122 move the transmission code from areaa repo

[ka-sarthak]

A plugin for Transmission Spectrophotometry has been developed in collaboration with IKZ (Hiroki Tanaka) in the last few months. It is currently available in the Area A modeling repo here: https://github.com/FAIRmat-NFDI/AreaA-data_modeling_and_schemas/tree/main/transmission/transmission_plugin

This PR aims to add this plugin as a module of nomad-measurements. To this end, the following steps are required:

• Copy the latest schema, parser to src/nomad_measurements/transmission
• Move readers to fairmat-readers-transmission https://github.com/FAIRmat-NFDI/readers-transmission/
• Allow for specialization of the plugin so that the general plugin can be specialized for IKZ in their repo 1 add ikz transmission IKZ-Berlin/nomad-ikz-plugin#3
• Add tests for transmission
• Use CompositeSystem for sample reference. This can be specialized in IKZ plugin for sample classes coming from specific growth techniques.

Some integration steps concerning this plugin moved to a separate issue #151

Summary by Sourcery

Move the transmission code from the Area A repository to the nomad-measurements repository.

New Features:

• Add a transmission plugin as a module of nomad-measurements.

Tests:

• Add tests for transmission.

[ka-sarthak]

Moved some IKZ specific stuff into the nomad-ikz-plugin. IKZ-Berlin/nomad-ikz-plugin#18

[ka-sarthak]

I have added the current version of the transmission plugin that was presented to the Area A TF on December 2, 2024. Some feedback from the discussions related to the refactoring of the quantities in TransmissionSampleReference has been integrated. Also, I have made a section called CrystallineTransmissionSampleReference which now contains the orientation of the sample surface where the light is incident.

[ka-sarthak]

TODO

• The UVVisNirTransmissionSettings.nir_gain sub-section needs further clarification. Currently, the sub-section for populated entries contains data not only for the NIR range but also for other wavelength ranges. Furthermore, gain is more of a general concept. Is it the amplification factor of the signal detected by the detector? Should it be renamed to gain?
  Renamed the sub-section to detector_gain. The gain is a setting for the detector in the Lambda series spectrophotometer: one setting per detector. For generality sake, it's better to have detector_gain setting as a separate subsection than putting it under a given detector. This allows to store multiple gain values for the same detector over different wavelength ranges.
  
  https://resources.perkinelmer.com/lab-solutions/resources/docs/app_highabsorbancescanninglambda1050950850.pdf

• Use/move the utils from/to nomad_measurements.utils. Currently, they are in nomad_measurements.transmission.utils

[ka-sarthak]

@hampusnasstrom @aalbino2 Finally ready for your reviews! :)

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request moves the transmission code from the Area A repository to the nomad-measurements repository. It copies the schema and parser, moves readers to a new repository, allows for specialization of the plugin, adds tests, and uses CompositeSystem for sample reference.

Class diagram for the Transmission Spectrophotometry data model

classDiagram
    class Measurement {
        <<abstract>>
    }
    class UVVisNirTransmission {
        +str user
        +str method
        +TransmissionSampleReference[] samples
        +UVVisNirTransmissionResult[] results
        +UVVisNirTransmissionSettings transmission_settings
    }
    class UVVisNirTransmissionResult {
        +float[] transmittance
        +float[] absorbance
        +float[] wavelength
        +generate_plots()
    }
    class TransmissionSampleReference {
        +CompositeSystem reference
        +float geometric_path_length
        +float optical_path_length
    }
    class UVVisNirTransmissionSettings {
        +str sample_beam_position
        +float common_beam_mask
        +bool common_beam_depolarizer
        +str detector_module
        +LampSettings[] light_sources
        +AttenuatorSettings attenuator
        +MonochromatorSettings[] monochromators
        +MonochromatorSlitWidth[] monochromator_slit_width
        +DetectorSettings[] detectors
        +DetectorGain[] detector_gain
        +DetectorIntegrationTime[] detector_integration_time
        +Accessory[] accessories
    }

    Measurement <|-- UVVisNirTransmission
    UVVisNirTransmission *-- TransmissionSampleReference
    UVVisNirTransmission *-- UVVisNirTransmissionResult
    UVVisNirTransmission *-- UVVisNirTransmissionSettings

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Class diagram for the Transmission Spectrophotometry instrument model

classDiagram
    class Entity {
        <<abstract>>
    }
    class Instrument {
        <<abstract>>
    }
    class Spectrophotometer {
        +str serial_number
        +str software_version
        +Detector[] detectors
        +Lamp[] light_sources
        +Monochromator[] monochromators
    }
    class Detector {
        +str type
    }
    class LightSource {
        +float power
    }
    class Lamp {
        +str type
    }
    class Monochromator {
    }
    class GratingMonochromator {
        +float groove_density
    }

    Entity <|-- Detector
    Entity <|-- LightSource
    LightSource <|-- Lamp
    Entity <|-- Monochromator
    Monochromator <|-- GratingMonochromator
    Instrument <|-- Spectrophotometer
    Spectrophotometer *-- Detector
    Spectrophotometer *-- Lamp
    Spectrophotometer *-- Monochromator

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File-Level Changes

Change	Details	Files
Copy the latest schema and parser to src/nomad_measurements/transmission	Added schema for transmission spectrophotometry, sample, and measurement. Added parser for transmission data files. Added transmission schema and parser to pyproject.toml	src/nomad_measurements/transmission/schema.py src/nomad_measurements/transmission/parser.py pyproject.toml
Move readers to fairmat-readers-transmission	Added fairmat-readers-transmission dependency to pyproject.toml	pyproject.toml
Allow for specialization of the plugin	Added plugin specialization to allow IKZ to specialize the plugin in their repository	src/nomad_measurements/transmission/schema.py
Add tests for transmission	Added tests for transmission spectrophotometry Added test data files	tests/test_transmission.py tests/data/transmission/3DM_test01.Probe.Raw.asc tests/data/transmission/F4-P3HT 1-10 0,5 mgml.Probe.Raw.asc tests/data/transmission/KTF-D.Probe.Raw.asc tests/data/transmission/Sample5926.Probe.Raw.asc tests/data/transmission/sphere_test01.Probe.Raw.asc
Use CompositeSystem for sample reference	Used CompositeSystem for sample reference, allowing specialization in IKZ plugin for sample classes	src/nomad_measurements/transmission/schema.py

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[sourcery-ai]

Hey @ka-sarthak - I've reviewed your changes and they look great!

Here's what I looked at during the review

• 🟡 General issues: 1 issue found
• 🟢 Security: all looks good
• 🟡 Testing: 2 issues found
• 🟢 Complexity: all looks good
• 🟢 Documentation: all looks good

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[aalbino2]

as commented this morning:

• need for a mechanism to be able so subclass this plugin

additionally:

• modify the toml of ikz-plugin and ikz-oasis!!

[ka-sarthak]

modify the toml of ikz-plugin and ikz-oasis!!

@aalbino2 Indeed, I made another issue yesterday to track this #151

[ka-sarthak]

need for a mechanism to be able so subclass this plugin

@aalbino2 Will handle this collectively for XRD and transmission in #131

[hampusnasstrom]

Looks good! Maybe just add a short description on what files the parser can currently parse. Then you can merge from my side.