timestamp>" footer text while reimplementing it, per
request ("ms precision is not needed"). Verified end-to-end with
bec_lib's real PDFWriter: a 300-line hook source forced a 7-page
report, with the logo correctly repeating on every page.

config(LamNI,flomni): add FZP params to the simulated device configs too

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56467682a9

simulated_lamni.yaml/simulated_flomni.yaml define their own separate
loptx/foptx (not shared with ptycho_lamni.yaml/ptycho_flomni.yaml) --
missed these when adding fzp_diameter/fzp_outermost_zone_width/
detector_distance earlier, so a simulated-only session wouldn't have
had them. Same values (170 micron, 60 nm, -1).

holler scheduled this pull request to auto merge when all checks succeed 2026-07-27 17:53:08 +02:00

holler canceled auto merging this pull request when all checks succeed 2026-07-28 09:35:04 +02:00

bec_bl_push-gitea added 1 commit 2026-07-28 09:54:02 +02:00

fix(LamNI): update tests for prompts/kwargs added earlier this branch

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13e9cb21e4

Several tomo_scan()/tomo_alignment_scan()/find_rotation_center() tests
started failing (CI) after recent commits on this branch introduced new
input()-backed confirmation/sample-name prompts, an
alignment_scan_progress GUI proxy, and tomo_queue_execute()'s
interactive=False kwarg -- none of which the existing test fixtures or
assertions were updated for. Mock/bypass the new prompts and GUI calls,
add the missing _alignment_scan_progress_proxy to the bare-object test
fixture, and update two assertions (tomo_queue interactive kwarg,
account-less sample registration) to match the intended new behavior.

holler merged commit 13e9cb21e4 into main

2026-07-28 09:56:28 +02:00

holler deleted branch fix/minor-fixes-lamni

2026-07-28 09:56:32 +02:00

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Reference: bec/csaxs_bec#278