HDF5 in Python

One way to gain a quick familiarity with NeXus is to start working with some data. For at least the first few examples in this section, we have a simple two-column set of 1-D data, collected as part of a series of alignment scans by the Advanced Photon Source USAXS instrument during the time it was stationed at beam line 32ID. We will show how to read and write this data in Python using both the nexusformat [1] and h5py [2] packages. The nexusformat package provides a simplified syntax for reading and writing NeXus-compliant files by automatically handling some of the features required by the NeXus standard, such as the attributes that define group classes and plottable data. However, it also uses the h5py package to read/write the HDF5 files on disk. We provide tabbed examples showing how to produce equivalent files either using nexusformat or directly in h5py.

The actual data to be written was extracted (elsewhere) from a spec [3] data file and read as a text block from a file by the Python source code. Our examples will start with the simplest case and add only mild complexity with each new case since these examples are meant for those who are unfamiliar with NeXus.

[1]

nexusformat: https://nexpy.github.io/nexpy/

[2]

h5py: https://www.h5py.org/

[3]

SPEC: http://certif.com/spec.html

Code examples

• Getting started
• Write a NeXus HDF5 file
• Write a NeXus HDF5 file with plottable data
• Write a NeXuS HDF5 File with links to external data
• Find plottable data in a NeXus HDF5 file

• Write examples with nexusformat for different NeXus classes

• Write examples with h5py for different NeXus classes

Example data used

The data shown plotted in the next figure will be written to the NeXus HDF5 file using only two NeXus base classes, NXentry and NXdata, in the first example and then minor variations on this structure in the next two examples. The data model is identical to the one in the Introduction chapter except that the names will be different, as shown below:

data structure of the simple example

/entry:NXentry
    /mr_scan:NXdata
       /mr : float64[31]
       /I00 : int32[31]

plot of the simple example data

Simple example values

17.92608    1037
17.92591    1318
17.92575    1704
17.92558    2857
17.92541    4516
17.92525    9998
17.92508    23819
17.92491    31662
17.92475    40458
17.92458    49087
17.92441    56514
17.92425    63499
17.92408    66802
17.92391    66863
17.92375    66599
17.92358    66206
17.92341    65747
17.92325    65250
17.92308    64129
17.92291    63044
17.92275    60796
17.92258    56795
17.92241    51550
17.92225    43710
17.92208    29315
17.92191    19782
17.92175    12992
17.92158    6622
17.92141    4198
17.92125    2248
17.92108    1321