vitessce 3.6.2__py3-none-any.whl → 3.6.4__py3-none-any.whl

vitessce/config.py

@@ -602,7 +602,7 @@ class VitessceConfigView:
             })
             spatial_view.use_coordination_by_dict(scopes)
         """
-        if "coordinationScopes" not in self.view["coordinationScopes"] or self.view["coordinationScopes"] is None:
+        if "coordinationScopes" not in self.view or self.view["coordinationScopes"] is None:
             self.view["coordinationScopes"] = {}
 
         if "coordinationScopesBy" not in self.view or self.view["coordinationScopesBy"] is None:

vitessce/data_utils/ome.py

@@ -99,7 +99,9 @@ def rgb_img_to_ome_zarr(img_arr, output_path, img_name="Image", chunks=(1, 256,
     z_root.attrs["omero"] = {
         "name": img_name,
         "version": "0.3",
-        "rdefs": {},
+        "rdefs": {
+            "model": "color",
+        },
         "channels": [
             {
                 "label": "R",
@@ -156,7 +158,9 @@ def multiplex_img_to_ome_zarr(img_arr, channel_names, output_path, img_name="Ima
     z_root.attrs["omero"] = {
         "name": img_name,
         "version": "0.3",
-        "rdefs": {},
+        "rdefs": {
+            "model": "greyscale",
+        },
         "channels": [
             {
                 "label": channel_name,

vitessce/file_def_utils.py

@@ -101,6 +101,17 @@ def gen_obs_labels_schema(options: dict, paths: Optional[list[str]] = None, name
     return options
 
 
+def gen_obs_feature_columns_schema(options: dict, obs_feature_column_paths: Optional[list[str]] = None):
+    if obs_feature_column_paths is not None:
+        options["obsFeatureColumns"] = [
+            {
+                "path": col_path
+            }
+            for col_path in obs_feature_column_paths
+        ]
+    return options
+
+
 def gen_path_schema(key: str, path: Optional[str], options: dict):
     if path is not None:
         options[key] = {

vitessce/widget.py

@@ -163,7 +163,7 @@ const { createRoot } = await importWithMap("react-dom/client", importMap);
 const e = React.createElement;
 
 function isAbsoluteUrl(s) {
-    return s.startsWith('http://') || s.startsWith('https://');
+    return s?.startsWith('http://') || s?.startsWith('https://');
 }
 const WORKSPACES_URL_KEYWORD = 'https://workspaces-pt';
 const OPTIONS_URL_KEYS = ['offsetsUrl', 'refSpecUrl'];
@@ -201,7 +201,7 @@ function prependBaseUrl(config, proxy, hasHostName) {
             ...d,
             files: d.files.map(f => {
                 const updatedFileDef = { ...f };
-                if (!isAbsoluteUrl(f.url)) {
+                if (f.url && !isAbsoluteUrl(f.url) ) {
                     // Update the main file URL if necessary.
                     updatedFileDef.url = `${origin}${baseUrl}${f.url}`;
                 }
@@ -214,6 +214,28 @@ function prependBaseUrl(config, proxy, hasHostName) {
                             updatedOptions[key] = `${origin}${baseUrl}${optionValue}`;
                         }
                     });
+
+                    // Update image URLs if they exist
+                    if ('images' in f.options && Array.isArray(f.options.images)) {
+                        const updatedImages = f.options.images.map(image => {
+                            const updatedImage = { ...image };
+
+                            if (image.url && !isAbsoluteUrl(image.url)) {
+                                updatedImage.url = `${origin}${baseUrl}${image.url}`;
+                            }
+
+                            const metadata = { ...image.metadata };
+                            if (metadata?.omeTiffOffsetsUrl && !isAbsoluteUrl(metadata.omeTiffOffsetsUrl)) {
+                                metadata.omeTiffOffsetsUrl = `${origin}${baseUrl}${metadata.omeTiffOffsetsUrl}`;
+                            }
+
+                            updatedImage.metadata = metadata;
+
+                            return updatedImage;
+                        });
+
+                        updatedOptions.images = updatedImages;
+                    }
                     updatedFileDef.options = updatedOptions;
                 }
                 return updatedFileDef;
@@ -232,6 +254,7 @@ async function render(view) {
     const storeUrls = view.model.get('store_urls');
     const invokeTimeout = view.model.get('invoke_timeout');
     const invokeBatched = view.model.get('invoke_batched');
+    const preventScroll = view.model.get('prevent_scroll');
 
     const pageMode = view.model.get('page_mode');
     const pageEsm = view.model.get('page_esm');
@@ -424,7 +447,7 @@ async function render(view) {
         const divRef = React.useRef();
 
         React.useEffect(() => {
-            if(!divRef.current) {
+            if(!divRef.current || !preventScroll) {
                 return () => {};
             }
 
@@ -450,7 +473,7 @@ async function render(view) {
                     divRef.current.removeEventListener("mouseleave", handleMouseLeave);
                 }
             };
-        }, [divRef]);
+        }, [divRef, preventScroll]);
 
         // Config changed on JS side (from within <Vitessce/>),
         // send updated config to Python side.
@@ -600,7 +623,7 @@ class VitessceWidget(anywidget.AnyWidget):
 
     next_port = DEFAULT_PORT
 
-    js_package_version = Unicode('3.6.3').tag(sync=True)
+    js_package_version = Unicode('3.6.4').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)
@@ -609,10 +632,11 @@ class VitessceWidget(anywidget.AnyWidget):
     page_esm = Unicode('').tag(sync=True)
     invoke_timeout = Int(300000).tag(sync=True)
     invoke_batched = Bool(True).tag(sync=True)
+    prevent_scroll = Bool(True).tag(sync=True)
 
     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='3.6.3', 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):
+    def __init__(self, config, height=600, theme='auto', uid=None, port=None, proxy=False, js_package_version='3.6.4', 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.
 
@@ -632,6 +656,7 @@ class VitessceWidget(anywidget.AnyWidget):
         :param bool invoke_batched: Should invocations (Zarr gets) be submitted in batch, or individually? By default, True.
         :param bool page_mode: Whether to render the <Vitessce/> component in grid-mode or page-mode. By default, False.
         :param str page_esm: The ES module string for the page component creation function. Optional.
+        :param bool prevent_scroll: Should mouseover in the Vitessce widget prevent disable the scrolling of the notebook? By default, True.
 
         .. code-block:: python
             :emphasize-lines: 4
@@ -665,7 +690,7 @@ class VitessceWidget(anywidget.AnyWidget):
             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),
-            invoke_timeout=invoke_timeout, invoke_batched=invoke_batched,
+            invoke_timeout=invoke_timeout, invoke_batched=invoke_batched, prevent_scroll=prevent_scroll,
             uid=uid_str, store_urls=list(self._stores.keys())
         )
 
@@ -747,7 +772,7 @@ class VitessceWidget(anywidget.AnyWidget):
 # 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='3.6.3', 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='3.6.4', 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)
 

vitessce/wrappers.py

@@ -33,6 +33,7 @@ from vitessce.file_def_utils import (
     gen_sdata_obs_spots_schema,
     gen_sdata_obs_sets_schema,
     gen_sdata_obs_feature_matrix_schema,
+    gen_obs_feature_columns_schema,
 )
 
 from .constants import (
@@ -1192,7 +1193,7 @@ def raise_error_if_more_than_one(inputs):
 
 
 class AnnDataWrapper(AbstractWrapper):
-    def __init__(self, adata_path=None, adata_url=None, adata_store=None, adata_artifact=None, ref_path=None, ref_url=None, ref_artifact=None, obs_feature_matrix_path=None, feature_filter_path=None, initial_feature_filter_path=None, obs_set_paths=None, obs_set_names=None, obs_locations_path=None, obs_segmentations_path=None, obs_embedding_paths=None, obs_embedding_names=None, obs_embedding_dims=None, obs_spots_path=None, obs_points_path=None, feature_labels_path=None, obs_labels_path=None, convert_to_dense=True, coordination_values=None, obs_labels_paths=None, obs_labels_names=None, is_zip=None, **kwargs):
+    def __init__(self, adata_path=None, adata_url=None, adata_store=None, adata_artifact=None, ref_path=None, ref_url=None, ref_artifact=None, obs_feature_matrix_path=None, obs_feature_column_paths=None, feature_filter_path=None, initial_feature_filter_path=None, obs_set_paths=None, obs_set_names=None, obs_locations_path=None, obs_segmentations_path=None, obs_embedding_paths=None, obs_embedding_names=None, obs_embedding_dims=None, obs_spots_path=None, obs_points_path=None, feature_labels_path=None, obs_labels_path=None, convert_to_dense=True, coordination_values=None, obs_labels_paths=None, obs_labels_names=None, is_zip=None, **kwargs):
         """
         Wrap an AnnData object by creating an instance of the ``AnnDataWrapper`` class.
 
@@ -1218,6 +1219,7 @@ class AnnDataWrapper(AbstractWrapper):
         :param str obs_labels_path: (DEPRECATED) The name of a column containing observation labels (e.g., alternate cell IDs), instead of the default index in `obs` of the AnnData store. Use `obs_labels_paths` and `obs_labels_names` instead. This arg will be removed in a future release.
         :param list[str] obs_labels_paths: The names of columns containing observation labels (e.g., alternate cell IDs), instead of the default index in `obs` of the AnnData store.
         :param list[str] obs_labels_names: The optional display names of columns containing observation labels (e.g., alternate cell IDs), instead of the default index in `obs` of the AnnData store.
+        :param list[str] obs_feature_column_paths: The paths to columns (typically in `obs`) that contain numerical values per observation (e.g., cell size, quality control metrics, etc.) which are not part of the main expression matrix.
         :param bool convert_to_dense: Whether or not to convert `X` to dense the zarr store (dense is faster but takes more disk space).
         :param coordination_values: Coordination values for the file definition.
         :param is_zip: Boolean indicating whether the Zarr store is in a zipped format.
@@ -1289,6 +1291,7 @@ class AnnDataWrapper(AbstractWrapper):
         self._spatial_spots_obsm = obs_spots_path
         self._spatial_points_obsm = obs_points_path
         self._feature_labels = feature_labels_path
+        self._obs_feature_column_paths = obs_feature_column_paths
         # Support legacy provision of single obs labels path
         if (obs_labels_path is not None):
             warnings.warn("`obs_labels_path` will be deprecated in a future release.", DeprecationWarning)
@@ -1357,6 +1360,7 @@ class AnnDataWrapper(AbstractWrapper):
             options = gen_obs_feature_matrix_schema(options, self._expression_matrix, self._gene_var_filter, self._matrix_gene_var_filter)
             options = gen_feature_labels_schema(self._feature_labels, options)
             options = gen_obs_labels_schema(options, self._obs_labels_elems, self._obs_labels_names)
+            options = gen_obs_feature_columns_schema(options, self._obs_feature_column_paths)
 
             if len(options.keys()) > 0:
                 if self.is_h5ad:
@@ -1397,7 +1401,7 @@ SpatialDataWrapperType = TypeVar('SpatialDataWrapperType', bound='SpatialDataWra
 
 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, obs_spots_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", coordination_values=None, **kwargs):
         """
         Wrap a SpatialData object.
 
@@ -1444,6 +1448,7 @@ class SpatialDataWrapper(AnnDataWrapper):
         if self._adata_path is not None:
             self.zarr_folder = 'spatialdata.zarr'
         self.obs_type_label = None
+        self._coordination_values = coordination_values
         if self._coordination_values is not None and "obsType" in self._coordination_values:
             self.obs_type_label = self._coordination_values["obsType"]
         self._table_path = table_path

{vitessce-3.6.2.dist-info → vitessce-3.6.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vitessce
-Version: 3.6.2
+Version: 3.6.4
 Summary: Jupyter widget facilitating interactive visualization of spatial single-cell data with Vitessce
 Project-URL: repository, https://github.com/vitessce/vitessce-python
 Author-email: Mark Keller <mark_keller@hms.harvard.edu>

{vitessce-3.6.2.dist-info → vitessce-3.6.4.dist-info}/RECORD

@@ -1,24 +1,24 @@
 vitessce/__init__.py,sha256=GWGahpQMOGFotQXilRccGT0Bnn3OyoCQUCUphW_DtTI,1632
-vitessce/config.py,sha256=vZX4k-kS3zspYVT08PRuLSBeB-tU4GJgbN93z1Ed1iY,81228
+vitessce/config.py,sha256=GLiFSYh-ACJvQhrEVu3-nqFj1HtlCF86V_mMDljvwFo,81206
 vitessce/config_converter.py,sha256=IRPnGPGaETvJbYZNUv2pe54SHHHsDY9VWo3JRjSI5FM,14681
 vitessce/constants.py,sha256=nBMH55TcnSavcpvYE-epyx3cJ0iDS31eHsL_1e9qb9M,15360
 vitessce/export.py,sha256=L7j5sVC0nBSqGocFWQyyHImSiAF4IjXhmqV1QtpuNc4,3874
-vitessce/file_def_utils.py,sha256=RM9Hj1uwPY-Y37JLOHiKA_acGY40p8C9WsDk8iVjDz8,6692
+vitessce/file_def_utils.py,sha256=0Q1jxTOBDtvbRJEDX3s80oPr1EYrwkqixjkA5-rzAFM,7028
 vitessce/repr.py,sha256=qMmefmZ3E-3sRVxeI5q1DTZnfuwbXKiA85eyqk5MCT4,2287
 vitessce/responses.py,sha256=Z6Wo4AXN-RyzmxMPhSuhpIsHTItHM4GyIgMLGoVEYcU,339
 vitessce/routes.py,sha256=U8T-L-3QCD_tAbPF8LsUlSMhPWNbyzbLNUnxP9Z9s9o,2140
 vitessce/utils.py,sha256=obzjj65qsagu60_yuhGc-0jmHO-BW0Y-bDs0FgrBqLY,981
-vitessce/widget.py,sha256=IGeYExc4XuSc4c23hwLGHxQUvT1hD--v33ensjzzF28,33210
-vitessce/wrappers.py,sha256=3ZNldH2uDhOzUl8ahil7GxnPcr0nKwqfrjjbgS2IL0Y,75010
+vitessce/widget.py,sha256=gvmfqTy99B7oafSIXM33x46q_5vXENwGd_hxOUA3nRY,34575
+vitessce/wrappers.py,sha256=garL6KfL5hEqGBQpf3NV_ZsZhaV_-RN1GrCmA1Fc_1I,75557
 vitessce/data_utils/__init__.py,sha256=3mWi1lMjoj4_dNbhMOvyE-HEJu0qpMzcmkhfz_5T6n8,361
 vitessce/data_utils/anndata.py,sha256=iLa5-bRezHgBzL_XCHO7w0pc0RQ4urzZbDsqJbBYeCk,10668
 vitessce/data_utils/entities.py,sha256=X8enC_TQbgwBzjgD1x53IPS6aVr9wyP0s-NLuYBeMeU,11705
 vitessce/data_utils/multivec.py,sha256=YVc68uKNdS-ga89GapQjY9lDjmje0dm-MExq1yT_6ZE,11571
-vitessce/data_utils/ome.py,sha256=aK-iGNgjUmUMsWgdZhW78VrtMBKMW_jIQDYnsupq6BE,5436
+vitessce/data_utils/ome.py,sha256=tJHlSHbZTxpjRgYfTxbYMS9zSnSHQwJVWPZpREAvHtU,5518
 vitessce/widget_plugins/__init__.py,sha256=lto2GXnc7KwjIoT-jvzyRYLj0XTJG3uxoX45Hc9EcWA,82
 vitessce/widget_plugins/demo_plugin.py,sha256=14S7nOxdlKSxIHw9DUcNCN83NE_U1EMPy2D4k0FDues,1797
 vitessce/widget_plugins/spatial_query.py,sha256=CYxvmMT1Je_jguikPROQxlegkPgIIzemKGbZSJfZMyI,12314
-vitessce-3.6.2.dist-info/METADATA,sha256=oFYSpxrfXHugNhDmIB_EBdJhIZBSRgCTKdxq5cLhAIQ,9826
-vitessce-3.6.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-vitessce-3.6.2.dist-info/licenses/LICENSE,sha256=sNNpI0PQ57AW8_XnTAjU5Yw8YBA_DRNkVHrHYpCIhRU,1067
-vitessce-3.6.2.dist-info/RECORD,,
+vitessce-3.6.4.dist-info/METADATA,sha256=sRseqTRfGZiMcogKRMZutfIMsMPcYPAIL0SliFhg8UU,9826
+vitessce-3.6.4.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+vitessce-3.6.4.dist-info/licenses/LICENSE,sha256=sNNpI0PQ57AW8_XnTAjU5Yw8YBA_DRNkVHrHYpCIhRU,1067
+vitessce-3.6.4.dist-info/RECORD,,