Merge pull request #38 from IKZ-Berlin/remove-transmission

Remove transmission schema, parser, entrypoint, dep

pyproject.toml

@@ -35,7 +35,6 @@ dependencies = [
     'nomad-analysis', # develop branch
     'lakeshore-nomad-plugin @ git+https://github.com/IKZ-Berlin/lakeshore-nomad-plugin.git@69a6deb3f0e99d7b0dc66714105dd62a56f157e9',
     'laytec_epitt_plugin @ git+https://github.com/IKZ-Berlin/laytec_epitt_nomad_plugin.git@f4953ac4ecb55b7003dee323d7d7f473e49ab4e3',
-    'transmission @ git+https://github.com/FAIRmat-NFDI/AreaA-data_modeling_and_schemas.git@2b2c38809e63e3578ef63d8c1d1fe9e27aa7a321#subdirectory=transmission/transmission_plugin/uv_vis_nir_transmission_plugin',
 ]
 
 [project.optional-dependencies]
@@ -144,7 +143,6 @@ where = ["src"]
 [project.entry-points.'nomad.plugin']
 general_schema = "nomad_ikz_plugin.general:schema"
 characterization_schema = "nomad_ikz_plugin.characterization:schema"
-characterization_transmission_parser = "nomad_ikz_plugin.characterization:transmission_parser"
 pld_schema = "nomad_ikz_plugin.pld:schema"
 movpe_schema = "nomad_ikz_plugin.movpe:schema"
 movpe2_growth_excel_parser = "nomad_ikz_plugin.movpe.movpe2.growth_excel:parser"

src/nomad_ikz_plugin/characterization/__init__.py

@@ -15,7 +15,7 @@
 # limitations under the License.
 #
 
-from nomad.config.models.plugins import ParserEntryPoint, SchemaPackageEntryPoint
+from nomad.config.models.plugins import SchemaPackageEntryPoint
 
 
 class CharacterizationEntryPoint(SchemaPackageEntryPoint):
@@ -25,25 +25,7 @@ def load(self):
         return m_package
 
 
-class TransmissionParserEntryPoint(ParserEntryPoint):
-    """
-    Entry point for lazy loading of the TransmissionParser.
-    """
-
-    def load(self):
-        from nomad_ikz_plugin.characterization.parser import TransmissionParser
-
-        return TransmissionParser(**self.dict())
-
-
 schema = CharacterizationEntryPoint(
     name='CharacterizationSchema',
     description='Schema package for general characterization methods used at IKZ.',
 )
-
-transmission_parser = TransmissionParserEntryPoint(
-    name='Transmission Parser',
-    description='Parser for data from Transmission Spectrophotometry.',
-    mainfile_mime_re='text/.*|application/zip',
-    mainfile_name_re='^.*\.asc$',
-)

src/nomad_ikz_plugin/characterization/schema.py

@@ -1,38 +1,17 @@
-from typing import TYPE_CHECKING
-
 import numpy as np
-import plotly.express as px
 from nomad.config import config
 from nomad.datamodel.data import EntryData
-from nomad.datamodel.metainfo.annotations import (
-    ELNAnnotation,
-    Filter,
-    SectionProperties,
-)
 from nomad.datamodel.metainfo.basesections import (
     Measurement,
     MeasurementResult,
 )
-from nomad.datamodel.metainfo.plot import (
-    PlotlyFigure,
-)
 from nomad.metainfo import Datetime, MEnum, Quantity, SchemaPackage, Section, SubSection
-from transmission.schema import (
-    ELNUVVisNirTransmission,
-    UVVisNirTransmissionResult,
-    UVVisNirTransmissionSettings,
-)
 
 from nomad_ikz_plugin.general.schema import (
     IKZCategory,
     SubstratePreparationStep,
 )
 
-if TYPE_CHECKING:
-    from nomad.datamodel.datamodel import EntryArchive
-    from structlog.stdlib import BoundLogger
-
-
 configuration = config.get_plugin_entry_point(
     'nomad_ikz_plugin.characterization:schema'
 )
@@ -157,182 +136,4 @@ class LightMicroscope(Measurement, SubstratePreparationStep, EntryData):
     )
 
 
-class IKZUVVisNirTransmissionSettings(UVVisNirTransmissionSettings):
-    """
-    A specialized section for IKZ based on the `UVVisNirTransmissionSettings` section.
-    """
-
-    ordinate_type = Quantity(
-        type=MEnum(['%T', 'A']),
-        description=(
-            'Specifies whether the ordinate (y-axis) of the measurement data is '
-            'percent transmittance (%T) or absorbance (A).'
-        ),
-        a_eln={'component': 'EnumEditQuantity'},
-    )
-
-
-class IKZUVVisNirTransmissionResult(UVVisNirTransmissionResult):
-    """
-    A specialized section for IKZ based on the `UVVisNirTransmissionResult` section.
-    """
-
-    m_def = Section(
-        a_eln=ELNAnnotation(
-            properties=SectionProperties(
-                order=[
-                    'transmittance',
-                    'absorbance',
-                    'wavelength',
-                    'extinction_coefficient',
-                ],
-                visible=Filter(
-                    exclude=[
-                        'array_index',
-                    ],
-                ),
-            )
-        )
-    )
-    extinction_coefficient = Quantity(
-        type=np.float64,
-        description=(
-            'Extinction coefficient calculated from transmittance and sample thickness '
-            'values: -log(T)/L. The coefficient includes the effects of '
-            'absorption, reflection, and scattering.'
-        ),
-        shape=['*'],
-        unit='1/m',
-        a_plot={'x': 'array_index', 'y': 'extinction_coefficient'},
-    )
-
-    def generate_plots(self) -> list[PlotlyFigure]:
-        """
-        Extends UVVisNirTransmissionResult.generate_plots() method to include the plotly
-        figures for the `IKZUVVisNirTransmissionResult` section.
-
-        Returns:
-            list[PlotlyFigure]: The plotly figures.
-        """
-        figures = super().generate_plots()
-        if self.wavelength is None:
-            return figures
-
-        # generate plot for extinction coefficient
-        if self.extinction_coefficient is None:
-            return figures
-
-        x = self.wavelength.to('nm').magnitude
-        x_label = 'Wavelength'
-        xaxis_title = x_label + ' (nm)'
-
-        y = self.extinction_coefficient.to('1/cm').magnitude
-        y_label = 'Extinction coefficient'
-        yaxis_title = y_label + ' (1/cm)'
-
-        line_linear = px.line(x=x, y=y)
-
-        line_linear.update_layout(
-            title=f'{y_label} over {x_label}',
-            xaxis_title=xaxis_title,
-            yaxis_title=yaxis_title,
-            xaxis=dict(
-                fixedrange=False,
-            ),
-            yaxis=dict(
-                fixedrange=False,
-            ),
-            template='plotly_white',
-        )
-
-        figures.append(
-            PlotlyFigure(
-                label=f'{y_label} linear plot',
-                figure=line_linear.to_plotly_json(),
-            ),
-        )
-
-        return figures
-
-    def calculate_extinction_coefficient(self, archive, logger):
-        """
-        Calculate the extinction coefficient from the transmittance and sample
-        thickness. The formula used is: -log( T[%] / 100 ) / L.
-
-        Args:
-            archive (EntryArchive): The archive containing the section.
-            logger (BoundLogger): A structlog logger.
-        """
-        self.extinction_coefficient = None
-        if not archive.data.samples:
-            logger.warning(
-                'Cannot calculate extinction coefficient as sample not found.'
-            )
-            return
-        if not archive.data.samples[0].thickness:
-            logger.warning(
-                'Cannot calculate extinction coefficient as sample thickness not found '
-                'or the value is 0.'
-            )
-            return
-
-        path_length = archive.data.samples[0].thickness
-        if self.transmittance is not None:
-            extinction_coeff = -np.log(self.transmittance) / path_length
-            # TODO: The if-block is a temperary fix to avoid processing of nans in
-            # the archive. The issue will be fixed in the future.
-            if np.any(np.isnan(extinction_coeff)):
-                logger.warning(
-                    'Failed to save extinction coefficient. '
-                    'Encountered NaN values in the calculation.'
-                )
-                return
-            self.extinction_coefficient = extinction_coeff
-
-    def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
-        """
-        The normalizer for the `IKZUVVisNirTransmissionResult` class.
-
-        Args:
-            archive (EntryArchive): The archive containing the section that is being
-            normalized.
-            logger (BoundLogger): A structlog logger.
-        """
-        super().normalize(archive, logger)
-        self.calculate_extinction_coefficient(archive, logger)
-
-
-class IKZELNUVVisNirTransmission(ELNUVVisNirTransmission):
-    """
-    A specialized section for IKZ based on the `ELNUVVisNirTransmission` section.
-    """
-
-    m_def = Section(
-        categories=[IKZCategory],
-        label='IKZ UV-Vis-NIR Transmission',
-        a_template={
-            'measurement_identifiers': {},
-        },
-    )
-    results = SubSection(
-        section_def=IKZUVVisNirTransmissionResult,
-        repeats=True,
-    )
-    transmission_settings = SubSection(
-        section_def=IKZUVVisNirTransmissionSettings,
-    )
-
-    def write_transmission_data(self, transmission, data_dict, archive, logger):
-        """
-        Specialized method to write the transmission data for the IKZ plugin. The method
-        overrides the `write_transmission_data` method of the parent
-        `ELNUVVisNirTransmission` class.
-        """
-        super().write_transmission_data(transmission, data_dict, archive, logger)
-        if data_dict['ordinate_type'] in ['%T', 'A']:
-            transmission.transmission_settings.ordinate_type = data_dict.get(
-                'ordinate_type'
-            )
-
-
 m_package.__init_metainfo__()