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Merged
keller-mark merged 2 commits into from
Oct 13, 2025
Merged

Support obs_points_path in SpatialDataWrapper #478

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Support obs_points_path in SpatialDataWrapper
keller-mark Oct 13, 2025
5953a0b
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keller-mark Oct 13, 2025
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35 changes: 34 additions & 1 deletion docs/notebooks/spatial_data_blobs.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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);"
]
Expand Down
2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -4,7 +4,7 @@ build-backend = "hatchling.build"

[project]
name = "vitessce"
version = "3.7.4"
version = "3.7.5"
authors = [
{ name="Mark Keller", email="mark_keller@hms.harvard.edu" },
]
Expand Down
12 changes: 12 additions & 0 deletions src/vitessce/file_def_utils.py
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Expand Up @@ -147,6 +147,18 @@ def gen_sdata_obs_segmentations_schema(options, path: str, table_path: str = "ta
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:
options['obsSpots'] = {
Expand Down
6 changes: 3 additions & 3 deletions src/vitessce/widget.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand All @@ -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``.

Expand Down Expand Up @@ -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)

Expand Down
7 changes: 6 additions & 1 deletion src/vitessce/wrappers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down Expand Up @@ -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.

Expand All @@ -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,
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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 = {
Expand Down