refactor!: rename NiiVue._meshes and NiiVue._volumes

These attributes are now public, and the underscore prefix has been removed. This is a breaking change; accessing `nv._meshes` and `nv._volumes` will no longer work.

Author: AnthonyAndroulakis

examples/draw.ui.ipynb

@@ -741,7 +741,7 @@
     "    # Update the previous_script_value\n",
     "    previous_script_value[0] = value\n",
     "\n",
-    "    nv._meshes = []\n",
+    "    nv.meshes = []\n",
     "    if value == \"FLAIR\":\n",
     "        volume_list1 = [{\"path\": DATA_FOLDER / \"FLAIR.nii.gz\"}]\n",
     "        nv.load_volumes(volume_list1)\n",

js/mesh.ts

@@ -351,7 +351,7 @@ export async function render_meshes(
 ) {
 	const mmodels = await lib.gather_models<MeshModel>(
 		model,
-		model.get("_meshes"),
+		model.get("meshes"),
 	);
 
 	const backend_meshes = mmodels;

js/types.ts

@@ -80,8 +80,8 @@ export type MeshLayerModel = AnyModel<{
 export type Model = AnyModel<{
 	id: string;
 	height: number;
-	_volumes: Array<string>;
-	_meshes: Array<string>;
+	volumes: Array<string>;
+	meshes: Array<string>;
 	opts: Partial<Record<keyof NVConfigOptions, unknown>>;
 
 	background_masks_overlays: number;

js/volume.ts

@@ -161,7 +161,7 @@ export async function render_volumes(
 ) {
 	const vmodels = await lib.gather_models<VolumeModel>(
 		model,
-		model.get("_volumes"),
+		model.get("volumes"),
 	);
 
 	const backend_volumes = vmodels;

js/widget.ts

@@ -45,12 +45,12 @@ function attachModelEventHandlers(
 	model: Model,
 	disposer: Disposer,
 ) {
-	model.on("change:_volumes", () => {
+	model.on("change:volumes", () => {
 		if (nv.canvas) {
 			render_volumes(nv, model, disposer);
 		}
 	});
-	model.on("change:_meshes", () => {
+	model.on("change:meshes", () => {
 		if (nv.canvas) {
 			render_meshes(nv, model, disposer);
 		}
@@ -211,7 +211,7 @@ function attachNiivueEventHandlers(nv: niivue.Niivue, model: Model) {
 		const volumeID = volume.id;
 		const volumeModels = await gather_models<VolumeModel>(
 			model,
-			model.get("_volumes"),
+			model.get("volumes"),
 		);
 
 		const backendVolumeIds = volumeModels.map(
@@ -256,7 +256,7 @@ function attachNiivueEventHandlers(nv: niivue.Niivue, model: Model) {
 		const meshID = mesh.id;
 		const meshModels = await gather_models<MeshModel>(
 			model,
-			model.get("_meshes"),
+			model.get("meshes"),
 		);
 
 		const backendMeshIds = meshModels.map((mmodel) => mmodel?.get("id") || "");
@@ -542,8 +542,8 @@ export default {
 		return () => {
 			disposer.disposeAll();
 
-			model.off("change:_volumes");
-			model.off("change:_meshes");
+			model.off("change:volumes");
+			model.off("change:meshes");
 			model.off("change:opts");
 			model.off("change:height");
 			model.off("msg:custom");

src/ipyniivue/widget.py

@@ -337,10 +337,10 @@ class NiiVue(anywidget.AnyWidget):
     opts = t.Instance(ConfigOptions).tag(
         sync=True, to_json=serialize_options, from_json=deserialize_options
     )
-    _volumes = t.List(t.Instance(Volume), default_value=[]).tag(
+    volumes = t.List(t.Instance(Volume), default_value=[]).tag(
         sync=True, **ipywidgets.widget_serialization
     )
-    _meshes = t.List(t.Instance(Mesh), default_value=[]).tag(
+    meshes = t.List(t.Instance(Mesh), default_value=[]).tag(
         sync=True, **ipywidgets.widget_serialization
     )
 
@@ -378,7 +378,7 @@ def __init__(self, height: int = 300, **options):  # noqa: D417
         """
         # convert to JS camelCase options
         opts = ConfigOptions(parent=self, **options)
-        super().__init__(height=height, opts=opts, _volumes=[], _meshes=[])
+        super().__init__(height=height, opts=opts, volumes=[], meshes=[])
 
         # handle messages coming from frontend
         self._event_handlers = {}
@@ -441,17 +441,17 @@ def _handle_custom_msg(self, content, buffers):
         elif event == "frame_change":
             idx = self.get_volume_index_by_id(data["id"])
             if idx != -1:
-                handler(self._volumes[idx], data["frame_index"])
+                handler(self.volumes[idx], data["frame_index"])
         elif event in {"image_loaded", "intensity_change"}:
             idx = self.get_volume_index_by_id(data["id"])
             if idx != -1:
-                handler(self._volumes[idx])
+                handler(self.volumes[idx])
             else:
                 handler(data)
         elif event == "mesh_loaded":
             idx = self.get_mesh_index_by_id(data["id"])
             if idx != -1:
-                handler(self._meshes[idx])
+                handler(self.meshes[idx])
             else:
                 handler(data)
         elif event == "mesh_added_from_url":
@@ -466,20 +466,20 @@ def _handle_custom_msg(self, content, buffers):
     def _add_volume_from_frontend(self, volume_data):
         index = volume_data.pop("index", None)
         volume = Volume(**volume_data)
-        if index is not None and 0 <= index <= len(self._volumes):
-            self._volumes = [*self._volumes[:index], volume, *self._volumes[index:]]
+        if index is not None and 0 <= index <= len(self.volumes):
+            self.volumes = [*self.volumes[:index], volume, *self.volumes[index:]]
         else:
-            self._volumes = [*self._volumes, volume]
+            self.volumes = [*self.volumes, volume]
 
     def _add_mesh_from_frontend(self, mesh_data):
         index = mesh_data.pop("index", None)
         layers_data = mesh_data.pop("layers", [])
         mesh = Mesh(**mesh_data)
         mesh.layers = [MeshLayer(**layer_data) for layer_data in layers_data]
-        if index is not None and 0 <= index <= len(self._meshes):
-            self._meshes = [*self._meshes[:index], mesh, *self._meshes[index:]]
+        if index is not None and 0 <= index <= len(self.meshes):
+            self.meshes = [*self.meshes[:index], mesh, *self.meshes[index:]]
         else:
-            self._meshes = [*self._meshes, mesh]
+            self.meshes = [*self.meshes, mesh]
 
     def close(self):
         """
@@ -506,7 +506,7 @@ def get_volume_index_by_id(self, volume_id: str) -> int:
         volume_id : str
             The id of the volume.
         """
-        for idx, vol in enumerate(self._volumes):
+        for idx, vol in enumerate(self.volumes):
             if vol.id == volume_id:
                 return idx
         return -1
@@ -519,7 +519,7 @@ def get_mesh_index_by_id(self, mesh_id: str) -> int:
         mesh_id : str
             The id of the mesh.
         """
-        for idx, mesh in enumerate(self._meshes):
+        for idx, mesh in enumerate(self.meshes):
             if mesh.id == mesh_id:
                 return idx
         return -1
@@ -546,7 +546,7 @@ def load_volumes(self, volumes: list):
 
         """
         volumes = [Volume(**item) for item in volumes]
-        self._volumes = volumes
+        self.volumes = volumes
 
     def add_volume(self, volume: dict):
         """
@@ -569,26 +569,7 @@ def add_volume(self, volume: dict):
             nv.add_volume({"path": "mni152.nii.gz"})
 
         """
-        self._volumes = [*self._volumes, Volume(**volume)]
-
-    @property
-    def volumes(self):
-        """
-        Returns the list of volumes.
-
-        Returns
-        -------
-        list
-            A list of dictionairies containing the volume information.
-
-        Examples
-        --------
-        ::
-
-            print(nv.volumes)
-
-        """
-        return list(self._volumes)
+        self.volumes = [*self.volumes, Volume(**volume)]
 
     def load_meshes(self, meshes: list):
         """
@@ -612,7 +593,7 @@ def load_meshes(self, meshes: list):
 
         """
         meshes = [Mesh(**item) for item in meshes]
-        self._meshes = meshes
+        self.meshes = meshes
 
     def add_mesh(self, mesh: Mesh):
         """
@@ -635,26 +616,7 @@ def add_mesh(self, mesh: Mesh):
             nv.add_mesh({"path": "BrainMesh_ICBM152.lh.mz3"})
 
         """
-        self._meshes = [*self._meshes, mesh]
-
-    @property
-    def meshes(self):
-        """
-        Returns the list of meshes.
-
-        Returns
-        -------
-        list
-            A list of dictionairies containing the mesh information.
-
-        Examples
-        --------
-        ::
-
-            print(nv.meshes)
-
-        """
-        return list(self._meshes)
+        self.meshes = [*self.meshes, mesh]
 
     """
     Other functions
@@ -804,7 +766,7 @@ def set_mesh_property(self, mesh_id: str, attribute: str, value: typing.Any):
         if idx == -1:
             raise ValueError(f"Mesh with id '{mesh_id}' not found.")
 
-        mesh = self._meshes[idx]
+        mesh = self.meshes[idx]
         setattr(mesh, attribute, value)
 
     def set_mesh_layer_property(
@@ -854,7 +816,7 @@ def set_mesh_layer_property(
         if idx == -1:
             raise ValueError(f"Mesh with id '{mesh_id}' not found.")
 
-        mesh = self._meshes[idx]
+        mesh = self.meshes[idx]
         if layer_index < 0 or layer_index >= len(mesh.layers):
             raise IndexError(f"Layer index {layer_index} out of range.")
 
@@ -955,7 +917,7 @@ def set_colormap(self, imageID: str, colormap: str):
         """
         idx = self.get_volume_index_by_id(imageID)
         if idx != -1:
-            self._volumes[idx].colormap = colormap
+            self.volumes[idx].colormap = colormap
         else:
             raise ValueError(f"Volume with ID '{imageID}' not found")