`ngff_zarr.v06.zarr_metadata`¶

Module Contents¶

Classes¶

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

Data¶

Transform

API¶

class ngff_zarr.v06.zarr_metadata.CoordinateSystem¶

name: str¶: None

axes: List[ngff_zarr.v04.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’

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, ) → tuple[ngff_zarr.v06.zarr_metadata.Metadata, list[ngff_zarr.ngff_image.NgffImage]]¶: Create Metadata instance from ome-zarr metadata dictionary.

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`¶