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')

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 0x7ff108024100>

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 0x7ff1080399c0>

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 0x7ff10803a320>,
 'bank103': <scippnexus.base.Group at 0x7ff10803a3e0>,
 'bank104': <scippnexus.base.Group at 0x7ff10803a4a0>,
 'bank105': <scippnexus.base.Group at 0x7ff10803a560>,
 'bank106': <scippnexus.base.Group at 0x7ff10803a620>,
 'bank123': <scippnexus.base.Group at 0x7ff10803a6e0>,
 'bank124': <scippnexus.base.Group at 0x7ff10803a7a0>,
 'bank143': <scippnexus.base.Group at 0x7ff10803a860>,
 'bank144': <scippnexus.base.Group at 0x7ff10803a920>,
 'bank164': <scippnexus.base.Group at 0x7ff10803a9e0>,
 'bank184': <scippnexus.base.Group at 0x7ff10803aaa0>,
 'bank22': <scippnexus.base.Group at 0x7ff10803ab60>,
 'bank23': <scippnexus.base.Group at 0x7ff10803ac20>,
 'bank24': <scippnexus.base.Group at 0x7ff10803ace0>,
 'bank42': <scippnexus.base.Group at 0x7ff10803ada0>,
 'bank43': <scippnexus.base.Group at 0x7ff10803ae60>,
 'bank44': <scippnexus.base.Group at 0x7ff10803af20>,
 'bank62': <scippnexus.base.Group at 0x7ff10803afe0>,
 'bank63': <scippnexus.base.Group at 0x7ff10803b0a0>,
 'bank64': <scippnexus.base.Group at 0x7ff10803b160>,
 'bank82': <scippnexus.base.Group at 0x7ff10803b220>,
 'bank83': <scippnexus.base.Group at 0x7ff10803b2e0>,
 'bank84': <scippnexus.base.Group at 0x7ff10803b3a0>}

Writing to files#

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

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#

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`#