vitessce 3.6.5__py3-none-any.whl → 3.6.7__py3-none-any.whl

vitessce/file_def_utils.py

@@ -3,8 +3,6 @@ from __future__ import annotations
 from functools import partial
 from typing import Optional
 
-import numpy as np
-
 
 def gen_obs_embedding_schema(options: dict, paths: Optional[list[str]] = None, names: Optional[list[str]] = None, dims: Optional[list[list[int]]] = None):
     if paths is not None:
@@ -127,29 +125,25 @@ gen_obs_points_schema = partial(gen_path_schema, "obsPoints")
 gen_feature_labels_schema = partial(gen_path_schema, "featureLabels")
 
 
-def gen_sdata_image_schema(options, path: str, coordinate_system: Optional[str] = None, affine_transformation: Optional[np.ndarray] = None) -> dict:
+def gen_sdata_image_schema(options, path: str, coordinate_system: Optional[str] = None) -> dict:
     if path is not None:
         options["image"] = {
             "path": path
         }
-        if affine_transformation is not None:
-            options["image"]['coordinateTransformations'] = affine_transformation
         if coordinate_system is not None:
             options["image"]['coordinateSystem'] = coordinate_system
     return options
 
 
-def gen_sdata_labels_schema(options, path: str, table_path: str = "tables/table", coordinate_system: Optional[str] = None, affine_transformation: Optional[np.ndarray] = None) -> dict:
+def gen_sdata_obs_segmentations_schema(options, path: str, table_path: str = "tables/table", coordinate_system: Optional[str] = None) -> dict:
     if path is not None:
-        options["labels"] = {
+        options["obsSegmentations"] = {
             "path": path
         }
         if table_path is not None:
-            options["labels"]['tablePath'] = table_path
-        if affine_transformation is not None:
-            options["labels"]['coordinateTransformations'] = affine_transformation
+            options["obsSegmentations"]['tablePath'] = table_path
         if coordinate_system is not None:
-            options["labels"]['coordinateSystem'] = coordinate_system
+            options["obsSegmentations"]['coordinateSystem'] = coordinate_system
     return options
 
 

vitessce/widget.py

@@ -131,6 +131,11 @@ def launch_vitessce_io(config, theme='light', port=None, base_url=None, host_nam
         port, DEFAULT_PORT, proxy=proxy, base_url=base_url, host_name=host_name)
     config_dict = config.to_dict(base_url=base_url)
     routes = config.get_routes()
+
+    stores = config.get_stores(base_url=base_url)
+    if len(stores) > 0:
+        raise ValueError('One or more files in this configuration have been provided via Zarr store, which can only be loaded via the widget. Either use VitessceConfig.widget or VitessceConfig.display (instead of .web_app), or provide the files via _path or _url (rather than _store) parameters.')
+
     serve_routes(config, routes, use_port)
     vitessce_url = f"http://vitessce.io/#?theme={theme}&url=data:," + quote_plus(
         json.dumps(config_dict))
@@ -147,6 +152,7 @@ def get_uid_str(uid):
     return uid_str
 
 
+# lang: js
 ESM = """
 import { importWithMap } from 'https://unpkg.com/dynamic-importmap@0.1.0';
 const importMap = {
@@ -539,6 +545,7 @@ async function render(view) {
 export default { render };
 """
 
+# lang: js
 DEFAULT_PLUGIN_ESM = """
 function createPlugins(utilsForPlugins) {
     const {
@@ -563,6 +570,7 @@ function createPlugins(utilsForPlugins) {
 export default { createPlugins };
 """
 
+# lang: js
 DEFAULT_PAGE_ESM = """
 function createPage(utilsForPage) {
     const {
@@ -623,7 +631,7 @@ class VitessceWidget(anywidget.AnyWidget):
 
     next_port = DEFAULT_PORT
 
-    js_package_version = Unicode('3.6.6').tag(sync=True)
+    js_package_version = Unicode('3.6.9').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)
@@ -636,7 +644,7 @@ 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='3.6.6', 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='3.6.9', 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.
 
@@ -772,7 +780,7 @@ 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='3.6.6', 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='3.6.9', 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

@@ -12,8 +12,6 @@ from pathlib import PurePath, PurePosixPath
 import warnings
 import zarr
 
-import numpy as np
-
 if TYPE_CHECKING:
     import lamindb as ln
     from spatialdata import SpatialData
@@ -29,7 +27,7 @@ from vitessce.file_def_utils import (
     gen_obs_labels_schema,
     gen_obs_sets_schema,
     gen_sdata_image_schema,
-    gen_sdata_labels_schema,
+    gen_sdata_obs_segmentations_schema,
     gen_sdata_obs_spots_schema,
     gen_sdata_obs_sets_schema,
     gen_sdata_obs_feature_matrix_schema,
@@ -1401,7 +1399,7 @@ 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", 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, table_path: str = "tables/table", coordination_values=None, **kwargs):
         """
         Wrap a SpatialData object.
 
@@ -1421,8 +1419,8 @@ class SpatialDataWrapper(AnnDataWrapper):
         :type affine_transformation: Optional[np.ndarray]
         :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]
+        :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]
         """
         raise_error_if_zero_or_more_than_one([
             sdata_path,
@@ -1437,14 +1435,21 @@ class SpatialDataWrapper(AnnDataWrapper):
             kwargs.get('adata_artifact', None)
         ])
         super().__init__(adata_path=sdata_path, adata_url=sdata_url, adata_store=sdata_store, adata_artifact=sdata_artifact, **kwargs)
+        if "labels_path" in kwargs:
+            warnings.warn("`labels_path` is deprecated. Use `obs_segmentations_path` instead.", DeprecationWarning)
+            self._obs_segmentations_path = kwargs["labels_path"]
+        if "shapes_path" in kwargs:
+            warnings.warn("`shapes_path` is deprecated. Use `obs_segmentations_path` instead.", DeprecationWarning)
+        if "affine_transformation" in kwargs:
+            warnings.warn("`affine_transformation` is deprecated. Store transformations in the SpatialData object, then specify `coordinate_system`.", DeprecationWarning)
+
         self.local_dir_uid = make_unique_filename(".sdata.zarr")
         self._image_path = image_path
         self._region = region
         self._coordinate_system = coordinate_system
-        self._affine_transformation = affine_transformation
         self._kwargs = kwargs
         self._obs_spots_path = obs_spots_path
-        self._labels_path = labels_path
+        self._obs_segmentations_path = obs_segmentations_path
         if self._adata_path is not None:
             self.zarr_folder = 'spatialdata.zarr'
         self.obs_type_label = None
@@ -1530,8 +1535,8 @@ class SpatialDataWrapper(AnnDataWrapper):
             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._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_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_feature_labels_schema(self._feature_labels, options)
             if len(options.keys()) > 0:
                 obj_file_def = {

{vitessce-3.6.5.dist-info → vitessce-3.6.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vitessce
-Version: 3.6.5
+Version: 3.6.7
 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-3.6.5.dist-info → vitessce-3.6.7.dist-info}/RECORD

@@ -3,13 +3,13 @@ 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=0Q1jxTOBDtvbRJEDX3s80oPr1EYrwkqixjkA5-rzAFM,7028
+vitessce/file_def_utils.py,sha256=heFDrJMO4fYoondtVALjUiIxe4swOiR24KVGEu8ZTM0,6688
 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=mTAXQR8QWPLwqQUSb077CF0CFUvrRpUDSpojsxQ8IBc,34575
-vitessce/wrappers.py,sha256=garL6KfL5hEqGBQpf3NV_ZsZhaV_-RN1GrCmA1Fc_1I,75557
+vitessce/widget.py,sha256=Tb9Llm2Nd5inFXsfRhLanb8jH8WLByrLHDa40Qjdj14,34982
+vitessce/wrappers.py,sha256=gbJggLGoFTRa1odnBvBDE5EspQ8vc_CpNq_eTbZBGSM,76091
 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
@@ -18,7 +18,7 @@ vitessce/data_utils/ome.py,sha256=tJHlSHbZTxpjRgYfTxbYMS9zSnSHQwJVWPZpREAvHtU,55
 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-3.6.5.dist-info/METADATA,sha256=k03oHmlKb_vZcnUwjHPovPxbUMikMSwSL365aX2dVdM,9826
-vitessce-3.6.5.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-vitessce-3.6.5.dist-info/licenses/LICENSE,sha256=sNNpI0PQ57AW8_XnTAjU5Yw8YBA_DRNkVHrHYpCIhRU,1067
-vitessce-3.6.5.dist-info/RECORD,,
+vitessce-3.6.7.dist-info/METADATA,sha256=MpjjO3VXVEwBQ770vTyExzNxCjUro_NLfXyB1qC0m7s,9826
+vitessce-3.6.7.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+vitessce-3.6.7.dist-info/licenses/LICENSE,sha256=sNNpI0PQ57AW8_XnTAjU5Yw8YBA_DRNkVHrHYpCIhRU,1067
+vitessce-3.6.7.dist-info/RECORD,,