Bluesky

The beamline uses Bluesky together with tomo bits for data acquisition and device control.

Environment setup

Activate the appropriate conda environment:

(base) 2bmb@arcturus ~ $ conda activate tomo-bits-decarlof

Start an IPython session:

(tomo-bits-decarlof) 2bmb@arcturus ~ $ ipython
Python 3.11.12 | packaged by conda-forge | (main, Apr 10 2025, 22:23:25) [GCC 13.3.0]
Type 'copyright', 'credits' or 'license' for more information
IPython 9.2.0 -- An enhanced Interactive Python. Type '?' for help.
Tip: The `%timeit` magic has a `-o` flag, which returns the results, making it easy to plot. See `%timeit?`.

Loading beamline devices

Initialize the beamline environment and load all devices:

In [1]: from tomo_instrument.startup import *
I Mon-15:25:45.117: **************************************** Bluesky Startup

IPython logging is configured automatically, for example:

Below are the IPython logging settings for your session.
These settings have no impact on your experiment.

Activating auto-logging. Current session state plus future input saved.
Filename       : /home/beams0/2BMB/.logs/ipython_log.py
Mode           : rotate
Output logging : True
Raw input log  : False
Timestamping   : True
State          : active
Exception reporting mode: Plain

End of IPython settings

The startup sequence loads configuration files and registers devices:

I Mon-15:25:52.441: Starting Instrument with iconfig: /home/beams0/2BMB/conda/tomo-bits-decarlof/src/tomo_instrument/configs/iconfig.yml
W Mon-15:25:52.462: APS DM setup file does not exist: '/home/dm/etc/dm.setup.sh'
I Mon-15:25:52.463: Registered Bluesky IPython magics
I Mon-15:25:53.067: Databroker catalog name: temp
I Mon-15:25:53.068: using ophyd control layer: 'pyepics'
I Mon-15:25:53.069: RunEngine metadata saved to: .re_md_dict.yml
I Mon-15:25:54.248: SPEC data file: /home/beams0/2BMB/20250512-152554.dat
Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use QT_QPA_PLATFORM=wayland to run on Wayland anyway.
I Mon-15:25:54.250: Loading device file: /home/beams0/2BMB/conda/tomo-bits-decarlof/src/tomo_instrument/configs/devices.yml
I Mon-15:25:54.828: Devices loaded in 0.577 s.
I Mon-15:25:54.829: Adding ophyd device 'shutter' to main namespace
I Mon-15:25:54.829: Adding ophyd device 'optics' to main namespace
I Mon-15:25:54.830: Adding ophyd device 'sim_motor' to main namespace
I Mon-15:25:54.830: Adding ophyd device 'sim_det' to main namespace
I Mon-15:25:55.883: Loading device file: /home/beams0/2BMB/conda/tomo-bits-decarlof/src/tomo_instrument/configs/devices_aps_only.yml
I Mon-15:25:55.894: Devices loaded in 0.010 s.
I Mon-15:25:55.898: Adding ophyd device 'shutter' to main namespace
I Mon-15:25:55.899: Adding ophyd device 'sim_motor' to main namespace
I Mon-15:25:55.900: Adding ophyd device 'optics' to main namespace
I Mon-15:25:55.901: Adding ophyd device 'aps' to main namespace
I Mon-15:25:55.901: Adding ophyd device 'sim_det' to main namespace

In [2]:

After startup, the following devices are available in the IPython namespace:

shutter
optics
sim_motor
sim_det
aps (from the APS-specific configuration)

Optical system control (optics)

The optics device provides Bluesky access to mctOptics, which controls the Optic Peter system (dual-camera, triple-lens optical assembly).

Lens selection

Read the current lens selection:

In [4]: optics.lens_select.get()
Out[4]: 2

Select a different lens:

In [10]: optics.lens_select.put(1)
In [11]: optics.lens_select.get()
Out[11]: 1

Camera selection

Read the current camera selection:

In [14]: optics.camera_select.get()
Out[14]: 0

Select a different camera:

In [15]: optics.camera_select.put(1)
In [16]: optics.camera_select.get()
Out[16]: 1

Tomoscan integration (under Bluesky)

The beamline can run tomography acquisition using tomoscan, a Python module for collecting computed tomography data at the APS. Tomoscan plans are executed through the Bluesky RunEngine.

Single tomoscan

Activate the conda environment, start IPython, load the tomoscan startup, and run a single scan:

(base) 2bmb@arcturus ~ $ conda activate tomo-bits-decarlof
(tomo-bits-decarlof) 2bmb@arcturus ~ $ ipython

In [1]: from tomo_2bm.startup import *
In [2]: RE(tomo_single_scan())