`ngff_zarr.v04.zarr_metadata`¶

Module Contents¶

Classes¶

`Axis`
`Identity`
`Scale`
`Translation`
`Dataset`
`OmeroWindow`
`OmeroChannel`
`Omero`
`MethodMetadata`
`PlateAcquisition`
`PlateColumn`
`PlateRow`
`PlateWell`
`Plate`
`WellImage`
`Well`
`Metadata`

Functions¶

`is_dimension_supported`	Helper for string validation
`is_unit_supported`	Helper for string validation
`_get_axis_fields`	Get the set of valid field names for the Axis dataclass.
`_filter_axis_dict`	Filter an axis dictionary to only include valid Axis fields.

Data¶

`logger`
`SupportedDims`
`SpatialDims`
`AxesType`
`SpaceUnits`
`TimeUnits`
`Units`
`supported_dims`
`space_units`
`time_units`
`Transform`
`_MULTISCALE_ENTRY_FIELDS`

API¶

ngff_zarr.v04.zarr_metadata.logger¶: ‘getLogger(…)’

ngff_zarr.v04.zarr_metadata.SupportedDims¶: None

ngff_zarr.v04.zarr_metadata.SpatialDims¶: None

ngff_zarr.v04.zarr_metadata.AxesType¶: None

ngff_zarr.v04.zarr_metadata.SpaceUnits¶: None

ngff_zarr.v04.zarr_metadata.TimeUnits¶: None

ngff_zarr.v04.zarr_metadata.Units¶: None

ngff_zarr.v04.zarr_metadata.supported_dims¶: [‘x’, ‘y’, ‘z’, ‘c’, ‘t’]

ngff_zarr.v04.zarr_metadata.space_units¶: [‘angstrom’, ‘attometer’, ‘centimeter’, ‘decimeter’, ‘exameter’, ‘femtometer’, ‘foot’, ‘gigameter’, …

ngff_zarr.v04.zarr_metadata.time_units¶: [‘attosecond’, ‘centisecond’, ‘day’, ‘decisecond’, ‘exasecond’, ‘femtosecond’, ‘gigasecond’, ‘hectos…

ngff_zarr.v04.zarr_metadata.is_dimension_supported(dim: str) → bool¶: Helper for string validation

ngff_zarr.v04.zarr_metadata.is_unit_supported(unit: str) → bool¶: Helper for string validation

ngff_zarr.v04.zarr_metadata._get_axis_fields() → set[str]¶

Get the set of valid field names for the Axis dataclass.

Cached to avoid repeated introspection.

ngff_zarr.v04.zarr_metadata._filter_axis_dict(axis_dict: dict) → dict¶

Filter an axis dictionary to only include valid Axis fields.

Logs a warning if unknown fields are encountered.

Raises: ValueError: If required fields ‘name’ or ‘type’ are missing from the axis dictionary.

class ngff_zarr.v04.zarr_metadata.Axis¶

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

type: ngff_zarr.v04.zarr_metadata.AxesType¶: None

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

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

class ngff_zarr.v04.zarr_metadata.Identity¶

type: str¶: ‘identity’

class ngff_zarr.v04.zarr_metadata.Scale¶

scale: list[float]¶: None

type: str¶: ‘scale’

class ngff_zarr.v04.zarr_metadata.Translation¶

translation: list[float]¶: None

type: str¶: ‘translation’

ngff_zarr.v04.zarr_metadata.Transform¶: None

class ngff_zarr.v04.zarr_metadata.Dataset¶

path: str¶: None

coordinateTransformations: list[ngff_zarr.v04.zarr_metadata.Transform]¶: None

class ngff_zarr.v04.zarr_metadata.OmeroWindow¶

min: float¶: None

max: float¶: None

start: float¶: None

end: float¶: None

class ngff_zarr.v04.zarr_metadata.OmeroChannel¶

color: str¶: None

window: ngff_zarr.v04.zarr_metadata.OmeroWindow¶: None

label: str | None¶: None

validate_color()¶

class ngff_zarr.v04.zarr_metadata.Omero¶

channels: list[ngff_zarr.v04.zarr_metadata.OmeroChannel]¶: None

class ngff_zarr.v04.zarr_metadata.MethodMetadata¶

description: str¶: None

method: str¶: None

version: str¶: None

class ngff_zarr.v04.zarr_metadata.PlateAcquisition¶

id: int¶: None

name: str | None¶: None

maximumfieldcount: int | None¶: None

description: str | None¶: None

starttime: int | None¶: None

endtime: int | None¶: None

class ngff_zarr.v04.zarr_metadata.PlateColumn¶

name: str¶: None

class ngff_zarr.v04.zarr_metadata.PlateRow¶

name: str¶: None

class ngff_zarr.v04.zarr_metadata.PlateWell¶

path: str¶: None

rowIndex: int¶: None

columnIndex: int¶: None

class ngff_zarr.v04.zarr_metadata.Plate¶

columns: list[ngff_zarr.v04.zarr_metadata.PlateColumn]¶: None

rows: list[ngff_zarr.v04.zarr_metadata.PlateRow]¶: None

wells: list[ngff_zarr.v04.zarr_metadata.PlateWell]¶: None

version: str¶: ‘0.4’

acquisitions: list[ngff_zarr.v04.zarr_metadata.PlateAcquisition] | None¶: None

field_count: int | None¶: None

name: str | None¶: None

class ngff_zarr.v04.zarr_metadata.WellImage¶

path: str¶: None

acquisition: int | None¶: None

class ngff_zarr.v04.zarr_metadata.Well¶

images: list[ngff_zarr.v04.zarr_metadata.WellImage]¶: None

version: str¶: ‘0.4’

ngff_zarr.v04.zarr_metadata._MULTISCALE_ENTRY_FIELDS¶: ‘frozenset(…)’

class ngff_zarr.v04.zarr_metadata.Metadata¶

axes: list[ngff_zarr.v04.zarr_metadata.Axis]¶: None

datasets: list[ngff_zarr.v04.zarr_metadata.Dataset]¶: None

coordinateTransformations: list[ngff_zarr.v04.zarr_metadata.Transform] | None¶: None

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

name: str¶: ‘image’

version: str¶: ‘0.4’

type: str | None¶: None

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

extra: dict¶: ‘field(…)’

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

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

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

classmethod _from_v05( metadata_v05: ngff_zarr.v05.zarr_metadata.Metadata, ) → ngff_zarr.v04.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.v04.zarr_metadata.Metadata, list[ngff_zarr.ngff_image.NgffImage]]¶

Create Metadata instance from ome-zarr metadata dictionary.

Parameters

root_attrs : dict The root attributes dictionary store : StoreLike The zarr store validate : bool Whether to validate the metadata subpath : str, optional Sub-path within the store for HCS well/image access (e.g., ‘A/1/0’)

property dimension_names: tuple¶

ngff_zarr.v04.zarr_metadata¶