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Suggested improvements to the NXdata base class definition #602

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Suggested improvements to the NXdata base class definition #602

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aee3827
Replace 'dataset' with 'field'
rayosborn Nov 27, 2017
619d077
Rename VARIABLE and AXISNAME
rayosborn Nov 27, 2017
7a0493c
Removed redundant fields
rayosborn Nov 27, 2017
b91e4d7
Removed redundant text
rayosborn Nov 27, 2017
0dec12d
Changed 'mandatory' to 'recommended'
rayosborn Nov 27, 2017
088ef4f
Update definition of uncertainties
rayosborn Nov 27, 2017
c0a593d
Add use of bin boundaries
rayosborn Nov 27, 2017
b81ae69
Miscellaneous edits
rayosborn Nov 27, 2017
59e55a4
Fix indentation
rayosborn Jan 30, 2018
4bac172
Fix typos and improve wording
rayosborn Jan 30, 2018
4c21ea8
Amend wording about uncertainties
rayosborn Jan 30, 2018
6b9413b
Fix indentation
rayosborn Jan 30, 2018
0359402
Merge branch 'master' of https://github.com/nexusformat/definitions i…
rayosborn Oct 19, 2020
4b7ccb3
Merge branch 'master' of https://github.com/nexusformat/definitions i…
rayosborn Oct 26, 2020
81634f1
Merge branch 'main' into osborn-suggestions
prjemian Sep 17, 2022
6ce74b0
DOC #602 reST syntax
prjemian Sep 19, 2022
6c56a38
Merge branch 'osborn-suggestions' of https://github.com/rayosborn/def…
prjemian Sep 19, 2022
4f7e06d
DOC #602 indentation
prjemian Sep 19, 2022
9e1b035
CI #602 spelling
prjemian Sep 19, 2022
5c37cbb
DOC #602 AXISNAME -> AXIS per commit 619d077
prjemian Sep 19, 2022
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226 changes: 111 additions & 115 deletions base_classes/NXdata.nxdl.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -42,25 +42,22 @@
-->

<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>
<doc>These symbols will be used below to coordinate fields with the same shape.</doc>
<symbol name="dataRank"><doc>rank of the ``DATA`` field</doc></symbol>
<symbol name="n"><doc>length of the ``AXIS`` 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).
Declares which field contains the default plottable data.
The value is the name of the field to be plotted.
A field of this name *must* exist (either as field
or as a link to a field in another group).

It is recommended (as of NIAC2014) to use this attribute
rather than adding a signal attribute to the dataset.
rather than adding a signal attribute to the field.
See http://wiki.nexusformat.org/2014_How_to_find_default_data
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that link goes nowhere

for a summary of the discussion.
</doc>
Expand All @@ -70,27 +67,28 @@
<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).
String array that defines the names of independent data fields used
in the default plot for each of the dimensions of the *signal* field.
One entry is provided for every dimension in the *signal* field.
The field(s) named in this attribute *must* exist.

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).
An axis slice is specified using a field named
``AXIS_indices`` as described below (where the text shown here
as ``AXIS`` 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::

@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.
In this example, since there are three items in the list, 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. If the dimension scale does not
exist, it is assumed the data will be plotted against the
corresponding array index.

See examples provided on the NeXus wiki:
http://wiki.nexusformat.org/2014_axes_and_uncertainties
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New URL: https://www.nexusformat.org/2014_axes_and_uncertainties.html

Expand All @@ -99,27 +97,28 @@
the axes attribute can be omitted.
</doc>
</attribute>
<attribute name="AXISNAME_indices">
<attribute name="AXIS_indices">
<!--
nxdl.xsd rules do not allow us to show this as a variable name
- we'll use ALL CAPS (see #562)
-->
<!-- AXISNAME_indices documentation copied from datarules.rst -->
<!-- AXIS_indices documentation copied from datarules.rst -->
<doc>
Each ``AXISNAME_indices`` attribute indicates the dependency
relationship of the ``AXISNAME`` field (where ``AXISNAME``
Each ``AXIS_indices`` attribute indicates the dependency
relationship of the ``AXIS`` field (where ``AXIS``
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
which need to be used in the *AXIS* field 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
Here, *AXIS* 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
Expand All @@ -131,14 +130,7 @@
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".
This attribute should be provided in all situations.

.. note:: Attributes potentially containing multiple values
(axes and _indices) are to be written as string or integer arrays,
Expand All @@ -151,25 +143,27 @@

.. index:: plotting

It is mandatory that there is at least one :ref:`NXdata` group
It is recommended 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.
The ``signal`` and ``axes`` attributes of the ``data`` group define
which fields are plottable data and which are the independent variables,
or *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.
to identify plottable data in each :ref:`NXentry`. The actual data
might be stored in another group and linked to the :ref:`NXdata` group.

..note :: Note that, in the following, ``DATA`` and ``AXIS``
represent the names of fields containing the plottable data and
axes, respectively. The names are not fixed by the standard.

* 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.
* Each :ref:`NXdata` group will define only one field
containing plottable data, one for each of the dimension scales, and,
optionally, associated uncertainties. Other fields 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 name of the plottable data will be defined by the value of
the group ``signal`` attribute, such as::

data:NXdata
Expand All @@ -180,29 +174,35 @@
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.
directly as a field 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 field of the same rank and dimensions, either with the
name ``DATA_errors`` or with a name specified in the data's
``uncertainties`` attribute.

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.
* For each data dimension of size ``n``, there should be a
one-dimensional array of size ``n`` or ``n+1``, which contain 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 (size ``n``) or the bin boundaries when the data is
histogrammed (size ``n+1 ``).
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.. index:: link
.. index:: axes (attribute)

* The group ``axes`` attribute will list these *dimension scales*.
associated with the plottable data in the order of their respective
dimension, *i.e.*, starting with the slowest-changing dimension in
row major order.

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
Here is an example for 2-D data, *data*, plotted
against *time*, and *pressure*. (An additional *temperature* data set
is provided and could be selected as an alternate for the *pressure* axis.)::
is provided and could be selected as an alternate for the *pressure*
axis.)::

data_2d:NXdata
@signal="data"
Expand All @@ -219,29 +219,32 @@

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
Neither should be used when writing new data files, but
client software should expect to see legacy data files
written with any of these methods.

* One method uses the ``axes``
attribute to specify the names of each *dimension scale*.
* One method adds the ``axes`` attribute to the data, rather than to
the group. This is not recommended because the data field could be
linked from another group, which does not contain all the
*dimension scales*.

* 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.
* The oldest method adds an ``axis`` attribute to each
*dimension scale* set to an integer corresponding to the
corresponding dimension.
</doc>
<field name="VARIABLE" type="NX_NUMBER" nameType="any">
<field name="AXIS" type="NX_NUMBER" nameType="any">
<doc>
Dimension scale defining an axis of the data.
Dimension scale defining an axis of the data. There should be one
of these for each dimension of the ``DATA`` field.
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``.
A *dimension scale* must have a rank of 1 and has length ``n``
or ``n+1``.
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</doc>
<dim index="1" value="n"/>
</dimensions>
Expand All @@ -259,24 +262,23 @@
<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.
N.B. The ``axis`` attribute is now deprecated and should not be
used in writing new files.
</doc>
</attribute>
</field>
<field name="VARIABLE_errors" type="NX_NUMBER" nameType="any">
<field name="AXIS_errors" type="NX_NUMBER" nameType="any">
<doc>
Errors (uncertainties) associated with axis ``VARIABLE``.
Errors (uncertainties) associated with axis ``AXIS``.
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*
but is matched with the *AXIS*
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``.
same as ``AXIS``.
</doc>
<dim index="1" value="n"/>
</dimensions>
Expand Down Expand Up @@ -305,10 +307,13 @@
<doc>
.. index:: plotting

Plottable (independent) axis, indicate index number.
Plottable (independent) axis, with a value designating its
priority in the :ref:`NXdata` group.
Only one field in a :ref:`NXdata` group may have the
``signal=1`` attribute.
Do not use the ``signal`` attribute with the ``axis`` attribute.

N.B. The ``signal`` attribute is now deprecated
and should not be used in writing new files.
</doc>
</attribute>
<attribute name="axes"
Expand All @@ -317,9 +322,9 @@
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.

N.B. The ``axes`` attribute is now deprecated and should not be
used in writing new files.
</doc>
</attribute>
<attribute name="uncertainties">
Expand Down Expand Up @@ -349,6 +354,24 @@
<doc>data label</doc>
</attribute>
</field>
<field name="DATA_errors" type="NX_NUMBER" nameType="any">
<doc>
Errors (uncertainties) associated with data ``DATA``. It is now
recommended that uncertainties are defined using the
``uncertainties`` attribute of the signal field. The name of this
field does not therefore have to conform to this pattern, i.e.,
the name of the signal field with ``_errors`` appended. However,
it does make the association of the two fields clear.
Client is responsible for defining the dimensions of the data.

</doc>
<dimensions rank="dataRank">
<doc>
The dimensions should match those of ``DATA``.
</doc>
<dim index="0" value="n"><!-- index="0": cannot know to which dimension this applies a priori --></dim>
</dimensions>
</field>
<field name="errors" type="NX_NUMBER">
<doc>
Standard deviations of data values -
Expand All @@ -360,8 +383,8 @@
<doc>
The ``errors`` must have
the same rank (``dataRank``)
as the ``data``.
At least one ``dim`` must have length "n".
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>
Expand All @@ -380,32 +403,5 @@
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>