x01dcandClaude Sonnet 5 7e8e807adc fix(flomni): stop duplicate 360deg tomo angles, add sample owner, fix abort crash
Three independent fixes:

- sub_tomo_scan(): in 360-degree tomo_type-1 mode, every sub-tomogram used
  to sweep the full 0-360 range, so each one's own fine grid contained
  angle pairs exactly 180deg apart -- redundant tomographic information.
  Sub-tomograms now each cover a 180deg span, split into low/high halves
  by subtomo_number % 4 with a bit-reversal-of-4 phase table, so adjacent
  pairs (1,2)/(3,4)/(5,6)/(7,8), either quartet, and all 8 combined each
  independently form a complete, evenly-spaced 360deg tomogram at
  successively finer spacing. Total projection count for a given
  tomo_angle_stepsize is now identical between 180 and 360 mode (same N,
  no longer doubled). Updated the 4 other consumers of the old N/step
  formula (zero-deg reference gating, _tomo_type1_actual_grid, the
  parameter wizard, the PDF report) to match. 180-degree mode is
  unchanged. Live-verified against the running flomni sim: real motor
  motion traces the expected boustrophedon path with no duplicate or
  180deg-apart angles.

- Sample storage: added an owner field, packed into the same EPICS DESC
  field as the sample name ("name | owner", via new sample_desc_codec.py)
  since there's no separate PV for it. Wired through
  FlomniSampleStorage, the CLI (flomni_modify_storage_non_interactive,
  ftransfer_modify_storage), the two transfer routines that forward a
  raw DESC value across a gripper move (now unpacked/repacked so owner
  survives the move instead of being dropped or double-packed), and
  SampleStorageWidget. Scoped to flomni only this session; OMNY's
  storage/transfer mixin is unchanged.

- ConsoleButtonsWidget's ABORT button used to send SIGINT then, 500ms
  later, a stop_devices() broadcast to ALL devices with no stop_id --
  an un-suppressed error from that broadcast landing on a queue-tracked
  instruction could kill the scan worker thread outright, requiring a
  full BEC restart. Replaced with: queue.request_scan_abortion() (safe
  no-op if idle, but registers a stop_id so expected errors are
  suppressed), then SIGINT, then a direct, immediate Galil hard stop via
  new GalilController.hard_abort_and_restore_positioning_mode() -- the
  same method ftransfer_abort() now delegates to, so the CLI and GUI
  paths can't drift apart again. SIGINT is sent before the hard stop:
  live testing showed that if the hard stop's mntprgs-clearing side
  effect lands first, a same-session polling loop can mistake it for
  normal completion and fall through into ensure_gripper_up(), which
  must not happen mid-transfer -- sending SIGINT first (near-instant)
  gives that loop's own KeyboardInterrupt handler a head start before
  the hard stop's own multi-step sequence completes. The button is
  labeled per beamline (e.g. "Flomni Motion Stop") and disabled rather
  than silently inert when no hard-stop device is configured/enabled.
  Scoped to flomni only this session (OMNY/LamNI wiring deferred).
  Live-verified against the running sim, including the exact
  stop-lands-mid-queued-instruction scenario that previously crashed
  the scan worker.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
2026-07-15 07:09:40 +02:00
2025-05-24 11:37:51 +02:00
2026-07-12 23:16:18 +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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