Increase rendering performance

examples/show_large_tree.py

@@ -24,7 +24,7 @@ def generate_binary_tree(max_depth: int):
     return nodes
 
 
-nodes = generate_binary_tree(6)
+nodes = generate_binary_tree(8)
 print(f"{len(nodes)} total nodes")
 
 

napari_arboretum/graph.py

@@ -16,7 +16,7 @@ class TreeNode:
     """TreeNode."""
 
     ID: int
-    t: Tuple[int, int]
+    t: np.ndarray
     generation: int
     children: List[int] = field(default_factory=list)
 
@@ -154,7 +154,8 @@ def build_subgraph(layer: napari.layers.Tracks, search_node: int) -> List[TreeNo
     def _node_from_graph(_id):
 
         idx = np.where(layer.data[:, 0] == _id)[0]
-        t = (np.min(layer.data[idx, 1]), np.max(layer.data[idx, 1]))
+        # t = (np.min(layer.data[idx, 1]), np.max(layer.data[idx, 1]))
+        t = layer.data[idx, 1]
         node = TreeNode(ID=_id, t=t, generation=1)
 
         if _id in reverse_graph:

napari_arboretum/plugin.py

@@ -93,7 +93,7 @@ def append_mouse_callback(self, track_layer: Tracks) -> None:
         when the layer is clicked.
         """
 
-        @track_layer.mouse_drag_callbacks.append
+        @track_layer.mouse_double_click_callbacks.append
         def show_tree(tracks: Tracks, event: Event) -> None:
             self.tracks = tracks
 

napari_arboretum/tree.py

@@ -30,6 +30,7 @@ class Edge:
     y: Tuple[float, float]
     color: np.ndarray = WHITE
     id: Optional[int] = None
+    node: Optional[TreeNode] = None
 
 
 def layout_tree(nodes: List[TreeNode]) -> Tuple[List[Edge], List[Annotation]]:
@@ -66,14 +67,15 @@ def layout_tree(nodes: List[TreeNode]) -> Tuple[List[Edge], List[Annotation]]:
         y = y_pos.pop(0)
 
         # draw the root of the tree
-        edges.append(Edge(y=(y, y), x=(node.t[0], node.t[-1]), id=node.ID))
+        edges.append(Edge(y=(y, y), x=(node.t[0], node.t[-1]), id=node.ID, node=node))
+
+        if node.is_root:
+            annotations.append(Annotation(y=y, x=node.t[0], label=str(node.ID)))
 
         # mark if this is an apoptotic tree
         if node.is_leaf:
             annotations.append(Annotation(y=y, x=node.t[-1], label=str(node.ID)))
-
-        if node.is_root:
-            annotations.append(Annotation(y=y, x=node.t[0], label=str(node.ID)))
+            continue
 
         children = [t for t in nodes if t.ID in node.children]
 
@@ -94,6 +96,11 @@ def layout_tree(nodes: List[TreeNode]) -> Tuple[List[Edge], List[Annotation]]:
 
                 # plot a linking line to the children
                 edges.append(Edge(y=(y, y_pos[-1]), x=(node.t[-1], child.t[0])))
+
+                # if it's a leaf don't plot the annotation
+                if child.is_leaf:
+                    continue
+
                 annotations.append(
                     Annotation(
                         y=y_pos[-1],
@@ -102,14 +109,4 @@ def layout_tree(nodes: List[TreeNode]) -> Tuple[List[Edge], List[Annotation]]:
                     )
                 )
 
-    # now that we have traversed the tree, calculate the span
-    tree_span = []
-    for edge in edges:
-        tree_span.append(edge.y[0])
-        tree_span.append(edge.y[1])
-
-    # # work out the span of the tree, we can modify positioning here
-    # min_x = min(tree_span)
-    # max_x = max(tree_span)
-
     return edges, annotations

napari_arboretum/visualisation/base_plotter.py

@@ -9,6 +9,8 @@
 from ..tree import Annotation, Edge, layout_tree
 from ..util import TrackPropertyMixin
 
+# from ..profiler import profiler
+
 GUI_MAXIMUM_WIDTH = 600
 
 __all__ = ["TreePlotterBase", "TreePlotterQWidgetBase"]
@@ -46,6 +48,7 @@ def draw_tree(self) -> None:
         subgraph_nodes = build_subgraph(self.tracks, self.track_id)
         self.draw_from_nodes(subgraph_nodes, self.track_id)
 
+    # @profiler("draw_from_nodes")
     def draw_from_nodes(
         self, tree_nodes: List[TreeNode], track_id: Optional[int] = None
     ):
@@ -61,6 +64,8 @@ def draw_from_nodes(
         for a in self.annotations:
             self.add_annotation(a)
 
+        self.draw_tree_visual()
+
     def update_edge_colors(self, update_live: bool = True) -> None:
         """
         Update tree edge colours from the track properties.
@@ -117,6 +122,13 @@ def draw_current_time_line(self, time: int) -> None:
         """
         raise NotImplementedError
 
+    @abc.abstractmethod
+    def draw_tree_visual(self) -> None:
+        """
+        Function to draw the visual after construction.
+        """
+        raise NotImplementedError
+
 
 class TreePlotterQWidgetBase(TreePlotterBase):
     """

napari_arboretum/visualisation/vispy_plotter.py

@@ -1,5 +1,4 @@
 from dataclasses import dataclass
-from typing import Optional
 
 import numpy as np
 from qtpy.QtWidgets import QWidget
@@ -11,6 +10,10 @@
 __all__ = ["VisPyPlotter"]
 
 
+DEFAULT_TEXT_SIZE = 8
+DEFAULT_BRANCH_WIDTH = 3
+
+
 @dataclass
 class Bounds:
     xmin: float
@@ -19,6 +22,31 @@ class Bounds:
     ymax: float
 
 
+@dataclass
+class TrackSubvisualProxy:
+    pos: np.ndarray
+    color: np.ndarray = np.array([1.0, 1.0, 1.0, 1.0])
+
+    @property
+    def connex(self):
+        connex = [True] * (self.pos.shape[0] - 1) + [False]
+        return connex
+
+    @property
+    def safe_color(self) -> np.ndarray:
+        if self.color.ndim != 2:
+            safe_color = np.repeat([self.color], self.pos.shape[0], axis=0)
+            return safe_color
+        return self.color
+
+
+@dataclass
+class AnnotationSubvisualProxy:
+    pos: np.ndarray
+    text: str
+    color: str = "white"
+
+
 class VisPyPlotter(TreePlotterQWidgetBase):
     """
     Tree plotter using pyqtgraph as the plotting backend.
@@ -71,6 +99,14 @@ def autoscale_view(self) -> None:
             width * (1 + 2 * padding),
             height * (1 + 2 * padding),
         )
+
+        # change the aspect ratio of the camera if we have just a single branch
+        # this will centre the camera on the single branch, otherwise, set the
+        # aspect ratio to match the data
+        if width == 0:
+            self.view.camera.aspect = 1.0
+        else:
+            self.view.camera.aspect = None
         self.view.camera.rect = rect
 
     def update_colors(self) -> None:
@@ -85,7 +121,8 @@ def add_branch(self, e: Edge) -> None:
         """
         Add a single branch to the tree.
         """
-        self.tree.add_track(e.id, np.column_stack((e.y, e.x)), e.color)
+        # self.tree.add_track(e.id, np.column_stack((e.y, e.x)), e.color)
+        self.tree.add_track(e)
         self.autoscale_view()
 
     def add_annotation(self, a: Annotation) -> None:
@@ -104,6 +141,12 @@ def draw_current_time_line(self, time: int) -> None:
             pos=np.array([[bounds.xmin - padding, time], [bounds.xmax + padding, time]])
         )
 
+    def draw_tree_visual(self) -> None:
+        """
+        Draw the whole tree.
+        """
+        self.tree.draw_tree()
+
 
 class TreeVisual(scene.visuals.Compound):
     """
@@ -116,7 +159,22 @@ def __init__(self, parent):
         self.unfreeze()
         # Keep a reference to tracks we add so their colour can be changed later
         self.tracks = {}
-        self.subvisuals = []
+        self.edges = []
+        self.annotations = []
+
+        subvisuals = [
+            scene.visuals.Line(color="white", width=DEFAULT_BRANCH_WIDTH),
+            scene.visuals.Text(
+                anchor_x="left",
+                anchor_y="top",
+                rotation=90,
+                font_size=DEFAULT_TEXT_SIZE,
+                color="white",
+            ),
+        ]
+
+        for visual in subvisuals:
+            self.add_subvisual(visual)
 
     def get_branch_color(self, branch_id: int) -> np.ndarray:
         return self.tracks[branch_id].color
@@ -125,9 +183,12 @@ def set_branch_color(self, branch_id: int, color: np.ndarray) -> None:
         """
         Set the color of an individual branch.
         """
-        self.tracks[branch_id].set_data(color=color)
+        self.tracks[branch_id].color = color
+        self._subvisuals[0].set_data(
+            color=np.row_stack([e.safe_color for e in self.edges]),
+        )
 
-    def add_track(self, id: Optional[int], pos: np.ndarray, color: np.ndarray) -> None:
+    def add_track(self, e: Edge) -> None:
         """
         Parameters
         ----------
@@ -139,35 +200,58 @@ def add_track(self, id: Optional[int], pos: np.ndarray, color: np.ndarray) -> No
             Array of shape (n, 4) specifying RGBA values in range [0, 1] along
             the track.
         """
-        if id is None:
-            visual = scene.visuals.Line(pos=pos, color=color, width=3)
+        color = e.color
+        pos = np.column_stack((e.y, e.x))
+
+        if e.node is None:
+            subvisual_proxy = TrackSubvisualProxy(
+                pos=pos,
+                color=np.array([1.0, 1.0, 1.0, 1.0]),
+            )
         else:
             # Split up line into individual time steps so color can vary
             # along the line
-            ys = np.arange(pos[0, 1], pos[1, 1] + 1)
+            ys = np.asarray(e.node.t)  # np.arange(pos[0, 1], pos[1, 1] + 1)
             xs = np.ones(ys.size) * pos[0, 0]
-            visual = scene.visuals.Line(
-                pos=np.column_stack((xs, ys)), color=color, width=3
+            subvisual_proxy = TrackSubvisualProxy(
+                pos=np.column_stack((xs, ys)),
+                color=color,
             )
-            self.tracks[id] = visual
+            # store a reference to this subvisual proxy
+            self.tracks[e.id] = subvisual_proxy
 
-        self.add_subvisual(visual)
-        self.subvisuals.append(visual)
+        self.edges.append(subvisual_proxy)
 
     def add_annotation(self, x: float, y: float, label: str, color):
-        visual = scene.visuals.Text(
+
+        subvisual_proxy = AnnotationSubvisualProxy(
             text=label,
-            color=color,
             pos=[y, x, 0],
-            anchor_x="left",
-            anchor_y="top",
-            font_size=10,
         )
-        self.add_subvisual(visual)
-        self.subvisuals.append(visual)
+
+        self.annotations.append(subvisual_proxy)
 
     def clear(self) -> None:
         """Remove all tracks."""
-        while self.subvisuals:
-            subvisual = self.subvisuals.pop()
-            self.remove_subvisual(subvisual)
+        self.tracks = {}
+        self.edges = []
+        self.annotations = []
+
+        for visual in self._subvisuals:
+            visual._pos = None
+
+            if hasattr(visual, "_text"):
+                visual._text = None
+
+    def draw_tree(self) -> None:
+        """Once the data is added, draw the tree."""
+
+        self._subvisuals[0].set_data(
+            pos=np.row_stack([e.pos for e in self.edges]),
+            color=np.row_stack([e.safe_color for e in self.edges]),
+            connect=np.concatenate([e.connex for e in self.edges]),
+        )
+
+        # TextVisual does not have a ``set_data`` method
+        self._subvisuals[1].pos = np.asarray([a.pos for a in self.annotations])
+        self._subvisuals[1].text = [a.text for a in self.annotations]