convert all graph data where necessary before saving to make it json serializable

src/motile_plugin/data_model/tracks.py

@@ -163,6 +163,7 @@ def get_time(self, node: Node) -> int:
         return int(self.get_times([node])[0])
 
     def set_times(self, nodes: Iterable[Node], times: Iterable[int]):
+        times = [int(t) for t in times]
         self._remove_from_seg_time_to_node(nodes)
         self._set_nodes_attr(nodes, self.time_attr, times)
         self._add_to_seg_time_to_node(nodes)
@@ -176,7 +177,7 @@ def set_time(self, node: Any, time: int):
             time (int): The time to set
 
         """
-        self.set_times([node], [time])
+        self.set_times([node], [int(time)])
 
     def get_seg_ids(
         self, nodes: Iterable[Node], required=False
@@ -205,12 +206,13 @@ def set_seg_ids(self, nodes: Iterable[Node], seg_ids: Iterable[int]):
             node (Any): The node id to set the seg id of
             seg_id (int): The segmentation id to set for the node
         """
+        seg_ids = [int(seg_id) for seg_id in seg_ids]
         self._remove_from_seg_time_to_node(nodes)
         self._set_nodes_attr(nodes, NodeAttr.SEG_ID.value, seg_ids)
         self._add_to_seg_time_to_node(nodes)
 
     def set_seg_id(self, node: Node, seg_id: int):
-        self.set_seg_ids([node], [seg_id])
+        self.set_seg_ids([node], [int(seg_id)])
 
     def add_nodes(
         self,
@@ -222,6 +224,8 @@ def add_nodes(
     ):
         if attrs is None:
             attrs = {}
+        for node in nodes:
+            print("add node", node)
         self.graph.add_nodes_from(nodes)
         self.set_times(nodes, times)
         final_pos: np.ndarray
@@ -493,8 +497,29 @@ def _save_graph(self, directory: Path):
             directory (Path): The directory in which to save the graph file.
         """
         graph_file = directory / self.GRAPH_FILE
+        graph_data = nx.node_link_data(self.graph)
+
+        def convert_np_types(data):
+            """Recursively convert numpy types to native Python types."""
+
+            if isinstance(data, dict):
+                return {key: convert_np_types(value) for key, value in data.items()}
+            elif isinstance(data, list):
+                return [convert_np_types(item) for item in data]
+            elif isinstance(data, np.ndarray):
+                return data.tolist()  # Convert numpy arrays to Python lists
+            elif isinstance(data, np.integer):
+                return int(data)  # Convert numpy integers to Python int
+            elif isinstance(data, np.floating):
+                return float(data)  # Convert numpy floats to Python float
+            else:
+                return (
+                    data  # Return the data as-is if it's already a native Python type
+                )
+
+        graph_data = convert_np_types(graph_data)
         with open(graph_file, "w") as f:
-            json.dump(nx.node_link_data(self.graph), f)
+            json.dump(graph_data, f)
 
     def _save_seg(self, directory: Path):
         """Save a segmentation as a numpy array using np.save. In the future,
@@ -514,9 +539,16 @@ def _save_attrs(self, directory: Path):
         """
         out_path = directory / self.ATTRS_FILE
         attrs_dict = {
-            "time_attr": self.time_attr
-            if not isinstance(self.time_attr, np.ndarray)
-            else self.time_attr.tolist(),
+            "time_attr": (
+                self.time_attr.astype(
+                    np.uint16
+                ).tolist()  # Convert to uint16 and convert to list
+                if isinstance(self.time_attr, np.ndarray)
+                and self.time_attr.dtype == np.int64
+                else self.time_attr.tolist()  # Convert to list if it's a numpy array
+                if isinstance(self.time_attr, np.ndarray)
+                else self.time_attr  # Otherwise, keep as is
+            ),
             "pos_attr": self.pos_attr
             if not isinstance(self.pos_attr, np.ndarray)
             else self.pos_attr.tolist(),