v1.1 cleanup

docs/source/getting_started.rst

@@ -104,8 +104,8 @@ It contains the following:
   If your input was a Points layer, the ``node_id`` is simply the index of the
   node in the list of points.
     - Note: This does not save the output segmentation. If you want to save
-  the relabeled segmentation, you can do so through napari by selecting the
-  layer and then selecting ``File``-> ``Save selected layers``
+    the relabeled segmentation, you can do so through napari by selecting the
+    layer and then selecting ``File``-> ``Save selected layers``
 - The ``Back to editing`` button, which will return you to the ``Run Editor`` in its
   previous state.
 - The ``Edit this run`` button. This button will take you back to the ``Run Editor``,
@@ -126,11 +126,7 @@ previous sessions do not appear here until you load them from disk with the
 
 The tracking results can also be visualized as a lineage tree.
 You can open the lineage tree widget via ``Plugins`` > ``Motile`` > ``Lineage View``.
-For more details, go to `this docs page`_.
+For more details, go to the :doc:`Tree View <tree_view>` documentation.
 
-
-
-.. _here: docs/source/key_bindings.rst
-.. _this docs page: docs/source/tree_view.rst
 .. _Issue #48: https://github.com/funkelab/motile_napari_plugin/issues/48
 .. _Cell Tracking Challenge: https://celltrackingchallenge.net/

src/motile_plugin/layers/track_graph.py

@@ -20,11 +20,7 @@ def __init__(
         name: str,
         colormap: CyclicLabelColormap,
     ):
-        if tracks is None or tracks.graph is None:
-            graph = nx.DiGraph()
-        else:
-            graph = tracks.graph
-
+        graph = nx.DiGraph() if tracks.graph is None else tracks.graph
         track_data, track_props, track_edges = to_napari_tracks_layer(
             graph, frame_key=tracks.time_attr, location_key=tracks.pos_attr
         )
@@ -40,6 +36,7 @@ def __init__(
 
         self.viewer = viewer
         self.colormaps_dict["track_id"] = colormap
+        self.colormap = "turbo"  # just to refresh the colormap
 
         self.tracks_layer_graph = copy.deepcopy(self.graph)  # for restoring graph later
 
@@ -63,6 +60,7 @@ def update_track_visibility(self, visible: list[int] | str) -> None:
             self.track_colors[:, 3] = 0
             self.track_colors[track_id_mask, 3] = 1
             if len(self.graph.items()) == 0:
-                self.display_graph = False  # empty dicts to not trigger update (bug?) so disable the graph entirely as a workaround
+                self.display_graph = False  # empty dicts to not trigger update (bug?)
+                # so disable the graph entirely as a workaround
             else:
                 self.display_graph = True

src/motile_plugin/utils/relabel_segmentation.py

@@ -30,7 +30,7 @@ def relabel_segmentation(
         previous_seg_id = solution_nx_graph.nodes[node][NodeAttr.SEG_ID.value]
         assert previous_seg_id != 0
         tracklet_id = solution_nx_graph.nodes[node]["tracklet_id"]
-        hypothesis_id = solution_nx_graph.nodes[node].get([NodeAttr.SEG_HYPO.value], 0)
+        hypothesis_id = solution_nx_graph.nodes[node].get(NodeAttr.SEG_HYPO.value, 0)
         previous_seg_mask = segmentation[time_frame, hypothesis_id] == previous_seg_id
         tracked_masks[time_frame, 0][previous_seg_mask] = tracklet_id
     return tracked_masks

src/motile_plugin/widgets/tracks_view/tree_widget.py

@@ -47,10 +47,7 @@ def mouseDragEvent(self, ev, axis=None):
             # Otherwise, disable rectangular zoom mode
             self.setMouseMode(self.PanMode)
 
-        if (
-            axis is not None
-            and ev.button() == QtCore.Qt.MouseButton.RightButton
-        ):
+        if axis is not None and ev.button() == QtCore.Qt.MouseButton.RightButton:
             ev.ignore()
         else:
             pg.ViewBox.mouseDragEvent(self, ev, axis=axis)
@@ -99,8 +96,8 @@ def update(
             feature (str): The feature to be plotted ('tree' or 'area')
             selected_nodes (list[Any]): The currently selected nodes to be highlighted
         """
-        self.set_data(track_df, feature)
         self.set_view(view_direction, feature)
+        self.set_data(track_df, feature)
         self._update_viewed_data()  # this can be expensive
         self.set_selection(selected_nodes, feature)
 
@@ -112,7 +109,7 @@ def set_view(self, view_direction: str, feature: str):
 
         Args:
             view_direction (str): "horizontal" or "vertical"
-            feature (str): the feature being displayed, it can be either 'tree' or 'area'
+            feature (str): the feature being displayed, it can be 'tree' or 'area'
         """
 
         if view_direction == self.view_direction and feature == self.feature:
@@ -127,7 +124,7 @@ def set_view(self, view_direction: str, feature: str):
                 self.setLabel("bottom", text="")
             else:
                 self.getAxis("bottom").setStyle(showValues=True)
-                self.setLabel("bottom", text="Number of pixels")
+                self.setLabel("bottom", text="Area in Scaled Pixels")
             self.invertY(True)  # to show tracks from top to bottom
         elif view_direction == "horizontal":
             self.setLabel("bottom", text="Time Point")
@@ -136,7 +133,7 @@ def set_view(self, view_direction: str, feature: str):
                 self.setLabel("left", text="")
                 self.getAxis("left").setStyle(showValues=False)
             else:
-                self.setLabel("left", text="Number of pixels")
+                self.setLabel("left", text="Area in Scaled Pixels")
                 self.getAxis("left").setStyle(showValues=True)
             self.invertY(False)
 
@@ -167,9 +164,9 @@ def set_data(self, track_df: pd.DataFrame, feature: str) -> None:
         self._create_pyqtgraph_content(track_df, feature)
 
     def _update_viewed_data(self):
-        self.g.scatter.setPen(
-            pg.mkPen(QColor(150, 150, 150))
-        )  # first reset the pen to avoid problems with length mismatch between the different properties
+        # first reset the pen to avoid problems with length mismatch between the
+        # different properties
+        self.g.scatter.setPen(pg.mkPen(QColor(150, 150, 150)))
         self.g.scatter.setSize(10)
         if len(self._pos) == 0 or self.view_direction == "vertical":
             pos_data = self._pos
@@ -188,9 +185,7 @@ def _update_viewed_data(self):
         self.g.scatter.setSize(self.sizes)
         self.autoRange()
 
-    def _create_pyqtgraph_content(
-        self, track_df: pd.DataFrame, feature: str
-    ) -> None:
+    def _create_pyqtgraph_content(self, track_df: pd.DataFrame, feature: str) -> None:
         """Parse the given track_df into the format that pyqtgraph expects
         and save the information as attributes.
 
@@ -320,9 +315,7 @@ class TreeWidget(QWidget):
     def __init__(self, viewer: napari.Viewer):
         super().__init__()
         self.track_df = pd.DataFrame()  # all tracks
-        self.lineage_df = (
-            pd.DataFrame()
-        )  # the currently viewed subset of lineages
+        self.lineage_df = pd.DataFrame()  # the currently viewed subset of lineages
         self.graph = None
         self.mode = "all"  # options: "all", "lineage"
         self.feature = "tree"  # options: "tree", "area"
@@ -436,8 +429,11 @@ def _update_track_data(self) -> None:
             )
             self.graph = self.tracks_viewer.tracks.graph
 
-        # check whether we have area measurements and therefore should activate the area button
+        # check whether we have area measurements and therefore should activate the area
+        # button
         if "area" not in self.track_df.columns:
+            if self.feature_widget.feature == "area":
+                self.feature_widget._toggle_feature_mode()
             self.feature_widget.show_area_radio.setEnabled(False)
         else:
             self.feature_widget.show_area_radio.setEnabled(True)
@@ -483,15 +479,14 @@ def _set_mode(self, mode: str) -> None:
         )
 
     def _set_feature(self, feature: str) -> None:
-        """Set the feature mode to 'tree' or 'area'. For this the view is always horizontal.
+        """Set the feature mode to 'tree' or 'area'. For this the view is always
+        horizontal.
 
         Args:
             feature (str): The feature to plot. Options are "tree" or "area"
         """
         if feature not in ["tree", "area"]:
-            raise ValueError(
-                f"Feature must be 'tree' or 'area', got {feature}"
-            )
+            raise ValueError(f"Feature must be 'tree' or 'area', got {feature}")
 
         self.feature = feature
         if feature == "tree" and self.mode == "all":