diff --git a/base_classes/NXdata.nxdl.xml b/base_classes/NXdata.nxdl.xml
index 67b54a7b0..3611a5e75 100644
--- a/base_classes/NXdata.nxdl.xml
+++ b/base_classes/NXdata.nxdl.xml
@@ -50,8 +50,8 @@
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*).
+ NXdata groups contain plottable data (also referred to as *signals* or *dependent variables*) and their
+ associated axis coordinates (also referred to as *axes* or *independent variables*).
The actual names of the :ref:`DATA </NXdata/DATA-field>` and :ref:`AXISNAME </NXdata/AXISNAME-field>` fields
can be chosen :ref:`freely <validItemName>`, as indicated by the upper case (this is a common convention in all NeXus classes).
@@ -60,176 +60,182 @@
does not describe how the data is to be plotted or even the dimensionality of the plot.
https://www.nexusformat.org/NIAC2018Minutes.html#nxdata-plottype--attribute
+ **Usage:**
+
+ .. admonition:: Plot data versus x axis
+
+ .. code-block::
+
+ data:NXdata
+ @signal = "data"
+ @axes = ["x"]
+ data: float[100]
+ x: float[100]
+
+ More complex cases are supported
+
+ * histogram data: ``x`` has one more value than ``data``.
+ * alternative axes: instead of a single ``x`` axis you can have several axes, one of which being the default.
+ * signals with more than one dimension: ``data`` could be 2D with axes ``x`` and ``y`` along each dimension.
+ * axes with more than one dimension: ``data`` could be 2D with axes ``x`` and ``y`` also being 2D, providing a
+ unique ``(x, y)`` coordinate for each ``data`` point.
+
**Signals:**
.. index:: plotting
-
+
+ .. admonition:: Defined by
+
+ * :ref:`DATA </NXdata/DATA-field>` fields
+ * the :ref:`signal </NXdata@signal-attribute>` attribute
+ * the :ref:`auxiliary_signals</NXdata@auxiliary_signals-attribute>` attribute
+
The :ref:`DATA </NXdata/DATA-field>` 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 </NXdata@signal-attribute>` attribute.
The names of the fields to be used as *secondary plot signals* are provided by the
:ref:`auxiliary_signals</NXdata@auxiliary_signals-attribute>` attribute.
- An example with three signals, one of which being the default
+ .. admonition:: An example with three signals, one of which being the default
- .. code-block::
+ .. 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]
+ 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 </NXdata/AXISNAME-field>` fields contain the axis coordinates associated with the data values.
- The names of all :ref:`AXISNAME </NXdata/AXISNAME-field>` fields are listed in the
- :ref:`axes </NXdata@axes-attribute>` attribute.
-
- `Rank`
-
- :ref:`AXISNAME </NXdata/AXISNAME-field>` fields are typically one-dimensional arrays, which annotate one of the dimensions.
+ .. admonition:: Defined by
- An example of this would be
+ * :ref:`AXISNAME </NXdata/AXISNAME-field>` fields
+ * the :ref:`axes </NXdata@axes-attribute>` attribute
+ * :ref:`AXISNAME_indices </NXdata@AXISNAME_indices-attribute>` attributes
- .. code-block::
+ The fields and attributes are defined as follows
- 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
+ 1. The :ref:`AXISNAME </NXdata/AXISNAME-field>` fields contain the axis coordinates associated with the signal values.
- In this example each data point ``data[i,j]`` has axis coordinates ``[x[i], y[j]]``.
+ 2. The :ref:`axes </NXdata@axes-attribute>` attribute provides the names of the :ref:`AXISNAME </NXdata/AXISNAME-field>`
+ fields to be used as the `default axis` for each dimension of the :ref:`DATA </NXdata/DATA-field>` fields.
- However, the fields can also have a rank greater than 1, in which case the rank of each
- :ref:`AXISNAME </NXdata/AXISNAME-field>` must be equal to the number of data dimensions it spans.
+ 3. The :ref:`AXISNAME_indices </NXdata@AXISNAME_indices-attribute>` attributes describe the :ref:`DATA </NXdata/DATA-field>`
+ dimensions spanned by the corresponding :ref:`AXISNAME </NXdata/AXISNAME-field>` fields.
- An example of this would be
+ Additional requirements for a complete definition
- .. code-block::
+ 1. The length of the :ref:`axes </NXdata@axes-attribute>` attribute must be equal to the rank of the :ref:`DATA </NXdata/DATA-field>`
+ fields. When a particular dimension has no default axis, the string “.” is used in that position.
- data:NXdata
- @signal = "data"
- @axes = ["x", "y"] --> the order does NOT matter
- @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 dimensions
+ 2. The number of values in :ref:`AXISNAME_indices </NXdata@AXISNAME_indices-attribute>` must be equal to the rank of the corresponding
+ :ref:`AXISNAME </NXdata/AXISNAME-field>` field.
- In this example each data point ``data[i,j]`` has axis coordinates ``[x[i,j], y[i,j]]``.
+ 3. When :ref:`AXISNAME_indices </NXdata@AXISNAME_indices-attribute>` is missing for a given
+ :ref:`AXISNAME </NXdata/AXISNAME-field>` field, the positions of the :ref:`AXISNAME </NXdata/AXISNAME-field>`
+ field name in the :ref:`axes </NXdata@axes-attribute>` attribute are used.
- `Dimensions`
+ 4. When :ref:`AXISNAME_indices </NXdata@AXISNAME_indices-attribute>` is the same as the indices of "AXISNAME" in the
+ :ref:`axes </NXdata@axes-attribute>` attribute, there is no need to provide
+ :ref:`AXISNAME_indices </NXdata@AXISNAME_indices-attribute>`.
- The data dimensions annotated by an :ref:`AXISNAME </NXdata/AXISNAME-field>` field are defined by the
- :ref:`AXISNAME_indices </NXdata@AXISNAME_indices-attribute>` attribute. When this attribute is missing,
- the position(s) of the :ref:`AXISNAME </NXdata/AXISNAME-field>` string in the
- :ref:`axes </NXdata@axes-attribute>` attribute are used.
+ 5. The indices of "AXISNAME" in the :ref:`axes </NXdata@axes-attribute>` attribute must be a subset of
+ :ref:`AXISNAME_indices </NXdata@AXISNAME_indices-attribute>`.
- When all :ref:`AXISNAME </NXdata/AXISNAME-field>` fields are one-dimensional, and none of the data dimensions
- have more than one axis, the :ref:`AXISNAME_indices </NXdata@AXISNAME_indices-attribute>` attributes
- are often omitted. If one of the data dimensions has no :ref:`AXISNAME </NXdata/AXISNAME-field>` field,
- the string “.” can be used in the corresponding index of the axes list.
+ 6. The shape of an :ref:`AXISNAME </NXdata/AXISNAME-field>` field must correspond to the shape of the
+ :ref:`DATA </NXdata/DATA-field>` dimensions it spans. This means that for each dimension ``i`` in ``[0, AXISNAME.ndim)``
+ spanned by axis field :ref:`AXISNAME </NXdata/AXISNAME-field>`, the number of axis values ``AXISNAME.shape[i]``
+ along dimension ``i`` must be equal to the number of data points ``DATA.shape[AXISNAME_indices[i]]`` along dimension ``i``
+ or one more than the number of data points ``DATA.shape[AXISNAME_indices[i]]+1`` in case the
+ :ref:`AXISNAME </NXdata/AXISNAME-field>` field contains histogram bin edges along dimension ``i``.
- An example of this would be
+ Highlight consequences that follow the definition
- .. code-block::
+ 1. An :ref:`AXISNAME </NXdata/AXISNAME-field>` field can have more than one dimension and can therefore span
+ more than one :ref:`DATA </NXdata/DATA-field>` dimension. Conversely, one :ref:`DATA </NXdata/DATA-field>` dimension
+ can be spanned by more than one :ref:`AXISNAME </NXdata/AXISNAME-field>` field. The default axis name (if any)
+ of each dimension can be found in the :ref:`axes </NXdata@axes-attribute>` attribute.
- data:NXdata
- @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
+ 2. A list of all available axes is not provided directly. All strings in the :ref:`axes </NXdata@axes-attribute>` attribute
+ (excluding the “.” string) are axis field names. In addition the prefix of an attribute ending with the string "_indices" is also
+ an axis field name.
- When using :ref:`AXISNAME_indices </NXdata@AXISNAME_indices-attribute>` this becomes
+ .. admonition:: The following example covers all axes features supported
- .. code-block::
+ .. code-block::
- data:NXdata
- @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
+ data:NXdata
+ @signal = "data"
+ @axes = ["x_set", "y_set", "."] --> default axes for all three dimensions
+ @x_encoder_indices = [0, 1]
+ @y_encoder_indices = 1 --> or [1]
+ data: float[10,7,1024]
+ x_encoder: float[11,7] --> coordinates along the first and second dimensions
+ y_encoder: float[7] --> coordinates along the second dimension
+ x_set: float[10] --> coordinates along the first dimension
+ y_set: float[7] --> coordinates along the second dimension
- When providing :ref:`AXISNAME_indices </NXdata@AXISNAME_indices-attribute>` attributes it is recommended
- to do it for all axes.
+ One scientific application that provided such data is 2D scanning X-Ray Fluorescence (XRF)
+ where the sample is scanned through a focussed X-ray beam in two dimensions and an XRF spectrum
+ with 1024 channels is recorded at each position. In addition the x motor is scanned
+ continuously and both motors have an encoder which records the actual motor position as
+ opposed to the requested or `set` position.
- `Non-trivial axes`
+ .. image:: data/example2D_hist.png
+ :width: 100%
- What follows are two examples where :ref:`AXISNAME_indices </NXdata@AXISNAME_indices-attribute>` attributes
- cannot be omitted.
+ 1. ``@axes`` has three values which corresponds to the ``data`` rank of three
- 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).
+ 2. ``x_set`` and ``y_set`` are the default axes for the first two dimensions while the third
+ dimension does not have a default axis or any axis for that matter.
- .. code-block::
+ 3. ``x_set_indices`` and ``y_set_indices`` are omitted because they would be equal to
+ the position of ``"x_set"`` and ``"y_set"`` in ``@axes``.
- data:NXdata
- @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
+ 4. The first dimension is spanned by two axes ``x_set`` and ``x_encoder``. Since
+ the x motor is scanned continuously, the encoder records the edge of every bin
+ on which an XRF spectrum is recorded yielding 11 values instead of 10 along the
+ first dimension. The ``x_encoder`` spans two dimensions because the actual x edges
+ are slightly different for every x motion at each y position.
- 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]]``.
+ 5. The second dimension is spanned by two axes ``y_set`` and ``y_encoder``. The axes
+ have as many values are there are data points along the second dimension. This is
+ because the y motor moves one step after each scan of the x motor. Since the y
+ motor does not move while scanning x, there is no need for ``y_encoder`` to span
+ the first dimension because the value along this dimension remains constant.
- .. code-block::
+ **Uncertainties:**
- data:NXdata
- @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
+ .. admonition:: Defined by
- **Uncertainties:**
+ * :ref:`FIELDNAME_errors </NXdata/FIELDNAME_errors-field>` fields
Standard deviations on data values as well as coordinates can be provided by
:ref:`FIELDNAME_errors </NXdata/FIELDNAME_errors-field>` fields where ``FIELDNAME`` is the name of a
:ref:`DATA </NXdata/DATA-field>` field or an :ref:`AXISNAME </NXdata/AXISNAME-field>` 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]
+ .. admonition:: 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"]
+ 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]
@@ -316,11 +322,13 @@
-->
- The ``AXISNAME_indices`` attribute is a single integer or an array of integers that defines which :ref:`data </NXdata/DATA-field>`
- dimension(s) are spanned by the corresponding axis. The first dimension index is ``0`` (zero).
+ The ``AXISNAME_indices`` attribute is a single integer or an array of integers that defines which :ref:`DATA </NXdata/DATA-field>`
+ dimensions are spanned by the corresponding axis. The first dimension index is ``0`` (zero).
+
+ The number of indices must be equal to the rank of the :ref:`AXISNAME </NXdata/AXISNAME-field>` field.
- When the ``AXISNAME_indices`` attribute is missing for an :ref:`AXISNAME </NXdata/AXISNAME-field>` field, its value becomes the index
- (or indices) of the :ref:`AXISNAME </NXdata/AXISNAME-field>` name in the :ref:`axes </NXdata@axes-attribute>` attribute.
+ When the ``AXISNAME_indices`` attribute is missing for a given :ref:`AXISNAME </NXdata/AXISNAME-field>` field, its value becomes
+ the index (or indices) of the :ref:`AXISNAME </NXdata/AXISNAME-field>` name in the :ref:`axes </NXdata@axes-attribute>` attribute.
.. note:: When ``AXISNAME_indices`` contains multiple integers, it must be saved as an actual array
of integers and not a comma separated string.
@@ -329,26 +337,33 @@
.. index:: plotting
-
+
The ``axes`` attribute is a list of strings which are the names of the :ref:`AXISNAME </NXdata/AXISNAME-field>` fields
- that contain the values of the coordinates along the :ref:`data </NXdata/DATA-field>` dimensions.
+ to be used as the default axis along every :ref:`DATA </NXdata/DATA-field>` dimension. As a result the length must
+ be equal to the rank of the :ref:`DATA </NXdata/DATA-field>` fields. The string "." can be used for
+ dimensions without a default axis.
.. note:: When ``axes`` contains multiple strings, it must be saved as an actual array
of strings and not a single comma separated string.
+
+
+
- Coordinate values along one or more :ref:`data </NXdata/DATA-field>` dimensions. The rank must be equal
- to the number of dimensions it spans.
-
+ Coordinate values along one or more :ref:`DATA </NXdata/DATA-field>` dimensions.
+
+ The shape of an ``AXISNAME`` field must correspond to the shape of the :ref:`DATA </NXdata/DATA-field>`
+ dimensions it spans. This means that for each ``i`` in ``[0, AXISNAME.ndim)`` the number of data points
+ ``DATA.shape[AXISNAME_indices[i]]`` must be equal to the number of coordinates ``AXISNAME.shape[i]`` or the
+ number of bin edges ``AXISNAME.shape[i]+1`` in case of histogram data.
+
As the upper case ``AXISNAME`` indicates, the names of the ``AXISNAME`` fields can be chosen :ref:`freely <validItemName>`.
- The :ref:`axes </NXdata@axes-attribute>` attribute can be used to find all datasets in the
- ``NXdata`` that contain coordinate values.
- Most AXISNAME fields will be sequences of numbers but if an axis is better represented using names, such as channel names,
+ Most ``AXISNAME`` fields will be sequences of numbers but if an axis is better represented using names, such as channel names,
an array of NX_CHAR can be provided.
Axis label
@@ -380,7 +395,7 @@
.. 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 <validItemName>`. The :ref:`signal attribute </NXdata@signal-attribute>`
and :ref:`auxiliary_signals attribute</NXdata@auxiliary_signals-attribute>` can be used to find all datasets in the ``NXdata``
@@ -424,10 +439,12 @@
"Errors" (meaning *uncertainties* or *standard deviations*)
associated with any field named ``FIELDNAME`` in this ``NXdata``
- group (e.g. an axis, signal or auxiliary signal).
+ group. This can be a :ref:`DATA </NXdata/DATA-field>` field
+ (signal or auxiliary signal) or a :ref:`AXISNAME </NXdata/AXISNAME-field>`
+ field (axis).
The dimensions of the ``FIELDNAME_errors`` field must match
- the dimensions of the ``FIELDNAME`` field.
+ the dimensions of the corresponding ``FIELDNAME`` field.
diff --git a/base_classes/data/example2D_hist.excalidraw b/base_classes/data/example2D_hist.excalidraw
new file mode 100644
index 000000000..a2ab01a92
--- /dev/null
+++ b/base_classes/data/example2D_hist.excalidraw
@@ -0,0 +1,2086 @@
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diff --git a/base_classes/data/example2D_hist.png b/base_classes/data/example2D_hist.png
new file mode 100644
index 000000000..8b35aeafb
Binary files /dev/null and b/base_classes/data/example2D_hist.png differ