CopickPicksFile
copick.models.CopickPicksFile
Bases: BaseModel
Datamodel for a collection of locations, orientations and other metadata for one pickable object.
Attributes:
-
pickable_object_name(str) –Pickable object name from CopickConfig.pickable_objects[X].name
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user_id(str) –Unique identifier for the user or tool name.
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session_id(Union[str, Literal['0']]) –Unique identifier for the pick session (prevent race if they run multiple instances of napari, ChimeraX, etc.) If it is 0, this pick was generated by a tool.
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run_name(Optional[str]) –Name of the run this pick belongs to.
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voxel_spacing(Optional[float]) –Voxel spacing for the tomogram this pick belongs to.
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unit(str) –Unit for the location of the pick.
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points(List[CopickPoint]) –References to the points for this pick.
-
trust_orientation(Optional[bool]) –Flag to indicate if the angles are known for this pick or should be ignored.
pickable_object_name: str
user_id: str
session_id: Union[str, Literal['0']]
run_name: Optional[str] = None
voxel_spacing: Optional[float] = None
unit: str = 'angstrom'
points: Optional[List[CopickPoint]] = None
trust_orientation: Optional[bool] = True
copick.models.CopickPoint
Bases: BaseModel
Point in 3D space with an associated orientation, score value and instance ID.
Attributes:
-
location(CopickLocation) –Location in 3D space.
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transformation(ndarray) –Transformation matrix.
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instance_id(Optional[int]) –Instance ID.
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score(Optional[float]) –Score value.
location: CopickLocation
transformation_: Optional[List[List[float]]] = [[1.0, 0.0, 0.0, 0.0], [0.0, 1.0, 0.0, 0.0], [0.0, 0.0, 1.0, 0.0], [0.0, 0.0, 0.0, 1.0]]
instance_id: Optional[int] = 0
score: Optional[float] = 1.0
model_config = {'arbitrary_types_allowed': True}
transformation: np.ndarray
The transformation necessary to transform coordinates from the object space to the tomogram space.
Returns:
-
ndarray–np.ndarray: 4x4 transformation matrix.
validate_transformation(v) -> List[List[float]]
Validate the transformation matrix.