NeXus validation¶
Work in progress
This page is intended to give more information about the validation tools that are part of pynxtools. Please also have a look at our comprehensive how-to guide on NeXus validation.
One of the main advantages of using pynxtools is that it comes with its own validation tools. That is, it can be used to validate that a given NeXus/HDF5 file is compliant with a NeXus application definition.
As part of the dataconverter¶
During data conversion, before writing the HDF5 file, the data is first checked against the provided application definition.
read_nexus: NeXus file reader and debugger¶
This utility outputs a debug log for a given NeXus file by annotating the data and metadata entries with the schema definitions from the respective NeXus base classes and application definitions to which the file refers to. See here for the API documentation.
The following example dataset can be used to test the read_nexus module: src/pynxtools/data/201805_WSe2_arpes.nxs.
This is an angular-resolved photoelectron spectroscopy (ARPES) dataset that is formatted according to the NXarpes application definition of NeXus.
Using a different set of NeXus definitions¶
The environment variable "NEXUS_DEF_PATH" can be set to a directory which contains the NeXus definitions as NXDL XML files. If this environment variable is not defined, the module will use the definitions in its bundle (see src/pynxtools/definitions)._
The environment variable can be set as follows:
A note to Windows users¶
If you run read_nexus from git bash, you need to set the environmental variable
MSYS_NO_PATHCONV to avoid the path translation in Windows Git MSys.
The easiest way is to prefix the read_nexus call with MSYS_NO_PATHCONV=1:
This workaround was tested with Windows 11, but should very likely also work with Windows 10 and lower.
Other approaches (not part of pynxtools)¶
Aside from the tools we developed within FAIRmat, the official NeXus website lists two more programs for the validation of NeXus files:
We will not discuss the details of these two programs here, but you can find some information about the in the how-to guide linked above.