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Axis

AxisType #

Bases: str, Enum

String enum representing the three axis types (space, time, channel) defined in the specification.

Axis #

Bases: SkipNoneBase, FrozenBase

Axis metadata.

See https://ngff.openmicroscopy.org/0.4/#axes-md for the specification of this data structure.

Attributes:

Name Type Description
_version Literal['0.4']

The current version of this metadata.
_skip_if_none tuple[str,...], default=("type", "unit")

Names of fields that will not be serialized if they are None.
name str

The name for this axis.
type str | None = None

The type for this axis, e.g. "space". If this is set to None, it will not be serialized.
unit str | None

The unit of measure associated with the interval defined by this axis. If this is set to None, it will not be serialized.

check_type_unit #

check_type_unit(model)

Check that the unit attribute of an Axis object is valid. This function emits warnings when the unit attribute of of an Axis object is spec-compliant but contravenes a "SHOULD" statement in the spec.

Source code in src/pydantic_ome_ngff/v04/axis.py 
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def check_type_unit(model: Axis) -> Axis:
    """
    Check that the `unit` attribute of an `Axis` object is valid.
    This function emits warnings when the `unit` attribute of of an `Axis` object
    is spec-compliant but contravenes a "SHOULD" statement in the spec.
    """

    typ = model.type
    unit = model.unit

    if typ == AxisType.space:
        if unit not in [e.value for e in SpaceUnit]:
            msg = (
                f"Unit '{unit}' is not recognized as a standard unit "
                f"for an axis with type '{typ}'."
            )
            warnings.warn(msg, stacklevel=1)
    elif typ == AxisType.time:
        if unit not in [e.value for e in TimeUnit]:
            msg = (
                f"Unit '{unit}' is not recognized as a standard unit "
                f"for an axis with type '{typ}'."
            )
            warnings.warn(msg, stacklevel=1)
    elif typ == AxisType.channel:
        pass
    elif typ is None:
        msg = (
            f"The `type` field of this axis was set to `None`. Version {model._version} of the OME-NGFF spec states "
            "that the 'type' field of an axis should be set to a string."
        )
        warnings.warn(msg, stacklevel=1)
    else:
        msg = (
            f"Unknown axis type '{typ}'. Version {model._version} of the OME-NGFF "
            " spec states that the 'type' field of an axis should be one of "
            f"{AxisType._member_names_}."
        )
        warnings.warn(msg, stacklevel=1)

    if unit is None:
        msg = (
            f"The `unit` field of this axis was set to `None`. Version {model._version} of the OME-NGFF spec states "
            "that the `unit` field of an axis should be set to a string."
        )
        warnings.warn(msg, stacklevel=1)
    return model