napari_track_edit.data_views.views.tree_view.tree_widget_utils

Functions

get_tracklets(→ list[set[int]])

Group nodes into tracklets by BFS, cutting at division nodes.

extract_sorted_tracks(→ pandas.DataFrame | None)

Extract the information of individual tracks required for constructing the tree

find_root(→ int)

Function to find the root associated with a track by tracing its lineage

order_roots_by_prev(→ list[int])

Order a list of root nodes by the previous order, insert missing orders immediately

get_sorted_track_ids(→ list[Any])

Extract the lineage tree plot order of the tracklet_ids on the graph, ensuring that

extract_lineage_tree(→ list[str])

Extract the entire lineage tree including horizontal relations for a given node

get_features_from_tracks(→ list[str])

Extract the regionprops feature display names currently activated on Tracks.

Module Contents

napari_track_edit.data_views.views.tree_view.tree_widget_utils.get_tracklets(parent_to_children: dict[int, list[int]], child_to_parent: dict[int, int], node_ids: list[int], dividing_node_set: set[int], node_to_track_id: dict[int, int]) → list[set[int]]

Group nodes into tracklets by BFS, cutting at division nodes.

A tracklet is a maximal linear segment of the track graph — it does not cross a division point. The returned sets contain node IDs; callers are responsible for sorting by time if needed.

Parameters:

  • parent_to_children – maps each parent node_id to its list of child node_ids.

  • child_to_parent – maps each child node_id to its single parent node_id.

  • node_ids – all node IDs to partition.

  • dividing_node_set – set of node IDs that have ≥2 children (division nodes).

  • node_to_track_id – maps each node_id to its pre-computed tracklet ID.

Returns:

List of sets, one set of node IDs per tracklet.

napari_track_edit.data_views.views.tree_view.tree_widget_utils.extract_sorted_tracks(tracks: funtracks.data_model.Tracks, colormap: napari_track_edit.data_views.colormap.TrackColormap, prev_axis_order: list[int] | None = None) → pandas.DataFrame | None

Extract the information of individual tracks required for constructing the tree plot. Follows the same logic as the relabel_segmentation function from the Motile toolbox.

Parameters:

  • tracks (funtracks.data_model.Tracks) – A tracks object containing a graph to be converted into a dataframe.

  • colormap (TrackColormap) – Colors tree-view nodes per node via colormap.get_colors(node_ids), so the tree follows whichever feature the colormap is coloring by, like every other view.

  • prev_axis_order (list[int], Optional)

Returns:

data frame with all the information needed to construct the tree plot. Columns are: ‘t’, ‘node_id’, ‘track_id’, ‘color’, ‘x’, ‘y’, (‘z’), ‘index’, ‘parent_id’, ‘parent_track_id’, ‘state’, ‘symbol’, and ‘x_axis_pos’

Return type:

pd.DataFrame | None

napari_track_edit.data_views.views.tree_view.tree_widget_utils.find_root(track_id: int, parent_map: dict) → int

Function to find the root associated with a track by tracing its lineage

napari_track_edit.data_views.views.tree_view.tree_widget_utils.order_roots_by_prev(prev_axis_order: list[int], roots: list[int]) → list[int]

Order a list of root nodes by the previous order, insert missing orders immediately to the right of the closest smaller numerical element.

Parameters:

  • prev_axis_order (list[int]) – the previous order of root nodes.

  • roots (list[int]) – the to be sorted list of root nodes.

Returns:

sorted list of root nodes.

Return type:

list[int]

napari_track_edit.data_views.views.tree_view.tree_widget_utils.get_sorted_track_ids(node_ids: list[int], node_to_track_id: dict, child_to_parent: dict[int, int], parent_to_children: dict[int, list[int]], prev_axis_order: list[int] | None = None) → list[Any]

Extract the lineage tree plot order of the tracklet_ids on the graph, ensuring that each tracklet_id is placed in between its daughter tracklet_ids and adjacent to its parent track id.

Parameters:

  • node_ids – list of all node IDs.

  • node_to_track_id (dict) – precomputed mapping from node_id to track_id.

  • child_to_parent – precomputed mapping from child node_id to parent node_id.

  • parent_to_children – precomputed mapping from parent node_id to child node_ids.

  • prev_axis_order (list[int], Optional)

Returns:

list[Any] of ordered tracklet_ids.

napari_track_edit.data_views.views.tree_view.tree_widget_utils.extract_lineage_tree(graph: tracksdata.GraphView, node_id: str) → list[str]

Extract the entire lineage tree including horizontal relations for a given node

napari_track_edit.data_views.views.tree_view.tree_widget_utils.get_features_from_tracks(tracks: funtracks.data_model.Tracks | None = None, features_to_ignore: list[str] | None = None) → list[str]

Extract the regionprops feature display names currently activated on Tracks.

Parameters:

tracks (Tracks | None) – the Tracks instance to extract features from

Returns:

list of the feature names to plot, or an empty list if tracks is None

Return type:

features_to_plot (list[str])