Add visium HD nb

Author: keller-mark

docs/notebooks/spatial_data_visium_hd.ipynb

@@ -137,33 +137,6 @@
     "sdata"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Test with spatialdata-plot"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import spatialdata_plot"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "sdata.pl.render_images(\"Visium_HD_Mouse_Small_Intestine_full_image\").pl.render_labels(\"rasterized_016um\").pl.show(\"Visium_HD_Mouse_Small_Intestine\")"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -209,8 +182,17 @@
     "        'photometricInterpretation': 'RGB',\n",
     "    }]),\n",
     "}, scope_prefix=get_initial_coordination_scope_prefix(\"A\", \"image\"))\n",
+    "vc.link_views_by_dict([spatial, layer_controller], {\n",
+    "    'segmentationLayer': CL([{\n",
+    "        'segmentationChannel': CL([{\n",
+    "            'spatialChannelOpacity': 0.5,\n",
+    "            'obsColorEncoding': 'geneSelection',\n",
+    "            'featureValueColormapRange': [0, 0.5],\n",
+    "        }])\n",
+    "    }]),\n",
+    "}, scope_prefix=get_initial_coordination_scope_prefix(\"A\", \"obsSegmentations\"))\n",
     "obs_sets = vc.add_view(vt.OBS_SETS, dataset=dataset)\n",
-    "vc.link_views([spatial, layer_controller, feature_list, obs_sets], ['obsType'], [wrapper.obs_type_label])\n",
+    "vc.link_views([spatial, layer_controller, feature_list, obs_sets], ['obsType', 'featureSelection'], [wrapper.obs_type_label, ['AA986860']])\n",
     "\n",
     "# Layout the views\n",
     "vc.layout(spatial | (feature_list / layer_controller / obs_sets));"
@@ -233,16 +215,6 @@
     "vw"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import json\n",
-    "print(json.dumps(vc.to_dict(base_url=f\"http://localhost:{vw.port}\")))"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,

src/vitessce/widget.py

@@ -445,7 +445,7 @@ def get_uid_str(uid):
     function VitessceWidget(props) {
         const { model, styleContainer } = props;
 
-        const [config, setConfig] = React.useState(prependBaseUrl(model.get('config'), model.get('proxy'), model.get('has_host_name')));
+        const [config, setConfig] = React.useState(prependBaseUrl(model.get('_config'), model.get('proxy'), model.get('has_host_name')));
         const [validateConfig, setValidateConfig] = React.useState(true);
         const height = model.get('height');
         const theme = model.get('theme') === 'auto' ? (prefersDark ? 'dark' : 'light') : model.get('theme');
@@ -484,16 +484,16 @@ def get_uid_str(uid):
         // Config changed on JS side (from within <Vitessce/>),
         // send updated config to Python side.
         const onConfigChange = React.useCallback((config) => {
-            model.set('config', config);
+            model.set('_config', config);
             setValidateConfig(false);
             model.save_changes();
         }, [model]);
 
         // Config changed on Python side,
         // pass to <Vitessce/> component to it is updated on JS side.
         React.useEffect(() => {
-            model.on('change:config', () => {
-                const newConfig = prependBaseUrl(model.get('config'), model.get('proxy'), model.get('has_host_name'));
+            model.on('change:_config', () => {
+                const newConfig = prependBaseUrl(model.get('_config'), model.get('proxy'), model.get('has_host_name'));
 
                 // Force a re-render and re-validation by setting a new config.uid value.
                 // TODO: make this conditional on a parameter from Python.
@@ -622,7 +622,12 @@ class VitessceWidget(anywidget.AnyWidget):
     # Widget properties are defined as traitlets. Any property tagged with `sync=True`
     # is automatically synced to the frontend *any* time it changes in Python.
     # It is synced back to Python from the frontend *any* time the model is touched.
-    config = Dict({}).tag(sync=True)
+    _config = Dict({}).tag(sync=True)
+    """dict: Dictionary representation of the Vitessce JSON configuration. Synced via traitlets upon interactions."""
+
+    config = None
+    """VitessceConfig: The VitessceConfig instance used to create this widget. Not synced upon interactions."""
+
     height = Int(600).tag(sync=True)
     theme = Unicode('auto').tag(sync=True)
     proxy = Bool(False).tag(sync=True)
@@ -631,7 +636,7 @@ class VitessceWidget(anywidget.AnyWidget):
 
     next_port = DEFAULT_PORT
 
-    js_package_version = Unicode('3.6.11').tag(sync=True)
+    js_package_version = Unicode('3.6.12').tag(sync=True)
     js_dev_mode = Bool(False).tag(sync=True)
     custom_js_url = Unicode('').tag(sync=True)
     plugin_esm = List(trait=Unicode(''), default_value=[]).tag(sync=True)
@@ -644,7 +649,7 @@ class VitessceWidget(anywidget.AnyWidget):
 
     store_urls = List(trait=Unicode(''), default_value=[]).tag(sync=True)
 
-    def __init__(self, config, height=600, theme='auto', uid=None, port=None, proxy=False, js_package_version='3.6.11', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, prefer_local=True, invoke_timeout=300000, invoke_batched=True, page_mode=False, page_esm=None, prevent_scroll=True):
+    def __init__(self, config, height=600, theme='auto', uid=None, port=None, proxy=False, js_package_version='3.6.12', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, prefer_local=True, invoke_timeout=300000, invoke_batched=True, page_mode=False, page_esm=None, prevent_scroll=True):
         """
         Construct a new Vitessce widget.
 
@@ -678,7 +683,11 @@ def __init__(self, config, height=600, theme='auto', uid=None, port=None, proxy=
 
         base_url, use_port, VitessceWidget.next_port = get_base_url_and_port(
             port, VitessceWidget.next_port, proxy=proxy)
-        self.config_obj = config
+        # Note:
+        # - self.config is the VitessceConfig instance.
+        # - self._config is the JSON configuration, synced via traitlets
+
+        self.config = config
         self.port = use_port
         config_dict = config.to_dict(base_url=base_url)
         routes = config.get_routes()
@@ -694,7 +703,7 @@ def __init__(self, config, height=600, theme='auto', uid=None, port=None, proxy=
         uid_str = get_uid_str(uid)
 
         super(VitessceWidget, self).__init__(
-            config=config_dict, height=height, theme=theme, proxy=proxy,
+            _config=config_dict, height=height, theme=theme, proxy=proxy,
             js_package_version=js_package_version, js_dev_mode=js_dev_mode, custom_js_url=custom_js_url,
             plugin_esm=plugin_esm, remount_on_uid_change=remount_on_uid_change,
             page_mode=page_mode, page_esm=('' if page_esm is None else page_esm),
@@ -712,14 +721,14 @@ def handle_config_change(change):
                     # It is optional for plugins to implement on_config_change.
                     pass
             if new_config is not None:
-                self.config = new_config
+                self._config = new_config
 
-        self.observe(handle_config_change, names=['config'])
+        self.observe(handle_config_change, names=['_config'])
 
         serve_routes(config, routes, use_port)
 
     def _get_coordination_value(self, coordination_type, coordination_scope):
-        obj = self.config['coordinationSpace'][coordination_type]
+        obj = self._config['coordinationSpace'][coordination_type]
         obj_scopes = list(obj.keys())
         if coordination_scope is not None:
             if coordination_scope in obj_scopes:
@@ -742,7 +751,7 @@ def get_cell_selection(self, scope=None):
         return self._get_coordination_value('cellSelection', scope)
 
     def close(self):
-        self.config_obj.stop_server(self.port)
+        self.config.stop_server(self.port)
         super().close()
 
     @anywidget.experimental.command
@@ -780,7 +789,7 @@ def _plugin_command(self, params, buffers):
 # Launch Vitessce using plain HTML representation (no ipywidgets)
 
 
-def ipython_display(config, height=600, theme='auto', base_url=None, host_name=None, uid=None, port=None, proxy=False, js_package_version='3.6.11', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, page_mode=False, page_esm=None):
+def ipython_display(config, height=600, theme='auto', base_url=None, host_name=None, uid=None, port=None, proxy=False, js_package_version='3.6.12', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, page_mode=False, page_esm=None):
     from IPython.display import display, HTML
     uid_str = "vitessce" + get_uid_str(uid)