Support obs_points_path in SpatialDataWrapper

Author: keller-mark

docs/notebooks/spatial_data_blobs.ipynb

@@ -60,6 +60,21 @@
     "sdata.write(spatialdata_filepath, overwrite=True)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Change data type of x and y columns from int64 to int32\n",
+    "# Temporary workaround, will be resolved by https://github.com/vitessce/vitessce/issues/2292\n",
+    "ddf = sdata[\"blobs_points\"]\n",
+    "ddf[\"x\"] = ddf[\"x\"].astype('int32')\n",
+    "ddf[\"y\"] = ddf[\"y\"].astype('int32')\n",
+    "sdata[\"blobs_points_2\"] = ddf\n",
+    "sdata.write_element(\"blobs_points_2\")"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -107,7 +122,17 @@
     "        \"fileUid\": \"my_unique_id\"\n",
     "    }\n",
     ")\n",
-    "dataset = vc.add_dataset(name='Blobs').add_object(wrapper)\n",
+    "points_wrapper = SpatialDataWrapper(\n",
+    "    sdata_store=spatialdata_filepath,\n",
+    "    # The following paths are relative to the root of the SpatialData zarr store on-disk.\n",
+    "    obs_points_path=\"points/blobs_points_2\",\n",
+    "    coordinate_system=\"global\",\n",
+    "    coordination_values={\n",
+    "        \"obsType\": \"point\",\n",
+    "        \"fileUid\": \"other_unique_id\"\n",
+    "    }\n",
+    ")\n",
+    "dataset = vc.add_dataset(name='Blobs').add_object(wrapper).add_object(points_wrapper)\n",
     "\n",
     "# Add views (visualizations) to the configuration:\n",
     "spatial = vc.add_view(\"spatialBeta\", dataset=dataset)\n",
@@ -148,6 +173,14 @@
     "    }]),\n",
     "}, scope_prefix=get_initial_coordination_scope_prefix(\"A\", \"obsSegmentations\"))\n",
     "\n",
+    "vc.link_views_by_dict([spatial, layer_controller], {\n",
+    "    'pointLayer': CL([{\n",
+    "        \"fileUid\": \"other_unique_id\",\n",
+    "        \"obsType\": \"point\",\n",
+    "        \"obsHighlight\": None,\n",
+    "    }]),\n",
+    "}, scope_prefix=get_initial_coordination_scope_prefix(\"A\", \"obsPoints\"))\n",
+    "\n",
     "# Layout the views\n",
     "vc.layout(spatial | layer_controller);"
    ]

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "vitessce"
-version = "3.7.4"
+version = "3.7.5"
 authors = [
   { name="Mark Keller", email="[email protected]" },
 ]

src/vitessce/file_def_utils.py

@@ -146,6 +146,16 @@ def gen_sdata_obs_segmentations_schema(options, path: str, table_path: str = "ta
             options["obsSegmentations"]['coordinateSystem'] = coordinate_system
     return options
 
+def gen_sdata_obs_points_schema(options, path: str, table_path: str = "tables/table", coordinate_system: Optional[str] = None) -> dict:
+    if path is not None:
+        options["obsPoints"] = {
+            "path": path
+        }
+        if table_path is not None:
+            options["obsPoints"]['tablePath'] = table_path
+        if coordinate_system is not None:
+            options["obsPoints"]['coordinateSystem'] = coordinate_system
+    return options
 
 def gen_sdata_obs_spots_schema(options: dict, shapes_path: str, table_path: str = "tables/table", region: Optional[str] = None, coordinate_system: Optional[str] = None) -> dict:
     if shapes_path is not None:

src/vitessce/widget.py

@@ -651,7 +651,7 @@ class VitessceWidget(anywidget.AnyWidget):
 
     next_port = DEFAULT_PORT
 
-    js_package_version = Unicode('3.6.18').tag(sync=True)
+    js_package_version = Unicode('3.8.3').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)
@@ -664,7 +664,7 @@ 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='3.6.18', 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, server_host=None):
+    def __init__(self, config, height=600, theme='auto', uid=None, port=None, proxy=False, js_package_version='3.8.3', 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, server_host=None):
         """
         Construct a new Vitessce widget. Not intended to be instantiated directly; instead, use ``VitessceConfig.widget``.
 
@@ -798,7 +798,7 @@ 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='3.6.18', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, page_mode=False, page_esm=None, server_host=None):
+def ipython_display(config, height=600, theme='auto', base_url=None, host_name=None, uid=None, port=None, proxy=False, js_package_version='3.8.3', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, page_mode=False, page_esm=None, server_host=None):
     from IPython.display import display, HTML
     uid_str = "vitessce" + get_uid_str(uid)
 

src/vitessce/wrappers.py

@@ -28,6 +28,7 @@
     gen_obs_sets_schema,
     gen_sdata_image_schema,
     gen_sdata_obs_segmentations_schema,
+    gen_sdata_obs_points_schema,
     gen_sdata_obs_spots_schema,
     gen_sdata_obs_sets_schema,
     gen_sdata_obs_feature_matrix_schema,
@@ -1399,7 +1400,7 @@ def auto_view_config(self, vc):
 
 class SpatialDataWrapper(AnnDataWrapper):
 
-    def __init__(self, sdata_path: Optional[str] = None, sdata_url: Optional[str] = None, sdata_store: Optional[Union[str, zarr.storage.StoreLike]] = None, sdata_artifact: Optional[ln.Artifact] = None, image_path: Optional[str] = None, region: Optional[str] = None, coordinate_system: Optional[str] = None, obs_spots_path: Optional[str] = None, obs_segmentations_path: Optional[str] = None, table_path: str = "tables/table", is_zip=None, coordination_values=None, **kwargs):
+    def __init__(self, sdata_path: Optional[str] = None, sdata_url: Optional[str] = None, sdata_store: Optional[Union[str, zarr.storage.StoreLike]] = None, sdata_artifact: Optional[ln.Artifact] = None, image_path: Optional[str] = None, region: Optional[str] = None, coordinate_system: Optional[str] = None, obs_spots_path: Optional[str] = None, obs_segmentations_path: Optional[str] = None, obs_points_path: Optional[str] = None, table_path: str = "tables/table", is_zip=None, coordination_values=None, **kwargs):
         """
         Wrap a SpatialData object.
 
@@ -1422,6 +1423,8 @@ def __init__(self, sdata_path: Optional[str] = None, sdata_url: Optional[str] =
         :type obs_spots_path: Optional[str]
         :param obs_segmentations_path: Path to a labels or shapes element (segmentation bitmask label image or segmentation polygon shapes), by default None
         :type obs_segmentations_path: Optional[str]
+        :param obs_points_path: Path to a points element, by default None
+        :type obs_points_path: Optional[str]
         """
         raise_error_if_zero_or_more_than_one([
             sdata_path,
@@ -1451,6 +1454,7 @@ def __init__(self, sdata_path: Optional[str] = None, sdata_url: Optional[str] =
         self._kwargs = kwargs
         self._obs_spots_path = obs_spots_path
         self._obs_segmentations_path = obs_segmentations_path
+        self._obs_points_path = obs_points_path
         if self._adata_path is not None:
             self.zarr_folder = 'spatialdata.zarr'
         self.obs_type_label = None
@@ -1538,6 +1542,7 @@ def generator(base_url):
             options = gen_sdata_obs_spots_schema(options, self._obs_spots_path, self._table_path, self._region, self._coordinate_system)
             options = gen_sdata_image_schema(options, self._image_path, self._coordinate_system)
             options = gen_sdata_obs_segmentations_schema(options, self._obs_segmentations_path, self._table_path, self._coordinate_system)
+            options = gen_sdata_obs_points_schema(options, self._obs_points_path, self._table_path, self._coordinate_system)
             options = gen_feature_labels_schema(self._feature_labels, options)
             if len(options.keys()) > 0:
                 obj_file_def = {