Updates

Author: keller-mark

docs/notebooks/spatial_data_kpmp.py

@@ -1,56 +1,15 @@
-#!/usr/bin/env python
-# coding: utf-8
-
-# # Vitessce Widget Tutorial
-
-# ## Import dependencies
-# 
-
-# https://github.com/vitessce/vitessce/blob/main/examples/configs/src/view-configs/spatial-beta/kpmp.js
-
-# In[2]:
-
-
 from os.path import join
-
-
-# In[1]:
-
-
-import spatialdata
 from spatialdata import SpatialData, to_polygons
 from spatialdata.models import Image2DModel, Labels2DModel, TableModel
 from spatialdata.transformations import (
-    Affine,
-    MapAxis,
     Scale,
-    Sequence,
-    Translation,
-    get_transformation,
     set_transformation,
 )
-from anndata import read_zarr, AnnData
-import tifffile
-from tifffile import imread, TiffFile
-import xml.etree.ElementTree
-import io
+from anndata import read_zarr
+from tifffile import imread
 import zarr
 
-
-
-# In[2]:
-
-
-
-
-# In[3]:
-
-
-base_dir = join("..", "..", "..", "kpmp-f2f-march-2023", "S-1905-017737")
-
-
-# In[ ]:
-
+base_dir = join("S-1905-017737")
 
 img_path = join(base_dir, "S-1905-017737_PAS_2of2_bf.ome.tif")
 seg_path = join(base_dir, "S-1905-017737_PAS_2of2.ome.tif")
@@ -65,29 +24,11 @@
     "peritubular_capillaries": join(base_dir, "Peritubular Capillaries renamed.adata.zarr"),
 }
 
-
-# In[ ]:
-
-
 # The shape of the data should be c(z)yx for 2D (3D) images
-
-
-# In[ ]:
-
-
 img_arr = imread(img_path)
-
-
-# In[ ]:
-
-
 seg_store = imread(seg_path, aszarr=True)
 seg_z = zarr.open(seg_store)
 
-
-# In[ ]:
-
-
 def clean_adata(adata):
     colnames = adata.obs.columns.tolist()
     adata.obs = adata.obs.rename(columns=dict([ (c, c.replace(" ", "_")) for c in colnames ]))
@@ -97,10 +38,6 @@ def clean_adata(adata):
         adata.obs.index = range(1, adata.obs.shape[0]+1)
     return adata
 
-
-# In[ ]:
-
-
 sdata = SpatialData(
     images={
         "image": Image2DModel.parse(img_arr, scale_factors=[2, 2, 2, 2, 2]),
@@ -118,26 +55,10 @@ def clean_adata(adata):
     scale = Scale([2.0, 2.0], axes=("y","x"))
     set_transformation(sdata[f"labels_{obs_type}"], scale, to_coordinate_system="global")
 
-
-# In[ ]:
-
 for labels_key in sdata.labels.keys():
     shapes_key = "shapes" + labels_key[labels_key.index("_"):]
     sdata.shapes[shapes_key] = to_polygons(sdata.labels[labels_key])
 
-
 sdata.write(join(base_dir, "sdata.zarr"), overwrite=True)
-print(join(base_dir, "sdata.zarr"))
+print(join(base_dir, "S-1905-017737.sdata.zarr"))
 print("Done")
-
-# In[ ]:
-
-
-
-
-
-# In[ ]:
-
-
-
-

src/vitessce/widget.py

@@ -232,6 +232,7 @@ def get_uid_str(uid):
     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 +425,7 @@ def get_uid_str(uid):
         const divRef = React.useRef();
 
         React.useEffect(() => {
-            if(!divRef.current || pageMode) {
+            if(!divRef.current || !preventScroll) {
                 return () => {};
             }
 
@@ -450,7 +451,7 @@ def get_uid_str(uid):
                     divRef.current.removeEventListener("mouseleave", handleMouseLeave);
                 }
             };
-        }, [divRef, pageMode]);
+        }, [divRef, preventScroll]);
 
         // Config changed on JS side (from within <Vitessce/>),
         // send updated config to Python side.
@@ -609,10 +610,11 @@ 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='3.6.3', 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):
         """
         Construct a new Vitessce widget.
 
@@ -632,6 +634,7 @@ def __init__(self, config, height=600, theme='auto', uid=None, port=None, proxy=
         :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 +668,7 @@ def __init__(self, config, height=600, theme='auto', uid=None, port=None, proxy=
             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())
         )