Tomotools Suite#
The tomotools suite is a set of developments focused on tomography. It was started with the EBS upgrade, and the goal is to allow scientists to reconstruct datasets acquired with the new machine.
We will only focus on the software side.
Raw Input Format#
The first targeted input is the Bliss files (using the HDF5 file format). The second target is the legacy format of ESRF data, Spec-EDF, for backward compatibility and because not all beamlines have moved to Bliss after the restart.
Nexus (NXtomo): Default Input Format#
As one of the goals of the ESRF is to create open-source and ‘sharable’ software, it has been decided that the default input format will be Nexus.
Since we are focusing on tomography, the Nexus application to use is the NXtomo application definition. It contains all the information necessary for data analysis.
From Raw Input to NXtomo (nxtomomill)#
To move from the Raw Input Format to the Nexus (NXtomo): Default Input Format, we developed a tool named nxtomomill. It can convert either Bliss files to NXtomo or EDF-Spec files to NXtomo.
Reading / Editing an NXtomo (nxtomo project)#
To allow users to easily edit an NXtomo, we created the nxtomo project. Its goal is to stay focused on the Nexus format while maintaining a simple and user-friendly interface.
Data Processing (nabu)#
To reconstruct a volume from radiographs, users can use nabu. The expected input is an NXtomo application definition, but for convenience, raw Spec files are also accepted.
Automating (tomwer)#
To automate processing (define and execute a workflow), users can define a workflow from the Canvas. It also allows direct connection with the acquisition and triggers a workflow once the acquisition is finished.
Tomoscan#
To abstract the reading of raw data (NXtomo or another format, if necessary), we built tomoscan. This was the primary goal of the library. Over time, it has also become a common library for most of the software (nabu and tomwer). Recently (2023), we also added code to handle reading/saving volumes.
