lamindb.curators.SpatialDataCatManager

class lamindb.curators.SpatialDataCatManager(sdata, var_index, categoricals=None, verbosity='hint', organism=None, sources=None, *, sample_metadata_key='sample')

Bases: CatManager

Categorical manager for SpatialData.

Attributes

property categoricals: dict[str, dict[str, DeferredAttribute]]

Return the categorical keys and fields to validate against.

property non_validated: dict[str, dict[str, list[str]]]

Return the non-validated features and labels.

property var_index: DeferredAttribute

Return the registry fields to validate variables indices against.

Class methods

classmethod from_anndata(data, var_index, categoricals=None, obs_columns=FieldAttr(Feature.name), verbosity='hint', organism=None, sources=None)
Return type:

AnnDataCatManager

classmethod from_df(df, categoricals=None, columns=FieldAttr(Feature.name), verbosity='hint', organism=None)
Return type:

DataFrameCatManager

classmethod from_mudata(mdata, var_index, categoricals=None, verbosity='hint', organism=None)
Return type:

MuDataCatManager

classmethod from_spatialdata(sdata, var_index, categoricals=None, organism=None, sources=None, verbosity='hint', *, sample_metadata_key='sample')
classmethod from_tiledbsoma(experiment_uri, var_index, categoricals=None, obs_columns=FieldAttr(Feature.name), organism=None, sources=None)
Return type:

TiledbsomaCatManager

Methods

add_new_from(key, accessor=None, **kwargs)

Save new values of categorical from sample level metadata or table.

Parameters:

  • key (str) – The key referencing the slot in the DataFrame.

  • accessor (str | None, default: None) – The accessor key such as ‘sample’ or ‘table x’.

  • organism – The organism name.

  • **kwargs – Additional keyword arguments to pass to create new records.

Return type:

None

add_new_from_var_index(table, **kwargs)

Save new values from .var.index of table.

Parameters:

  • table (str) – The table key.

  • organism – The organism name.

  • **kwargs – Additional keyword arguments to pass to create new records.

Return type:

None

lookup(public=False)

Look up categories.

Parameters:

public (bool, default: False) – Whether the lookup is performed on the public reference.

Return type:

CatLookup

save_artifact(*, key=None, description=None, revises=None, run=None)

Save the validated SpatialData store and metadata.

Parameters:

  • description (str | None, default: None) – A description of the dataset.

  • key (str | None, default: None) – A path-like key to reference artifact in default storage, e.g., "myartifact.zarr". Artifacts with the same key form a version family.

  • revises (Artifact | None, default: None) – Previous version of the artifact. Triggers a revision.

  • run (Run | None, default: None) – The run that creates the artifact.

Return type:

Artifact

Returns:

A saved artifact record.

standardize(key, accessor=None)

Replace synonyms with canonical values.

Modifies the dataset inplace.

Parameters:

  • key (str) – The key referencing the slot in the table or sample metadata.

  • accessor (str | None, default: None) – The accessor key such as ‘sample_key’ or ‘table_key’.

Return type:

None

validate()

Validate variables and categorical observations.

This method also registers the validated records in the current instance: - from public sources

Parameters:

organism – The organism name.

Return type:

bool

Returns:

Whether the SpatialData object is validated.