pynxtools-raman 0.1.1

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

A reader for raman data

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 thus should be installed together with pynxtools:

pip install pynxtools[raman]

for the latest development version.

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

Download the repository via git clone:

git clone https://github.com/FAIRmat-NFDI/pynxtools-raman.git

Switch to the project root folder:

cd pynxtools-raman

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 as well 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 Multiformat Reader to the NeXus concepts. These config files allow individual adjustments, as different laboratories may have different electronic lab notebook structures.

Consider setting up an individual python environment, to separate the python functionalities of this package from the python functionalities of your operating system: For Ubuntu-based systems:

python -m venv .pyenv
source .pyenv/bin/activate

Verify its location via:

which python

It should point to the python folder, you created above with the name .pyenv.

Install the python package:

pip install .

Perform a data conversion for the WITec dataset via:

dataconverter 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:

dataconverter 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

Extensive documentation of this pynxtools plugin is available here. You can 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

Ron Hildebrandt