Add ORSO providers

src/essreflectometry/amor/load.py

@@ -153,32 +153,7 @@ def extract_events(
     data.coords['position'].fields.y += data.coords['position'].fields.z * sc.tan(
         2.0 * data.coords['sample_rotation'] - (0.955 * sc.units.deg)
     )
-    return RawData[Run](data)
-
-
-# TODO
-# def populate_orso(orso: Any, data: sc.DataGroup, filename: str) -> Any:
-#    """
-#    Populate the Orso object, by calling the :code:`base_orso` and adding data from the
-#    file.
-#
-#    Parameters
-#    ----------
-#    orso:
-#        The orso object to be populated by additional information from the loaded file.
-#    data:
-#        Data group to source information from.
-#        Should mimic the structure of the NeXus file.
-#    filename:
-#        Path of the file to load.
-#    """
-#    orso.data_source.experiment.title = data['title']
-#    orso.data_source.experiment.instrument = data['name']
-#    orso.data_source.experiment.start_date = datetime.strftime(
-#        datetime.strptime(data['start_time'][:-3], '%Y-%m-%dT%H:%M:%S.%f'),
-#        '%Y-%m-%d',
-#    )
-#    orso.data_source.measurement.data_files = [filename]
+    return RawEvents[Run](data)
 
 
 providers = (extract_events, load_raw_nexus)

src/essreflectometry/amor/orso.py

@@ -1,60 +1,79 @@
 # SPDX-License-Identifier: BSD-3-Clause
 # Copyright (c) 2023 Scipp contributors (https://github.com/scipp)
-import platform
-from datetime import datetime
-
-from orsopy import fileio
-
-from .. import __version__
-
-
-def make_orso(
-    owner: fileio.base.Person,
-    sample: fileio.data_source.Sample,
-    creator: fileio.base.Person,
-    reduction_script: str,
-) -> fileio.orso.Orso:
-    """
-    Generate the base Orso object for the Amor instrument.
-    Populate the Orso object for metadata storage.
-
-    Parameters
-    ----------
-    owner:
-        The owner of the data set, i.e. the main proposer of the measurement.
-    sample:
-        A description of the sample.
-    creator:
-        The creator of the reduced data, the person responsible for the
-        reduction process.
-    reduction_script:
-        The script or notebook used for reduction.
-
-    Returns
-    -------
-    :
-        Orso object with the default parameters for the Amor instrument.
-    """
-    orso = fileio.orso.Orso.empty()
-    orso.data_source.experiment.probe = 'neutrons'
-    orso.data_source.experiment.facility = 'Paul Scherrer Institut'
-    orso.data_source.measurement.scheme = 'angle- and energy-dispersive'
-    orso.reduction.software = fileio.reduction.Software(
-        'scipp-ess', __version__, platform.platform()
+"""ORSO utilities for Amor."""
+import os
+from typing import Optional
+
+from dateutil.parser import parse as parse_datetime
+from orsopy.fileio import base as orso_base
+from orsopy.fileio import data_source
+
+from ..orso import (
+    OrsoExperiment,
+    OrsoInstrument,
+    OrsoMeasurement,
+    OrsoOwner,
+    OrsoSample,
+)
+from ..types import Filename, RawData, Reference, Run, Sample
+
+
+def parse_orso_experiment(raw_data: RawData[Run]) -> OrsoExperiment[Run]:
+    """Parse ORSO experiment data from raw Amor NeXus data."""
+    return OrsoExperiment(
+        data_source.Experiment(
+            title=raw_data['title'],
+            instrument=raw_data['name'],
+            facility=raw_data['facility'],
+            start_date=parse_datetime(raw_data['start_time']),
+            probe='neutron',
+        )
+    )
+
+
+def parse_orso_owner(raw_data: RawData[Run]) -> OrsoOwner[Run]:
+    """Parse ORSO owner data from raw Amor NeXus data."""
+    return OrsoOwner(
+        orso_base.Person(
+            name=raw_data['user']['name'],
+            contact=raw_data['user']['email'],
+            affiliation=None,
+        )
     )
-    orso.reduction.timestep = datetime.now()
-    orso.reduction.corrections = []
-    orso.reduction.computer = platform.node()
-    orso.columns = [
-        fileio.base.Column('Qz', '1/angstrom', 'wavevector transfer'),
-        fileio.base.Column('R', None, 'reflectivity'),
-        fileio.base.Column('sR', None, 'standard deivation of reflectivity'),
-        fileio.base.Column(
-            'sQz', '1/angstrom', 'standard deviation of wavevector transfer resolution'
-        ),
-    ]
-    orso.data_source.owner = owner
-    orso.data_source.sample = sample
-    orso.reduction.creator = creator
-    orso.reduction.script = reduction_script
-    return orso
+
+
+def parse_orso_sample(raw_data: RawData[Run]) -> OrsoSample[Run]:
+    """Parse ORSO sample data from raw Amor NeXus data."""
+    if not raw_data.get('sample'):
+        return OrsoSample(data_source.Sample.empty())
+    raise NotImplementedError('Amor NsXus sample parsing is not implemented')
+
+
+def build_orso_measurement(
+    sample_filename: Filename[Sample],
+    reference_filename: Filename[Reference],
+    instrument: Optional[OrsoInstrument],
+) -> OrsoMeasurement:
+    """Assemble ORSO measurement data."""
+    # TODO populate timestamp
+    #      doesn't work with a local file because we need the timestamp of the original,
+    #      SciCat can provide that
+    return OrsoMeasurement(
+        data_source.Measurement(
+            instrument_settings=instrument,
+            data_files=[orso_base.File(file=os.path.basename(sample_filename))],
+            additional_files=[
+                orso_base.File(
+                    file=os.path.basename(reference_filename), comment='supermirror'
+                )
+            ],
+        )
+    )
+
+
+providers = (
+    parse_orso_experiment,
+    build_orso_measurement,
+    parse_orso_owner,
+    parse_orso_sample,
+)

src/essreflectometry/orso.py

@@ -1,15 +1,101 @@
 # SPDX-License-Identifier: BSD-3-Clause
 # Copyright (c) 2023 Scipp contributors (https://github.com/scipp)
-import warnings
+"""ORSO utilities for reflectometry."""
+import platform
+from datetime import datetime, timezone
+from typing import NewType, Optional
 
+import sciline
+from orsopy.fileio import base as orso_base
+from orsopy.fileio import data_source, reduction
 
-def not_found_warning():
+from . import __version__
+from .types import Reference, Run, Sample
+
+
+class OrsoExperiment(
+    sciline.Scope[Run, data_source.Experiment], data_source.Experiment
+):
+    """ORSO experiment for a run."""
+
+
+class OrsoInstrument(
+    sciline.Scope[Run, data_source.InstrumentSettings], data_source.InstrumentSettings
+):
+    """ORSO instrument settings for a run."""
+
+
+class OrsoOwner(sciline.Scope[Run, orso_base.Person], orso_base.Person):
+    """ORSO owner of a file."""
+
+
+class OrsoReduction(sciline.Scope[Run, reduction.Reduction], reduction.Reduction):
+    """ORSO measurement for a run."""
+
+
+class OrsoSample(sciline.Scope[Run, data_source.Sample], data_source.Sample):
+    """ORSO sample of a run."""
+
+
+OrsoCreator = NewType('OrsoCreator', orso_base.Person)
+"""ORSO creator, that is, the person who processed the data."""
+
+OrsoDataSource = NewType('OrsoDataSource', data_source.DataSource)
+"""ORSO data source."""
+
+OrsoMeasurement = NewType('OrsoMeasurement', data_source.Measurement)
+"""ORSO measurement."""
+
+
+def build_orso_reduction(creator: Optional[OrsoCreator]) -> OrsoReduction:
+    """Construct ORSO reduction data.
+
+    This assumes that ess.reflectometry is the primary piece of software
+    used to reduce the data.
     """
-    A function to raise a orso specific error if necessary.
+    return OrsoReduction(
+        reduction.Reduction(
+            software=reduction.Software(
+                name='ess.reflectometry',
+                version=str(__version__),
+                platform=platform.system(),
+            ),
+            timestamp=datetime.now(tz=timezone.utc),
+            creator=creator,
+            corrections=[],
+        )
+    )
+
+
+def build_orso_data_source(
+    owner: Optional[OrsoOwner[Sample]],
+    sample: Optional[OrsoSample[Sample]],
+    sample_experiment: Optional[OrsoExperiment[Sample]],
+    reference_experiment: Optional[OrsoExperiment[Reference]],
+    measurement: Optional[OrsoMeasurement],
+) -> OrsoDataSource:
+    """Judiciously assemble an ORSO DataSource.
+
+    Makes some assumptions about how sample and reference runs should be merged,
+    giving precedence to the sample run.
     """
-    warnings.warn(
-        "For metadata to be logged in the data array, "
-        "it is necessary to install the orsopy package.",
-        UserWarning,
-        stacklevel=2,
+    # We simply assume that the owner of the reference measurement
+    # has no claim on this data.
+    if (sample_experiment.facility != reference_experiment.facility) or (
+        sample_experiment.instrument != reference_experiment.instrument
+    ):
+        raise ValueError(
+            'The sample and reference experiments were done at different instruments'
+        )
+
+    return OrsoDataSource(
+        data_source.DataSource(
+            owner=owner,
+            sample=sample,
+            experiment=sample_experiment,
+            measurement=measurement,
+        )
     )
+
+
+providers = (build_orso_reduction, build_orso_data_source)