Merge pull request #6 from funkelab/tracks_layer_update

Use single attribute for location when making tracks layer

src/motile_toolbox/visualization/napari_utils.py

@@ -1,6 +1,8 @@
 import networkx as nx
 import numpy as np
 
+from motile_toolbox.candidate_graph import NodeAttr
+
 
 def assign_tracklet_ids(graph: nx.DiGraph) -> nx.DiGraph:
     """Add a tracklet_id attribute to a graph by removing division edges,
@@ -36,17 +38,17 @@ def assign_tracklet_ids(graph: nx.DiGraph) -> nx.DiGraph:
 
 
 def to_napari_tracks_layer(
-    graph, frame_key="t", location_keys=("y", "x"), properties=()
+    graph, frame_key=NodeAttr.TIME.value, location_key=NodeAttr.POS.value, properties=()
 ):
     """Function to take a networkx graph and return the data needed to add to
     a napari tracks layer.
 
     Args:
         graph (nx.DiGraph): _description_
         frame_key (str, optional): Key in graph attributes containing time frame.
-            Defaults to "t".
-        location_keys (tuple, optional): Keys in graph node attributes containing
-            location. Should be in order: (Z), Y, X. Defaults to ("y", "x").
+            Defaults to NodeAttr.TIME.value.
+        location_key (str, optional): Key in graph node attributes containing
+            location. Defaults to NodeAttr.POS.value.
         properties (tuple, optional): Keys in graph node attributes to add
             to the visualization layer. Defaults to (). NOTE: not working now :(
 
@@ -65,13 +67,16 @@ def to_napari_tracks_layer(
             case of track splitting, or more than one (the track has multiple
             parents, but only one child) in the case of track merging.
     """
-    napari_data = np.zeros((graph.number_of_nodes(), len(location_keys) + 2))
+    for _, loc in graph.nodes(data=location_key):
+        ndim = len(loc)
+        break
+    napari_data = np.zeros((graph.number_of_nodes(), ndim + 2))
     napari_properties = {prop: np.zeros(graph.number_of_nodes()) for prop in properties}
     napari_edges = {}
     graph, intertrack_edges = assign_tracklet_ids(graph)
     for index, node in enumerate(graph.nodes(data=True)):
         node_id, data = node
-        location = [data[loc_key] for loc_key in location_keys]
+        location = data[location_key]
         napari_data[index] = [data["tracklet_id"], data[frame_key], *location]
         for prop in properties:
             if prop in data: