organoid_tracker.core.position_collection module

class organoid_tracker.core.position_collection.PositionCollection(positions: Iterable[Position] = ())

Bases: object

add(position: Position)

Adds a position, optionally with the given shape. The position must have a time point specified.

add_positions(other: PositionCollection)

Adds all positions and shapes of the other collection to this collection.

contains_position(position: Position) → bool

Returns whether the given position is part of the experiment.

copy() → PositionCollection

Creates a copy of this positions collection. Changes made to the copy will not affect this instance and vice versa.

count_positions(*, time_point: Optional[TimePoint], z: Optional[int])

Counts the number of positions at the given time point and the given z. If no z or time point is given, positions at all time points and/or all z will be counted.

detach_all_for_time_point(time_point: TimePoint)

Removes all positions for a given time point, if any.

detach_position(position: Position)

Removes a position from a time point. Does nothing if the position is not in this collection.

first_time_point() → Optional[TimePoint]

Gets the first time point that contains positions, or None if there are no positions stored.

first_time_point_number() → Optional[int]

Gets the first time point that contains positions, or None if there are no positions stored.

has_positions() → bool

Returns True if there are any positions stored here.

highest_z() → Optional[int]

Returns the lowest z in use, or None if there are no positions in this collection.

last_time_point() → Optional[TimePoint]

Gets the last time point (inclusive) that contains positions, or None if there are no positions stored.

last_time_point_number() → Optional[int]

Gets the last time point (inclusive) that contains positions, or None if there are no positions stored.

lowest_z() → Optional[int]

Returns the lowest z in use, or None if there are no positions in this collection.

move_in_time(time_point_delta: int)

Moves all data with the given time point delta.

move_position(old_position: Position, new_position: Position)

Moves a position, keeping its shape. Does nothing if the position is not in this collection. Raises a value error if the time points the provided positions are None or if they do not match.

nearby_z(z: int) → Iterable[Position]

Returns all positions (for any time point) for which round(position.z) == z.

of_time_point(time_point: TimePoint) → AbstractSet[Position]

Returns all positions for a given time point. Returns an empty set if that time point doesn’t exist.

of_time_point_and_z(time_point: TimePoint, z_min: Optional[int] = None, z_max: Optional[int] = None) → Iterable[Position]

Gets all positions that are nearby the given min to max z, inclusive.

time_points() → Iterable[TimePoint]

Returns all time points that have at least one position.