API for command line tools

pynxtools supports a number of command line applications. This page provides documentation for their current API.

Data conversion

Note that simply calling dataconverter defaults to dataconverter convert.

dataconverter

Usage:

dataconverter [OPTIONS] COMMAND [ARGS]...

Options:

Name	Type	Description	Default
--help	boolean	Show this message and exit.	False

Subcommands

• convert: This command allows you to use the converter functionality of the dataconverter.
• generate-template: Generates and prints a template to use for your nxdl.
• get-readers: Prints a list of all installed readers.

dataconverter convert

This command allows you to use the converter functionality of the dataconverter.

Usage:

dataconverter convert [OPTIONS] [FILES]...

Options:

Name	Type	Description	Default
--input-file	text	Deprecated: Please use the positional file arguments instead. The path to the input data file to read. Repeat for more than one file. default=[] This option is required if no '--params-file' is supplied.	[]
--reader	choice (example | json_map | json_yml | multi)	The reader to use. Examples are json_map or readers from a pynxtools plugin. default='json_map' This option is required if no '--params-file' is supplied.	json_map
--nxdl	text	The name of the NeXus application definition file to use without the extension nxdl.xml. This option is required if no '--params-file' is supplied.	None
--output	text	The path to the output NeXus file to be generated. default='output.nxs'	output.nxs
--params-file	filename	Allows to pass a .yaml file with all the parameters the converter supports.	None
--ignore-undocumented	boolean	Ignore all undocumented fields during validation.	False
--fail	boolean	Fail conversion and don't create an output file if the validation fails.	False
--skip-verify	boolean	Skips the verification routine during conversion.	False
--mapping	text	Takes a .mapping.json file and converts data from given input files.	None
-c, --config	file	A json config file for the reader	None
--help	boolean	Show this message and exit.	False

dataconverter generate-template

Generates and prints a template to use for your nxdl.

Usage:

dataconverter generate-template [OPTIONS]

Options:

Name	Type	Description	Default
--nxdl	text	The name of the NeXus application definition file to use without extension. For example: NXmpes	_required
--required	boolean	Use this flag to only get the required template.	False
--pythonic	boolean	Prints a valid Python dictionary instead of JSON	False
--output	path	Writes the output into the filepath provided.	None
--help	boolean	Show this message and exit.	False

dataconverter get-readers

Prints a list of all installed readers.

Usage:

dataconverter get-readers [OPTIONS]

Options:

Name	Type	Description	Default
--help	boolean	Show this message and exit.	False

NeXus file validation

read_nexus

Functionality to extract documentation and concept definition information about the individual parts of a NeXus/HDF5 file.

Usage:

read_nexus [OPTIONS]

Options:

Name	Type	Description	Default
-f, --nexus-file	text	NeXus file with extension .nxs.	None
-d, --documentation	text	Definition path in nexus output (.nxs) file. Returns debug log relevant with that definition path. Example: /entry/data/delays	None
-c, --concept	text	Concept path from application definition file (.nxdl,xml). Finds out all the available concept definition (IS-A realation) for rendered concept path. Example: /NXarpes/ENTRY/INSTRUMENT/analyser	None
--help	boolean	Show this message and exit.	False

NOTE: Only one option from (-d and -c) is acceptable.

ELN generation

generate_eln

Helper tool for generating ELN files in YAML format.

Usage:

generate_eln [OPTIONS]

Options:

Name	Type	Description	Default
--nxdl	text	Name of NeXus definition without extension (.nxdl.xml).	_required
--skip-top-levels	integer	To skip the level of parent hierarchy level. E.g. for default 1 the part Entry[ENTRY] from /Entry[ENTRY]/Instrument[INSTRUMENT]/... will be skiped.	1
--output-file	text	Name of file that is neede to generated output file.	eln_data
--eln-type	choice (eln | scheme_eln)	Choose a type of ELN output (eln or scheme_eln).	eln
--help	boolean	Show this message and exit.	False