Fairmat 2024: several new base classes in NXsample and NXsample_component #1413
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sanbrock
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sanbrock
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sanbrock
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| # For further information, see http://www.nexusformat.org | ||
| --> | ||
| <definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" name="NXsubstance" extends="NXobject" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd"> | ||
| <doc> |
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can now also inherit IDENTIFIER
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will be implemented when #1486 has been discussed
sanbrock
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Sep 29, 2024
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NXsample can now hold several base classes that split the sample description into 1) description of its components down to the chemical substance level -> NXsample_component, NXsample_component_set, NXsubstance, NXsample_surface_dopant as an example for an NXsubstance 2) any physical process that was performed prior/during the experiment -> NXphysical_process, NXsample_synthesis_step, ... -> can also be stored in NXsample_history 3) a description of the sample history -> NXsample_history, made up of one or more NXphysical_process instances 4) sample environment -> for now still allowed as NXenvironment in NXsample, but should eventually be on the level of the application definitions # Conflicts: # base_classes/NXsample.nxdl.xml # base_classes/NXsample_component.nxdl.xml
New(changed base classes: - NXsample - NXsample_component - NXsample_history - NXactivtiy - NXphysical_process - NXsample_synthesis_step # Conflicts: # base_classes/NXsample_component.nxdl.xml # base_classes/nyaml/NXsample.yaml # base_classes/nyaml/NXsample_component.yaml # contributed_definitions/NXsample_history.nxdl.xml # contributed_definitions/nyaml/NXphysical_process.yaml # contributed_definitions/nyaml/NXsample_history.yaml
- Update some links/terms - Remove non-supported base class inheritance wrt. NXactivity # Conflicts: # base_classes/nyaml/NXsample.yaml # contributed_definitions/NXphysical_process.nxdl.xml # contributed_definitions/NXsample_component_set.nxdl.xml # contributed_definitions/nyaml/NXphysical_process.yaml # contributed_definitions/nyaml/NXsample_component_set.yaml # contributed_definitions/nyaml/NXsample_history.yaml # contributed_definitions/nyaml/NXsubstance.yaml
There can only ever be one NXsample_component_set in any NXsample or NXsample_component. There can only ever be one NXsubstance in any NXsample or NXsample_component -> in this case, we are talking about a pure material # Conflicts: # base_classes/NXsample_component.nxdl.xml # base_classes/nyaml/NXsample.yaml # base_classes/nyaml/NXsample_component.yaml
# Conflicts: # base_classes/NXsample_component.nxdl.xml # base_classes/nyaml/NXsample.yaml # base_classes/nyaml/NXsample_component.yaml # contributed_definitions/NXsample_component_set.nxdl.xml # contributed_definitions/NXsample_history.nxdl.xml # contributed_definitions/NXsample_synthesis_step.nxdl.xml # contributed_definitions/NXsubstance.nxdl.xml # contributed_definitions/nyaml/NXphysical_process.yaml # contributed_definitions/nyaml/NXsample_component_set.yaml # contributed_definitions/nyaml/NXsample_history.yaml # contributed_definitions/nyaml/NXsubstance.yaml
currently not possible for base_classes # Conflicts: # base_classes/NXsample_component.nxdl.xml # base_classes/nyaml/NXsample.yaml # base_classes/nyaml/NXsample_component.yaml
# Conflicts: # base_classes/NXsample.nxdl.xml # contributed_definitions/NXsingle_crystal.nxdl.xml
# Conflicts: # base_classes/NXsample_component.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
Since we have substantial changes on the NXsample base class now, here we remove any changes to NXsample in this PR.
# Conflicts: # contributed_definitions/NXmpes.nxdl.xml # contributed_definitions/nyaml/NXmpes.yaml
# Conflicts: # base_classes/NXsample_component.nxdl.xml # base_classes/nyaml/NXsample.yaml # base_classes/nyaml/NXsample_component.yaml
# Conflicts: # base_classes/NXsample_component.nxdl.xml # base_classes/nyaml/NXsample.yaml # base_classes/nyaml/NXsample_component.yaml
# Conflicts: # base_classes/nyaml/NXsample.yaml
# Conflicts: # base_classes/NXuser.nxdl.xml # base_classes/nyaml/NXsample.yaml # base_classes/nyaml/NXuser.yaml # contributed_definitions/NXapm.nxdl.xml # contributed_definitions/NXfabrication.nxdl.xml # contributed_definitions/NXidentifier.nxdl.xml # contributed_definitions/NXoptical_spectroscopy.nxdl.xml # contributed_definitions/nyaml/NXapm.yaml # contributed_definitions/nyaml/NXfabrication.yaml # contributed_definitions/nyaml/NXidentifier.yaml # contributed_definitions/nyaml/NXoptical_spectroscopy.yaml
# Conflicts: # base_classes/NXactivity.nxdl.xml # contributed_definitions/NXactivity.nxdl.xml # contributed_definitions/NXaperture_em.nxdl.xml # contributed_definitions/NXchemical_process.nxdl.xml # contributed_definitions/NXelectronanalyser.nxdl.xml # contributed_definitions/NXrotation_set.nxdl.xml # contributed_definitions/NXunit_cell.nxdl.xml
pull in cited base classes pull in cited base classes
lukaspie
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discussion needed
NIAC vote needed
This was referenced Dec 6, 2024
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This PR is aimed at a more detailed description of the components of a sample. It introduces the following new base classes:
NXsample_component_set,NXsubstance,NXunit_cell,NXsingle_crystal,NXrotation_setNXsample_component_set: this is meant as a wrapper that takes in all the sub sample components (i.e. instances ofNXsample_component) and their relationships (mass fractions, volume fractions, etc.)NXsubstance: this is meant to describe a chemical substance. Examples can be single chemical elements, chemical compunds, or alloys (e.g. CuO, C,). It is envisioned that if such a substance is crystalline, it could have an instance ofNXunit_cell: Description of a unit cell, i.e., the crystal structure of a single thermodynamic phase. This was can be used withinNXsample_(component)and/or inNXsingle_crystal: this is for describing a single crystalline material/phase within another material. It makes use of the new base_classNXrotation_set, which provides a rigorous way of describing rotations, orientations, and disorientations.Eventually, it is envisioned that each sample can contain one or more instances
NXsample_component_set, each of which has one or more instances ofNXsample_component. This component is either not mixed (and thus can contain an instance ofNXsubstance) or it by itself contains one or more instancesNXsample_component_setwith multiple instances ofNXsample_component. The image provides a useful visualization of this nesting.One thing to consider here is the naming of the base classes:
NXsample_component_setandNXrotation_setare probably not the best idea as_setis a reserved suffix and will now also be formally added toNXobject, see #1507.In addition to the description of the sample component hierarchy, this PR also brings in
NXhistoryandNXactivity, which are used to describe the history of physical activities that have happened on the sample (preparation, calcination, in situ treatment, ...). It is the same concept as described in #1419, but it is now added toNXsampleas well.