Tomotools suite#
The tomotools suite is a set of developments focus on tomography. It was started with the EBS upgrade and the goal is to allow scientist to reconstruct dataset acquired with the new machine.
We will only focus on the software side.
Raw Input format#
First targetted input are the bliss files (using HDF5 file format) Second target is spec - EDF - legacy format of ESRF data. For backward compatibility but also because not all beamlines have been moved to bliss for the restart
Nexus (NXtomo): default input format#
As one of the goal of the ESRF is to create open source and ‘sharable’ software it has been decided that the default input format will be Nexus
And as we are focusing in tomography the nexus application to use is the NXtomo application definition It contains all informations necessary to do the data analysis.
From raw input to NXtomo (nxtomomill)#
To move from the:ref:raw input format to the Nexus (NXtomo): default input format we develop a tool named nxtomomill It can convert either bliss files to NXtomo or edf-spec files to NXtomo
Reading / editing an NXtomo (nxtomo project)#
In order to let users edit easily an NXtomo we created the nxtomo project It intends to keep focus on Nexus format and keep a simple and user friendly interface.
Data processing (nabu)#
In order to reconstruct a volume from radios user can use nabu The expected input is an NXtomo application definition but for convenience raw spec-file are also accepted.
Automating (tomwer)#
In order to automate processing (define and execute a processing workflow) users can define a processing workflow from the Canvas It also allow to be connected directly with the acquisition and trigger a workflow once an acquisition is finished
tomoscan#
In order to abstract reading of raw data (NXtomo or another if necessary) we build tomoscan This is the first goal of the library. But with time it has also became a common library to most of the software (nabu and tomwer). Recently (2023) we also added code to handle reading / saving volumes there.
