Convert X-ray spectroscopy data and metadata to NeXus¶

Who is this tutorial for?¶

This document is for people who want to use this reader as a standalone standardize their research data by converting these into a NeXus standardized format.

What should you should know before this tutorial?¶

You should have a basic understanding of FAIRmat NeXus and pynxtools
You should have a basic understanding of using Python and Jupyter notebooks via JupyterLab

What you will know at the end of this tutorial?¶

You will have a basic understanding how to use pynxtools-xps for converting your XPS data to a NeXus/HDF5 file.

Steps¶

Installation¶

See here for how to install pynxtools together with the XPS reader plugin.

Running the reader from the command line¶

An example script to run the XPS reader in pynxtools:

user@box:~$ dataconverter $<xps-file path> $<xps-file path> $<eln-file path> --reader xps --nxdl NXxps --output <output-file path>.nxs

Note that none of the supported file format have data/values for all required and recommended fields and attributes in NXxps. In order for the validation step of the XPS reader to pass, you need to provide an ELN file that contains the missing values.

Examples¶

You can find examples how to use pynxtools-xps for your XPS research data pipeline in src/pynxtools-xps/nomad/examples. These are designed for working with NOMAD and its NOMAD Remote Tools Hub (NORTH). Feel invited to try out the respective tutorial here.

There are also small example files with raw and converted data for using the pynxtools dataconverter with the mpes reader and the NXmpes application definition in the examples folder.

For this tutorial, we will work with the example data for the VAMAS reader (see here ). You can run the conversion as

dataconverter \\
    --reader xps \\
    --nxdl NXmpes \\
    regular.vms \\
    eln_data_vms.yaml \\
    -c  config_file.json \\
    --output regular.vms.nxs

TODO: add more steps!

Congrats! You now have a FAIR NeXus file!