Quick Start Guide#

Overview#

The NeXus Data Format is typically used to structure HDF5 files. An HDF5 file is a container for datasets and groups. Groups are folder-like and work like Python dictionaries. Datasets work like NumPy arrays. In addition, groups and datasets have a dictionary of attributes.

NeXus extends this with the following:

Definitions for attributes for datasets, in particular a units attribute. In NeXus, datasets are referred to as field.
Definitions for attributes and structure of groups. This includes:
- An NX_class attribute, identifying a group as an instance of a particular NeXus class such as NXdata or NXlog.
- Attributes that identify which fields contained in the group hold signal values, and which hold axis labels.

In the following we use a file from the POWGEN instrument at SNS. It is bundled with ScippNexus and will be downloaded automatically using pooch if it is not cached already:

[1]:

from scippnexus import data

filename = data.get_path('PG3_4844_event.nxs')

Downloading file 'PG3_4844_event.nxs' from 'https://public.esss.dk/groups/scipp/scippnexus/1/PG3_4844_event.nxs' to '/home/runner/.cache/scippnexus/1'.

Opening files#

It is often useful to only load part of a file or inspecting the file structure without loading any data. ScippNexus provides an interface that is similar to h5py for this purpose.

We first need to open the file using snx.File. Wherever possible this should be done using a context manager as follows:

[4]:

import scippnexus as snx

with snx.File(filename) as f:
    print(list(f.keys()))

['entry']

Unfortunately working with a context manager in a Jupyter Notebook is cumbersome, so for the following we open the file directly instead:

[5]:

f = snx.File(filename)

Navigating files#

Name-based access#

If there are multiple children with a specific NX_class attribute then the aforementioned properties cannot be used. Above we saw that the file contains a single key, 'entry' (the name could be anything, it just happens to match the class name here). When we access it we can see that it belongs to the class NXentry which is found on the top level in any NeXus file:

[6]:

entry = f['entry']
entry

[6]:

<scippnexus.base.Group at 0x7fc272d71a20>

We could continue inspecting keys, until we find a group we are interested in. For this example we use the 'proton_charge' log found within 'DASlogs':

[7]:

proton_charge = entry['DASlogs']['proton_charge']
proton_charge

[7]:

<scippnexus.base.Group at 0x7fc272dc30d0>

Getting all children of a specific `NX_class`#

The __getitem__ method can be used with a class imported from scippnexus to obtain a dict of all children with a matching NX_class attribute. For example, we can get all detectors within the NXintrument using:

[8]:

f['entry/instrument'][snx.NXdetector]

[8]:

{'bank102': <scippnexus.base.Group at 0x7fc272dc3bb0>,
 'bank103': <scippnexus.base.Group at 0x7fc272dc3c70>,
 'bank104': <scippnexus.base.Group at 0x7fc272dc3d30>,
 'bank105': <scippnexus.base.Group at 0x7fc272dc3df0>,
 'bank106': <scippnexus.base.Group at 0x7fc272dc3eb0>,
 'bank123': <scippnexus.base.Group at 0x7fc272dc3f70>,
 'bank124': <scippnexus.base.Group at 0x7fc272dd0070>,
 'bank143': <scippnexus.base.Group at 0x7fc272dd0130>,
 'bank144': <scippnexus.base.Group at 0x7fc272dd01f0>,
 'bank164': <scippnexus.base.Group at 0x7fc272dd02b0>,
 'bank184': <scippnexus.base.Group at 0x7fc272dd0370>,
 'bank22': <scippnexus.base.Group at 0x7fc272dd0430>,
 'bank23': <scippnexus.base.Group at 0x7fc272dd04f0>,
 'bank24': <scippnexus.base.Group at 0x7fc272dd05b0>,
 'bank42': <scippnexus.base.Group at 0x7fc272dd0670>,
 'bank43': <scippnexus.base.Group at 0x7fc272dd0730>,
 'bank44': <scippnexus.base.Group at 0x7fc272dd07f0>,
 'bank62': <scippnexus.base.Group at 0x7fc272dd08b0>,
 'bank63': <scippnexus.base.Group at 0x7fc272dd0970>,
 'bank64': <scippnexus.base.Group at 0x7fc272dd0a30>,
 'bank82': <scippnexus.base.Group at 0x7fc272dd0af0>,
 'bank83': <scippnexus.base.Group at 0x7fc272dd0bb0>,
 'bank84': <scippnexus.base.Group at 0x7fc272dd0c70>}

Writing to files#

See application definitions section for documentation about how to write to Nexus files.

This Page

Quick Start Guide#

Overview#

Loading files#

Opening files#

Navigating files#

Name-based access#

Getting all children of a specific `NX_class`#

Loading groups and datasets#

Writing to files#

This Page

Quick Start Guide#

Overview#

Loading files#

Opening files#

Navigating files#

Name-based access#

Getting all children of a specific NX_class#

Loading groups and datasets#

Writing to files#

Getting all children of a specific `NX_class`#