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NXdata linking of signal #205

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Jul 15, 2024
Merged

NXdata linking of signal #205

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ca6cbc9
Add depends for data field
domna Mar 28, 2024
8b419b3
Use `@reference`
domna Apr 10, 2024
2d0fcd7
use reference attribute in NXmpes and NXmpes_arpes
lukaspie Jul 3, 2024
653dd26
change text style
lukaspie Jul 3, 2024
6db20ea
fix duplicated in reference attribute
lukaspie Jul 4, 2024
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82 changes: 55 additions & 27 deletions base_classes/NXdata.nxdl.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -235,6 +235,20 @@ without this attribute being set to "true".-->
the axes attribute can be omitted.
</doc>
</attribute>
<attribute name="reference">
<doc>
Points to the path of a field defining the data to which the `DATA` group refers.

This concept allows to link the data to a respective field in the NeXus hierarchy, thereby
defining the physical quantity it represents.

Example:
If the data corresponds to a readout of a detector, ``@reference`` links
to that detectors data:

@reference: '/entry/instrument/detector/data' for a 2D detector
</doc>
</attribute>
<attribute name="AXISNAME_indices" type="NX_INT">
<!--
nxdl.xsd rules do not allow us to show this as a variable name
Expand Down Expand Up @@ -283,33 +297,6 @@ AXISNAME_indices documentation copied from datarules.rst
to avoid string parsing in reading applications.
</doc>
</attribute>
<attribute name="AXISNAME_depends">
<doc>
Points to the path of a field defining the axis on which the ``AXISNAME`` axis depends.

This concept allows to link an axis to a respective field in the NeXus hierarchy, thereby
defining the physical quantity it represents.

Here, *AXISNAME* is to be replaced by the name of each
field described in the ``axes`` attribute.

Examples:
If a calibration has been performed, ``@AXISNAME_depends`` links to the result of
that calibration:

@AXISNAME_depends: '/entry/process/calibration/calibrated_axis'

If the axis corresponds to a coordinate of a detector, ``@AXISNAME_depends`` links
to that detector axis:

@AXISNAME_depends: '/entry/instrument/detector/axis/some_axis' for a 2D detector

If the axis is a scanned motor, ``@AXISNAME_depends`` links to the transformation
describing the respective motion, e.g.:

@AXISNAME_depends: '/entry/instrument/detector/transformations/some_transformation' for a motion of the detector
</doc>
</attribute>
<field name="AXISNAME" type="NX_NUMBER" nameType="any">
<doc>
Dimension scale defining an axis of the data.
Expand Down Expand Up @@ -354,6 +341,30 @@ AXISNAME_indices documentation copied from datarules.rst
The ``axes`` *group* attribute is now preferred.
</doc>
</attribute>
<attribute name="reference">
<doc>
Points to the path of a field defining the axis to which the ``AXISNAME`` axis refers.

This concept allows to link an axis to a respective field in the NeXus hierarchy, thereby
defining the physical quantity it represents.

Examples:
If a calibration has been performed, ``@reference`` links to the result of
that calibration:

@reference: '/entry/process/calibration/calibrated_axis'

If the axis corresponds to a coordinate of a detector, ``@reference`` links
to that detector axis:

@reference: '/entry/instrument/detector/axis/some_axis' for a 2D detector

If the axis is a scanned motor, ``@reference`` links to the transformation
describing the respective motion, e.g.:

@reference: '/entry/instrument/detector/transformations/some_transformation' for a motion of the detector
</doc>
</attribute>
</field>
<field name="FIELDNAME_errors" type="NX_NUMBER" nameType="any">
<doc>
Expand Down Expand Up @@ -408,6 +419,23 @@ AXISNAME_indices documentation copied from datarules.rst
data label
</doc>
</attribute>
<attribute name="reference">
<doc>
Points to the path of a field defining the data to which the `DATA` field refers.

This concept allows to link the data to a respective field in the NeXus hierarchy, thereby
defining the physical quantity it represents.

Here, *DATA* is to be replaced by the name of each
data field.

Example:
If the data corresponds to a readout of a detector, ``@reference`` links
to that detectors data:

@reference: '/entry/instrument/detector/data' for a 2D detector
</doc>
</attribute>
</field>
<field name="errors" type="NX_NUMBER" deprecated="Use ``DATA_errors`` instead (NIAC2018)">
<doc>
Expand Down
74 changes: 49 additions & 25 deletions base_classes/nyaml/NXdata.yaml
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Expand Up @@ -193,6 +193,18 @@ NXdata(NXobject):

If there are no axes at all (such as with a stack of images),
the axes attribute can be omitted.
\@reference:
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doc: |
Points to the path of a field defining the data to which the `DATA` group refers.

This concept allows to link the data to a respective field in the NeXus hierarchy, thereby
defining the physical quantity it represents.

Example:
If the data corresponds to a readout of a detector, ``@reference`` links
to that detectors data:

@reference: '/entry/instrument/detector/data' for a 2D detector
\@AXISNAME_indices:
type: NX_INT

Expand Down Expand Up @@ -238,31 +250,6 @@ NXdata(NXobject):
.. 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.
\@AXISNAME_depends:
doc: |
Points to the path of a field defining the axis on which the ``AXISNAME`` axis depends.

This concept allows to link an axis to a respective field in the NeXus hierarchy, thereby
defining the physical quantity it represents.

Here, *AXISNAME* is to be replaced by the name of each
field described in the ``axes`` attribute.

Examples:
If a calibration has been performed, ``@AXISNAME_depends`` links to the result of
that calibration:

@AXISNAME_depends: '/entry/process/calibration/calibrated_axis'

If the axis corresponds to a coordinate of a detector, ``@AXISNAME_depends`` links
to that detector axis:

@AXISNAME_depends: '/entry/instrument/detector/axis/some_axis' for a 2D detector

If the axis is a scanned motor, ``@AXISNAME_depends`` links to the transformation
describing the respective motion, e.g.:

@AXISNAME_depends: '/entry/instrument/detector/transformations/some_transformation' for a motion of the detector
AXISNAME(NX_NUMBER):
nameType: any
doc: |
Expand Down Expand Up @@ -301,6 +288,28 @@ NXdata(NXobject):
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.
\@reference:
doc: |
Points to the path of a field defining the axis to which the ``AXISNAME`` axis refers.

This concept allows to link an axis to a respective field in the NeXus hierarchy, thereby
defining the physical quantity it represents.

Examples:
If a calibration has been performed, ``@reference`` links to the result of
that calibration:

@reference: '/entry/process/calibration/calibrated_axis'

If the axis corresponds to a coordinate of a detector, ``@reference`` links
to that detector axis:

@reference: '/entry/instrument/detector/axis/some_axis' for a 2D detector

If the axis is a scanned motor, ``@reference`` links to the transformation
describing the respective motion, e.g.:

@reference: '/entry/instrument/detector/transformations/some_transformation' for a motion of the detector
FIELDNAME_errors(NX_NUMBER):
nameType: any
doc: |
Expand Down Expand Up @@ -350,6 +359,21 @@ NXdata(NXobject):
\@long_name:
doc: |
data label
\@reference:
doc: |
Points to the path of a field defining the data to which the `DATA` field refers.

This concept allows to link the data to a respective field in the NeXus hierarchy, thereby
defining the physical quantity it represents.

Here, *DATA* is to be replaced by the name of each
data field.

Example:
If the data corresponds to a readout of a detector, ``@reference`` links
to that detectors data:

@reference: '/entry/instrument/detector/data' for a 2D detector
errors(NX_NUMBER):
deprecated: Use ``DATA_errors`` instead (NIAC2018)
doc: |
Expand Down
14 changes: 11 additions & 3 deletions contributed_definitions/NXdata_mpes.nxdl.xml
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Expand Up @@ -33,9 +33,7 @@
<doc>
Calibrated energy axis.

In an application definition, this could be a link to either
/entry/process/energy_calibration/calibrated_axis or
/entry/process/energy_correction/calibrated_axis.
Could be linked from the respective '@reference' field.
</doc>
<attribute name="type" type="NX_CHAR">
<doc>
Expand All @@ -62,6 +60,16 @@
</item>
</enumeration>
</attribute>
<attribute name="reference">
<doc>
The energy can be dispersed according to different strategies. ``@reference`` points to
the path of a field defining the calibrated axis which the ``energy`` axis refers.

For example:
@reference: 'entry/process/energy_calibration/calibrated_axis'
@reference: 'entry/process/energy_referencing/calibrated_axis'
</doc>
</attribute>
</field>
<field name="kN" type="NX_NUMBER" units="NX_WAVENUMBER">
<doc>
Expand Down
53 changes: 40 additions & 13 deletions contributed_definitions/NXmpes.nxdl.xml
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Expand Up @@ -870,21 +870,48 @@
<doc>
Calibrated energy axis.

This could be a link to either
/entry/process/energy_calibration/calibrated_axis or
/entry/process/energy_correction/calibrated_axis.
Could be linked from the respective '@reference' field.
</doc>
<attribute name="type" recommended="true"/>
<attribute name="type" type="NX_CHAR">
<doc>
The energy can be either stored as kinetic or as binding energy.
</doc>
<enumeration>
<item value="kinetic">
<doc>
Calibrated kinetic energy axis.

In case the kinetic energy axis is referenced to the Fermi level :math:`E_F`
(e.g., in entry/process/energy_referencing), kinetic energies :math:`E` are
provided as :math:`E-E_F`.

This concept is related to term `3.35`_ of the ISO 18115-1:2023 standard.

.. _3.35: https://www.iso.org/obp/ui/en/#iso:std:iso:18115:-1:ed-3:v1:en:term:3.35
</doc>
</item>
<item value="binding">
<doc>
Calibrated binding energy axis.

This concept is related to term `12.16`_ of the ISO 18115-1:2023 standard.

.. _12.16: https://www.iso.org/obp/ui/en/#iso:std:iso:18115:-1:ed-3:v1:en:term:12.16
</doc>
</item>
</enumeration>
</attribute>
<attribute name="reference" type="NX_CHAR" recommended="true">
<doc>
The energy can be dispersed according to different strategies. ``@reference`` points to
the path of a field defining the calibrated axis which the ``energy`` axis refers.

For example:
@reference: 'entry/process/energy_calibration/calibrated_axis'
</doc>
</attribute>
</field>
<attribute name="energy_depends" type="NX_CHAR" optional="true">
<doc>
The energy can be dispersed according to different strategies. ``energy_depends`` points to
the path of a field defining the calibrated axis on which the energy axis depends.

For example:
@energy_depends: 'entry/process/energy_calibration'
</doc>
</attribute>
<attribute name="energy_indices" recommended="true"/>
</group>
</group>
</definition>
67 changes: 35 additions & 32 deletions contributed_definitions/NXmpes_arpes.nxdl.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -355,52 +355,55 @@ with higher granularity in the data description.
<attribute name="energy_indices"/>
<attribute name="angular0_indices"/>
<attribute name="angular1_indices"/>
<attribute name="angular0_depends">
<doc>
Points to the path to a field defining the axis on which the angular axis depends.
For example:
@angular0_depends: '/entry/sample/transformations/sample_tilt' for a manipulator angular scan
@angular0_depends: '/entry/instrument/detector/sensor_x' for a 2D detector
@angular0_depends: '/entry/instrument/collectioncolumn/deflector' for a deflector scan
@angular0_depends: '/entry/process/calibration/angular0_calibration/calibrated_axis' for a preprocessed axis.
</doc>
</attribute>
<attribute name="angular1_depends">
<doc>
Points to the path to a field defining the axis on which the angular axis depends.
For example:
@angular1_depends: '/entry/sample/transformations/sample_polar' for a manipulator angular scan
@angular1_depends: '/entry/instrument/detector/sensor_x' for a 2D detector
@angular1_depends: '/entry/instrument/collectioncolumn/deflector' for a deflector scan
@angular1_depends: '/entry/process/calibration/angular1_calibration/calibrated_axis' for a preprocessed axis.
</doc>
</attribute>
<attribute name="energy_depends">
<doc>
Points to the path to a field defining the axis on which the energy axis depends.
For example:
@energy_depends: '/entry/instrument/detector/sensor_y' for a 2D detector
@energy_depends: '/entry/instrument/energydispersion/center_kinetic_energy' for a swept scan
@energy_depends: '/entry/process/calibration/energy_calibration/calibrated_axis' for a preprocessed axis.
</doc>
</attribute>
<field name="energy" type="NX_NUMBER" units="NX_ENERGY">
<doc>
Trace of the energy axis. Could be linked from the respective 'AXISNAME_depends'
Trace of the energy axis. Could be linked from the respective ``@reference``
field.
</doc>
<attribute name="reference" recommended="true">
<doc>
Points to the path of a field defining the calibrated axis which the energy axis refers.

For example:
@reference: '/entry/instrument/detector/sensor_y' for a 2D detector
@reference: '/entry/instrument/energydispersion/center_kinetic_energy' for a swept scan
@reference: '/entry/process/calibration/energy_calibration/calibrated_axis' for a preprocessed axis.
</doc>
</attribute>
</field>
<field name="angular0" type="NX_NUMBER" units="NX_ANGLE">
<doc>
Trace of the first angular axis. Could be linked from the respective
'AXISNAME_depends' field.
``@reference`` field.
</doc>
<attribute name="reference" recommended="true">
<doc>
Points to the path of a field defining the calibrated axis which the ``angular0`` axis refers.

For example:
@reference: '/entry/sample/transformations/sample_tilt' for a manipulator angular scan
@reference: '/entry/instrument/detector/sensor_x' for a 2D detector
@reference: '/entry/instrument/collectioncolumn/deflector' for a deflector scan
@reference: '/entry/process/calibration/angular0_calibration/calibrated_axis' for a preprocessed axis.
</doc>
</attribute>
</field>
<field name="angular1" type="NX_NUMBER" units="NX_ANGLE">
<doc>
Trace of the second axis. Could be linked from the respective 'AXISNAME_depends'
Trace of the second axis. Could be linked from the respective ``@reference``
field.
</doc>
<attribute name="reference" recommended="true">
<doc>
Points to the path of a field defining the calibrated axis which the ``angular1`` axis refers.

For example:
@reference: '/entry/sample/transformations/sample_polar' for a manipulator angular scan
@reference: '/entry/instrument/detector/sensor_y' for a 2D detector
@reference: '/entry/instrument/collectioncolumn/deflector' for a deflector scan
@reference: '/entry/process/calibration/angular1_calibration/calibrated_axis' for a preprocessed axis.
</doc>
</attribute>
</field>
<field name="data" type="NX_NUMBER" units="NX_ANY">
<doc>
Expand Down
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