organoid_tracker.core.beacon_collection module

class organoid_tracker.core.beacon_collection.Beacon(position: Position, beacon_type: Optional[str])

Bases: NamedTuple

A beacon is a named point in space.

beacon_type: Optional[str]: Alias for field number 1

position: Position: Alias for field number 0

class organoid_tracker.core.beacon_collection.BeaconCollection

Bases: object

Ordered list of beacons per time point.

add(position: Position, beacon_type: Optional[str] = None): Adds a new beacon. If there is already a beacon at the given position, it is overwritten.

add_beacons(beacons: BeaconCollection): Adds all beacons from the given collection to this collection.

contains_position(beacon: Position) → bool: Gets whether the given beacon exists in this collection.

count_beacons_at_time_point(time_point: TimePoint) → int: Gets the number of beacons at the given time point.

find_closest_beacon(position: Position, resolution: ImageResolution) → Optional[ClosestBeacon]: Finds the closest beacon at the same time point as the position. Returns None if there are no beacons at that time point.

find_single_beacon() → Optional[Position]: If there is only one beacon in the entire experiment, return it. Otherwise, it returns None.

find_single_beacon_of_time_point(time_point: TimePoint) → Optional[Position]: If there is only one beacon in the given time point, return it. Otherwise, it returns None.

get_beacon_type(beacon_position: Position) → Optional[str]: Gets the name of the beacon at the given position.

has_beacons() → bool: Checks whether there are any beacons stored.

move(old_position: Position, new_position: Position) → bool: Moves a beacon from its old to its new position. The old and new positions must have the same time point. Does nothing and returns False if there was no beacon at old_position. Returns True if successful.

move_in_time(time_point_delta: int): Moves all data with the given time point delta.

of_time_point(time_point: TimePoint) → Iterable[Position]: Gets all beacons at the given time point.

of_time_point_with_type(time_point: TimePoint) → Iterable[Beacon]: Gets all beacons at the given time point, including their beacon types.

remove(position: Position) → bool: Removes the beacon at the given position. Returns True if succesful, returns False if there was no beacon at that position.

set_beacon_type(beacon_position: Position, name: Optional[str]): Sets the name of the beacon at the given position. Does nothing if there is no beacon at that position.

time_points() → Iterable[TimePoint]: Gets all used time points.

class organoid_tracker.core.beacon_collection.ClosestBeacon(search_position: Position, beacon_position: Position, beacon_type: Optional[str], distance_um: float, resolution: ImageResolution)

Bases: object

Used to represent the distance towards, the identity and the position of the closest beacon.

property beacon: Beacon: Gets the beacon as a Beacon object.

beacon_index: int

beacon_position: Position

beacon_type: str

difference_um() → Vector3: Gets the difference between the search position and the beacon position in micrometers.

distance_um: float

resolution: ImageResolution

search_position: Position