AtlasPackagingData#

class brainglobe_atlasapi.atlas_generation.atlas_packaging_data.AtlasPackagingData(atlas_name: str, atlas_version: str, citation: str, atlas_link: str, species: str, resolution: ~typing.Tuple[int | float, int | float, int | float] | ~typing.List[~typing.Tuple[int | float, int | float, int | float]], root_id: int, working_dir: ~pathlib.Path, reference_stack: str | ~pathlib.Path | ~numpy.ndarray[tuple[~typing.Any, ...], ~numpy.dtype[~numpy._typing._array_like._ScalarT]] | ~typing.List[str | ~pathlib.Path | ~numpy.ndarray[tuple[~typing.Any, ...], ~numpy.dtype[~numpy._typing._array_like._ScalarT]]], annotation_stack: str | ~pathlib.Path | ~numpy.ndarray[tuple[~typing.Any, ...], ~numpy.dtype[~numpy._typing._array_like._ScalarT]] | ~typing.List[str | ~pathlib.Path | ~numpy.ndarray[tuple[~typing.Any, ...], ~numpy.dtype[~numpy._typing._array_like._ScalarT]]], structures_list: ~typing.List[~typing.Dict], meshes_dict: ~typing.Dict[int | str, str | ~pathlib.Path], template_info: ~brainglobe_atlasapi.atlas_generation.atlas_packaging_data.TemplateInfo, annotation_info: ~brainglobe_atlasapi.atlas_generation.atlas_packaging_data.AnnotationInfo, terminology_info: ~brainglobe_atlasapi.atlas_generation.atlas_packaging_data.TerminologyInfo, coordinate_space_info: ~brainglobe_atlasapi.atlas_generation.atlas_packaging_data.CoordinateSpaceInfo, orientation: str = 'asr', space_convention: ~brainglobe_space.core.AnatomicalSpace | None = None, atlas_version_underscore: str | None = None, atlas_packager: str | None = None, hemispheres_stack: str | ~pathlib.Path | ~numpy.ndarray[tuple[~typing.Any, ...], ~numpy.dtype[~numpy._typing._array_like._ScalarT]] | ~typing.List[str | ~pathlib.Path | ~numpy.ndarray[tuple[~typing.Any, ...], ~numpy.dtype[~numpy._typing._array_like._ScalarT]]] = None, additional_references: ~typing.List[~typing.Tuple[~brainglobe_atlasapi.atlas_generation.atlas_packaging_data.TemplateInfo, str | ~pathlib.Path | ~numpy.ndarray[tuple[~typing.Any, ...], ~numpy.dtype[~numpy._typing._array_like._ScalarT]] | ~typing.List[str | ~pathlib.Path | ~numpy.ndarray[tuple[~typing.Any, ...], ~numpy.dtype[~numpy._typing._array_like._ScalarT]]]]] = <factory>, additional_metadata: ~typing.Dict = <factory>)[source]#

Bases: object

Container for all data required to package a BrainGlobe atlas.

This dataclass is an internal implementation detail of the atlas packaging pipeline. It collects all atlas data in one place to avoid threading individual arguments through many function signatures.

atlas_name#

Atlas name in the form author_species.

Type:: str

atlas_minor_version#

Minor version number for this particular atlas.

Type:: int or str

citation#

Citation for the atlas, if unpublished specify “unpublished”.

Type:: str

atlas_link#

Valid URL for the atlas.

Type:: str

species#

Species name formatted as “CommonName (Genus species)”.

Type:: str

resolution#

Resolution on three axes, or a list of such tuples for multi-scale.

Type:: Resolution | ResolutionList

orientation#

Orientation of the original atlas (tuple describing origin for BGSpace).

Type:: str

root_id#

Id of the root element of the atlas.

Type:: int

reference_stack#

Reference stack for the atlas. If str or Path, will be read with tifffile. If list, should be ordered from highest to lowest resolution.

Type:: ValidComponentData

annotation_stack#

Annotation stack for the atlas. If str or Path, will be read with tifffile. If list, should be ordered from highest to lowest resolution.

Type:: ValidComponentData

structures_list#

List of valid dictionaries for structures.

Type:: List[Dict]

meshes_dict#

Dict of meshio-compatible mesh file paths in the form {struct_id: meshpath}.

Type:: Dict[int | str, str | Path]

atlas_packager#

Credit for those responsible for converting the atlas into the BrainGlobe format.

Type:: str, optional

hemispheres_stack#

Hemisphere stack for the atlas. If None, atlas is assumed symmetric.

Type:: ValidComponentData, optional

additional_references#

List of tuples containing metadata and arrays for secondary templates.

Type:: List[Tuple[TemplateInfo, ValidComponentData]], optional

additional_metadata#

Additional metadata to write to metadata.json.

Type:: Dict, optional

symmetric#

Whether the atlas is symmetric across the midline.

Type:: bool, optional

Attributes

`atlas_packager`
`atlas_version_underscore`
`hemispheres_stack`
`orientation`
`space_convention`
`atlas_name`
`atlas_version`
`citation`
`atlas_link`
`species`
`resolution`
`root_id`
`working_dir`
`reference_stack`
`annotation_stack`
`structures_list`
`meshes_dict`
`template_info`
`annotation_info`
`terminology_info`
`coordinate_space_info`
`additional_references`
`additional_metadata`