FAIRmat NeXus documentation¶
Within FAIRmat, we are extending the NeXus data format standard to support the FAIR data principles for experimental data in materials science (covering solid-state physics and the chemical physics of solids, as well as materials engineering). This is the documentation for both our contribution to the NeXus standard and for our tools for data conversion and verification.
pynxtools, the main tool under development, provides a data converter that maps experimental data and metadata to the NeXus format, performing parsing, normalization, visualization, and ontology matching. It combines various instrument output formats and electronic lab notebook (ELN) formats to an HDF5 file according to NeXus application definitions. In addition, pynxtools can be used to validate and verify NeXus files.
pynxtools offers scientists a convenient way to use the NeXus format and solves the challenge of unstructured and non-standardized data in experimental materials science. We consider this package useful for meeting the following FAIR principle as defined in FAIR Principles: Interpretations and Implementation Considerations: F2-4, I2-I3, and R1.
FAIRmat's contribution to the existing NeXus standard, together with the tools provided through pynxtools, enable scientists and research groups working with data, as well as helping communities implement standardized FAIR research data.
Additionally, the software is used as a plugin in the research data management system NOMAD for making experimental data searchable and publishable. NOMAD is developed by the FAIRmat consortium, as a part of the German National Research Data Infrastructure (NFDI).
Tutorial¶
A series of tutorials giving you an overview on how to store or convert your data to NeXus-compliant files.
How-to guides¶
How-to guides provide step-by-step instructions for a wide range of tasks.
- Build your own pynxtools plugin
- Implement a reader based on the MultiFormatReader
- Validation of NeXus files
- Creation of NeXus files in python via hard-coding
- Using pynxtools test framework for plugins
- Using pynxtools tests in parallel
The following How-to guides are still under development:
Learn¶
An introduction to NeXus and its design principles¶
- An introduction to NeXus
- Rules for storing data in NeXus
- The concept of multiple application definitions
- The MultiFormatReader as a reader superclass
pynxtools¶
Reference¶
NeXus definitions¶
Here, you find the detailed list of application definitions and base classes and their respective fields.
Or go directly to the official NIAC or latest FAIRmat definitions.
Note: To connect NeXus concepts with semantic web tools, efforts are underway to represent them using the W3C Web Ontology Language (OWL). See the NeXusOntology for more details.
pynxtools¶
pynxtools has a number of command line tools that can be used to convert data and verify NeXus files. You can find more information about the API here.
Within FAIRmat, we maintain a number of generic built-in pynxtools readers, together with reader plugins for different experimental techniques. Here you can find more information: