Write a NeXus HDF5 file¶

In this example, the 1-D scan data will be written into the simplest possible NeXus HDF5 data file, containing only the required NeXus components. NeXus requires at least one NXentry group at the root level of an HDF5 file. The NXentry group contains all the data and associated information that comprise a single measurement. NXdata is used to describe the plottable data in the NXentry group. The simplest place to store data in a NeXus file is directly in the NXdata group, as shown in the next figure.

fig.simple-example-python — Simple Example¶

In the above figure, the data file (simple_example_write1_h5py.hdf5) contains a hierarchy of items, starting with an NXentry named entry. (The full HDF5 path reference, /entry in this case, is shown to the right of each component in the data structure.) The next h5py code example will show how to build an HDF5 data file with this structure. Starting with the numerical data described above, the only information written to the file is the absolute minimum information NeXus requires. In this example, you can see how the HDF5 file is created, how Groups and datasets (Fields) are created, and how Attributes are assigned. Note particularly the NX_class attribute on each HDF5 group that describes which of the NeXus Base Class Definitions is being used. When the next Python program (simple_example_write1_h5py.py) is run from the command line (and there are no problems), the simple_example_write1_h5py.hdf5 file is generated.

#!/usr/bin/env python
"""
Writes the simplest NeXus HDF5 file using h5py

Uses method accepted at 2014NIAC
according to the example from Figure 1.3
in the Introduction chapter
"""

from pathlib import Path

import numpy

from nexusformat.nexus import NXdata, NXentry, NXfield, nxopen

filename = str(Path(__file__).absolute().parent.parent / "simple_example.dat")
buffer = numpy.loadtxt(filename).T
tthData = buffer[0]
countsData = numpy.asarray(buffer[1], "int32")

with nxopen("simple_example_write1.hdf5", "w") as f:  # create the NeXus file
    f["Scan"] = NXentry()
    tth = NXfield(tthData, name="two_theta", units="degrees")
    counts = NXfield(countsData, name="counts", units="counts")
    f["Scan/data"] = NXdata(counts, tth)

#!/usr/bin/env python
"""
Writes the simplest NeXus HDF5 file using h5py

Uses method accepted at 2014NIAC
according to the example from Figure 1.3
in the Introduction chapter
"""

from pathlib import Path
import h5py
import numpy

filename = str(Path(__file__).absolute().parent.parent / "simple_example.dat")
buffer = numpy.loadtxt(filename).T
tthData = buffer[0]  # float[]
countsData = numpy.asarray(buffer[1], "int32")  # int[]

with h5py.File("simple_example_write1.hdf5", "w") as f:  # create the HDF5 NeXus file
    # since this is a simple example, no attributes are used at this point

    nxentry = f.create_group("Scan")
    nxentry.attrs["NX_class"] = "NXentry"

    nxdata = nxentry.create_group("data")
    nxdata.attrs["NX_class"] = "NXdata"
    nxdata.attrs["signal"] = "counts"
    nxdata.attrs["axes"] = "two_theta"
    nxdata.attrs["two_theta_indices"] = [
        0,
    ]

    tth = nxdata.create_dataset("two_theta", data=tthData)
    tth.attrs["units"] = "degrees"

    counts = nxdata.create_dataset("counts", data=countsData)
    counts.attrs["units"] = "counts"

One of the tools provided with the HDF5 support libraries is the h5dump command, a command-line tool to print out the contents of an HDF5 data file. With no better tool in place (the output is verbose), this is a good tool to investigate what has been written to the HDF5 file. View this output from the command line using h5dump simple_example_write1.hdf5. Compare the data contents with the numbers shown above. Note that the various HDF5 data types have all been decided by the h5py support package.

Note

The only difference between this file and one written using the NAPI is that the NAPI file will have some additional, optional attributes set at the root level of the file that tells the original file name, time it was written, and some version information about the software involved.

Since the output of h5dump is verbose (see the Downloads section below), the punx tree tool [1] was used to print out the structure of HDF5 data files. This tool provides a simplified view of the NeXus file. Here is the output:

  Scan:NXentry
    @NX_class = "NXentry"
    data:NXdata
      @NX_class = "NXdata"
      @axes = "two_theta"
      @signal = "counts"
      @two_theta_indices = [0]
      counts:NX_INT32[31] = [1037, 1318, 1704, '...', 1321]
        @units = "counts"
      two_theta:NX_FLOAT64[31] = [17.92608, 17.92591, 17.92575, '...', 17.92108]
        @units = "degrees"

As the data files in these examples become more complex, you will appreciate the information density provided by punx tree.

downloads¶

The Python code and files related to this section may be downloaded from the following table.

file	description
`../simple_example.dat`	2-column ASCII data used in this section
`simple_example_write1.py`	h5py code to write example simple_example_write1
`nexusformat/simple_example_write1.py`	nexusformat code to write example simple_example_write1
`simple_example_write1.hdf5`	NeXus file written by this code
`simple_example_write1_h5dump.txt`	h5dump analysis of the NeXus file
`simple_example_write1_structure.txt`	punx tree analysis of the NeXus file

Write a NeXus HDF5 file¶

downloads¶

NeXus-FAIRmat

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