CopickPicks

copick.models.CopickPicks

Encapsulates all data pertaining to a specific set of picked points. This includes the locations, orientations, and other metadata for the set of points.

Attributes:

• run (CopickRun) –

  Reference to the run this pick belongs to.

• meta (CopickPicksFile) –

  Metadata for this pick.

• points (List[CopickPoint]) –

  Points for this pick. Either populated from storage or lazily loaded when CopickPicks.points is accessed for the first time.

• from_tool (bool) –

  Flag to indicate if this pick was generated by a tool.

• pickable_object_name (str) –

  Pickable object name from CopickConfig.pickable_objects[...].name

• user_id (str) –

  Unique identifier for the user or tool name.

• session_id (str) –

  Unique identifier for the pick session

• trust_orientation (bool) –

  Flag to indicate if the angles are known for this pick or should be ignored.

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

  Color of the pickable object this pick belongs to.

__init__

__init__(run: CopickRun, file: CopickPicksFile)

Parameters:

• run (CopickRun) –

  Reference to the run this pick belongs to.

• file (CopickPicksFile) –

  Metadata for this set of points.

load

load() -> CopickPicksFile

Load the points from storage.

Returns:

• CopickPicksFile ( CopickPicksFile ) –

  The loaded points.

store

store()

Store the points (set using CopickPicks.points property).

refresh

refresh() -> None

Refresh the points from storage.

delete

delete() -> None

Delete the pick record.

numpy

numpy() -> Tuple[np.ndarray, np.ndarray]

Return the points as a [N, 3] numpy array (N, [x, y, z]) and the transforms as a [N, 4, 4] numpy array. Format of the transforms is:

[[rxx, rxy, rxz, tx],
 [ryx, ryy, ryz, ty],
 [rzx, rzy, rzz, tz],
 [  0,   0,   0,  1]]

Returns:

• Tuple[ndarray, ndarray] –

  Tuple[np.ndarray, np.ndarray]: The picks and transforms as numpy arrays.

from_numpy

from_numpy(positions: ndarray, transforms: Optional[ndarray] = None) -> None

Set the points and transforms from numpy arrays.

Parameters:

• positions (ndarray) –

  [N, 3] numpy array of positions (N, [x, y, z]).

• transforms (Optional[ndarray], default: None ) –

  [N, 4, 4] numpy array of orientations. If None, transforms will be set to the identity matrix. Format of the transforms is:

  [[rxx, rxy, rxz, tx],
   [ryx, ryy, ryz, ty],
   [rzx, rzy, rzz, tz],
   [  0,   0,   0,  1]]
  

df

df(format: str = 'relion') -> pd.DataFrame

Returns the points as a pandas DataFrame with columns based on the format.

from_df

from_df(df: DataFrame, format: str = 'relion') -> None

Set the points from a pandas DataFrame with columns based on the format.