Merge branch 'main' into faster_edge_errors

.github/workflows/ci.yml

@@ -13,7 +13,7 @@ jobs:
   # check-manifest:
   #   runs-on: ubuntu-latest
   #   steps:
-  #     - uses: actions/checkout@v3
+  #     - uses: actions/checkout@v4
   #     - run: pipx run check-manifest
 
   test:
@@ -26,7 +26,7 @@ jobs:
         platform: [ubuntu-latest, macos-latest, windows-latest]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
@@ -111,7 +111,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python
         uses: actions/setup-python@v4

src/traccuracy/_tracking_graph.py

@@ -159,13 +159,42 @@ def __init__(
                 )
         self.location_keys = location_keys
 
-        # Define empty attributes that will be set by update_graph
-        self.graph = None
-        self.nodes_by_frame = None
-        self.start_frame = None
-        self.end_frame = None
+        self.graph = graph
 
-        self._update_graph(graph)
+        # construct dictionaries from attributes to nodes/edges for easy lookup
+        self.nodes_by_frame = {}
+        self.nodes_by_flag = {flag: set() for flag in NodeAttr}
+        self.edges_by_flag = {flag: set() for flag in EdgeAttr}
+        for node, attrs in self.graph.nodes.items():
+            # check that every node has the time frame and location specified
+            assert (
+                self.frame_key in attrs.keys()
+            ), f"Frame key {self.frame_key} not present for node {node}."
+            for key in self.location_keys:
+                assert (
+                    key in attrs.keys()
+                ), f"Location key {key} not present for node {node}."
+
+            # store node id in nodes_by_frame mapping
+            frame = attrs[self.frame_key]
+            if frame not in self.nodes_by_frame.keys():
+                self.nodes_by_frame[frame] = {node}
+            else:
+                self.nodes_by_frame[frame].add(node)
+            # store node id in nodes_by_flag mapping
+            for flag in NodeAttr:
+                if flag in attrs and attrs[flag]:
+                    self.nodes_by_flag[flag].add(node)
+
+        # store edge id in edges_by_flag
+        for edge, attrs in self.graph.edges.items():
+            for flag in EdgeAttr:
+                if flag in attrs and attrs[flag]:
+                    self.edges_by_flag[flag].add(edge)
+
+        # Store first and last frames for reference
+        self.start_frame = min(self.nodes_by_frame.keys())
+        self.end_frame = max(self.nodes_by_frame.keys()) + 1
 
         # Record types of annotations that have been calculated
         self.division_annotations = False
@@ -223,7 +252,7 @@ def get_nodes_in_frame(self, frame):
             list of node_ids: A list of node ids for all nodes in frame.
         """
         if frame in self.nodes_by_frame.keys():
-            return self.nodes_by_frame[frame]
+            return list(self.nodes_by_frame[frame])
         else:
             return []
 
@@ -250,12 +279,7 @@ def get_nodes_with_flag(self, attr):
         """
         if not isinstance(attr, NodeAttr):
             raise ValueError(f"Function takes NodeAttr arguments, not {type(attr)}.")
-        nodes_with_flag = [
-            node
-            for node, attrs in self.nodes().items()
-            if attr in attrs.keys() and attrs[attr] is True
-        ]
-        return nodes_with_flag
+        return list(self.nodes_by_flag[attr])
 
     def get_edges_with_flag(self, attr):
         """Get all edges with specified EdgeAttr set to True.
@@ -269,12 +293,7 @@ def get_edges_with_flag(self, attr):
         """
         if not isinstance(attr, EdgeAttr):
             raise ValueError(f"Function takes EdgeAttr arguments, not {type(attr)}.")
-        edges_with_flag = [
-            edge
-            for edge, attrs in self.edges().items()
-            if attr in attrs.keys() and attrs[attr] is True
-        ]
-        return edges_with_flag
+        return list(self.edges_by_flag[attr])
 
     def get_nodes_by_roi(self, **kwargs):
         """Gets the nodes in a given region of interest (ROI). The ROI is
@@ -292,6 +311,7 @@ def get_nodes_by_roi(self, **kwargs):
         Returns:
             list of hashable: A list of node_ids for all nodes in the ROI.
         """
+        frames = None
         dimensions = []
         for dim, limit in kwargs.items():
             if not (dim == self.frame_key or dim in self.location_keys):
@@ -300,9 +320,25 @@ def get_nodes_by_roi(self, **kwargs):
                     f" {self.frame_key} or one of the location keys"
                     f" {self.location_keys}."
                 )
-            dimensions.append((dim, limit[0], limit[1]))
+            if dim == self.frame_key:
+                frames = list(limit)
+            else:
+                dimensions.append((dim, limit[0], limit[1]))
         nodes = []
-        for node, attrs in self.graph.nodes().items():
+        if frames:
+            if frames[0] is None:
+                frames[0] = self.start_frame
+            if frames[1] is None:
+                frames[1] = self.end_frame
+            possible_nodes = []
+            for frame in range(frames[0], frames[1]):
+                if frame in self.nodes_by_frame:
+                    possible_nodes.extend(self.nodes_by_frame[frame])
+        else:
+            possible_nodes = self.graph.nodes()
+
+        for node in possible_nodes:
+            attrs = self.graph.nodes[node]
             inside = True
             for dim, start, end in dimensions:
                 if start is not None and attrs[dim] < start:
@@ -450,41 +486,27 @@ def get_subgraph(self, nodes):
 
         new_graph = self.graph.subgraph(nodes).copy()
         new_trackgraph = copy.deepcopy(self)
-        new_trackgraph._update_graph(new_graph)
-
-        return new_trackgraph
-
-    def _update_graph(self, graph):
-        """Given a new graph, which is expected to be a subgraph of the current graph,
-        update attributes which are dependent on the graph.
-
-        Args:
-            graph (nx.DiGraph): A networkx graph that is a subgraph of the original graph
-        """
-        self.graph = graph
+        new_trackgraph.graph = new_graph
+        for frame, nodes_in_frame in self.nodes_by_frame.items():
+            new_nodes_in_frame = nodes_in_frame.intersection(nodes)
+            if new_nodes_in_frame:
+                new_trackgraph.nodes_by_frame[frame] = new_nodes_in_frame
+            else:
+                del new_trackgraph.nodes_by_frame[frame]
 
-        # construct a dictionary from frames to node ids for easy lookup
-        self.nodes_by_frame = {}
-        for node, attrs in self.graph.nodes.items():
-            # check that every node has the time frame and location specified
-            assert (
-                self.frame_key in attrs.keys()
-            ), f"Frame key {self.frame_key} not present for node {node}."
-            for key in self.location_keys:
-                assert (
-                    key in attrs.keys()
-                ), f"Location key {key} not present for node {node}."
+        for attr in NodeAttr:
+            new_trackgraph.nodes_by_flag[attr] = self.nodes_by_flag[attr].intersection(
+                nodes
+            )
+        for attr in EdgeAttr:
+            new_trackgraph.edges_by_flag[attr] = self.edges_by_flag[attr].intersection(
+                nodes
+            )
 
-            # store node id in nodes_by_frame mapping
-            frame = attrs[self.frame_key]
-            if frame not in self.nodes_by_frame.keys():
-                self.nodes_by_frame[frame] = [node]
-            else:
-                self.nodes_by_frame[frame].append(node)
+        new_trackgraph.start_frame = min(new_trackgraph.nodes_by_frame.keys())
+        new_trackgraph.end_frame = max(new_trackgraph.nodes_by_frame.keys()) + 1
 
-        # Store first and last frames for reference
-        self.start_frame = min(self.nodes_by_frame.keys())
-        self.end_frame = max(self.nodes_by_frame.keys()) + 1
+        return new_trackgraph
 
     def set_node_attribute(self, ids, attr, value=True):
         """Set an attribute flag for a set of nodes specified by
@@ -510,6 +532,10 @@ def set_node_attribute(self, ids, attr, value=True):
             )
         for _id in ids:
             self.graph.nodes[_id][attr] = value
+            if value:
+                self.nodes_by_flag[attr].add(_id)
+            else:
+                self.nodes_by_flag[attr].discard(_id)
 
     def set_edge_attribute(self, ids, attr, value=True):
         """Set an attribute flag for a set of edges specified by
@@ -535,6 +561,60 @@ def set_edge_attribute(self, ids, attr, value=True):
             )
         for _id in ids:
             self.graph.edges[_id][attr] = value
+            if value:
+                self.edges_by_flag[attr].add(_id)
+            else:
+                self.edges_by_flag[attr].discard(_id)
+
+    def get_node_attribute(self, _id, attr):
+        """Get the boolean value of a given attribute for a given node.
+
+        Args:
+            _id (hashable): node id
+            attr (NodeAttr): Node attribute to fetch the value of
+
+        Raises:
+            ValueError: if attr is not a NodeAttr
+
+        Returns:
+            bool: The value of the attribute for that node. If the attribute
+                is not present on the graph, the value is presumed False.
+        """
+        if not isinstance(attr, NodeAttr):
+            raise ValueError(
+                f"Provided attribute {attr} is not of type NodeAttr. "
+                "Please use the enum instead of passing string values, "
+                "and add new attributes to the class to avoid key collision."
+            )
+
+        if attr not in self.graph.nodes[_id]:
+            return False
+        return self.graph.nodes[_id][attr]
+
+    def get_edge_attribute(self, _id, attr):
+        """Get the boolean value of a given attribute for a given edge.
+
+        Args:
+            _id (hashable): node id
+            attr (EdgeAttr): Edge attribute to fetch the value of
+
+        Raises:
+            ValueError: if attr is not a EdgeAttr
+
+        Returns:
+            bool: The value of the attribute for that edge. If the attribute
+                is not present on the graph, the value is presumed False.
+        """
+        if not isinstance(attr, EdgeAttr):
+            raise ValueError(
+                f"Provided attribute {attr} is not of type EdgeAttr. "
+                "Please use the enum instead of passing string values, "
+                "and add new attributes to the class to avoid key collision."
+            )
+
+        if attr not in self.graph.edges[_id]:
+            return False
+        return self.graph.edges[_id][attr]
 
     def get_tracklets(self):
         """Gets a list of new TrackingGraph objects containing all tracklets of the current graph.

tests/test_tracking_graph.py

@@ -1,3 +1,5 @@
+from collections import Counter
+
 import networkx as nx
 import pytest
 from traccuracy import EdgeAttr, NodeAttr, TrackingGraph
@@ -114,10 +116,10 @@ def test_constructor(nx_comp1):
     assert tracking_graph.start_frame == 0
     assert tracking_graph.end_frame == 4
     assert tracking_graph.nodes_by_frame == {
-        0: ["1_0"],
-        1: ["1_1"],
-        2: ["1_2", "1_3"],
-        3: ["1_4"],
+        0: {"1_0"},
+        1: {"1_1"},
+        2: {"1_2", "1_3"},
+        3: {"1_4"},
     }
 
     # raise AssertionError if frame key not present or ValueError if overlaps
@@ -134,14 +136,18 @@ def test_constructor(nx_comp1):
 
 def test_get_cells_by_frame(simple_graph):
     assert simple_graph.get_nodes_in_frame(0) == ["1_0"]
-    assert simple_graph.get_nodes_in_frame(2) == ["1_2", "1_3"]
+    assert Counter(simple_graph.get_nodes_in_frame(2)) == Counter(["1_2", "1_3"])
     assert simple_graph.get_nodes_in_frame(5) == []
 
 
 def test_get_nodes_by_roi(simple_graph):
     assert simple_graph.get_nodes_by_roi(t=(0, 1)) == ["1_0"]
-    assert simple_graph.get_nodes_by_roi(x=(1, None)) == ["1_0", "1_1", "1_3", "1_4"]
-    assert simple_graph.get_nodes_by_roi(x=(None, 2), t=(1, None)) == ["1_1", "1_2"]
+    assert Counter(simple_graph.get_nodes_by_roi(x=(1, None))) == Counter(
+        ["1_0", "1_1", "1_3", "1_4"]
+    )
+    assert Counter(simple_graph.get_nodes_by_roi(x=(None, 2), t=(1, None))) == Counter(
+        ["1_1", "1_2"]
+    )
 
 
 def test_get_location(nx_comp1):
@@ -219,7 +225,7 @@ def test_get_preds(simple_graph, merge_graph):
 
 def test_get_succs(simple_graph):
     assert simple_graph.get_succs("1_0") == ["1_1"]
-    assert simple_graph.get_succs("1_1") == ["1_2", "1_3"]
+    assert Counter(simple_graph.get_succs("1_1")) == Counter(["1_2", "1_3"])
     assert simple_graph.get_succs("1_2") == []