motile_plugin.data_model.solution_tracks

Classes

SolutionTracks

Difference from Tracks: every node must have a track_id

Module Contents

class motile_plugin.data_model.solution_tracks.SolutionTracks(graph: networkx.DiGraph, segmentation: numpy.ndarray | None = None, time_attr: str = NodeAttr.TIME.value, pos_attr: str | tuple[str] | list[str] = NodeAttr.POS.value, scale: list[float] | None = None, ndim: int | None = None)

Bases: motile_plugin.data_model.tracks.Tracks

Difference from Tracks: every node must have a track_id

max_track_id: int

classmethod from_tracks(tracks: motile_plugin.data_model.tracks.Tracks)

property node_id_to_track_id: dict[motile_plugin.data_model.tracks.Node, int]

get_next_track_id() → int

Return the next available track_id and update self.max_track_id

get_track_id(node) → int

set_track_id(node: motile_plugin.data_model.tracks.Node, value: int)

_initialize_track_ids()

_assign_tracklet_ids()

Add a track_id attribute to a graph by removing division edges, assigning one id to each connected component. Also sets the max_track_id and initializes a dictionary from track_id to nodes

export_tracks(outfile: pathlib.Path | str)

Export the tracks from this run to a csv with the following columns: t,[z],y,x,id,parent_id,track_id Cells without a parent_id will have an empty string for the parent_id. Whether or not to include z is inferred from self.ndim