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CopickFilaments

copick.models.CopickFilaments

The traced filaments (ordered centrelines) of one pickable object in one run.

Attributes:

  • run (CopickRun) –

    Reference to the run these filaments belong to.

  • meta (CopickFilamentsFile) –

    The filaments and their metadata. Loaded from storage when CopickFilaments.filaments is first accessed.

__init__ 

__init__(run: CopickRun, file: CopickFilamentsFile)

Parameters:

load 

load() -> CopickFilamentsFile

Load the filaments from storage.

store 

store() -> None

Store the filaments. A curve of a known kind that no longer describes its filament's points is dropped, with a warning, rather than stored.

refresh 

refresh() -> None

Reload the filaments from storage.

delete 

delete() -> None

Delete the filaments.

get 

get(instance_id: int) -> Optional[CopickFilament]

The filament with this instance ID, or None.

instance_ids 

instance_ids() -> np.ndarray

The filaments' instance IDs, in file order.

numpy 

numpy() -> List[np.ndarray]

The centrelines as a list of (M, 3) arrays of [x, y, z] in Angstrom, in file order.

from_numpy 

from_numpy(polylines: List[ndarray], instance_ids: Optional[List[int]] = None, polarity_known: Optional[List[bool]] = None, scores: Optional[List[float]] = None, radii: Optional[List[Optional[float]]] = None, voxel_spacing: Optional[float] = None, metadata: Optional[List[Optional[Dict[str, Any]]]] = None) -> None

Set the filaments from (M, 3) arrays of ordered points in Angstrom, and store them. The filaments have no curves; use from_control_points or from_curves for editable ones.

Parameters:

  • polylines (List[ndarray]) –

    One (M, 3) array per filament, M >= 2, in order along the filament.

  • instance_ids (Optional[List[int]], default: None ) –

    Filament IDs (>= 1, unique). Default 1..K.

  • polarity_known (Optional[List[bool]], default: None ) –

    Per filament, whether the point order follows the polarity. Default False.

  • scores (Optional[List[float]], default: None ) –

    Per filament score. Default 1.0.

  • radii (Optional[List[Optional[float]]], default: None ) –

    Per filament tube radius in Angstrom, or None.

  • voxel_spacing (Optional[float], default: None ) –

    Voxel spacing the filaments were traced in, recorded in the file.

  • metadata (Optional[List[Optional[Dict[str, Any]]]], default: None ) –

    Per filament metadata, or None.

Raises:

  • ValueError –

    If the arguments' lengths differ or a filament is invalid.

from_curves 

from_curves(curves: List[CopickFilamentCurve], instance_ids: Optional[List[int]] = None, polarity_known: Optional[List[bool]] = None, scores: Optional[List[float]] = None, radii: Optional[List[Optional[float]]] = None, voxel_spacing: Optional[float] = None, metadata: Optional[List[Optional[Dict[str, Any]]]] = None) -> None

Set the filaments from curves, regenerating their points, and store them.

Parameters:

  • curves (List[CopickFilamentCurve]) –

    One CopickFilamentCurve (or dict of its fields) per filament, of a known kind; for example CopickFilamentCurve.from_tck(...) for a scipy spline fit.

  • instance_ids, polarity_known, scores, radii, voxel_spacing, metadata –

    As for from_numpy.

from_control_points 

from_control_points(control_points: List[ndarray], instance_ids: Optional[List[int]] = None, step: Optional[float] = None, kind: str = 'catmull-rom', alpha: float = 0.5, polarity_known: Optional[List[bool]] = None, scores: Optional[List[float]] = None, radii: Optional[List[Optional[float]]] = None, voxel_spacing: Optional[float] = None, metadata: Optional[List[Optional[Dict[str, Any]]]] = None) -> None

Set the filaments from traced control points (catmull-rom or linear curves), regenerating their points, and store them.

Parameters:

  • control_points (List[ndarray]) –

    One (n, 3) array per filament, n >= 2, in order along the filament, in Angstrom.

  • instance_ids (Optional[List[int]], default: None ) –

    Filament IDs (>= 1, unique). Default 1..K.

  • step (Optional[float], default: None ) –

    Arc-length spacing of the regenerated points; default voxel_spacing (or the file's).

  • kind (str, default: 'catmull-rom' ) –

    "catmull-rom" or "linear".

  • alpha (float, default: 0.5 ) –

    Catmull-Rom parameterisation.

  • polarity_known, scores, radii, voxel_spacing, metadata –

    As for from_numpy.

control_points 

control_points() -> List[Optional[np.ndarray]]

Per filament, in file order, the (n, 3) control points of its current curve, or None.

editable_curve 

editable_curve(instance_id: int, tolerance: Optional[float] = None, kinds: Iterable[str] = CURVE_KINDS) -> CopickFilamentCurve

CopickFilament.editable_curve for one filament, deriving a curve at the file's voxel spacing: points voxel_spacing apart, within half of it of the stored points.

Raises:

  • KeyError –

    If no filament has this ID.