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woutdenolf committed Jun 21, 2023
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<doc>
The :ref:`NXdata` class is designed to encapsulate all the information required for a set of data to be plotted.
NXdata groups contain plottable data (sometimes referred to as *signals* or *dependent variables*) and their
associated axis coordinates (sometimes referred to as *axes* or *independent variables*)."
associated axis coordinates (sometimes referred to as *axes* or *independent variables*).

The actual names of the :ref:`DATA &lt;/NXdata/DATA-field&gt;` and :ref:`AXISNAME &lt;/NXdata/AXISNAME-field&gt;` fields
can be chosen :ref:`freely &lt;validItemName>`, as indicated by the upper case (this is a common convention in all NeXus classes).
can be chosen :ref:`freely &lt;validItemName&gt;`, as indicated by the upper case (this is a common convention in all NeXus classes).

.. note:: ``NXdata`` provides data and coordinates to be plotted but
does not describe how the data is to be plotted or even the dimensionality of the plot.
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The :ref:`DATA &lt;/NXdata/DATA-field&gt;` fields contain the signal values to be plotted. The name of the field
to be used as the *default plot signal* is provided by the :ref:`signal &lt;/NXdata@signal-attribute&gt;` attribute.
The names of the fields to be used as *secondary plot signals* are provided by the :ref:`auxiliary_signals&lt;/NXdata@auxiliary_signals-attribute&gt;` attribute.

The names of the fields to be used as *secondary plot signals* are provided by the
:ref:`auxiliary_signals&lt;/NXdata@auxiliary_signals-attribute&gt;` attribute.

An example with three signals, one of which being the default

.. code-block::

data:NXdata
@signal = "data1"
@auxiliary_signals = ["data2", "data3"]
data1: float[10,20,30] --> the default signal
data2: float[10,20,30]
data3: float[10,20,30]

**Axes:**

.. index:: axes (attribute)
.. index:: coordinates

The :ref:`AXISNAME &lt;/NXdata/AXISNAME-field&gt;` fields contain the axis coordinates associated with the data values. The names of all :ref:`AXISNAME &lt;/NXdata/AXISNAME-field&gt;`
fields are listed in the :ref:`axes &lt;/NXdata@axes-attribute&gt;` attribute.
The :ref:`AXISNAME &lt;/NXdata/AXISNAME-field&gt;` fields contain the axis coordinates associated with the data values.
The names of all :ref:`AXISNAME &lt;/NXdata/AXISNAME-field&gt;` fields are listed in the
:ref:`axes &lt;/NXdata@axes-attribute&gt;` attribute.

`Rank`

:ref:`AXISNAME &lt;/NXdata/AXISNAME-field&gt;` fields are typically one-dimensional arrays, which annotate one of the dimensions. However, the fields can also have a rank greater than 1,
in which case the rank of each :ref:`AXISNAME &lt;/NXdata/AXISNAME-field&gt;` must be equal to the number of data dimensions it spans.
:ref:`AXISNAME &lt;/NXdata/AXISNAME-field&gt;` fields are typically one-dimensional arrays, which annotate one of the dimensions.

`Dimensions`
An example of this would be

The data dimensions annotated by an :ref:`AXISNAME &lt;/NXdata/AXISNAME-field&gt;` field are defined by the :ref:`AXISNAME_indices &lt;/NXdata@AXISNAME_indices-attribute&gt;` attribute.
When this attribute is missing, the position(s) of the :ref:`AXISNAME &lt;/NXdata/AXISNAME-field&gt;` string in the :ref:`axes &lt;/NXdata@axes-attribute&gt;` attribute are used.
.. code-block::

When all :ref:`AXISNAME &lt;/NXdata/AXISNAME-field&gt;` fields are one-dimensional, and none of the data dimensions have more than one axis, the
:ref:`AXISNAME_indices &lt;/NXdata@AXISNAME_indices-attribute&gt;` attributes are often omitted. If one of the data dimensions has no :ref:`AXISNAME &lt;/NXdata/AXISNAME-field&gt;` field,
the string “.” can be used in the corresponding index of the axes list.
data:NXdata
@signal = "data"
@axes = ["x", "y"] --> the order matters
data: float[10,20]
x: float[10] --> coordinates along the first dimension
y: float[20] --> coordinates along the second dimension

When providing :ref:`AXISNAME_indices &lt;/NXdata@AXISNAME_indices-attribute&gt;` attributes it is recommended to do it for all axes.
In this example each data point ``data[i,j]`` has axis coordinates ``[x[i], y[j]]``.

**Uncertainties:**
However, the fields can also have a rank greater than 1, in which case the rank of each
:ref:`AXISNAME &lt;/NXdata/AXISNAME-field&gt;` must be equal to the number of data dimensions it spans.

Standard deviations on data values as well as coordinates can be provided by :ref:`FIELDNAME_errors &lt;/NXdata/FIELDNAME_errors-field&gt;` fields
where ``FIELDNAME`` is the name of a :ref:`DATA &lt;/NXdata/DATA-field&gt;` field or an :ref:`AXISNAME &lt;/NXdata/AXISNAME-field&gt;` field.
An example of this would be

**Examples:**
.. code-block::

1. Two-dimensional data with coordinates on both data dimensions::

data:NXdata
@signal = "data"
@axes = ["y", "x"] --> the order does matter
data: float[10,20] --> the default signal
y: float[10] --> coordinates along the first dimension
x: float[20] --> coordinates along the second dimension
@signal = "data"
@axes = ["x", "y"] --> the order does NOT matters
@x_indices = [0, 1]
@y_indices = [0, 1]
data: float[10,20]
x: float[10,20] --> coordinates along both dimensions
y: float[10,20] --> coordinates along both dimension

In this example each data point ``data[i,j]`` has axis coordinates ``[x[i,j], y[i,j]]``.

`Dimensions`

The data dimensions annotated by an :ref:`AXISNAME &lt;/NXdata/AXISNAME-field&gt;` field are defined by the
:ref:`AXISNAME_indices &lt;/NXdata@AXISNAME_indices-attribute&gt;` attribute. When this attribute is missing,
the position(s) of the :ref:`AXISNAME &lt;/NXdata/AXISNAME-field&gt;` string in the
:ref:`axes &lt;/NXdata@axes-attribute&gt;` attribute are used.

When all :ref:`AXISNAME &lt;/NXdata/AXISNAME-field&gt;` fields are one-dimensional, and none of the data dimensions
have more than one axis, the :ref:`AXISNAME_indices &lt;/NXdata@AXISNAME_indices-attribute&gt;` attributes
are often omitted. If one of the data dimensions has no :ref:`AXISNAME &lt;/NXdata/AXISNAME-field&gt;` field,
the string “.” can be used in the corresponding index of the axes list.

An example of this would be

.. code-block::

2. Three-dimensional data with coordinates and uncertainties::

data:NXdata
@signal = "data1"
@auxiliary_signals = ["data2", "data3"]
@axes = ["x", "z"] --> the order does NOT matter
@x_indices = 0
@z_indices = 2
data1: float[10,20,30] --> the default signal
data2: float[10,20,30]
data3: float[10,20,30]
x: float[10] --> coordinates along the first dimension
z: float[30] --> coordinates along the last dimension
data1_errors: float[10,20,30]
data2_errors: float[10,20,30]
data3_errors: float[10,20,30]
x_errors: float[10]
z_errors: float[30]

Note that the second data dimension has no coordinates.

3. An example with a data dimension with more than one axis::
@signal = "data"
@axes = ["x", ".", "z"] --> the order matters
data: float[10,20,30]
x: float[10] --> coordinates along the first dimension
z: float[30] --> coordinates along the third dimension

When using :ref:`AXISNAME_indices &lt;/NXdata@AXISNAME_indices-attribute&gt;` this becomes

.. code-block::

data:NXdata
@signal = "data1"
@auxiliary_signals = ["data2", "data3"]
@axes = ["x", "y", "z", "time"] --> the order does NOT matter
@x_indices = 0
@y_indices = 1
@z_indices = 2
@time_indices = 2
data1: float[10,20,30] --> the default signal
data2: float[10,20,30]
data3: float[10,20,30]
x: float[10] --> coordinates along the first dimension
y: float[20] --> coordinates along the second dimension
z: float[30] --> coordinates along the last dimension
time: float[30] --> coordinates along the last dimension

Note that ``time`` is an alternative axis of ``z`` for the last dimension (or vice versa).

4. An example with coordinates that span more than one data dimension::

@signal = "data"
@axes = ["x", "z"] --> the order does NOT matter
data: float[10,20,30]
@x_indices = 0
@z_indices = 2
x: float[10] --> coordinates along the first dimension
z: float[30] --> coordinates along the third dimension

When providing :ref:`AXISNAME_indices &lt;/NXdata@AXISNAME_indices-attribute&gt;` attributes it is recommended
to do it for all axes.

`Non-trivial axes`

What follows are two examples where :ref:`AXISNAME_indices &lt;/NXdata@AXISNAME_indices-attribute&gt;` attributes
cannot be omitted.

The first is an example where data dimensions have alternative axis coordinates. The NXdata group represents
a stack of images collected at different energies. The ``wavelength`` is an alternative axis of ``energy``
for the last dimension (or vice versa).

.. code-block::

data:NXdata
@signal = "data1"
@auxiliary_signals = ["data2", "data3"]
@axes = ["x", "y", "z"] --> the order does NOT matter
@x_indices = [0, 1]
@y_indices = [0, 1]
@z_indices = 2
data1: float[10,20,30] --> the default signal
data2: float[10,20,30]
data3: float[10,20,30]
x: float[10,20] --> coordinates along the first two dimensions
y: float[10,20] --> coordinates along the first two dimensions
z: float[30] --> coordinates along the last dimension

Note that each signal value ``data1[i,j,k]`` has axis coordinates ``[x[i,j], y[i,j], z[k]]``.
The same goes for the auxiliary signals ``data2`` and ``data3``.

5. An example without :ref:`AXISNAME_indices &lt;/NXdata@AXISNAME_indices-attribute&gt;` attributes
and a data dimension without axis coordinates::

@signal = "data"
@axes = ["x", "y", "energy", "wavelength"] --> the order does NOT matter
@x_indices = 0
@y_indices = 1
@energy_indices = 2
@wavelength_indices = 2
data: float[10,20,30]
x: float[10] --> coordinates along the first dimension
y: float[20] --> coordinates along the second dimension
energy: float[30] --> coordinates along the third dimension
wavelength: float[30] --> coordinates along the third dimension

The second is an example with coordinates that span more than one dimension. The NXdata group represents data
from 2D mesh scans performed at multiple energies. Each data point ``data[i,j,k]`` has axis coordinates
``[x[i,j,k], y[i,j,k], energy[k]]``.

.. code-block::

data:NXdata
@signal = "data1"
@auxiliary_signals = ["data2", "data3"]
@axes = ["x", ".", "z"] --> the order matters
data1: float[10,20,30] --> the default signal
data2: float[10,20,30]
data3: float[10,20,30]
x: float[10] --> coordinates along the first dimension
z: float[30] --> coordinates along the last dimension
@signal = "data"
@axes = ["x", "y", "energy"] --> the order does NOT matter
@x_indices = [0, 1, 2]
@y_indices = [0, 1, 2]
@energy_indices = 2
data: float[10,20,30]
x: float[10,20,30] --> coordinates along all dimensions
y: float[10,20,30] --> coordinates along all dimensions
energy: float[30] --> coordinates along the third dimension

**Uncertainties:**

This implicitely defines ``@x_indices = 0`` and ``@z_indices = 2``. Note that the second data dimension has no coordinates.
Standard deviations on data values as well as coordinates can be provided by
:ref:`FIELDNAME_errors &lt;/NXdata/FIELDNAME_errors-field&gt;` fields where ``FIELDNAME`` is the name of a
:ref:`DATA &lt;/NXdata/DATA-field&gt;` field or an :ref:`AXISNAME &lt;/NXdata/AXISNAME-field&gt;` field.

An example of uncertainties on the signal, auxiliary signals and axis coordinates

.. code-block::

data:NXdata
@signal = "data1"
@auxiliary_signals = ["data2", "data3"]
@axes = ["x", "z"]
@x_indices = 0
@z_indices = 2
data1: float[10,20,30]
data2: float[10,20,30]
data3: float[10,20,30]
x: float[10]
z: float[30]
data1_errors: float[10,20,30]
data2_errors: float[10,20,30]
data3_errors: float[10,20,30]
x_errors: float[10]
z_errors: float[30]

</doc>

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.. index:: plotting
.. index:: signal attribute value

The value is the :ref:`name &lt;validItemName>` of the signal that contains
The value is the :ref:`name &lt;validItemName&gt;` of the signal that contains
the default plottable data. This field or link *must* exist and be a direct child
of this NXdata group.

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<doc>
.. index:: plotting

Array of strings holding the :ref:`names &lt;validItemName>` of additional
Array of strings holding the :ref:`names &lt;validItemName&gt;` of additional
signals to be plotted with the :ref:`default signal &lt;/NXdata@signal-attribute&gt;`.
These fields or links *must* exist and be direct children of this NXdata group.

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Coordinate values along one or more :ref:`data &lt;/NXdata/DATA-field&gt;` dimensions. The rank must be equal
to the number of dimensions it spans.

As the upper case ``AXISNAME`` indicates, the names of the ``AXISNAME`` fields can be chosen :ref:`freely &lt;validItemName>`.
As the upper case ``AXISNAME`` indicates, the names of the ``AXISNAME`` fields can be chosen :ref:`freely &lt;validItemName&gt;`.
The :ref:`axes &lt;/NXdata@axes-attribute&gt;` attribute can be used to find all datasets in the
``NXdata`` that contain coordinate values.
</doc>
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.. index:: plotting

Data values to be used as the NeXus *plottable data*. As the upper case ``DATA``
indicates, the names of the ``DATA`` fields can be chosen :ref:`freely &lt;validItemName>`. The :ref:`signal attribute &lt;/NXdata@signal-attribute&gt;`
indicates, the names of the ``DATA`` fields can be chosen :ref:`freely &lt;validItemName&gt;`. The :ref:`signal attribute &lt;/NXdata@signal-attribute&gt;`
and :ref:`auxiliary_signals attribute&lt;/NXdata@auxiliary_signals-attribute&gt;` can be used to find all datasets in the ``NXdata``
that contain data values.

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