Installation#

Tomwer relies on nabu to process the tomographic reconstruction.

As of today, the software is only compatible with Linux.

../_images/Tux.svg

Step 1 - Install Tomwer#

To install Tomwer with all features, use:

pip install tomwer[full]

Alternatively, you can install the main branch directly from GitLab:

pip install git+https://gitlab.esrf.fr/tomotools/tomwer/#egg=tomwer[full]

Step 2 - Update Forks for Orange-Canvas-Core and Orange-Widget-Base#

To access processing wheels and the reprocess action, you might want to install forks of orange-canvas-core and orange-widget-base. This is optional; the project works with native Orange projects as well.

pip install git+https://github.com/payno/orange-canvas-core --no-deps --upgrade
pip install git+https://github.com/payno/orange-widget-base --no-deps --upgrade

Launching Applications#

After installation, Tomwer includes several applications that can be launched with:

tomwer appName {options}

Note

If you call tomwer without any arguments, the man page will be displayed.

Note

You can access help for each application using:

tomwer appName --help

Tomwer Canvas#

You can launch the canvas to create workflows from the different ‘bricks’:

tomwer canvas

Note

tomwer canvas launches ‘orange-canvas’ with additional processing (such as setting log levels for some libraries). It is recommended to use tomwer canvas instead of orange-canvas.

Documentation#

To build the documentation, use:

sphinx-build doc build/html

The documentation will be built in build/html, and the entry point is index.html:

firefox build/html/index.html

Note

Building the documentation requires Sphinx. If it is not installed, you may need to install it separately.

To generate documentation accessible from the Orange GUI (by pressing F1), use:

sphinx-build doc build/html -b htmlhelp

Tomwer with BLISS Bliss-Tomo#

Tomwer and Bliss-Tomo (a tomography framework for BLISS) can share information.

  • With the scan listener using RPC commands. When a scan is started and finished, it will send a command for Tomwer to process it. This requires the Bliss-Tomo framework to be activated at the beamline. Please check with the beamline supervisor.

Tomwer Installation at ESRF#

Installation is managed using automatix.

On the SLURM Cluster#

Users can activate Python virtual environments within the Tomotools suite by sourcing the script /scisoft/tomotools/activate {version} with the desired version. This script handles the node architecture and special version names such as dev or stable.

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

At Beamlines#

On beamlines, installations are typically done in /nobackup partitions. Locations can be found in https://gitlab.esrf.fr/tomotools/automatix/-/blob/master/deployment/cfg_esrf_envs.py.

To simplify activation and launching of the Orange Canvas, a tomwer-{version} alias is usually created:

tomwer-dev canvas [options]