FAIRmat 2024: additional base classes in NXinstrument #1419

lukaspie · 2024-09-23T16:34:01Z

Note that the CI/CD is failing here because we are bringing in several new base classes, which by themselves cite additional new base classes. This PR will only be ready once a decision on these new base classes has been reached.

phyy-nx · 2024-09-30T09:02:50Z

base_classes/NXhistory.nxdl.xml

+        <doc>
+             Any activity that was performed on the physical entity prior or during the experiment. In
+             the future, if there is base class inheritance, this can describe any activity,
+             including processes and measurements.


Remove the comment on the future

phyy-nx · 2024-09-30T09:03:37Z

base_classes/NXhistory.nxdl.xml

+subentry(NXsuxbentry):
+doc: |
+Any activity that was performed on the physical entity prior or during the experiment.
+definition: ["NXactivity"]-->


Remove comment

phyy-nx · 2024-09-30T09:04:02Z

base_classes/NXhistory.nxdl.xml

+        <doc>
+             Any chemical process that was performed on the physical entity prior or during the
+             experiment.
+        </doc>


Remove physical and chemical process as that will be covered by the NXactivity

phyy-nx · 2024-09-30T09:05:40Z

base_classes/NXhistory.nxdl.xml

+             persistent) identifier of e.g. another file which gives
+             as many as possible details of the history event.
+        </doc>
+    </group>


Remove NXidentifier

phyy-nx · 2024-09-30T09:06:47Z

base_classes/NXhistory.nxdl.xml

+             as many as possible details of the history event.
+        </doc>
+    </group>
+    <!--There should be more activities here, like measurement.-->


Remove comment

phyy-nx · 2024-09-30T09:07:51Z

base_classes/NXhistory.nxdl.xml

+             reference to the location or a unique identifier or other metadata file. In the
+             case these are not available, free-text description.
+             This should only be used in case that there is no rigorous description
+             using the base classes above. This field can also be used to pull in any activities


Suggested change

using the base classes above. This field can also be used to pull in any activities

using the base classes above. This group can also be used to pull in any activities

phyy-nx · 2024-09-30T09:13:21Z

base_classes/NXhistory.nxdl.xml

+        </doc>
+    </group>
+    <!--There should be more activities here, like measurement.-->
+    <group name="notes" type="NXnote">


Remove name="notes"

Replaced by <group type="NXnote" nameType="any">

phyy-nx · 2024-09-30T09:14:42Z

base_classes/NXhistory.nxdl.xml

+             case these are not available, free-text description.
+             This should only be used in case that there is no rigorous description
+             using the base classes above. This field can also be used to pull in any activities
+             that are not well described by an existing base class definition.


Add comment that any number of NXnotes are allowed for extra details.

phyy-nx · 2024-09-30T09:16:22Z

base_classes/NXactivity.nxdl.xml

+
+         This class is planned be used in the future as the super class for all other activities if inheritance 
+         in base classes is supported in NeXus.
+    </doc>


Remove reference to the future. "This class is a super class..."

phyy-nx · 2024-09-30T09:16:45Z

base_classes/NXactivity.nxdl.xml

+    </doc>
+    <field name="start_time" type="NX_DATE_TIME">
+        <doc>
+             ISO 8601 formatted time code (with local time zone offset to UTC information


Remove ISO reference. "Start time of activity"

Inclusion of time zone should be a recommendation, even a strong recommendation but not a requirement.

Implemented as
"Start time of this activity. It is recommended to include local time zone information."

phyy-nx · 2024-09-30T09:17:01Z

base_classes/NXactivity.nxdl.xml

+        <doc>
+             ISO 8601 formatted time code (with local time zone offset to UTC information
+             included) when this activity ended.
+        </doc>


Remove ISO reference. "End time of activity"

See start time

phyy-nx · 2024-09-30T09:17:17Z

base_classes/NXactivity.nxdl.xml

+             Short description of the activity.
+        </doc>
+    </field>
+    <group name="notes" type="NXnote">


Remove name="notes"

phyy-nx · 2024-09-30T09:19:40Z

base_classes/NXactivity.nxdl.xml

+             ISO 8601 formatted time code (with local time zone offset to UTC information
+             included) when this activity ended.
+        </doc>
+    </field>


Add end_time_estimated or add an estimated attribute on end_time.

Added as

<attribute name="estimated" type="NX_BOOLEAN"> <doc> In some cases, the end time of an activity can only be estimated. In this case, this attribute shall be True. </doc> </attribute>

phyy-nx · 2024-09-30T09:25:39Z

base_classes/NXactivity.nxdl.xml

+             This can be any data or other descriptor acquired during the activity
+             (NXnote allows to add pictures, audio, movies). Alternatively, a
+             reference to the location or a unique identifier or other metadata file. In the
+             case these are not available, free-text description.


Add comment that any number of NXnotes are allowed for extra details.

phyy-nx · 2024-09-30T09:29:51Z

base_classes/NXresolution.nxdl.xml

+    </field>
+    <field name="relative_resolution" type="NX_FLOAT" units="NX_ANY">
+        <doc>
+             Ratio of the resolution at a specified measurand value to that measurand value,


Suggested change

Ratio of the resolution at a specified measurand value to that measurand value,

Ratio of the resolution at a specified measurand value to that measurand value

lukaspie · 2024-09-30T09:30:49Z

base_classes/NXresolution.nxdl.xml

+    </group>
+    <field name="formula_SYMBOL" type="NX_CHAR">
+        <doc>
+             A symbol linking to another path in this appdef to be referred to from the


This should be "A symbol linking to another path in the NeXus tree to be referred to from the..."

phyy-nx · 2024-09-30T09:31:30Z

base_classes/NXresolution.nxdl.xml

+    </group>
+    <field name="formula_SYMBOL" type="NX_CHAR">
+        <doc>
+             A symbol linking to another path in this appdef to be referred to from the


spell out appdef

See above, changed to "A symbol linking to another path in the NeXus tree to be referred to from the..."

woutdenolf · 2024-09-30T09:31:50Z

base_classes/NXresolution.nxdl.xml

+    <field name="physical_quantity">
+        <doc>
+             The physical quantity of the resolution, e.g.,
+             energy, momentum, time, etc.


Can we include spatial resolution as an example (e.g. imaging techniques)?

added "area" to the examples

phyy-nx · 2024-09-30T09:37:30Z

base_classes/NXinstrument.nxdl.xml

    <group type="NXinsertion_device" />
    <group type="NXmirror" />
    <group type="NXmoderator" />
    <group type="NXmonochromator" />
    <group type="NXpolarizer" />
    <group type="NXpositioner" />
+    <group type="NXresolution"/>


Remove NXresolution from NXinstrument

woutdenolf · 2024-09-30T09:38:32Z

base_classes/NXresolution.nxdl.xml

+    </field>
+    <field name="relative_resolution" type="NX_FLOAT" units="NX_ANY">
+        <doc>
+             Ratio of the resolution at a specified measurand value to that measurand value,


measurand -> measured?

We intentionally used measurand here because we are not talking about measured values, but rather what resolution we will have given any value of a given measurand.

phyy-nx · 2024-09-30T09:39:16Z

base_classes/NXresolution.nxdl.xml

+    </field>
+    <group name="response_function" type="NXdata">
+        <doc>
+             The response of the instrument or part to a infinitesimally sharp input signal


Suggested change

The response of the instrument or part to a infinitesimally sharp input signal

The response of the instrument or part of the instrument to a infinitesimally sharp input signal

phyy-nx · 2024-09-30T09:42:00Z

base_classes/NXresolution.nxdl.xml

+                 in the input axis or grid.
+                 This field should have the same dimensions as `input`.
+            </doc>
+        </field>


Remove input and magnitude, and expand doc string to describe how this should be used.

phyy-nx · 2024-09-30T09:57:00Z

base_classes/NXresolution.nxdl.xml

+             entered by the `formula_...` fields.
+             The output unit should match the provided unit of this field.
+        </doc>
+    </field>


Remove formula_SYMBOL and change resolution_formula to resolution_description, update doc to indicate an english description of the math used.

Actually use NXparameters for formula_SYMBOL

lukaspie · 2024-09-30T10:01:25Z

base_classes/NXcalibration.nxdl.xml

+             calibration method but no actual calibration data.
+        </doc>
+    </group>
+    <group name="calibration_reference" type="NXidentifier">


to be replaced by identifier attribute

changed to <attribute name="identifier_calibration_reference">

base_classes/NXcalibration.nxdl.xml

phyy-nx · 2024-09-30T13:28:44Z

base_classes/NXcalibration.nxdl.xml

+             The axis values may be copied or linked in the appropriate NXcalibration fields for reference.
+        </doc>
+    </group>
+    <group name="calibration_object" type="NXserialized">


Use NXnote instead

lukaspie · 2024-10-01T14:10:13Z

Dev notes to keep track:

NXhistory: implemented suggested edits
NXactivity: implemented suggested edits
NXresolution: implemented suggested edits
NXcalibration: ok following edits
NXserialization: removed -> moved needed parameters to NXnote
NXinstrument: implemented suggested edits
NXcalibration: implemented suggested edits (using NXparameters in formula_SYMBOL and formula_description)

depends on / blocked by:

identifierNAME in NXobject -> add identifierNAME to NXobject #1486
~~changes to dev_tools -> name_type="partial" in dev tools #1491~~ -> done
~~implementation of nameType in groups -> UPPERCASE to indicate flexible names #1485~~ -> done

# Conflicts: # base_classes/NXaperture.nxdl.xml

… version of yaml. Removing unintensional comments # Conflicts: # base_classes/NXbeam.nxdl.xml # base_classes/NXdetector.nxdl.xml # base_classes/NXentry.nxdl.xml # base_classes/NXinstrument.nxdl.xml # base_classes/NXprocess.nxdl.xml # base_classes/NXsample.nxdl.xml # base_classes/NXsource.nxdl.xml # contributed_definitions/NXcollectioncolumn.nxdl.xml # contributed_definitions/NXmpes.nxdl.xml

# Conflicts: # contributed_definitions/NXmpes.nxdl.xml # contributed_definitions/nyaml/NXmpes.yaml

# Conflicts: # base_classes/NXenvironment.nxdl.xml # base_classes/nyaml/NXinstrument.yaml # contributed_definitions/NXmpes.nxdl.xml # contributed_definitions/nyaml/NXmanipulator.yaml # contributed_definitions/nyaml/NXmpes.yaml

# Conflicts: # base_classes/NXdetector.nxdl.xml # base_classes/NXsensor.nxdl.xml # base_classes/NXsource.nxdl.xml

# Conflicts: # base_classes/NXinstrument.nxdl.xml

# Conflicts: # base_classes/nyaml/NXinstrument.yaml

…ersion # Conflicts: # applications/NXarpes.nxdl.xml # applications/nyaml/NXarpes.yaml # base_classes/NXaperture.nxdl.xml # base_classes/NXbeam.nxdl.xml # base_classes/NXdata.nxdl.xml # base_classes/NXdetector.nxdl.xml # base_classes/NXentry.nxdl.xml # base_classes/NXenvironment.nxdl.xml # base_classes/NXinstrument.nxdl.xml # base_classes/NXmonochromator.nxdl.xml # base_classes/NXroot.nxdl.xml # base_classes/NXsample.nxdl.xml # base_classes/NXsample_component.nxdl.xml # base_classes/NXsensor.nxdl.xml # base_classes/NXsource.nxdl.xml # base_classes/NXsubentry.nxdl.xml # base_classes/NXtransformations.nxdl.xml # base_classes/NXuser.nxdl.xml # base_classes/nyaml/NXaperture.yaml # base_classes/nyaml/NXbeam.yaml # base_classes/nyaml/NXdata.yaml # base_classes/nyaml/NXdetector.yaml # base_classes/nyaml/NXentry.yaml # base_classes/nyaml/NXenvironment.yaml # base_classes/nyaml/NXmonochromator.yaml # base_classes/nyaml/NXprocess.yaml # base_classes/nyaml/NXroot.yaml # base_classes/nyaml/NXsample.yaml # base_classes/nyaml/NXsample_component.yaml # base_classes/nyaml/NXsensor.yaml # base_classes/nyaml/NXsource.yaml # base_classes/nyaml/NXsubentry.yaml # base_classes/nyaml/NXtransformations.yaml # base_classes/nyaml/NXuser.yaml # contributed_definitions/nyaml/NXinstrument.yaml

move NXfabrication to base_classes pull out base classes cited in NXinstrument

Co-authored-by: Aaron S. Brewster <[email protected]> Co-authored-by: Thomas A Caswell <[email protected]>

lukaspie marked this pull request as draft September 23, 2024 16:45

lukaspie changed the title ~~Fairmat 2024: additional base classes in NXinstrument~~ FAIRmat 2024: additional base classes in NXinstrument Sep 23, 2024

lukaspie force-pushed the fairmat-2024-nxinstrument branch from 64226dd to 5f5b269 Compare September 23, 2024 16:53

sanbrock mentioned this pull request Sep 29, 2024

NXinstrument #1452

Open

lukaspie linked an issue Sep 29, 2024 that may be closed by this pull request

NXinstrument #1452

Open

phyy-nx reviewed Sep 30, 2024

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lukaspie commented Sep 30, 2024

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phyy-nx reviewed Sep 30, 2024

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woutdenolf reviewed Sep 30, 2024

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phyy-nx reviewed Sep 30, 2024

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woutdenolf reviewed Sep 30, 2024

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phyy-nx reviewed Sep 30, 2024

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lukaspie commented Sep 30, 2024

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base_classes/NXcalibration.nxdl.xml Show resolved Hide resolved

phyy-nx reviewed Sep 30, 2024

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This was referenced Oct 1, 2024

Fairmat 2024: add base classes to NXprocess #1420

Open

Fairmat 2024: several new base classes in NXsample and NXsample_component #1413

Open

NXmpes #1464

Open

prjemian mentioned this pull request Oct 13, 2024

UPPERCASE to indicate flexible names #1485

Merged

6 tasks

lukaspie force-pushed the fairmat-2024-nxinstrument branch from 47d5f4a to ea5c4f5 Compare October 16, 2024 08:19

domna and others added 20 commits October 17, 2024 16:03

Readds base classes for mpes (from commit 843283a)

1be94c5

# Conflicts: # base_classes/NXaperture.nxdl.xml

Store NXsensor on NXinstrument (and NXmanipulator) instead of NXsample

19b73ca

# Conflicts: # contributed_definitions/NXmpes.nxdl.xml # contributed_definitions/nyaml/NXmpes.yaml

Add NXactuator base class

f8d6dec

# Conflicts: # base_classes/NXenvironment.nxdl.xml # base_classes/nyaml/NXinstrument.yaml # contributed_definitions/NXmpes.nxdl.xml # contributed_definitions/nyaml/NXmanipulator.yaml # contributed_definitions/nyaml/NXmpes.yaml

Add NXfabrication to all MPES instrument-related base classes

06d8bb6

# Conflicts: # base_classes/NXdetector.nxdl.xml # base_classes/NXsensor.nxdl.xml # base_classes/NXsource.nxdl.xml

remove explicit resolution names from NXinstrument

d5de6d6

# Conflicts: # base_classes/NXinstrument.nxdl.xml

add NXhistory to NXinstrument

c0db855

# Conflicts: # base_classes/nyaml/NXinstrument.yaml

revert unintentional changes from cherry-pick

f54a81d

pull out base classes cited in NXinstrument

5967df7

move NXfabrication to base_classes pull out base classes cited in NXinstrument

bring in NXactivity

63ed671

bring in NXcalibration

3a0eb72

bring in NXserialized

c82eb1d

Apply suggestions from code review on NXserialized

aef694c

Co-authored-by: Aaron S. Brewster <[email protected]> Co-authored-by: Thomas A Caswell <[email protected]>

address review from NIAC meeting

8e5e6fb

move new fields from NXserialized to NXnote

0c961a9

remove NXidentfier from NXfabrication and NXcalibration

51cf4ff

remove future comment from NXhistory

24c0d3e

use NXparameters and fit_formula_desription

74011bd

use NXparameters in NXresolution

d79ccf5

lukaspie force-pushed the fairmat-2024-nxinstrument branch from ea5c4f5 to d79ccf5 Compare October 17, 2024 14:03

lukaspie added 2 commits October 17, 2024 16:18

reformat docstrings in NXnote

e7af7a2

remove NXcalibration from contributed

ede44f3

	using the base classes above. This field can also be used to pull in any activities
	using the base classes above. This group can also be used to pull in any activities

	Ratio of the resolution at a specified measurand value to that measurand value,
	Ratio of the resolution at a specified measurand value to that measurand value

	The response of the instrument or part to a infinitesimally sharp input signal
	The response of the instrument or part of the instrument to a infinitesimally sharp input signal

FAIRmat 2024: additional base classes in NXinstrument #1419

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FAIRmat 2024: additional base classes in NXinstrument #1419

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lukaspie commented Sep 23, 2024 • edited Loading

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lukaspie commented Oct 1, 2024 • edited Loading

lukaspie commented Sep 23, 2024 •

edited

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lukaspie commented Oct 1, 2024 •

edited

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