`ngff_zarr.v06.zarr_metadata`¶

Module Contents¶

Classes¶

`Axis`
`CoordinateSystem`
`CoordinateSystemIdentifier`	CoordinateSystemIdentifier field used in transformations metadata.
`BaseTransform`
`Identity`
`Scale`
`Translation`
`Rotation`
`Affine`
`Coordinates`
`Displacements`
`TransformSequence`
`Dataset`	Dataset in the multiscales metadata.
`Metadata`

Data¶

`AxesType`
`Transform`

API¶

ngff_zarr.v06.zarr_metadata.AxesType¶: None

class ngff_zarr.v06.zarr_metadata.Axis¶

name: ngff_zarr.v04.zarr_metadata.SupportedDims¶: None

type: ngff_zarr.v06.zarr_metadata.AxesType¶: None

unit: ngff_zarr.v04.zarr_metadata.Units | None¶: None

orientation: ngff_zarr.rfc4.AnatomicalOrientation | None¶: None

discrete: bool | None¶: None

class ngff_zarr.v06.zarr_metadata.CoordinateSystem¶

name: str¶: None

axes: List[ngff_zarr.v06.zarr_metadata.Axis]¶: None

class ngff_zarr.v06.zarr_metadata.CoordinateSystemIdentifier¶

CoordinateSystemIdentifier field used in transformations metadata.

There, the input/output fields of transformations must be an object with ‘path’ and ‘name’ fields.

path: str | None¶: None

name: str | None¶: None

class ngff_zarr.v06.zarr_metadata.BaseTransform¶

Bases: abc.ABC

input: ngff_zarr.v06.zarr_metadata.CoordinateSystemIdentifier | None¶: None

output: ngff_zarr.v06.zarr_metadata.CoordinateSystemIdentifier | None¶: None

name: str | None¶: None

type: str | None¶: None

to_dict() → dict¶

classmethod from_dict(data: dict) → ngff_zarr.v06.zarr_metadata.BaseTransform¶

class ngff_zarr.v06.zarr_metadata.Identity¶

Bases: ngff_zarr.v06.zarr_metadata.BaseTransform

type: str¶: ‘identity’

class ngff_zarr.v06.zarr_metadata.Scale¶

Bases: ngff_zarr.v06.zarr_metadata.BaseTransform

scale: List[float]¶: None

type: str¶: ‘scale’

class ngff_zarr.v06.zarr_metadata.Translation¶

Bases: ngff_zarr.v06.zarr_metadata.BaseTransform

translation: List[float]¶: None

type: str¶: ‘translation’

class ngff_zarr.v06.zarr_metadata.Rotation¶

Bases: ngff_zarr.v06.zarr_metadata.BaseTransform

rotation: List[List[float]]¶: None

path: str | None¶: None

type: str¶: ‘rotation’

class ngff_zarr.v06.zarr_metadata.Affine¶

Bases: ngff_zarr.v06.zarr_metadata.BaseTransform

affine: List[List[float]]¶: None

path: str | None¶: None

type: str¶: ‘affine’

class ngff_zarr.v06.zarr_metadata.Coordinates¶

Bases: ngff_zarr.v06.zarr_metadata.BaseTransform

path: str¶: None

interpolation: str | None¶: None

type: str¶: ‘coordinates’

class ngff_zarr.v06.zarr_metadata.Displacements¶

Bases: ngff_zarr.v06.zarr_metadata.BaseTransform

path: str¶: None

interpolation: str | None¶: None

type: str¶: ‘displacements’

ngff_zarr.v06.zarr_metadata.Transform¶: None

class ngff_zarr.v06.zarr_metadata.TransformSequence¶

Bases: ngff_zarr.v06.zarr_metadata.BaseTransform

transformations: List[ngff_zarr.v06.zarr_metadata.Transform]¶: None

name: str | None¶: ‘transformSequence’

type: str¶: ‘sequence’

class ngff_zarr.v06.zarr_metadata.Dataset¶

Dataset in the multiscales metadata.

path: Path to the dataset within the Zarr store. coordinateTransformations: List of transformations to map from dataset. Must be one of - Single identity - single scale - sequence of scale and translation

path: str¶: None

coordinateTransformations: List[ngff_zarr.v06.zarr_metadata.Transform]¶: None

class ngff_zarr.v06.zarr_metadata.Metadata¶

coordinateSystems: List[ngff_zarr.v06.zarr_metadata.CoordinateSystem]¶: None

datasets: List[ngff_zarr.v06.zarr_metadata.Dataset]¶: None

coordinateTransformations: List[ngff_zarr.v06.zarr_metadata.Transform] | None¶: None

omero: ngff_zarr.v04.zarr_metadata.Omero | None¶: None

name: str¶: ‘image’

type: str | None¶: None

metadata: ngff_zarr.v04.zarr_metadata.MethodMetadata | None¶: None

extra: dict¶: ‘field(…)’

__post_init__()¶: We use the post-init to do some on-the-fly validation that is not covered by the json schemas well.

property intrinsic_coordinate_system: ngff_zarr.v06.zarr_metadata.CoordinateSystem¶

to_version( version: Union[str, ngff_zarr._supported_versions.NgffVersion], ) → Union[ngff_zarr.v06.zarr_metadata.Metadata, ngff_zarr.v05.zarr_metadata.Metadata, ngff_zarr.v04.zarr_metadata.Metadata]¶

classmethod from_version( metadata: Union[ngff_zarr.v06.zarr_metadata.Metadata, ngff_zarr.v05.zarr_metadata.Metadata, ngff_zarr.v04.zarr_metadata.Metadata], ) → ngff_zarr.v06.zarr_metadata.Metadata¶

_to_v05() → ngff_zarr.v05.zarr_metadata.Metadata¶

classmethod _from_v05( metadata_v05: ngff_zarr.v05.zarr_metadata.Metadata, ) → ngff_zarr.v06.zarr_metadata.Metadata¶

classmethod _from_zarr_attrs( root_attrs: dict, store: ngff_zarr._zarr_types.StoreLike, validate: bool = False, subpath: str | None = None, ) → tuple[ngff_zarr.v06.zarr_metadata.Metadata, list[ngff_zarr.ngff_image.NgffImage]]¶

Create Metadata instance from ome-zarr metadata dictionary.

When the multiscales group is nested inside the store (e.g. a displacement field written next to its image), subpath locates the group so dataset arrays resolve against the right prefix. Dataset paths in the returned metadata stay relative to the group.

classmethod _parse_transforms( transforms: List[dict], coordinateSystems: List[ngff_zarr.v06.zarr_metadata.CoordinateSystem], ) → List[ngff_zarr.v06.zarr_metadata.Transform]¶: Parse a list of possibly nested transformation dictionaries into Transform instances.

property dimension_names: tuple¶

ngff_zarr.v06.zarr_metadata¶

Module Contents¶

Classes¶

Data¶

API¶

`ngff_zarr.v06.zarr_metadata`¶