https://github.com/dials/nxmx

https://github.com/dials/nxmx

Last synced: about 2 months ago
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• Host: GitHub
• URL: https://github.com/dials/nxmx
• Owner: dials
• License: bsd-3-clause
• Created: 2022-10-28T10:24:04.000Z (about 2 years ago)
• Default Branch: main
• Last Pushed: 2024-11-04T19:58:24.000Z (2 months ago)
• Last Synced: 2024-11-04T20:36:24.095Z (2 months ago)
• Language: Python
• Size: 98.6 KB
• Stars: 1
• Watchers: 11
• Forks: 0
• Open Issues: 3
• Metadata Files:
  • Readme: README.md

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README

        
# Read NXmx-flavour NeXus HDF5 data in Python

[![PyPI release](https://img.shields.io/pypi/v/nxmx.svg)](https://pypi.python.org/pypi/nxmx)

[![Supported Python versions](https://img.shields.io/pypi/pyversions/nxmx.svg)](https://pypi.org/project/nxmx)

[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)]( https://github.com/ambv/black)

This package provides a neat and tidy Python interface for reading data from [HDF5 files](https://www.hdfgroup.org/solutions/hdf5/) that are structured according to the [NXmx application definition](https://manual.nexusformat.org/classes/applications/NXmx.html) of the [NeXus standard](https://www.nexusformat.org/).

## Installation

`python-nxmx` is available as `nxmx` on PyPI, so you just need Pip.

```Bash

$ pip install nxmx

```

## Getting started

If you have an HDF5 file in NXmx format, inspecting it with `h5ls` will look something like this:

```Bash

$ h5ls -r my-nxmx-file.h5 

/                        Group

/entry                   Group

/entry/data              Group

/entry/definition        Dataset {SCALAR}

/entry/end_time          Dataset {SCALAR}

/entry/end_time_estimated Dataset {SCALAR}

/entry/instrument        Group

/entry/instrument/beam   Group

/entry/instrument/beam/incident_beam_size Dataset {2}

/entry/instrument/beam/incident_wavelength Dataset {SCALAR}

/entry/instrument/beam/total_flux Dataset {SCALAR}

/entry/instrument/detector Group

... etc. ...

```

With `nxmx`, you can access the NXmx data in Python like this:

```Python

import h5py

import nxmx

with h5py.File("my-nxmx-file.h5") as f:

    nxmx_data = nxmx.NXmx(f)

```

## A slightly more detailed example

```Python

import h5py

import nxmx

with h5py.File("my-nxmx-file.h5") as f:

    nxmx_data = nxmx.NXmx(f)

    # Explore the NXmx data structure.

    entry, *_ = nxmx_data.entries

    print(entry.definition)  # Prints "NXmx".

    instrument, *_ = entry.instruments

    detector, *_ = instrument.detectors

    

    # Get the h5py object underlying an instance of a NX class.

    entry_group = entry._handle  # entry_group == f["entry"]

    # Find instances of a given NX class in a h5py.Group.

    beams = nxmx.find_class(instrument._handle, "NXbeam")

    # The equivalent for more than one NX class.

    beams, detectors = nxmx.find_classes(instrument._handle, "NXbeam", "NXdetector")

    # Query attributes of an object in the normal h5py way.

    # Suppose out detector has a transformation called "det_z".

    transformations, *_ = nxmx.find_class(detector._handle, "NXtransformations")

    attrs = transformations["det_z"].attrs  # Get the attributes of the "det_z" dataset.

```