organoid_tracker.core.link_data module

class organoid_tracker.core.link_data.LinkData

Bases: object

Used to supply additional metadata to links.

copy() → LinkData

Creates a copy of this linking dataset. Changes to the copy will not affect this object, and vice versa.

find_all_data_names() → Set[str]

Finds all data_names

find_all_data_of_link(position1: Position, position2: Position) → Iterable[Tuple[str, Union[float, int, str, bool, List[float], List[int], List[str], List[bool]]]]

Finds all data associated with the given link. Raises ValueError if the two positions are not in consecutive time points.

find_all_links_with_data(data_name: str) → ItemsView[Tuple[Position, Position], Union[float, int, str, bool, List[float], List[int], List[str], List[bool]]]

Gets a dictionary of all positions with the given data marker. Do not modify the returned dictionary.

get_link_data(position1: Position, position2: Position, data_name: str) → Optional[Union[float, int, str, bool, List[float], List[int], List[str], List[bool]]]

Gets the attribute of the link with the given name. Returns None if not found. Raises ValueError if the two positions are not in consecutive time points.

has_link_data() → bool

Gets whether there is any link data stored here.

merge_data(other: LinkData)

Merges all data from the given dataset into this one. Changes to the other dataset made afterwards may “write-through” into this dataset.

move_in_time(time_point_delta: int)

Moves all data with the given time point delta.

remove_link(position1: Position, position2: Position)

Removes all data of the given link. Raises ValueError if the two positions are not in consecutive time points.

replace_link(position_old1: Position, position_old2: Position, position_new1: Position, position_new2: Position)

Replaces a link, for example if the position moved. Raises ValueError if any of the two links are not between consecutive time points. Raises ValueError if the time points of the links are changed.

set_link_data(position1: Position, position2: Position, data_name: str, value: Optional[Union[float, int, str, bool, List[float], List[int], List[str], List[bool]]])

Adds or overwrites the given attribute for the given position. Set value to None to delete the attribute. Raises ValueError if the two positions are not in consecutive time points.

Note: this is a low-level API. See the linking_markers module for more high-level methods, for example for how to read end markers, error markers, etc.