Nxsample refactoring #56
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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
This also contains a NXsample_without_deprecated.yaml file that show the new NXsample without the many deprecated fields.
lukaspie
requested review from
domna,
sherjeelshabih,
mkuehbach,
RubelMozumder,
sanbrock,
rettigl and
aalbino2
- Fix small error in intendation in NXsingle_crystal.yaml - Create nxdl once again
There a </field> missing
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Hi @lukaspie, thank you very much for pushing this. |
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For all to support you with finding some of the base class suggestions, I have made in the comments above, I am talking about nyaml files in the contributed/nyaml of the following PR #51 |
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This is a very good start. What I don't quite understand is the intended use/hierarchy of the Nx_sample_component/NX_physical_process subclasses. As far as I understand they are not cited in the base class hierarchy.
Does Nexus Inheritance also work in the sense that you can substitute a cited base class with an instance of a child class of that base class? I always thought the inheritance only goes as far as it includes all the super class elements.
Change base classes: - NXsample_component_set - NXsubstance - NXunit_cell
New(changed base classes: - NXsample - NXsample_component - NXsample_history - NXactivtiy - NXphysical_process - NXsample_synthesis_step
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In the most recent commits, I have distilled the changes to simply adding the new base classes on NXsample and Nxsample_component, without deprecating anything (as @sanbrock suggested). |
- Update some links/terms - Remove non-supported base class inheritance wrt. NXactivity
All activity-related base classes now contain a NXnote for any data or other descriptors acquired during the activity.
These will be addressed by a new PR.
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
Describe the dependancy of the sample_ component to an instance of the NXsample_component_set (at the same level of granularity where the instance of component is located).
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Any description of single crystals and unit cells has been removed for now and will be addressed in the branch crystal_structure_refactor. |
In order to know the ordering of components in the concentaration, volume_Fraction, ... fields, we need an array of strings refering to the names of the NXsample_components. The order of these components serves as an index (starting at 1).
currently not possible for base_classes
Initial draft for major refactoring of NXsample.
NXsample can now hold several base classes that split the sample description into
In general, most of the new base classes in contributed_definitions don't contain much information yet and will be fleshed out in the future. This process will also heavily involve input from Area A's base sections, especially for description of physical processes and substances/sample components.
There are also new base classes for descriptions of single crystals (NXsingle_crystal) and related unit cell (NXunit_cell), based on what was available already in the old NXsample. So far, they are not in use anywhere, but one could imagine that in the future, they may be part of a larger ecosystem describing the shape and type of the sample (components), including other types of samples like liquids, powders, pellets, ...
For better discussion, the new/changed nyaml files have also been added. This also includes a NXsample_without_deprecated.yaml file that show the new NXsample without the many deprecated fields. They should obviously be cleared later on.