x01dcandClaude Sonnet 5 906e9f5318
CI for csaxs_bec / test (push) Failing after 5s
feat(omny): port tomo-queue backend from flomni/lamni (Phase 1 of 2)
Mirko wants the tomo params GUI widget available for OMNY before running
real tomo scans. That widget (Phase 2, separate follow-up) needs a working
job queue and scan progress visible outside the CLI session that started
it -- neither existed for OMNY. OMNY now inherits TomoQueueMixin
(OMNY_shared/tomo_queue_mixin.py), the same shared backend flomni/lamni
already use, giving it tomo_queue_add/delete/move/clear/show/execute/
reacquire, at_each_angle_hook registration, and tomo_scan_resume() for the
first time.

self.progress is now a global-var-backed proxy (_ProgressProxy, byte-for-
byte port of flomni's/lamni's own), not a plain in-memory dict -- the
load-bearing change the queue mixin and the eventual widget's busy-banner
both depend on. tomo_queue_mixin.py's tomo_queue_reacquire() hardcoded
tomo_type == 1; generalized via a new _TOMO_TYPE_1_LIKE class attribute
(default frozenset({1}), flomni/lamni unaffected) since OMNY has three
"equally spaced sub-tomograms" flavors (types 1/4/5), not just one.

Along the way, fixed several real bugs in tomo_scan()/write_pdf_report()
that predate this session and would have crashed on a real account/
real energy read (bec.active_account.decode() -- active_account is str
not bytes; dev.mokev doesn't exist for OMNY, only dev.ccm_energy; an
unguarded logbook send; a stale "LamNI" logo/tag copy-paste leftover) --
all direct ports of fixes flomni/lamni already needed and got. Also added
the missing unconditional omnygui_show_progress() call and heartbeat-
clearing try/finally in tomo_scan(), matching both.

Verification: 23 new tests (test_omny_tomo_queue.py, test_omny_tomo_scan.py)
covering the mixin wiring, hook dispatch/resolution, tomo_scan_resume()/
_resolve_type1_projection()/reacquire() across all three sub-tomogram
flavors, account handling, and heartbeat clearing on both normal completion
and a mid-scan exception. Full suite: 702 passed. Not yet live-tested
against a running session (the local bec-server may be in active use by
Mirko's own parallel session) -- next step is his own pull-and-test.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01QLrD7sVYGLAzsQjLVJpCgt
2026-09-02 14:42:35 +02:00
2026-08-19 12:03:18 +02:00
2025-05-24 11:37:51 +02:00

cSAXS BEC

cSAXS specific plugins and configs for BEC This document guides you through the procedure to spin up BEC at the beamline for a new experiment (e-account). You might want to run cSAXS copy scripts before in case you want to have the former data structure to be preserved.

Overview

  • Clone cSAXS BEC repository into e-account (e.g. into ~/Data10/software/.)
  • Start Epics iocs
  • Start BEC, BEC server and load/modify the device config with relevant hardware
  • BEC commands

Clone cSAXS BEC repository

Clone the current cSAXS BEC repository from GIT into the new e-account. Create directory

mkdir ~/Data10/software
cd ~/Data10/software

Clone repository

git clone https://gitlab.psi.ch/bec/csaxs_bec.git

Start epics iocs

You can start up the iocs while the ./setup_bec.sh script is running. Be aware though that the scripts requires you to interact with it.

DelayGenerator

Open a new tab in a terminal in comp1/comp2 or cons1 and follow the commands below:

ssh gac-x12sa@localhost
cd ~/delaygen
iocsh -7.0.6 startup.script

Be aware -7.0.6 is referring to the current epics version and might change in future (SLS 2.0). To start the epics panel (only if needed), run in a new shell

caqtdm -noMsg -macro P=delaygen:,R=DG1: srsDG645.ui

More notes on usages and cabelling of DDGs. Currently 3 generators are used:

  • DDG1 for detectors (EXT Enable from SGalil stages, T0 to DDG2, AB for eiger, CD for Falcon, EF for Pilatus_2)
  • DDG2 for mcs card (ext. enable from DDG1, AB to mcs card)
  • DDG3 for fast shutter and mcs enable (AB short pulse to enable MCS (needed!!), CD to keep FSH open )

Eiger

Open a new tab in a terminal in comp1/comp2 or cons1 and follow the commands below:

ssh gac-x12sa@localhost
cd ~/Software/Eiger/
./launch_ioc

A live view of status and images for std_daq can be found here xbl-daq-29:5000.

Pilatus_2

First, start the cam server. Connect to the computer and follow the instructions printed after connecting:

ssh det@x12sa-pd-2 (Pilatus2)

The cam server will open, wait until you see **. Nex step, open a new tab in a terminal in comp1/comp2 or cons1 and follow the commands below:

ssh gac-x12sa@localhost
cd ~/Software/Pilatus300K/
./launch_epics

FalconX1

Open a new tab in a terminal in comp1/comp2 or cons1 (logged in as the current e-account) and follow the commands:

ssh x12sa-cons-01
cd /ioc/X12SA-PC-FALCONX1/
iocsh -7.0.6 startup.script

Be aware -7.0.6 is referring to the current epics version and might change in future (SLS 2.0)

Start BEC, BEC server and load device config

Step 1 needs to have finished for continuing with these steps. What remains now is to start the bec server. Connect to pc15543 and open a new terminal to run:

cd ~/Data10/software
source bec_venv/bin/activate
bec-server start
tmux attach -t bec

Open another teminal on pc15543 and start BEC:

cd ~/Data10/software
source bec_venv/bin/activate
bec

Note: In case there is a warning after starting BEC that it was not able to import scilog, you will have to pip install scilog in the bec_venv to be able to send printouts to scilog from the command line. Within a new terminal:

cd ~/Data10/software
source bec_venv/bin/activate
pip install scilog

Device config from csaxs-bec plugins

bec.config.update_session_with_file('/sls/X12SA/data/e20639/Data10/software/csaxs-bec/bec_plugins/configs/bec_device_config_sastt.yaml')
bec.config.save_current_session('~/Data10/software/current_config.yaml')

The second command is helpful if you adjust limits of motors, which will then be stored in the config and loaded if a reload of the configuration is needed.

BEC commands

A number of commands that are useful:

To move devices that are added in the config:

umv(dev.samx, 0) #absolute
umvr(dev.samx, 0) #relative
dev.samx.wm #print motor position and limits
dev.samx.limits = [low_limit, high_limit] # To set limits, note, same lower and higher limit, e.g. [0, 0] means no limits!!

Scans:

scans.acquire(exp_time = 0.5, frames_per_trigger=10, readout_time=3e-3) # equivalent to a loopscan 30 0.5
scans.line_scan(dev.samx, -1, 1, steps=20, exp_time=0.5, readout_time=3e-3, relative=True) # optional, add frames_per_trigger =10 for burst acquisition at each step
#Scan 2 motors in a step scan at the same time
scans.line_scan(dev.samx, -1, 1, dev.samy, -1, 1, steps=20, exp_time=0.5, readout_time =3e-3, relative=True) # step scan with 20 steps, again frames_per_trigger can be added for burst at each point
scans.sgalil_grid(start_y = , end_y = , interval_y = , start_x=, end_x=, interval_x =, exp_time=0.5, readout_time=3e-3, relative=True)
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