Usage in NOMAD¶

Who is this tutorial for?¶

This tutorial is for researchers who want to use pynxtools-xps inside NOMAD to convert, store, search, and analyze their XPS data in a full research data management system.

What should you know before this tutorial?¶

You should have pynxtools-xps installed with the NOMAD extras — see Tutorial > Installation guide.
Basic familiarity with NOMAD uploads is helpful but not required.

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

You will understand:

How to create an XPS example upload in NOMAD
What files the example contains and what each one does
How to inspect the converted NeXus file and the parsed data
How to run the analysis notebooks in NORTH

Steps¶

1. Open NOMAD central¶

Go to https://nomad-lab.eu/prod/v1/gui/ and sign in (or register for a free account).

2. Create the XPS example upload¶

Navigate to Publish → Uploads and click + Upload. In the dialog, select Use an example upload and choose X-ray Photoelectron Spectroscopy (XPS) from the NeXus Experiment Examples category.

NOMAD creates a new upload pre-populated with all example files.

3. Explore the example files¶

The upload contains:

File	Role
`EX439_S718_Au_in_25_mbar_O2.sle`	Raw SPECS SLE measurement file (Au in 25 mbar O₂, NAP-XPS)
`xps.scheme.archive.yaml`	ELN schema — defines all NXxps fields not present in the raw file
`eln_conversion.archive.json`	Converts the ELN schema to `eln_data.yaml`
`nexus_conversion.archive.json`	Converts SLE + ELN to an `NXxps` NeXus file
`E1 XPS data conversion to NeXus.ipynb`	Notebook: conversion pipeline walkthrough
`E2 XPS data analysis and fitting.ipynb`	Notebook: peak fitting with `lmfit`, Shirley background

Open the FILES tab to inspect the raw and generated files. NeXus files (.nxs) can be explored interactively with the built-in H5Web HDF5 viewer.

4. Review the ELN and trigger conversion¶

Click on eln_conversion.archive.json to view and edit the prefilled ELN metadata (instrument, sample, user information). NOMAD runs the ElnYamlConverter automatically, producing eln_data.yaml.

Then open nexus_conversion.archive.json. NOMAD invokes the XPS reader and produces the standardized NeXus file (Au_25_mbar_O2_no_align.nxs) according to the NXxps application definition.

The full pipeline in the example:

EX439_S718_Au_in_25_mbar_O2.sle  +  eln_data.yaml
        │
        ▼  NexusDataConverter (reader: xps, nxdl: NXxps)
        │
  Au_25_mbar_O2_no_align.nxs
        │
        ├──► NexusParser → NOMAD Metainfo (DATA tab, search)
        ├──► H5Web viewer (FILES tab)
        └──► NORTH Jupyter analysis (E1 · E2 notebooks)

5. Inspect the parsed data¶

Open the DATA tab of the upload. The NexusParser has extracted the NXxps structure into NOMAD Metainfo, making instrument parameters, sample details, and spectral data browsable and searchable.

6. Run the analysis notebooks in NORTH¶

If NOMAD is deployed with NORTH, open Analyze → NORTH and launch a JupyterLab container. Navigate to the upload directory and open:

E1 XPS data conversion to NeXus.ipynb — step-by-step notebook showing how the conversion is orchestrated.
E2 XPS data analysis and fitting.ipynb — loads the NeXus file, performs Shirley background subtraction, and fits peaks with lmfit.

Using your own data¶

The example uses a SPECS SLE file, but the same workflow applies to any format supported by pynxtools-xps (VMS, TXT, IBW, XML, …). Replace the raw measurement file in the upload, update the input_files field in nexus_conversion.archive.json, and adjust the ELN metadata to match your instrument.