Merge pull request #89 from funkelab/bugfixes

Bugfixes - scaling centroid, warn if no tracks found

src/motile_plugin/application_menus/__init__.py

@@ -1,2 +1,3 @@
 from .main_app import MainApp  # noqa
 from .editing_menu import EditingMenu  # noqa
+from .menu_widget import MenuWidget  # noqa

src/motile_plugin/data_model/tracks.py

@@ -638,11 +638,11 @@ def _create_seg_time_to_node(self) -> dict[int, dict[int, Node]]:
 
         for node in self.graph.nodes():
             seg_id = self.get_seg_id(node)
-            if seg_id is None:
+            time = self.get_time(node)
+            if seg_id is None or time is None:
                 continue
             if seg_id not in self.seg_time_to_node:
                 self.seg_time_to_node[seg_id] = {}
-            time = self.get_time(node)
             self.seg_time_to_node[seg_id][time] = node
 
     def _set_node_attr(self, node: Node, attr: NodeAttr, value: Any):
@@ -733,12 +733,13 @@ def _compute_node_attrs(
                 pos = None
             else:
                 seg = self.segmentation[time][0] == seg_id
+                pos_scale = self.scale[1:] if self.scale is not None else None
                 area = np.sum(seg)
-                if self.scale is not None:
-                    area *= np.prod(self.scale)
+                if pos_scale is not None:
+                    area *= np.prod(pos_scale)
                 # only include the position if the segmentation was actually there
                 pos = (
-                    measure.centroid(seg, spacing=self.scale)
+                    measure.centroid(seg, spacing=pos_scale)
                     if area > 0
                     else np.array(
                         [

src/motile_plugin/data_views/views/__init__.py

@@ -1,4 +0,0 @@
-from .tree_view.tree_widget import TreeWidget  # noqa
-from .layers.track_graph import TrackGraph  # noqa
-from .layers.track_labels import TrackLabels  # noqa
-from .layers.track_points import TrackPoints  # noqa

src/motile_plugin/data_views/views_coordinator/__init__.py

@@ -1,2 +0,0 @@
-from .node_selection_list import NodeSelectionList  # noqa
-from .tracks_viewer import TracksViewer  # noqa

src/motile_plugin/motile/backend/solve.py

@@ -16,7 +16,6 @@
     get_candidate_graph_from_points_list,
     graph_to_nx,
 )
-from motile_toolbox.visualization.napari_utils import assign_tracklet_ids
 
 from .solver_params import SolverParams
 
@@ -71,7 +70,8 @@ def solve(
 
     solution_graph = solver.get_selected_subgraph(solution=solution)
     solution_nx_graph = graph_to_nx(solution_graph)
-    solution_nx_graph, _, _ = assign_tracklet_ids(solution_nx_graph)
+    logger.debug("Solution graph has %d nodes", solution_nx_graph.number_of_nodes())
+    # solution_nx_graph, _, _ = assign_tracklet_ids(solution_nx_graph)
     return solution_nx_graph
 
 

src/motile_plugin/motile/menus/motile_widget.py

@@ -166,13 +166,18 @@ def solve_with_motile(self, run: MotileRun) -> MotileRun:
             lambda event_data: self._on_solver_event(run, event_data),
             scale=run.scale,
         )
+
+        run._initialize_track_ids()
         if run.input_segmentation is not None:
             run.segmentation = self.relabel_segmentation(
                 run.graph, run.input_segmentation
             )
-
         run._create_seg_time_to_node()
-        run._initialize_track_ids()
+
+        if run.graph.number_of_nodes() == 0:
+            show_warning(
+                "No tracks found - try making your edge selection value more negative"
+            )
         return run
 
     def _on_solver_event(self, run: MotileRun, event_data: dict) -> None: