NXdata.nxdl.xml

<?xml version="1.0" encoding="UTF-8"?>
<?xml-stylesheet type="text/xsl" href="nxdlformat.xsl" ?>
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# NeXus - Neutron and X-ray Common Data Format
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<definition name="NXdata" 
	version="1.0"
	type="group" 
	extends="NXobject"
	category="base"
	ignoreExtraFields="true"
	ignoreExtraAttributes="true" 
	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"
	>
	
	<!-- 
		The ignoreExtra* attributes are used in the definition to
		avoid warning messages that would be generated from unexpected fields or attributes.
		Since common use of NXdata indicates field names of any value, _many_
		instances of this class would generate a warning message during validation
		without this attribute being set to "true".
	-->

	<symbols>
		<doc>These symbols will be used below to coordinate datasets with the same shape.</doc>
		<symbol name="dataRank"><doc>rank of the ``data`` field</doc></symbol>
		<symbol name="n"><doc>length of the ``variable`` field</doc></symbol>
		<symbol name="nx"><doc>length of the ``x`` field</doc></symbol>
		<symbol name="ny"><doc>length of the ``y`` field</doc></symbol>
		<symbol name="nz"><doc>length of the ``z`` field</doc></symbol>
	</symbols>
	
	<attribute name="signal">
		<doc>
			.. index:: plotting
			
			Declares which dataset is the default. 
			The value is the name of the dataset to be plotted.
			A field of this name *must* exist (either as dataset 
			or as a link to a dataset).
			
			It is recommended (as of NIAC2014) to use this attribute
			rather than adding a signal attribute to the dataset.
			See http://wiki.nexusformat.org/2014_How_to_find_default_data
			for a summary of the discussion.
		</doc>
	</attribute>
	<attribute name="axes">
		<!-- http://wiki.nexusformat.org/2014_axes_and_uncertainties -->
		<doc>
			.. index:: plotting
			
			String array that defines the independent data fields used in 
			the default plot for all of the dimensions of the *signal* field
			(the *signal* field is the field in this group that is named by
			the ``signal`` attribute of this group). 
			One entry is provided for every dimension in the *signal* field.
			
			The field(s) named as values (known as "axes") of this attribute 
			*must* exist. An axis slice is specified using a field named 
			``AXISNAME_indices`` as described below (where the text shown here
			as ``AXISNAME`` is to be replaced by the actual field name).
			
			When no default axis is available for a particular dimension 
			of the plottable data, use a "." in that position.  
			Such as::
			
				@I_axes="time", ".", "."
			
			Since there are three items in the list, the the *signal* field
			must must be a three-dimensional array (rank=3).  The first dimension
			is described by the values of a one-dimensional array named ``time``
			while the other two dimensions have no fields to be used as dimension scales.
			
			See examples provided on the NeXus wiki:
			http://wiki.nexusformat.org/2014_axes_and_uncertainties
			
			If there are no axes at all (such as with a stack of images), 
			the axes attribute can be omitted.
		</doc>
	</attribute>
	<attribute name="AXISNAME_indices">
		<!-- 
			nxdl.xsd rules do not allow us to show this as a variable name 
			- we'll use ALL CAPS 
		-->
		<!-- AXISNAME_indices documentation copied from datarules.rst -->
		<doc>
			Each ``AXISNAME_indices`` attribute indicates the dependency
			relationship of the ``AXISNAME`` field (where ``AXISNAME`` 
			is the name of a field that exists in this ``NXdata`` group) 
			with one or more dimensions of the plottable data.
		
			Integer array that defines the indices of the *signal* field 
			(that field will be a multidimensional array)
			which need to be used in the *AXISNAME* dataset in 
			order to reference the corresponding axis value.
			
			The first index of an array is ``0`` (zero).
			
			Here, *AXISNAME* is to be replaced by the name of each 
			field described in the ``axes`` attribute.  
			An example with 2-D data, :math:`d(t,P)`, will illustrate::
			
			  data_2d:NXdata
				@signal="data"
				@axes="time","pressure"
				@time_indices=0
				@pressure_indices=1
				data: float[1000,20]
				time: float[1000]
				pressure: float[20]
			
			This attribute is to be provided in all situations. 
			However, if the indices attributes are missing 
			(such as for data files written before this specification), 
			file readers are encouraged to make their best efforts 
			to plot the data. 	
			Thus the implementation of the 
			``AXISNAME_indices`` attribute is based on the model of 
			"strict writer, liberal reader". 
			
			.. note::  Attributes potentially containing multiple values 
			   (axes and _indices) are to be written as string or integer arrays, 
			   to avoid string parsing in reading applications.
		</doc>
	</attribute>
	
	<doc>
		:ref:`NXdata` describes the plottable data and related dimension scales. 
		
		.. index:: plotting
		
		It is mandatory  that there is at least one :ref:`NXdata` group 
		in each :ref:`NXentry` group.  
		Note that the ``variable`` and ``data`` 
		can be defined with different names.  
		The ``signal`` and ``axes`` attributes of the 
		``data`` group define which items 
		are plottable data and which are *dimension scales*, respectively.
		
		:ref:`NXdata` is used to implement one of the basic motivations in NeXus,
		to provide a default plot for the data of this :ref:`NXentry`.  The actual data
		might be stored in another group and (hard) linked to the :ref:`NXdata` group.

		* Each :ref:`NXdata` group will define only one data set
		  containing plottable data, dimension scales, and 
		  possibly associated standard deviations.
		  Other data sets may be present in the group.
		* The plottable data may be of arbitrary rank up to a maximum
		  of ``NX_MAXRANK=32``.
		* The plottable data will be named as the value of 
		  the group ``signal`` attribute, such as::
		  
		    data:NXdata
		      @signal = "counts"
		      @axes = "mr"
		      @mr_indices = 0
		      counts: float[100]  --> the default dependent data
		      mr: float[100]  --> the default independent data
		  
		  The field named in the ``signal`` attribute **must** exist, either
		  directly as a dataset or defined through a link.
		
		* The group ``axes`` attribute will name the
		  *dimension scale* associated with the plottable data.

		If available, the standard deviations of the data are to be
		stored in a data set of the same rank and dimensions, with the name ``errors``. 

		* For each data dimension, there should be a one-dimensional array
		  of the same length.
		* These one-dimensional arrays are the *dimension scales* of the
		  data,  *i.e*. the values of the independent variables at which the data
		  is measured, such as scattering angle or energy transfer.
		
		.. index:: link
		.. index:: axes (attribute)
		
		The preferred method to associate each data dimension with
		its respective dimension scale is to specify the field name
		of each dimension scale in the group ``axes`` attribute as a string list.
		Here is an example for a 2-D data set *data* plotted 
		against *time*, and *pressure*.  (An additional *temperature* data set 
		is provided and could be selected as an alternate for the *pressure* axis.)::

		  data_2d:NXdata
		    @signal="data"
		    @axes="time","pressure"
		    @pressure_indices=1
		    @temperature_indices=1
		    @time_indices=0
		    data: float[1000,20]
		    pressure: float[20]
		    temperature: float[20]
		    time: float[1000]

		.. rubric:: Old methods to identify the plottable data
		
		There are two older methods of associating 
		each data dimension to its respective dimension scale.
		Both are now out of date and
		should not be used when writing new data files.
		However, client software should expect to see data files
		written with any of these methods.
		
		  * One method uses the ``axes`` 
		    attribute to specify the names of each *dimension scale*.
		
		  * The oldest method uses the ``axis`` attribute on each
		    *dimension scale* to identify
		    with an integer the axis whose value is the number of the dimension.
	</doc>
	<field name="variable" type="NX_NUMBER">
		<doc>
	 		Dimension scale defining an axis of the data.
	 		Client is responsible for defining the dimensions of the data.
	 		The name of this field may be changed to fit the circumstances.
	 		Standard NeXus client tools will use the attributes to determine
	 		how to use this field.
	 	</doc>
		<dimensions rank="1">
			<doc>
				A *dimension scale* must have a rank of 1 and has length ``n``.
			</doc>
			<dim index="1" value="n"/>
		</dimensions>
		<attribute name="long_name"><doc>Axis label</doc></attribute>
		<attribute name="distribution" type="NX_BOOLEAN">
			<doc>
				``0|false``: single value, 
				``1|true``: multiple values
			</doc>
		</attribute>
		<attribute name="first_good" type="NX_INT"><doc>Index of first good value</doc></attribute>
		<attribute name="last_good" type="NX_INT"><doc>Index of last good value</doc></attribute>
		<attribute name="axis" type="NX_POSINT"
			deprecated="Use the group ``axes`` attribute   (NIAC2014)">
			<doc>
				Index (positive integer) identifying this specific set of numbers.
				
				N.B. The ``axis`` attribute is the old way of designating a link.  
				Do not use the ``axes`` attribute with the ``axis`` attribute.
				The ``axes`` *group* attribute is now preferred.
			</doc>
		</attribute>
	</field>
	<field name="variable_errors" type="NX_NUMBER">
		<doc>
			Errors (uncertainties) associated with axis ``variable``.
			Client is responsible for defining the dimensions of the data.
			The name of this field may be changed to fit the circumstances 
			but is matched with the *variable*
			field with ``_errors`` appended.
		</doc>
		<dimensions rank="1">
			<doc>
				A dimension scale must have a rank of 1 and has length ``n``, 
				same as ``variable``.
			</doc>
			<dim index="1" value="n"/>
		</dimensions>
	</field>
	<field name="data" type="NX_NUMBER">
		<doc>
			.. index:: plotting
		
			This field contains the data values to be used as the 
			NeXus *plottable data*.
			Client is responsible for defining the dimensions of the data.
			The name of this field may be changed to fit the circumstances.
			Standard NeXus client tools will use the attributes to determine
			how to use this field.
		</doc>
		<dimensions rank="dataRank">
			<doc>
				The rank (``dataRank``) of the ``data`` must satisfy
				``1 &lt;= dataRank &lt;= NX_MAXRANK=32``.  
				At least one ``dim`` must have length ``n``.
			</doc>
			<dim index="0" value="n"><!-- index="0": cannot know to which dimension this applies a priori --></dim>
		</dimensions>
		<attribute name="signal" type="NX_POSINT"
			deprecated="Use the group ``signal`` attribute   (NIAC2014)">
			<doc>
				.. index:: plotting
	
				Plottable (independent) axis, indicate index number.
				Only one field in a :ref:`NXdata` group may have the
				``signal=1`` attribute.
				Do not use the ``signal`` attribute with the ``axis`` attribute.
			</doc>
		</attribute>
		<attribute name="axes"
			deprecated="Use the group ``axes`` attribute   (NIAC2014)">
			<doc>
				Defines the names of the dimension scales
				(independent axes) for this data set
				as a colon-delimited array.
				NOTE: The ``axes`` attribute is the preferred
				method of designating a link.
				Do not use the ``axes`` attribute with the ``axis`` attribute.
			</doc>
		</attribute>
		<attribute name="uncertainties">
			<!-- 
				see http://wiki.nexusformat.org/2014_axes_and_uncertainties
				not accepted at NIAC2014
				"NIAC will see a proposal when experience has been gained with all variations."
			-->
			<doc>
				Specify the name (or names) of the uncertainties (errors) 
				of the dependent axes as plottable data.
				NOTE: The ``uncertainties`` attribute uses the same syntax
				as the ``axes`` attribute, a string or an array of strings 
				for multiple uncertainties.
				
				Examples::
				
					@I_uncertainties="Idev"
					
					@Q_uncertainties="dQw", "dQl"		
		
			</doc>
		</attribute>
		<attribute name="long_name">
			<doc>data label</doc>
		</attribute>
	</field>
	<field name="errors" type="NX_NUMBER">
		<doc>
			Standard deviations of data values - 
			the data array is identified by the group attribute ``signal``. 
			The ``errors`` array must have the same dimensions as ``data``.
			Client is responsible for defining the dimensions of the data.
		</doc>
		<dimensions rank="dataRank">
			<doc>
				The ``errors`` must have 
				the same rank (``dataRank``) 
				as the ``data``.  
				At least one ``dim`` must have length "n".
			</doc>
			<dim index="0" value="n"><!-- index="0": cannot know to which dimension this applies a priori --></dim>
		</dimensions>
	</field>
	<field name="scaling_factor" type="NX_FLOAT">
		<doc>
			The elements in data are usually float values really. For
			efficiency reasons these are usually stored as integers
			after scaling with a scale factor. This value is the scale
			factor. It is required to get the actual physical value,
			when necessary.
		</doc>
	</field>
	<field name="offset" type="NX_FLOAT">
		<doc>
			An optional offset to apply to the values in data.
		</doc>
	</field>
	<field name="x" type="NX_FLOAT" units="NX_ANY">
		<doc>
			This is an array holding the values to use for the x-axis of
			data.  The units must be appropriate for the measurement.
		</doc>
		<dimensions rank="1">
			<dim index="1" value="nx" />
		</dimensions>
	</field>
	<field name="y" type="NX_FLOAT" units="NX_ANY">
		<doc>
			This is an array holding the values to use for the y-axis of
			data.  The units must be appropriate for the measurement.
		</doc>
		<dimensions rank="1">
			<dim index="1" value="ny" />
		</dimensions>
	</field>
	<field name="z" type="NX_FLOAT" units="NX_ANY">
		<doc>
			This is an array holding the values to use for the z-axis of
			data.  The units must be appropriate for the measurement.
		</doc>
		<dimensions rank="1">
			<dim index="1" value="nz" />
		</dimensions>
	</field>
</definition>