Merge pull request #298 from funkelab/295-decouple-selection-and-zoom-to-this-node

295 decouple selection and zoom to this node

Author: cmalinmayor

docs/source/key_bindings.rst

@@ -11,9 +11,11 @@ Napari viewer and layer key bindings and mouse functions
    * - Mouse / Key binding
      - Action
    * - Click on a point or label
-     - Select this node (center view if necessary)
+     - Select this node (centers view if only one node selected)
    * - SHIFT + click on point or label
-     - Add this node to selection
+     - Add this node to selection (does not center view)
+   * - CTRL + click on point or label
+     - Center view on this node (does not change selection)
    * - Mouse drag with point layer selection tool active
      - Select multiple nodes at once
    * - Q
@@ -30,9 +32,11 @@ Tree view key and mouse functions
    * - Mouse / Key binding
      - Action
    * - Click on a node
-     - Select this node (center view if necessary)
+     - Select this node (centers view if only one node selected)
    * - SHIFT + click on a node
-     - Add this node to selection
+     - Add this node to selection (does not center view)
+   * - CTRL/CMD + click on a node
+     - Center view on this node (does not change selection)
    * - Scroll
      - Zoom in or out
    * - Scroll + X / Right mouse click + drag horizontally

docs/source/tree_view.rst

@@ -10,7 +10,11 @@ through the motile widget in the tree view, you can open the tree widget from th
 via ``Plugins`` > ``Motile`` > ``Lineage View``.
 
 Clicking on individual nodes in the tree widget or in the napari Points or Labels layer will select that node,
-highlighting it both in the tree view and in the napari layers, and centering the view if necessary.
+highlighting it both in the tree view and in the napari layers. The view is centered on the selected node
+only when a single node is selected. Use ``SHIFT + click`` to add nodes to the selection without centering,
+or ``CTRL + click`` to center the view on a node without changing the selection.
+When multiple nodes are selected, you can cycle through them using the "Next selected node" and
+"Previous selected node" buttons in the Groups widget.
 You can navigate and select nodes in the tree view using the arrow keys (make sure to click on the tree widget first).
 Optionally, you can display only selected lineages in the tree view and/or napari layers (press ``Q`` in the tree widget and/or in the napari viewer).
 If you used a Labels layer as input for tracking, you will also have the option to plot the object sizes (area or volume) in calibrated units

src/motile_tracker/__main__.py

@@ -9,7 +9,7 @@ def main() -> None:
     # Auto-load the motile tracker
     viewer = napari.Viewer()
     main_app = MainApp(viewer)
-    viewer.window.add_dock_widget(main_app)
+    viewer.window.add_dock_widget(main_app, name="Motile Tracker")
 
     # Start napari event loop
     napari.run()

src/motile_tracker/application_menus/menu_widget.py

@@ -1,5 +1,12 @@
 import napari
-from qtpy.QtWidgets import QScrollArea, QTabWidget, QVBoxLayout
+from qtpy.QtWidgets import (
+    QHBoxLayout,
+    QLabel,
+    QScrollArea,
+    QTabWidget,
+    QVBoxLayout,
+    QWidget,
+)
 
 from motile_tracker.application_menus.editing_menu import EditingMenu
 from motile_tracker.application_menus.visualization_widget import (
@@ -8,6 +15,9 @@
 from motile_tracker.data_views.views_coordinator.tracks_viewer import TracksViewer
 from motile_tracker.motile.menus.motile_widget import MotileWidget
 
+DOCS_URL = "https://funkelab.github.io/motile_tracker"
+KEYBINDINGS_URL = f"{DOCS_URL}/key_bindings.html"
+
 
 class MenuWidget(QScrollArea):
     """Combines the different tracker menus into tabs for cleaner UI"""
@@ -25,19 +35,35 @@ def __init__(self, viewer: napari.Viewer):
 
         self.tabwidget = QTabWidget()
 
-        self.tabwidget.addTab(motile_widget, "Track with Motile")
+        self.tabwidget.addTab(motile_widget, "Tracking")
         self.tabwidget.addTab(self.tracks_viewer.tracks_list, "Tracks List")
         self.tabwidget.addTab(editing_widget, "Edit Tracks")
         self.tabwidget.addTab(self.tracks_viewer.collection_widget, "Groups")
 
-        layout = QVBoxLayout()
-        layout.addWidget(self.tabwidget)
-
-        self.setWidget(self.tabwidget)
+        # Header with title and help links
+        header_layout = QHBoxLayout()
+        header_layout.setContentsMargins(5, 5, 5, 0)
+        header_label = QLabel(
+            f"<b>Motile Tracker</b> · "
+            f'<a href="{DOCS_URL}"><font color=yellow>Docs</font></a> · '
+            f'<a href="{KEYBINDINGS_URL}"><font color=yellow>Keybindings</font></a>'
+        )
+        header_label.setOpenExternalLinks(True)
+        header_layout.addWidget(header_label)
+        header_layout.addStretch()
+
+        # Container widget with header + tabs
+        container = QWidget()
+        container_layout = QVBoxLayout()
+        container_layout.setContentsMargins(0, 0, 0, 0)
+        container_layout.setSpacing(2)
+        container_layout.addLayout(header_layout)
+        container_layout.addWidget(self.tabwidget)
+        container.setLayout(container_layout)
+
+        self.setWidget(container)
         self.setWidgetResizable(True)
 
-        self.setLayout(layout)
-
     def _has_visualization_tab(self):
         return self.tabwidget.indexOf(self.visualization_widget) != -1
 

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

@@ -147,7 +147,11 @@ def process_click(self, event: Event, label: int):
             label is not None and label != 0 and self.colormap.map(label)[-1] != 0
         ):  # check opacity (=visibility) in the colormap
             append = "Shift" in event.modifiers
-            self.tracks_viewer.selected_nodes.add(label, append)
+            jump = "Control" in event.modifiers
+            if jump:
+                self.tracks_viewer.center_on_node(label)
+            else:
+                self.tracks_viewer.selected_nodes.add(label, append)
 
     def _get_colormap(self) -> DirectLabelColormap:
         """Get a DirectLabelColormap that maps node ids to their track ids, and then

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

@@ -130,7 +130,11 @@ def process_click(self, event: Event, point_index: int | None):
         else:
             node_id = self.nodes[point_index]
             append = "Shift" in event.modifiers
-            self.tracks_viewer.selected_nodes.add(node_id, append)
+            jump = "Control" in event.modifiers
+            if jump:
+                self.tracks_viewer.center_on_node(node_id)
+            else:
+                self.tracks_viewer.selected_nodes.add(node_id, append)
 
     def set_point_size(self, size: int) -> None:
         """Sets a new default point size.

src/motile_tracker/data_views/views/tree_view/tree_widget.py

@@ -91,6 +91,7 @@ def mouseDragEvent(self, ev, axis=None):
 
 class TreePlot(pg.PlotWidget):
     node_clicked = Signal(Any, bool)  # node_id, append
+    jump_to_node = Signal(int)  # node to jump to
     nodes_selected = Signal(list, bool)
 
     def __init__(self) -> pg.PlotWidget:
@@ -230,8 +231,12 @@ def _on_click(self, _, points: np.ndarray, ev: QMouseEvent) -> None:
         modifiers = ev.modifiers()
         node_id = points[0].data()
         append = Qt.ShiftModifier == modifiers
-        self.node_clicked.emit(node_id, append)
-        self.setFocus()
+        jump = Qt.ControlModifier == modifiers
+        if jump:
+            self.jump_to_node.emit(node_id)
+        else:
+            self.node_clicked.emit(node_id, append)
+            self.setFocus()
 
     def set_data(self, track_df: pd.DataFrame, plot_type: str, feature: str) -> None:
         """Updates the stored pyqtgraph content based on the given dataframe.
@@ -323,12 +328,14 @@ def _create_pyqtgraph_content(
 
     def set_selection(self, selected_nodes: list[Any], plot_type: str) -> None:
         """Set the provided list of nodes to be selected. Increases the size
-        and highlights the outline with blue. Also centers the view
-        if the first selected node is not visible in the current canvas.
+        and highlights the outline with blue.
+
+        Note: Single-node centering is handled separately via the center_node signal
+        from TracksViewer. Multi-node range centering is handled here.
 
         Args:
             selected_nodes (list[Any]): A list of node ids to be selected.
-            feature (str): the feature that is being plotted, either 'tree' or 'area'
+            plot_type (str): the plot type being displayed, either 'tree' or 'feature'
         """
 
         # reset to default size and color to avoid problems with the array lengths
@@ -340,9 +347,7 @@ def set_selection(self, selected_nodes: list[Any], plot_type: str) -> None:
         )  # just copy the size here to keep the original self.sizes intact
 
         outlines = self.outline_pen.copy()
-        axis_label = (
-            self.feature if plot_type == "feature" else "x_axis_pos"
-        )  # check what is currently being shown, to know how to scale  the view
+        axis_label = self.feature if plot_type == "feature" else "x_axis_pos"
 
         if len(selected_nodes) > 0:
             x_values = []
@@ -361,11 +366,9 @@ def set_selection(self, selected_nodes: list[Any], plot_type: str) -> None:
                     size[index] += 5
                     outlines[index] = pg.mkPen(color="c", width=2)
 
-            # Center point if a single node is selected, center range if multiple nodes
-            # are selected
-            if len(selected_nodes) == 1:
-                self._center_view(x_axis_value, t)
-            else:
+            # Center range if multiple nodes are selected (single-node centering
+            # is handled by the center_node signal)
+            if len(x_values) > 1:
                 min_x = np.min(x_values)
                 max_x = np.max(x_values)
                 min_t = np.min(t_values)
@@ -398,8 +401,27 @@ def _center_range(self, min_x: int, max_x: int, min_t: int, max_t: int):
         else:
             self.autoRange()
 
+    def center_on_node(self, node_id: int) -> None:
+        """Center the view on a specific node by ID.
+
+        Args:
+            node_id: The node ID to center on.
+        """
+        if not hasattr(self, "track_df") or self.track_df is None:
+            return
+        node_df = self.track_df.loc[self.track_df["node_id"] == node_id]
+        if node_df.empty:
+            return
+        axis_label = self.feature if self.plot_type == "feature" else "x_axis_pos"
+        x_axis_value = node_df[axis_label].values[0]
+        t = node_df["t"].values[0]
+        self._center_view(x_axis_value, t)
+
     def _center_view(self, center_x: int, center_y: int):
-        """Center the Viewbox on given coordinates"""
+        """Center the Viewbox on given coordinates, preserving the current zoom level.
+
+        Only pans if the point is outside the current view.
+        """
 
         if self.view_direction == "horizontal":
             center_x, center_y = (
@@ -420,7 +442,12 @@ def _center_view(self, center_x: int, center_y: int):
         ):
             return
 
-        self.autoRange()
+        # Pan to center the point while preserving current zoom level
+        x_width = x_range[1] - x_range[0]
+        y_width = y_range[1] - y_range[0]
+        new_x_range = (center_x - x_width / 2, center_x + x_width / 2)
+        new_y_range = (center_y - y_width / 2, center_y + y_width / 2)
+        view_box.setRange(xRange=new_x_range, yRange=new_y_range, padding=0)
 
 
 class TreeWidget(QWidget):
@@ -445,7 +472,9 @@ def __init__(self, viewer: napari.Viewer):
 
         self.tree_widget: TreePlot = TreePlot()
         self.tree_widget.node_clicked.connect(self.selected_nodes.add)
+        self.tree_widget.jump_to_node.connect(self.tracks_viewer.center_on_node)
         self.tree_widget.nodes_selected.connect(self.selected_nodes.add_list)
+        self.tracks_viewer.center_node.connect(self.tree_widget.center_on_node)
 
         # Add radiobuttons for switching between different display modes
         self.mode_widget = TreeViewModeWidget()

src/motile_tracker/data_views/views_coordinator/groups.py

@@ -94,26 +94,34 @@ def __init__(self, tracks_viewer: TracksViewer):
 
         # Select widget group
         select_widget = QGroupBox("Selection")
-        selection_layout = QVBoxLayout()
+        selection_layout = QHBoxLayout()
 
-        row1_layout = QHBoxLayout()
+        col1_layout = QVBoxLayout()
         self.select_btn = QPushButton("Select nodes in group")
         self.select_btn.clicked.connect(self._select_nodes)
         self.invert_btn = QPushButton("Invert selection")
         self.invert_btn.clicked.connect(self._invert_selection)
-        row1_layout.addWidget(self.select_btn)
-        row1_layout.addWidget(self.invert_btn)
+        self.jump_to_next_btn = QPushButton("Next selected node")
+        self.jump_to_next_btn.clicked.connect(lambda: self._jump_to_node(forward=True))
+        col1_layout.addWidget(self.select_btn)
+        col1_layout.addWidget(self.invert_btn)
+        col1_layout.addWidget(self.jump_to_next_btn)
 
-        row2_layout = QHBoxLayout()
+        col2_layout = QVBoxLayout()
         self.deselect_btn = QPushButton("Deselect")
         self.deselect_btn.clicked.connect(self.tracks_viewer.selected_nodes.reset)
         self.reselect_btn = QPushButton("Restore selection")
         self.reselect_btn.clicked.connect(self.tracks_viewer.selected_nodes.restore)
-        row2_layout.addWidget(self.deselect_btn)
-        row2_layout.addWidget(self.reselect_btn)
+        self.jump_to_previous_btn = QPushButton("Previous selected node")
+        self.jump_to_previous_btn.clicked.connect(
+            lambda: self._jump_to_node(forward=False)
+        )
+        col2_layout.addWidget(self.deselect_btn)
+        col2_layout.addWidget(self.reselect_btn)
+        col2_layout.addWidget(self.jump_to_previous_btn)
 
-        selection_layout.addLayout(row1_layout)
-        selection_layout.addLayout(row2_layout)
+        selection_layout.addLayout(col1_layout)
+        selection_layout.addLayout(col2_layout)
         select_widget.setLayout(selection_layout)
 
         # edit layout
@@ -201,14 +209,25 @@ def _update_buttons_and_node_count(self) -> None:
 
         if len(self.tracks_viewer.selected_nodes) > 0:
             self.deselect_btn.setEnabled(True)
+            self.jump_to_next_btn.setEnabled(True)
+            self.jump_to_previous_btn.setEnabled(True)
         else:
             self.deselect_btn.setEnabled(False)
+            self.jump_to_next_btn.setEnabled(False)
+            self.jump_to_previous_btn.setEnabled(False)
 
         if self.tracks_viewer.tracks is not None:
             self.new_group_button.setEnabled(True)
         else:
             self.new_group_button.setEnabled(False)
 
+    def _jump_to_node(self, forward: bool) -> None:
+        """Jump to the next/previous selected node in the list"""
+
+        node = self.tracks_viewer.selected_nodes.next_node(forward)
+        if node:
+            self.tracks_viewer.center_on_node(node)
+
     def _invert_selection(self) -> None:
         """Invert the current selection"""