nxvalidate 0.3.0b1

A Python package for validating NeXus files

Introduction

This package provides a Python API to inspect and validate NeXus files written in the HDF5 format.

The latest development version is always available from NeXpy's GitHub repository.

Installation

Released versions of nxvalidate can be installed using

    % pip install nxvalidate

The source code can be downloaded from the NeXpy Git repository:

    % git clone http://github.com/nexpy/nxvalidate.git

Prerequisites

The only prerequisite required to install the nxvalidate package is the nexusformat package. There are more details of further dependencies in the NeXpy documentation.

Usage

At the moment, the nxvalidate package provides a single command-line script.

% nxinspect -h
usage: nxinspect [-h] [-f FILENAME] [-p PATH] [-a [APPLICATION]]
                 [-b BASECLASS] [-i] [-w] [-e] [-v]

Inspects and validates NeXus files.

options:
  -h, --help            show this help message and exit
  -f FILENAME, --filename FILENAME
                        name of the NeXus file to be validated
  -p PATH, --path PATH  path to group to be validated in the NeXus file
  -b BASECLASS, --baseclass BASECLASS
                        name of the base class to be listed
  -a [APPLICATION], --application [APPLICATION]
                        validate the NeXus file against its application definition
  -d DEFINITIONS, --definitions DEFINITIONS
                        path to the directory containing NeXus definitions
  -i, --info            output info messages in addition to warnings and errors
  -w, --warning         output info messages in addition to warnings and errors
  -e, --error           output info messages in addition to warnings and errors
  -v, --version         show program's version number and exit

N.B., the command is nxinspect, rather than nxvalidate to avoid confusion with the C-library.

Examples

1. To compare the contents of a NeXus file with the base classes defined by the NeXus standard and print conflicting fields or groups, type:

   % nxinspect -f <filename.nxs> -e
   

   The --info, --warning and --error switches control how much information is output. The default is --warning.
2. To compare the contents of a NeXus file with the base classes defined in a different directory to the installed package, type:

   % nxinspect -f <filename.nxs> -d /path/to/definitions
   

   The directory should contain two sub-directories, applications and base_classes containing the NXDL files needed to validate the specified NeXus file.
3. To check whether the contents of the NeXus file conform to the required contents of the application definition specified in the file, type:

   % nxinspect -f <filename.nxs> -a
   

4. To check whether the contents of the NeXus file conform to the required contents of an application definition file, type:

   % nxinspect -f <filename.nxs> -a <application.nxdl.xml>
   

5. To print the contents of a base class, type:

   % nxinspect -b <base-class-name>
   

User Support

Information about the Python API for reading and writing NeXus files is available as part of the NeXpy documentation. If you have any general questions concerning the use of this package, please address them to the NeXus Mailing List. If you discover any bugs, please submit a Github issue, preferably with relevant tracebacks.

Acknowledgements

This package was developed jointly by Kaitlyn Marlor, Justin Wozniak, and Ray Osborn. The NeXus data format standard has been developed under the supervision of the NeXus International Advisory Committee.