Transmission modify sample #167
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… physical props; refactor normalize
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…to atomic fraction
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* Order quantities; revert modification of basesection quantities * Modify description of quantities * Populate elements and components based on chemical_composition * Add overwrite_quantity in merge_sections * Include merge section capability to allow GUI interaction in `components` * Restrict component class to `PureSubstanceComponent` * Move material system as sub-section in TransmissionSample * Add module for material_system and classes for Solid Solution * Create TransmissionSampleReference class and use it in samples subsection * Make SolidSolution as an entry class; reference it in TransmissionSample * Bugfix: logic of adjusting composition * Rearrange imports * Add physical properties classes * Refactor Transmission sample to be a section containing reference and physical props; refactor normalize * Fixing rebase * Changing warn to warning * Move Physical properties to schema * Rename section names; add docstring for naming convention * Add crystal, polycrystal, mixed crystal, mixed polycrystal sections * Ruff * Add material system entry point; rename dopant as impurity * Refine the ELN properties of sample related schemas * Refine ELN properties for material system; make atomic percentage in to atomic fraction * Remove materials_system: they will be moved to nomad-material-processing * Align TransmissionSampleReference with CompositeSystemReference * Compose a Sample class based on composite system * Refactor extinction coefficient calc and plot * Temporary bugfix for extinction coeff calc; minor changes in schema * Update nomad * Bugfix schema import; ignore search when in client context * Add caplog conftest * Bugfix: updating schema in search_quantities * Add aliases * Add previous archives to test for backward compatibility * Add test for backward compatibility * Add fixes for backward compatibility * Move RawFileTransmissionData to schema
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* Order quantities; revert modification of basesection quantities * Modify description of quantities * Populate elements and components based on chemical_composition * Add overwrite_quantity in merge_sections * Include merge section capability to allow GUI interaction in `components` * Restrict component class to `PureSubstanceComponent` * Move material system as sub-section in TransmissionSample * Add module for material_system and classes for Solid Solution * Create TransmissionSampleReference class and use it in samples subsection * Make SolidSolution as an entry class; reference it in TransmissionSample * Bugfix: logic of adjusting composition * Rearrange imports * Add physical properties classes * Refactor Transmission sample to be a section containing reference and physical props; refactor normalize * Fixing rebase * Changing warn to warning * Move Physical properties to schema * Rename section names; add docstring for naming convention * Add crystal, polycrystal, mixed crystal, mixed polycrystal sections * Ruff * Add material system entry point; rename dopant as impurity * Refine the ELN properties of sample related schemas * Refine ELN properties for material system; make atomic percentage in to atomic fraction * Remove materials_system: they will be moved to nomad-material-processing * Align TransmissionSampleReference with CompositeSystemReference * Compose a Sample class based on composite system * Refactor extinction coefficient calc and plot * Temporary bugfix for extinction coeff calc; minor changes in schema * Update nomad * Bugfix schema import; ignore search when in client context * Add caplog conftest * Bugfix: updating schema in search_quantities * Add aliases * Add previous archives to test for backward compatibility * Add test for backward compatibility * Add fixes for backward compatibility * Move RawFileTransmissionData to schema
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* Order quantities; revert modification of basesection quantities * Modify description of quantities * Populate elements and components based on chemical_composition * Add overwrite_quantity in merge_sections * Include merge section capability to allow GUI interaction in `components` * Restrict component class to `PureSubstanceComponent` * Move material system as sub-section in TransmissionSample * Add module for material_system and classes for Solid Solution * Create TransmissionSampleReference class and use it in samples subsection * Make SolidSolution as an entry class; reference it in TransmissionSample * Bugfix: logic of adjusting composition * Rearrange imports * Add physical properties classes * Refactor Transmission sample to be a section containing reference and physical props; refactor normalize * Fixing rebase * Changing warn to warning * Move Physical properties to schema * Rename section names; add docstring for naming convention * Add crystal, polycrystal, mixed crystal, mixed polycrystal sections * Ruff * Add material system entry point; rename dopant as impurity * Refine the ELN properties of sample related schemas * Refine ELN properties for material system; make atomic percentage in to atomic fraction * Remove materials_system: they will be moved to nomad-material-processing * Align TransmissionSampleReference with CompositeSystemReference * Compose a Sample class based on composite system * Refactor extinction coefficient calc and plot * Temporary bugfix for extinction coeff calc; minor changes in schema * Update nomad * Bugfix schema import; ignore search when in client context * Add caplog conftest * Bugfix: updating schema in search_quantities * Add aliases * Add previous archives to test for backward compatibility * Add test for backward compatibility * Add fixes for backward compatibility * Move RawFileTransmissionData to schema
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This brings the following changes in the schema
Refactors around sample
Sampleis a composite system containing information about the sample id, geometry, and reference to the material system undercomponentssub-section.TransmissionSampleReferenceis a composite system reference containing information related to the sample that is specific to the Transmission. It has a reference toSample, thickness or path length, and orientation of the sample with respect to the light beam. Path length can be taken from the sample geometry. Orientation is expected to be in miller indices.Adds the tests for backward compatibility
Moves
RawFileTransmissionDatato schema.pyRenames the classes for consistency
The material system classes, originally planned to be written here, will be handled in
nomad-material-processingFAIRmat-NFDI/nomad-material-processing#77.