Python dataclasses for the OME data model
Project description
ome-types: OME dataclasses for python
autogenerated dataclasses for a pythonic interface into the OME data model: http://www.openmicroscopy.org/Schemas/OME/2016-06
It converts the ome.xsd schema into a set of python dataclasses and types.
As an example, the
OME/Image
model will be rendered as the following dataclass in ome_types/model/image.py
from dataclasses import field
from datetime import datetime
from typing import List, Optional
from pydantic.dataclasses import dataclass
from .annotation_ref import AnnotationRef
from .experiment_ref import ExperimentRef
from .experimenter_group_ref import ExperimenterGroupRef
from .experimenter_ref import ExperimenterRef
from .imaging_environment import ImagingEnvironment
from .instrument_ref import InstrumentRef
from .microbeam_manipulation_ref import MicrobeamManipulationRef
from .objective_settings import ObjectiveSettings
from .pixels import Pixels
from .roi_ref import ROIRef
from .simple_types import ImageID
from .stage_label import StageLabel
@dataclass
class Image:
id: ImageID
pixels: Pixels
acquisition_date: Optional[datetime] = None
annotation_ref: List[AnnotationRef] = field(default_factory=list)
description: Optional[str] = None
experiment_ref: Optional[ExperimentRef] = None
experimenter_group_ref: Optional[ExperimenterGroupRef] = None
experimenter_ref: Optional[ExperimenterRef] = None
imaging_environment: Optional[ImagingEnvironment] = None
instrument_ref: Optional[InstrumentRef] = None
microbeam_manipulation_ref: List[MicrobeamManipulationRef] = field(default_factory=list)
name: Optional[str] = None
objective_settings: Optional[ObjectiveSettings] = None
roi_ref: List[ROIRef] = field(default_factory=list)
stage_label: Optional[StageLabel] = None
ome_autogen.convert_schema(url, target) is the main function. It accepts an
xsd file path (only test on an ome.xsd), and a target directory, and writes a
human-readable module, that will validate OME XML, provide pythonic method
naming, and provides full typing support for IDEs, etc...
Usage
The model is not checked into source, but it is included when you pip install
the package (and it will be built automatically at ome_types/model if it
doesn't exist the first time you import the package.)
from ome_types import OME # the root class
# or specific objects
from ome_types.model import Image, Pixels, Plate # etc...
There is a convenience function that accepts xml, and outputs a validated OME model (if it fails validation, an exception is raised):
from ome_types import from_xml
metadata = from_xml(xml)
where xml in that example can be a path to a file, a URI of a
resource, an opened file-like object, an Element instance, an ElementTree
instance, or a literal string containing the XML data.
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