ome-types 0.0.1rc4

Python dataclasses for the OME data model

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.