Keller mark/spatial data2

tests/test_wrappers.py

@@ -394,13 +394,69 @@ def test_multivec_zarr_with_base_dir(self):
     def test_spatial_data_with_base_dir(self):
 
         spatial_data_path = 'test.spatialdata.zarr'
-        w = SpatialDataWrapper(sdata_path=spatial_data_path, image_path="images/picture", obs_set_paths=['obs/CellType'], obs_set_names=['Cell Type'], obs_embedding_paths=[
-            'obsm/X_umap'], obs_embedding_names=['UMAP'])
+        w = SpatialDataWrapper(
+            sdata_path=spatial_data_path,
+            image_path="images/picture",
+            obs_set_paths=['obs/CellType'],
+            obs_set_names=['Cell Type'],
+            obs_embedding_paths=['obsm/X_umap'],
+            obs_embedding_names=['UMAP']
+        )
         w.base_dir = data_path
         w.local_dir_uid = 'spatialdata.zarr'
 
         file_def_creator = w.make_file_def_creator('A', 0)
         file_def = file_def_creator('http://localhost:8000')
-        print(file_def)
-        self.assertEqual(file_def,
-                         {'fileType': 'spatialdata.zarr', 'url': 'http://localhost:8000/test.spatialdata.zarr', 'options': {'obsSets': {'obsSets': [{'name': 'Cell Type', 'path': 'obs/CellType'}], 'tablePath': 'tables/table'}, 'image': {'path': 'images/picture'}}})
+        self.assertEqual(file_def, {
+            'fileType': 'spatialdata.zarr',
+            'url': 'http://localhost:8000/test.spatialdata.zarr',
+            'options': {
+                'obsSets': {
+                    'obsSets': [{'name': 'Cell Type', 'path': 'obs/CellType'}],
+                    'tablePath': 'tables/table'
+                },
+                'image': {'path': 'images/picture'}
+            }})
+
+    def test_spatial_data_with_base_dir_2(self):
+        spatial_data_path = 'test.spatialdata.zarr'
+        w = SpatialDataWrapper(
+            sdata_path=spatial_data_path,
+            image_path='images/CytAssist_FFPE_Human_Breast_Cancer_full_image',
+            coordinate_system='aligned',
+            region='CytAssist_FFPE_Human_Breast_Cancer',
+            obs_feature_matrix_path='tables/table/X',
+            obs_spots_path='shapes/CytAssist_FFPE_Human_Breast_Cancer',
+            table_path='tables/table',
+            coordination_values={
+                "obsType": "spot"
+            }
+        )
+        w.base_dir = data_path
+        w.local_dir_uid = 'spatialdata.zarr'
+
+        file_def_creator = w.make_file_def_creator('A', 0)
+        file_def = file_def_creator('http://localhost:8000')
+        self.assertDictEqual(file_def, {
+            'fileType': 'spatialdata.zarr',
+            'url': 'http://localhost:8000/test.spatialdata.zarr',
+            'options': {
+                'image': {
+                    'path': 'images/CytAssist_FFPE_Human_Breast_Cancer_full_image',
+                    'coordinateSystem': 'aligned',
+                },
+                'obsFeatureMatrix': {
+                    'path': 'tables/table/X',
+                    'region': 'CytAssist_FFPE_Human_Breast_Cancer'
+                },
+                'obsSpots': {
+                    'path': 'shapes/CytAssist_FFPE_Human_Breast_Cancer',
+                    'tablePath': 'tables/table',
+                    'region': 'CytAssist_FFPE_Human_Breast_Cancer',
+                    'coordinateSystem': 'aligned',
+                }
+            },
+            'coordinationValues': {
+                "obsType": "spot"
+            }
+        })

vitessce/file_def_utils.py

@@ -142,13 +142,28 @@ def gen_sdata_labels_schema(options, path: str, table_path: str = "tables/table"
     return options
 
 
-def gen_sdata_obs_spots_schema(options: dict, shapes_path: Optional[str] = None, table_path: str = "tables/table", region: Optional[str] = None, coordinate_system: Optional[str] = None) -> dict:
+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'] = {
             "path": shapes_path,
-            "tablePath": table_path,
-            "region": region
+            "tablePath": table_path
         }
+        if region is not None:
+            options['obsSpots']['region'] = region
         if coordinate_system is not None:
             options['obsSpots']['coordinateSystem'] = coordinate_system
     return options
+
+
+def gen_sdata_obs_feature_matrix_schema(options: dict, matrix_path: Optional[str] = None, var_filter_path: Optional[str] = None, init_var_filter_path: Optional[str] = None, region: Optional[str] = None):
+    if matrix_path is not None:
+        options["obsFeatureMatrix"] = {
+            "path": matrix_path
+        }
+        if region is not None:
+            options['obsFeatureMatrix']['region'] = region
+        if var_filter_path is not None:
+            options["obsFeatureMatrix"]["featureFilterPath"] = var_filter_path
+        if init_var_filter_path is not None:
+            options["obsFeatureMatrix"]["initialFeatureFilterPath"] = init_var_filter_path
+    return options

vitessce/widget.py

@@ -454,7 +454,7 @@ class VitessceWidget(anywidget.AnyWidget):
 
     next_port = DEFAULT_PORT
 
-    js_package_version = Unicode('3.4.12').tag(sync=True)
+    js_package_version = Unicode('3.4.14').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)
@@ -463,7 +463,7 @@ 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='3.4.12', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, invoke_timeout=30000):
+    def __init__(self, config, height=600, theme='auto', uid=None, port=None, proxy=False, js_package_version='3.4.14', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, invoke_timeout=30000):
         """
         Construct a new Vitessce widget.
 
@@ -576,7 +576,7 @@ 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='3.4.12', js_dev_mode=False, custom_js_url='', plugin_esm=DEFAULT_PLUGIN_ESM, remount_on_uid_change=True):
+def ipython_display(config, height=600, theme='auto', base_url=None, host_name=None, uid=None, port=None, proxy=False, js_package_version='3.4.14', js_dev_mode=False, custom_js_url='', plugin_esm=DEFAULT_PLUGIN_ESM, remount_on_uid_change=True):
     from IPython.display import display, HTML
     uid_str = "vitessce" + get_uid_str(uid)
 

vitessce/wrappers.py

@@ -31,7 +31,8 @@
     gen_sdata_image_schema,
     gen_sdata_labels_schema,
     gen_sdata_obs_spots_schema,
-    gen_sdata_obs_sets_schema
+    gen_sdata_obs_sets_schema,
+    gen_sdata_obs_feature_matrix_schema,
 )
 
 from .constants import (
@@ -1289,7 +1290,7 @@ 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, affine_transformation: Optional[np.ndarray] = None, spot_shapes_path: Optional[str] = None, labels_path: Optional[str] = None, table_path: str = "tables/table", **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, affine_transformation: Optional[np.ndarray] = None, obs_spots_path: Optional[str] = None, labels_path: Optional[str] = None, table_path: str = "tables/table", **kwargs):
         """
         Wrap a SpatialData object.
 
@@ -1301,16 +1302,16 @@ def __init__(self, sdata_path: Optional[str] = None, sdata_url: Optional[str] =
         :type sdata_store: Optional[Union[str, zarr.storage.StoreLike]]
         :param sdata_artifact: Artifact that corresponds to a SpatialData object.
         :type sdata_artifact: Optional[ln.Artifact]
-        :param image_elem: Name of the image element of interest. By default, None.
-        :type image_elem: Optional[str]
+        :param image_path: Path to the image element of interest. By default, None.
+        :type image_path: Optional[str]
         :param coordinate_system: Name of a target coordinate system.
         :type coordinate_system: Optional[str]
         :param affine_transformation: Transformation to be applied to the image. By default, None. Prefer coordinate_system.
         :type affine_transformation: Optional[np.ndarray]
-        :param shapes_elem: location of the shapes, by default None
-        :type shapes_elem: Optional[str]
-        :param labels_elem: location of the labels, by default None
-        :type labels_elem: Optional[str]
+        :param obs_spots_path: Location of shapes that should be interpreted as spot observations, by default None
+        :type obs_spots_path: Optional[str]
+        :param labels_path: Location of the labels (segmentation bitmask image), by default None
+        :type labels_path: Optional[str]
         """
         raise_error_if_zero_or_more_than_one([
             sdata_path,
@@ -1331,7 +1332,7 @@ def __init__(self, sdata_path: Optional[str] = None, sdata_url: Optional[str] =
         self._coordinate_system = coordinate_system
         self._affine_transformation = affine_transformation
         self._kwargs = kwargs
-        self._spot_shapes_path = spot_shapes_path
+        self._obs_spots_path = obs_spots_path
         self._labels_path = labels_path
         if self._adata_path is not None:
             self.zarr_folder = 'spatialdata.zarr'
@@ -1402,7 +1403,7 @@ def from_object(cls: Type[SpatialDataWrapperType], sdata: SpatialData, table_key
                     image_path=str(image_elem) if image_elem is not None else None,
                     labels_path=str(labels_elem) if labels_elem is not None else None,
                     obs_feature_matrix_path=str(obs_feature_matrix_elem),
-                    spot_shapes_path=str(spot_shapes_elem) if spot_shapes_elem is not None else None,
+                    obs_spots_path=str(spot_shapes_elem) if spot_shapes_elem is not None else None,
                     initial_feature_filter_path=initial_feature_filter_elem,
                     obs_set_paths=obs_set_elems,
                     coordination_values={"obsType": "spot"}  # TODO: should we remove?
@@ -1414,9 +1415,9 @@ def make_file_def_creator(self, dataset_uid: str, obj_i: str) -> Optional[Callab
         def generator(base_url):
             options = {}
             options = gen_obs_labels_schema(options, self._obs_labels_elems, self._obs_labels_names)
-            options = gen_obs_feature_matrix_schema(options, self._expression_matrix, self._gene_var_filter, self._matrix_gene_var_filter)
+            options = gen_sdata_obs_feature_matrix_schema(options, self._expression_matrix, self._gene_var_filter, self._matrix_gene_var_filter, self._region)
             options = gen_sdata_obs_sets_schema(options, self._obs_set_elems, self._obs_set_names, self._table_path, self._region)
-            options = gen_sdata_obs_spots_schema(options, self._spot_shapes_path, self._table_path, self._region, self._coordinate_system)
+            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, self._affine_transformation)
             options = gen_sdata_labels_schema(options, self._labels_path, self._table_path, self._coordinate_system, self._affine_transformation)
             options = gen_feature_labels_schema(self._feature_labels, options)