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CopickFeatures

copick.models.CopickFeatures

Encapsulates all data pertaining to a specific feature map, i.e. the Zarr-store for the feature map.

Attributes:

  • tomogram (CopickTomogram) –

    Reference to the tomogram this feature map belongs to.

  • meta (CopickFeaturesMeta) –

    Metadata for this feature map.

  • tomo_type (str) –

    Type of the tomogram that the features were computed on.

  • feature_type (str) –

    Type of the features contained.

__init__(tomogram: CopickTomogram, meta: CopickFeaturesMeta)

Parameters:

zarr() -> MutableMapping

Override to return the Zarr store for this feature set. Also needs to handle creating the store if it doesn't exist.

numpy(zarr_group: str = '0', slices: Tuple[slice, ...] = None) -> np.ndarray

Returns the content of the Zarr-File for this feature map as a numpy array. Multiscale group and slices are supported.

Parameters:

  • zarr_group (str, default: '0' ) –

    Zarr group to access.

  • slices (Tuple[slice, ...], default: None ) –

    Tuple of slices for the axes.

Returns:

  • ndarray –

    np.ndarray: The object as a numpy array.

set_region(data: np.ndarray, zarr_group: str = '0', slices: Tuple[slice, ...] = None) -> None

Set the content of the Zarr-File for this feature map from a numpy array. Multiscale group and slices are supported.

Parameters:

  • data (ndarray) –

    The data to set.

  • zarr_group (str, default: '0' ) –

    Zarr group to access.

  • slices (Tuple[slice, ...], default: None ) –

    Tuple of slices for the axes.