pynxtools-raman: A pynxtools reader for Raman data

A pynxtools reader plugin for transferring Raman data from vendor formats to NeXus and NOMAD.

+This pynxtools plugin was generated with cookiecutter using the pynxtools-plugin-template template.

Installation

It is recommended to use python 3.12 with a dedicated virtual environment for this package. Learn how to manage python versions and virtual environments.

This package is a reader plugin for pynxtools and should be installed together with pynxtools:

uv pip install pynxtools[raman]

Purpose

This reader plugin for pynxtools is used to translate diverse file formats from the scientific community and technology partners within the field of raman into a standardized representation using the NeXus application definition NXraman.

Step-by-Step Example

You see three Folders:

• examples: contains example datasets to show how the data conversion is done (currently one example from WITec and one example from the Raman Open Database)
• tests: contains a test procedure and files, which are required for software development
• src/pynxtools_raman: source files, which contain the sub-reader function for Raman experiments. This only works in combination with the Python package pynxtools. This is a specialization of the Multiformat Reader. There are also sub-reader functions for a WITec device and files from the Raman Open Database. In addition, config.json files are located in src/pynxtools_raman/config. These are necessary to map the input data via the MultiformatReader to the NeXus concepts. These config files allow individual adjustments, as different laboratories may have different electronic lab notebook structures.

Perform a data conversion

for the WITec dataset via:

pynx convert examples/witec/txt/eln_data.yaml examples/witec/txt/Si-wafer-Raman-Spectrum-1.txt src/pynxtools_raman/config/config_file_witec.json --reader raman --nxdl NXraman --output new_witec_example_nexus.nxs

and for the Raman Open Database dataset set via:

pynx convert examples/database/rod/rod_file_1000679.rod src/pynxtools_raman/config/config_file_rod.json --reader raman --nxdl NXraman --output new_rod_example_nexus.nxs

For Example for the Raman Open Database command:

• You assign the reader name via --reader raman.
• You assign the NeXus application definition, on which the output will be based via --nxdl NXraman.
• You specify the name and path of the output file via --output new_rod_example_nexus.nxs.
• You assign an individualized config file via src/pynxtools_raman/config/config_file_rod.json. The config file is detected by its extension .json.
• You give the file which includes the meta and measurement data via examples/database/rod/rod_file_1000679.rod. The parser is specified to detect the .rod file, and handle the content appropriately.

Then you can inspect the generated file at this website or in VScode via the extension "H5web".

Docs

More information about this pynxtools plugin is available in the documentation. You will find information about getting started, how-to guides, the supported file formats, how to get involved, and much more there.

Contact person in FAIRmat for this reader

Lukas Pielsticker