Merge pull request #262 from funkelab/55-add-user-defined-groups-for-viewing

55 add user defined groups for viewing

Author: cmalinmayor

src/motile_tracker/application_menus/menu_widget.py

@@ -22,6 +22,7 @@ def __init__(self, viewer: napari.Viewer):
         self.tabwidget.addTab(motile_widget, "Track with Motile")
         self.tabwidget.addTab(tracks_viewer.tracks_list, "Tracks List")
         self.tabwidget.addTab(editing_widget, "Edit Tracks")
+        self.tabwidget.addTab(tracks_viewer.collection_widget, "Groups")
 
         layout = QVBoxLayout()
         layout.addWidget(self.tabwidget)

src/motile_tracker/data_views/views/layers/track_points.py

@@ -232,7 +232,7 @@ def _update_data(self, event: Event):
 
         elif event.action == "removed":
             self.tracks_viewer.tracks_controller.delete_nodes(
-                self.tracks_viewer.selected_nodes._list
+                self.tracks_viewer.selected_nodes.as_list
             )
 
         elif event.action == "changed":
@@ -273,18 +273,24 @@ def get_symbols(self, tracks: Tracks, symbolmap: dict[NodeType, str]) -> list[st
         symbols = [symbolmap[statemap[degree]] for _, degree in tracks.graph.out_degree]
         return symbols
 
-    def update_point_outline(self, visible: list[int] | str) -> None:
+    def update_point_outline(self, visible_nodes: list[int] | str) -> None:
         """Update the outline color of the selected points and visibility according to
         display mode
 
         Args:
-            visible (list[int] | str): A list of track ids, or "all"
+            visible_nodes (list[int] | str): A list of node ids, or "all"
         """
-        # filter out the non-selected tracks if in lineage mode
-        if visible == "all":
+
+        if isinstance(visible_nodes, str):
             self.shown[:] = True
         else:
-            indices = np.where(np.isin(self.properties["track_id"], visible))[
+            # For lineage or group mode, visible_nodes is a list of node IDs
+            # In group mode, also include selected nodes so they remain visible
+            if self.tracks_viewer.mode == "group":
+                visible_nodes = (
+                    list(visible_nodes) + self.tracks_viewer.selected_nodes.as_list
+                )
+            indices = np.where(np.isin(self.properties["node_id"], visible_nodes))[
                 0
             ].tolist()
             self.shown[:] = False

src/motile_tracker/data_views/views/layers/tracks_layer_group.py

@@ -123,12 +123,19 @@ def _refresh(self) -> None:
         if self.points_layer is not None:
             self.points_layer._refresh()
 
-    def update_visible(self, visible_tracks: list[int], visible_nodes: list[int]):
+    def update_visible(self, visible_nodes: list[int] | str):
         if self.seg_layer is not None:
             self.seg_layer.update_label_colormap(visible_nodes)
         if self.points_layer is not None:
-            self.points_layer.update_point_outline(visible_tracks)
+            self.points_layer.update_point_outline(visible_nodes)
         if self.tracks_layer is not None:
+            # Convert node IDs to track IDs for the tracks layer
+            if isinstance(visible_nodes, str):
+                visible_tracks = visible_nodes  # "all"
+            else:
+                visible_tracks = list(
+                    {self.tracks.get_track_id(node) for node in visible_nodes}
+                )
             self.tracks_layer.update_track_visibility(visible_tracks)
 
     def center_view(self, node):