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1.3
  • youtube
  • pypi
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  • youtube
  • pypi
  • gitlab

Overview#

tomwer tomwer is offering tools to automate acquisition and reconstruction processes for Tomography. It contains:

  • a library to access each acquisition process individually

  • gui and applications to control main processes (reconstruction, data transfert…) and execute them as a stand alone application.

  • an orange add-on to help users defining their own workflow (http://orange.biolab.si)

Be aware that some demo/tutorial videos are available on https://www.youtube.com/@tomotools This notebooks focus on how to run thinks with tomwer 1.x versions

It is available from the cluster by 1. allocating a node with a gpu like:

salloc --partition gpu --gres=gpu:1 --mem=256G srun --pty bash -l

  1. load ‘tomotools’ module

module load tomotools  # or module load tomotools/{version==dev|stable|1.x} for a specific version

version can be dev, stable, 1.0 for example

  1. launching tomwer

tomwer {command} {options}

like to launch the canvas with a workflow file as a parameter:

tomwer canvas my_file.ows

Be aware that on beamlines computer you can have your own (editable / dedicated) python virtual environment with tomotools installed. They are usually on the /nobackup partition. Furthermore some aliases to those virtual environment can exists like

tomwer-1.0 {command} {options}

documentation can be found in https://tomotools.gitlab-pages.esrf.fr/tomwer/

troubleshooting - x forwarding#

if you end up with the following error:

qt.qpa.xcb: could not connect to display
qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, xcb.

Aborted (core dumped)

It most probably mean that you have troubles with the X forwarding.

As a reminder usually to connect to the cluster users must go with

ssh -XC {user}@cluster-access

Then some OS you might need to add the X forwarding (--x11 option) like:

salloc --partition gpu --x11 --gres=gpu:1 --mem=256G srun --pty bash -l
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