BEATS Computing Infrastructure

DAQ workstation - BEATS-control-ws

The data acquisition (DAQ) workstation is used to control the beamline and scan settings. Visit the section Data Acquisition (DAQ) for more information.

Useful commands

Mount PETRA:

sudo mount -t nfs 10.1.14.100:/PETRA/SED/BEATS/IH /PETRA/SED/BEATS/IH

SMB mount of SSCAN data folder:

sudo mount -t cifs -o vers=3,username=beats.smb '\\10.1.14.100\pco-flir-ws' /home/control/Desktop/SSCAN

Start the Energy GUI:

cd /home/control/energy/iocBoot/iocEnergy_2BM
python3 -i start_energy.py

Data analysis workstation - BL-BEATS-WS01

The data analysis workstation is used for several purposes including:

• Inspection of sinograms and CT reconstruction

• Submit reconstruction jobs on the cluster rum@sesame.org.jo

• 3D image visualization and processing

The list of software available on the workstation is listed in the section on :ref:’Data analysis software’ below.

Useful commands

Start alrecon CT reconstruction environment:

conda activate tomopy
solara run alrecon.pages --host localhost

Start reconstruction pipeline on Jupyter Lab. Available pipelines are described in section Tomographic reconstruction at BEATS:

conda activate tomopy
jupyter lab

Mount proposal ExpData and recon folders on BL-BEATS-WS01:

cd ~
./petra_prop_mounter.sh

Mount proposal ExpData and recon folders on User-BEATS-Dispenser and Dragonfly Dispenser 2:

./petra_prop_recon_smb_mounter.sh

Mount proposal ExpData and recon folders on Dragonfly Dispenser 1 for remote access:

./petra_prop_recon_smb_mounter_vizserver.sh

Check mount points:

df -h

Unmount proposal folders:

umount /PETRA/SED/BEATS/SEM_6/20235010
umount /PETRA/SED/BEATS/SEM_6_recon/20235010

Mount proposal ExpData and recon folders on Win Data Dispenser and Dragonfly VizServer:

./petra_prop_recon_smb_mounter.sh

Note

For proposals belonging to a different semester the scripts petra_prop_mounter.sh and petra_prop_recon_smb_mounter.sh must be modified.

Data analysis software

The software in the table below can be used to inspect and process 3D image data (sinograms and CT reconstructions) at SESAME BEATS.

Name	URL	Open source	Features
ImageJ	https://fiji.sc/	yes	Essential for data collection and reconstruction
Paraview	https://www.paraview.org/	yes	3D image rendering
Dragonfly	https://www.theobjects.com/dragonfly/index.html	no	3D image analysis and visualization
3D Slicer	https://www.slicer.org/	yes	3D image analysis and visualization
TomoPy	https://tomopy.readthedocs.io/en/stable/	yes	CT reconstruction in Python
Alrecon	https://github.com/gianthk/alrecon/tree/master	yes	Web app for CT reconstruction
Jupyter	https://jupyter.org/	yes	Interface for Python reconstruction pipelines (notebooks)

Load reconstructed volume with ImageJ

Reconstructions at SESAME BEATS are generally saved as a stack of .TIFF images contained in a reconstruction folder. To load a reconstruction in ImageJ use the command File › Import › Image Sequence. You can follow this video for a detailed explanation on how to import image sequences.

Note

Always select the option Use Virtual Stack when you import large image stacks in ImageJ!

rum - BEATS reconstruction cluster

Access the reconstruction cluster rum@sesame.org.jo with:

ssh -X beatsbs@rum.sesame.org.jo

Data dispenser PC - User-BEATS-Dispenser

The data dispencer Windows PC (User-BEATS-Dispenser) can be used to access, visualize, and copy your beamtime data. You can also use this PC to launch the Dragonfly VizServer 2, reserved to the beamline users during their shifts.

ORS Dragonfly VizServer

We offer the following 2 seats for image processing using ORS Dragonfly to our users.

	CPU	RAM	GPU	Note
VizServer 1	Intel Xeon Silver 4314 CPU@2.40 GHz	256 GB	(1×) NVIDIA RTX A6000	Contact the beamline staff to request access (see below)
VizServer 2	Intel Xeon Silver 4314 CPU@2.40 GHz	256 GB	(1×) NVIDIA RTX A6000	Reserved for users at the beamline

BEATS data portal / Dragonfly VizServer 1

SESAME BEATS data portal: visit https://access.sesame.org.jo/beats.

On the portal you will find instructions on how to access BEATS data and our Dragonfly VizServer 1.