CopickObject

copick.models.CopickObject

Object that can be picked or segmented in a tomogram.

Attributes:

• meta (PickableObject) –

  Metadata for this object.

• root (CopickRoot) –

  Reference to the root this object belongs to.

• name (str) –

  Name of the object.

• is_particle (bool) –

  Whether this object should be represented by points (True) or segmentation masks (False).

• label (Union[int, None]) –

  Numeric label/id for the object, as used in multilabel segmentation masks. Must be unique.

• color (Union[Tuple[int, int, int, int], None]) –

  RGBA color for the object.

• emdb_id (Union[str, None]) –

  EMDB ID for the object.

• pdb_id (Union[str, None]) –

  PDB ID for the object.

• map_threshold (Union[float, None]) –

  Threshold to apply to the map when rendering the isosurface.

• radius (Union[float, None]) –

  Radius of the particle, when displaying as a sphere.

__init__(root: CopickRoot, meta: PickableObject)

Parameters:

• root(CopickRoot) –

  The copick project root.

• meta (PickableObject) –

  The metadata for this object.

zarr() -> Union[None, MutableMapping]

Override this method to return a zarr store for this object. Should return None if CopickObject.is_particle is False or there is no associated map.

numpy(zarr_group: str = '0', x: slice = slice(None, None), y: slice = slice(None, None), z: slice = slice(None, None)) -> Union[None, np.ndarray]

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

Parameters:

• zarr_group (str, default: '0' ) –

  Zarr group to access.

• x (slice, default: slice(None, None) ) –

  Slice for the x-axis.

• y (slice, default: slice(None, None) ) –

  Slice for the y-axis.

• z (slice, default: slice(None, None) ) –

  Slice for the z-axis.

Returns:

• Union[None, ndarray] –

  np.ndarray: The object as a numpy array.

from_numpy(data: np.ndarray, voxel_size: float, dtype: Optional[np.dtype] = np.float32) -> None

Set the object from a numpy array.

Parameters:

• data (ndarray) –

  The segmentation as a numpy array.

• voxel_size (float) –

  Voxel size of the object.

• dtype (Optional[dtype], default: float32 ) –

  Data type of the segmentation. Default is np.float32.

set_region(data: np.ndarray, zarr_group: str = '0', x: slice = slice(None, None), y: slice = slice(None, None), z: slice = slice(None, None)) -> None

Set a region of the object from a numpy array.

Parameters:

• data (ndarray) –

  The object's subregion as a numpy array.

• zarr_group (str, default: '0' ) –

  Zarr group to access.

• x (slice, default: slice(None, None) ) –

  Slice for the x-axis.

• y (slice, default: slice(None, None) ) –

  Slice for the y-axis.

• z (slice, default: slice(None, None) ) –

  Slice for the z-axis.