1.3. Constructing NeXus Files and Application Definitions

In NeXus Design, we discussed the design of the NeXus format in general terms. In this section a more tutorial style introduction in how to construct a NeXus file is given. As an example a hypothetical instrument named WONI will be used.

Note

If you are looking for a tutorial on reading or writing NeXus data files using the NeXus API, consult the NAPI: NeXus Application Programmer Interface (frozen) chapter. For code examples, refer to Code Examples that use the NeXus API (NAPI) chapter. Alternatively, there are examples in the Example NeXus C programs using native HDF5 commands chapter of writing and reading NeXus data files using the native HDF5 interfaces in C. Further, there are also some Python examples using the h5py package in the Python Examples using h5py section.

1.3.1. The WOnderful New Instrument (WONI)

Consider yourself to be responsible for some hypothetical WOnderful New Instrument (WONI). You are tasked to ensure that WONI will record data according to the NeXus standard. For the sake of simplicity, WONI bears a strong resemblance to a simple powder diffractometer, but let’s pretend that WONI cannot use any of the existing NXDL application definitions.

FigWoniSchematic :width: 90% :align: center

The (fictional) WONI example powder diffractometer

WONI uses collimators and a monochromator to illuminate the sample with neutrons of a selected wavelength as described in The (fictional) WONI example powder diffractometer. The diffracted beam is collected in a large, banana-shaped, position sensitive detector. Typical data looks like Example Powder Diffraction Plot from (fictional) WONI at HYNES. There is a generous background to the data plus quite a number of diffraction peaks.

FigWoniPowderData :width: 90% :align: center

Example Powder Diffraction Plot from (fictional) WONI at HYNES

1.3.2. Constructing a NeXus file for WONI

The starting point for a NeXus file for WONI will be an empty basic NeXus file hierarchy as documented in the next figure. In order to arrive at a full NeXus file, the following steps are required:

  1. For each instrument component, decide which parameters need to be stored
  2. Map the component parameters to NeXus groups and parameters and add the components to the NXinstrument hierarchy
  3. Decide what needs to go into NXdata. While this group is optional, you are urged strongly to provide an NXdata group to support default plotting.
  4. Fill the NXsample and NXmonitor groups

Basic structure of a NeXus file

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  entry:NXentry
    NXdata
    NXinstrument
    NXmonitor
    NXsample

1.3.2.1. Decide which parameters need to be stored

Now the various groups of this empty NeXus file shell need to be filled. The next step is to look at a design drawing of WONI. Identify all the instrument components like collimators, detectors, monochromators etc. For each component decide which values need to be stored. As NeXus aims to describe the experiment as good as possible, strive to capture as much information as practical.

1.3.2.2. Mapping parameters to NeXus

With the list of parameters to store for each component, consult the reference manual section on the NeXus base classes. You will find that for each of your instruments components there will be a suitable NeXus base class. Add this base class together with a name as a group under NXinstrument in your NeXus file hierarchy. Then consult the possible parameter names in the NeXus base class and match them with the parameters you wish to store for your instruments components.

As an example, consider the monochromator. You may wish to store: the wavelength, the d-value of the reflection used, the type of the monochromator and its angle towards the incoming beam. The reference manual tells you that NXcrystal is the right base class to use. Suitable fields for your parameters can be found in there to. After adding them to the basic NeXus file, the file looks like in the next figure:

Basic structure of a NeXus file with a monochromator added

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  entry:NXentry
    NXdata
    NXinstrument
       monochromator:Nxcrystal
          wavelength
          d_spacing
          rotation_angle
          reflection
          type
    NXmonitor
    NXsample

If a parameter or even a whole group is missing in order to describe your experiment, do not despair! Contact the NIAC and suggest to add the group or parameter. Give a little documentation what it is for. The NIAC will check that your suggestion is no duplicate and sufficiently documented and will then proceed to enhance the base classes with your suggestion.

A more elaborate example of the mapping process is given in the section Creating a NXDL Specification.

1.3.2.3. Decide on NXdata

The NXdata/ group is supposed to contain the data required to put up a quick plot. For WONI this is a plot of counts versus two theta (polar_angle in NeXus) as can be seen in Example Powder Diffraction Plot from (fictional) WONI at HYNES. Now, in NXdata, create links to the appropriate data items in the NXinstrument hierarchy. In the case of WONI, both parameters live in the detector:NXdetector group.

1.3.2.4. Fill in auxiliary Information

Look at the section on NXsample in the NeXus reference manual. Choose appropriate parameters to store for your samples. Probably at least the name will be needed.

In order to normalize various experimental runs against each other it is necessary to know about the counting conditions and especially the monitor counts of the monitor used for normalization. The NeXus convention is to store such information in a control:NXmonitor group at NXentry level. Consult the reference for NXmonitor for field names. If additional monitors exist within your experiment, they will be stored as additional NXmonitor groups at entry level.

Consult the documentation for NXentry in order to find out under which names to store information such as titles, user names, experiment times etc.

A more elaborate example of this process can be found in the following section on creating an application definition.

1.3.3. Creating a NXDL Specification

An NXDL specification for a NeXus file is required if you desire to standardize NeXus files from various sources. Another name for a NXDL description is application definition. A NXDL specification can be used to verify NeXus files to conform to the standard encapsulated in the application definition. The process for constructing a NXDL specification is similar to the one described above for the construction of NeXus files.

One easy way to describe how to store data in the NeXus class structure and to create a NXDL specification is to work through an example. Along the way, we will describe some key decisions that influence our particular choices of metadata selection and data organization. So, on with the example ...

1.3.3.1. Application Definition Steps

With all this introductory stuff out of the way, let us look at the process required to define an application definition:

  1. Think! hard about what has to go into the data file.
  2. Map the required fields into the NeXus hierarchy
  3. Describe this map in a NXDL file
  4. Standardize your definition through communication with the NIAC

1.3.3.2. Step 1: Think! hard about data

This is actually the hard bit. There are two things to consider:

  1. What has to go into the data file?
  2. What is the normal plot for this type of data?

For the first part, one of the NeXus guiding principles gives us - Guidance! “A NeXus file must contain all the data necessary for standard data analysis.”

Not more and not less for an application definition. Of course the definition of standard data for analysis or a standard plot depends on the science and the type of data being described. Consult senior scientists in the field about this is if you are unsure. Perhaps you must call an international meeting with domain experts to haggle that out. When considering this, people tend to put in everything which might come up. This is not the way to go.

A key test question is: Is this data item necessary for common data analysis? Only these necessary data items belong in an application definition.

The purpose of an application definition is that an author of upstream software who consumes the file can expect certain data items to be there at well defined places. On the other hand if there is a development in your field which analyzes data in a novel way and requires more data to do it, then it is better to err towards the side of more data.

Now for the case of WONI, the standard data analysis is either Rietveld refinement or profile analysis. For both purposes, the kind of radiation used to probe the sample (for WONI, neutrons), the wavelength of the radiation, the monitor (which tells us how long we counted) used to normalize the data, the counts and the two theta angle of each detector element are all required. Usually, it is desirable to know what is being analyzed, so some metadata would be nice: a title, the sample name and the sample temperature. The data typically being plotted is two theta against counts, as shown in Example Powder Diffraction Plot from (fictional) WONI at HYNES above. Summarizing, the basic information required from WONI is given next.

  • title of measurement
  • sample name
  • sample temperature
  • counts from the incident beam monitor
  • type of radiation probe
  • wavelength (\(\lambda\)) of radiation incident on sample
  • angle (\(2\theta\) or two theta) of detector elements
  • counts for each detector element

If you start to worry that this is too little information, hold on, the section on Using an Application Definition (Using an Application Definition) will reveal the secret how to go from an application definition to a practical file.

1.3.3.3. Step 2: Map Data into the NeXus Hierarchy

This step is actually easier then the first one. We need to map the data items which were collected in Step 1 into the NeXus hierarchy. A NeXus file hierarchy starts with an NXentry group. At this stage it is advisable to pull up the base class definition for NXentry and study it. The first thing you might notice is that NXentry contains a field named title. Reading the documentation, you quickly realize that this is a good place to store our title. So the first mapping has been found.

title = /NXentry/title

Note

In this example, the mapping descriptions just contain the path strings into the NeXus file hierarchy with the class names of the groups to use. As it turns out, this is the syntax used in NXDL link specifications. How convenient!

Another thing to notice in the NXentry base class is the existence of a group of class NXsample. This looks like a great place to store information about the sample. Studying the NXsample base class confirms this view and there are two new mappings:

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sample name = /NXentry/NXsample/name
sample temperature = /NXentry/NXsample/temperature

Scanning the NXentry base class further reveals there can be a NXmonitor group at this level. Looking up the base class for NXmonitor reveals that this is the place to store our monitor information.

monitor = /NXentry/NXmonitor/data

For the other data items, there seem to be no solutions in NXentry. But each of these data items describe the instrument in more detail. NeXus stores instrument descriptions in the /NXentry/NXinstrument branch of the hierarchy. Thus, we continue by looking at the definition of the NXinstrument base class. In there we find further groups for all possible instrument components. Looking at the schematic of WONI (The (fictional) WONI example powder diffractometer), we realize that there is a source, a monochromator and a detector. Suitable groups can be found for these components in NXinstrument and further inspection of the appropriate base classes reveals the following further mappings:

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probe = /NXentry/NXinstrument/NXsource/probe
wavelength = /NXentry/NXinstrument/NXcrystal/wavelength
two theta of detector elements = /NXentry/NXinstrument/NXdetector/polar angle
counts for each detector element = /NXentry/NXinstrument/NXdetector/data

Thus we mapped all our data items into the NeXus hierarchy! What still needs to be done is to decide upon the content of the NXdata group in NXentry. This group describes the data necessary to make a quick plot of the data. For WONI this is counts versus two theta. Thus we add this mapping:

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two theta of detector elements = /NXentry/NXdata/polar angle
counts for each detector element = /NXentry/NXdata/data

The full mapping of WONI data into NeXus is documented in the next table:

WONI data NeXus path
title of measurement /NXentry/title
sample name /NXentry/NXsample/name
sample temperature /NXentry/NXsample/temperature
monitor /NXentry/NXmonitor/data
type of radiation probe /NXentry/MXinstrument/NXsource/probe
wavelength of radiation incident on sample /NXentry/MXinstrument/NXcrystal/wavelength
two theta of detector elements /NXentry/NXinstrument/NXdetector/polar_angle
counts for each detector element /NXentry/NXinstrument/NXdetector/data
two theta of detector elements /NXentry/NXdata/polar_angle
counts for each detector element /NXentry/NXdata/data

Looking at this table, one might get concerned that the two theta and counts data is stored in two places and thus duplicated. Stop worrying, this problem is solved at the NeXus API level. Typically NXdata will only hold links to the corresponding data items in /NXentry/NXinstrument/NXdetector.

In this step problems might occur. The first is that the base class definitions contain a bewildering number of parameters. This is on purpose: the base classes serve as dictionaries which define names for most things which possibly can occur. You do not have to give all that information. Keep it simple and only require data that is needed for typical data analysis for this type of application.

Another problem which can occur is that you require to store information for which there is no name in one of the existing base classes or you have a new instrument component for which there is no base class altogether. New fields and base classes can be introduced if necessary.

In any case please feel free to contact the NIAC via the mailing list with questions or suggestions.

1.3.3.4. Step 3: Describe this map in a NXDL file

This is even easier. Some XML editing is necessary. Fire up your XML editor of choice and open a file. If your XML editor supports XML schema while editing XML, it is worth to load nxdl.xsd. Now your XML editor can help you to create a proper NXDL file. As always, the start is an empty template file. This looks like the XML code below.

Note

This is just the basic XML for a NXDL definition. It is advisable to change some of the documentation strings.

NXDL template file

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<?xml version="1.0" encoding="UTF-8"?>
<!--
# NeXus - Neutron and X-ray Common Data Format
# 
# Copyright (C) 2008-2017 NeXus International Advisory Committee (NIAC)
# 
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 3 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
#
# For further information, see http://www.nexusformat.org
-->
<definition name="NX__template__" extends="NXobject" type="group"
    category="application"
    xmlns="http://definition.nexusformat.org/nxdl/3.1"
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd"
    version="1.0b"
    >
    <doc>template for a NXDL application definition</doc>
</definition>

For example, copy and rename the file to NXwoni.nxdl.xml. Then, locate the XML root element definition and change the name attribute (the XML shorthand for this attribute is /definition/@name) to NXwoni. Change the doc as well. Also consider keeping track of /definition/@version as suits your development of this NXDL file.

The next thing which needs to be done is adding groups into the definition. A group is defined by some XML, as in this example:

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<group type="NXdata">

</group>

The type is the actual NeXus base class this group belongs to. Optionally a name attribute may be given (default is data).

Next, one needs to include data items, too. The XML for such a data item looks similar to this:

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<field name="polar_angle" type="NX_FLOAT units="NX_ANGLE">
  <doc>Link to polar angle in /NXentry/NXinstrument/NXdetector</doc>
  <dimensions rank="1">
    <dim index="1" value="ndet"/>
  </dimensions>
</field>

The meaning of the name attribute is intuitive, the type can be looked up in the relevant base class definition. A field definition can optionally contain a doc element which contains a description of the data item. The dimensions entry specifies the dimensions of the data set. The size attribute in the dimensions tag sets the rank of the data, in this example: rank="1". In the dimensions group there must be rank dim fields. Each dim tag holds two attributes: index determines to which dimension this tag belongs, the 1 means the first dimension. The value attribute then describes the size of the dimension. These can be plain integers, variables, such as in the example ndet or even expressions like tof+1.

Thus a NXDL file can be constructed. The full NXDL file for the WONI example is given in Full listing of the WONI Application Definition. Clever readers may have noticed the strong similarity between our working example NXwoni and NXmonopd since they are essentially identical. Give yourselves a cookie if you spotted this.

1.3.3.5. Step 4: Standardize with the NIAC

Basically you are done. Your first application definition for NeXus is constructed. In order to make your work a standard for that particular application type, some more steps are required:

  • Send your application definition to the NIAC for review
  • Correct your definition per the comments of the NIAC
  • Cure and use the definition for a year
  • After a final review, it becomes the standard

The NIAC must review an application definition before it is accepted as a standard. The one year curation period is in place in order to gain practical experience with the definition and to sort out bugs from Step 1. In this period, data shall be written and analyzed using the new application definition.

1.3.3.6. Full listing of the WONI Application Definition

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<?xml version="1.0" encoding="UTF-8"?>
<?xml-stylesheet type="text/xsl" href="nxdlformat.xsl" ?>
<!--
# NeXus - Neutron and X-ray Common Data Format
# 
# Copyright (C) 2008-2017 NeXus International Advisory Committee (NIAC)
# 
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 3 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
#
# For further information, see http://www.nexusformat.org
-->
<definition name="NXmonopd" extends="NXobject" type="group"
    category="application"
    xmlns="http://definition.nexusformat.org/nxdl/3.1"
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd"
    version="1.0b"
    >
    <doc>
        Monochromatic Neutron and X-Ray Powder diffractometer 
        
        Instrument 
        definition for a powder diffractometer at a monochromatic neutron 
        or X-ray beam. This is both suited for a powder diffractometer 
        with a single detector or a powder diffractometer with a position 
        sensitive detector.
    </doc>
    <group type="NXentry" name="entry">
        <field name="title"/>
        <field name="start_time" type="NX_DATE_TIME"/>
        <field name="definition">
            <doc> Official NeXus NXDL schema to which this file conforms </doc>
            <enumeration>
                <item value="NXmonopd"/>
            </enumeration>
        </field>
        <group type="NXinstrument">
            <group type="NXsource">
                <field name="type"/>
                <field name="name"/>
                <field name="probe">
                    <enumeration>
                        <item value="neutron"/>
                        <item value="x-ray"/>
                        <item value="electron"/>
                    </enumeration>
                </field>
            </group>
            <group type="NXcrystal">
                <field name="wavelength" type="NX_FLOAT" units="NX_WAVELENGTH">
                    <doc>Optimum diffracted wavelength</doc>
                    <dimensions rank="1">
                        <dim index="1" value="i"/>
                    </dimensions>
                </field>
            </group>
            <group type="NXdetector">
                <field name="polar_angle" type="NX_FLOAT" axis="1">
                  <doc>where ndet = number of detectors</doc>
                  <dimensions rank="1">
                    <dim index="1" value="ndet" />
                  </dimensions>
                </field>
                <field name="data" type="NX_INT" signal="1">
                  <doc>
                    detector signal (usually counts) are already
                    corrected for detector efficiency
                  </doc>
                  <dimensions rank="1">
                    <dim index="1" value="ndet" />
                  </dimensions>
                </field>
            </group>
        </group>
        <group type="NXsample">
            <field name="name">
                <doc>Descriptive name of sample</doc>
            </field>
            <field name="rotation_angle" type="NX_FLOAT" units="NX_ANGLE">
                <doc>
                    Optional rotation angle for the case when the powder diagram 
                    has been obtained through an omega-2theta scan like from a 
                    traditional single detector powder diffractometer
                </doc>
            </field>
        </group>
        <group type="NXmonitor">
            <field name="mode">
                <doc>
                    Count to a preset value based on either clock time (timer) 
                    or received monitor counts (monitor).
                </doc>
                <enumeration>
                    <item value="monitor"/>
                    <item value="timer"/>
                </enumeration>
            </field>
            <field name="preset" type="NX_FLOAT">
                <doc>preset value for time or monitor</doc>
            </field>
            <field name="integral" type="NX_FLOAT" units="NX_ANY">
                <doc>Total integral monitor counts</doc>
            </field>
        </group>
        <group type="NXdata">
            <link name="polar_angle" target="/NXentry/NXinstrument/NXdetector/polar_angle">
                <doc>Link to polar angle in /NXentry/NXinstrument/NXdetector</doc>
            </link>
            <link name="data" target="/NXentry/NXinstrument/NXdetector/data">
                <doc>Link to data in /NXentry/NXinstrument/NXdetector</doc>
            </link>
        </group>
    </group>
</definition>

1.3.3.7. Using an Application Definition

The application definition is like an interface for your data file. In practice files will contain far more information. For this, the extendable capability of NeXus comes in handy. More data can be added, and upstream software relying on the interface defined by the application definition can still retrieve the necessary information without any changes to their code.

NeXus application definitions only standardize classes. You are free to decide upon names of groups, subject to them matching regular expression for NeXus name attributes (see the regular expression pattern for NXDL group and field names in the Naming Conventions section). Note the length limit of 63 characters imposed by HDF5. Please use sensible, descriptive names and separate multi worded names with underscores.

Something most people wish to add is more metadata, for example in order to index files into a database of some sort. Go ahead, do so, if applicable, scan the NeXus base classes for standardized names. For metadata, consider to use the NXarchive definition. In this context, it is worth to mention that a practical NeXus file might adhere to more then one application definition. For example, WONI data files may adhere to both the NXmonopd and NXarchive definitions. The first for data analysis, the second for indexing into the database.

Often, instrument scientists want to store the complete state of their instrument in data files in order to be able to find out what went wrong if the data is unsatisfactory. Go ahead, do so, please use names from the NeXus base classes.

Site policy might require you to store the names of all your bosses up to the current head of state in data files. Go ahead, add as many NXuser classes as required to store that information. Knock yourselves silly over this.

Your Scientific Accounting Department (SAD) may ask of you the preposterous; to store billing information into data files. Go ahead, do so if your judgment allows. Just do not expect the NIAC to provide base classes for this and do not use the prefix NX for your classes.

In most cases, NeXus files will just have one NXentry class group. But it may be required to store multiple related data sets of the results of data analysis into the same data file. In this case create more entries. Each entry should be interpretable standalone, i.e. contain all the information of a complete NXentry class. Please keep in mind that groups or data items which stay constant across entries can always be linked in.

1.3.4. Processed Data

Data reduction and analysis programs are encouraged to store their results in NeXus data files. As far as the necessary, the normal NeXus hierarchy is to be implemented. In addition, processed data files must contain a NXprocess group. This group, that documents and preserves data provenance, contains the name of the data processing program and the parameters used to run this program in order to achieve the results stored in this entry. Multiple processing steps must have a separate entry each.