nomad-measurements 1.3.5

A plugin for NOMAD containing base sections for measurements.

NOMAD's Measurements Plugin

This is a plugin for NOMAD which contains base sections for materials science measurements.

The nomad_measurements.xrd module supports parsing of following vendor-specific file formats:

• .rasx (Rigaku)
• .xrdml (Malvern Panalytical)
• .brml (Bruker)
• .raw (Bruker RAW v4)

The nomad_measurements.transmission module supports parsing of following vendor-specific file formats:

• .asc (generated by Perkin Elmer UV WinLab software)

The nomad_measurements.quantumdesign module supports parsing of following file format:

• .dat (in the structure of the QuantumDesign)

Getting started

nomad-measurements can be installed from PyPI using pip. Currently we require features in nomad-lab which are not published to PyPI. In order to install these a --index-url needs to be provided:

pip install nomad-measurements --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple

Setting up your OASIS

Read the NOMAD oasis documentation for details on how to add the plugin on your NOMAD instance.

You don't need to modify the nomad.yaml configuration file of your NOMAD instance, because the package is pip installed and all the available modules (entry points) are loaded. To include, instead, only some of the entry points, you need to specify them in the include section of the nomad.yaml. In the following lines, a list of all the available entry points:

plugins:
  include:
    - "nomad_measurements.general:schema_entry_point"
    - "nomad_measurements.xrd:schema_entry_point"
    - "nomad_measurements.xrd.parser:parser_entry_point"
    - "nomad_measurements.transmission:schema_entry_point"
    - "nomad_measurements.transmission:parser_entry_point"
    - "nomad_measurements.quantumdesign:eto_schema"
    - "nomad_measurements.quantumdesign:act_schema"
    - "nomad_measurements.quantumdesign:acms_schema"
    - "nomad_measurements.quantumdesign:eto_parser"
    - "nomad_measurements.quantumdesign:act_parser"
    - "nomad_measurements.quantumdesign:acms_parser"
    - "nomad_measurements.quantumdesign:sequence_parser"

X-ray diffraction ELN allows to generate a nexus .nxs file from the entry data by clicking on Switch To/From HDF5 Results button. This is useful for high-resolution or RSM scans, where the data is large and slows down the interaction with the entry. Once the data is moved to a nexus file, the entry only stores references to it, rather than the data itself, making the ELNs responsive. However, this requires that the plugin is installed with nexus dependencies. When adding this plugin to your oasis, nexus dependencies can be included by adding the following line in the pyproject.toml:

...
dependencies = [
  ...
  "nomad-measurements[nexus]",
]

If the nexus dependencies are not included, the functionality above still works but uses a plain .h5 file rather than a .nxs file.

Development

This code is currently under development and for installing and contributing you should clone the repository:

git clone [e-mail]:FAIRmat-NFDI/nomad-measurements.git
cd nomad-measurements

And install the package in editable mode with the development ('dev') dependencies:

pip install -e .[dev] --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple