Expected width to be in interval error im.calculate_image_features #989
Description
Description
Firstly, thank you for this wonderful package.
The error I'm encountering looks like the same as the one reported in #878 which was closed without an answer.
When running sq.im.calculate_image_features on certain Visium slides it fails with some version of the following error:
ValueError: Expected `width` to be in interval `[0, 1985]`, found `2026`.
This currently happens for 50% of the samples that I'm working with, for the other 50% the function works as expected.
Minimal example
adata = sc.read_visium('/path/to/Aligned/spaceranger/' + 'sample' + '/outs/',
count_file='filtered_feature_bc_matrix.h5',
source_image_path='/path/to/Aligned/spaceranger/' + 'sample' + '/outs/spatial/tissue_hires_image.png')
scale = adata.uns["spatial"]['sample']["scalefactors"]["tissue_hires_scalef"]
img = sq.im.ImageContainer(adata.uns["spatial"]['sample']["images"]["hires"], scale = scale)
sq.im.calculate_image_features(
adata,
img,
layer= "image",
features="summary",
key_added="features_summary_mean",
mask_circle = True
)The result of img.shape is (2000, 1985)
Traceback
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[8], line 1
----> 1 sq.im.calculate_image_features(
2 adata,
3 img,
4 layer= "image",
5 features="summary",
6 key_added="features_summary_mean",
7 mask_circle = True
8 )
File /path/to/squidpy_env/lib/python3.9/site-packages/squidpy/im/_feature.py:90, in calculate_image_features(adata, img, layer, library_id, features, features_kwargs, key_added, copy, n_jobs, backend, show_progress_bar, **kwargs)
87 n_jobs = _get_n_cores(n_jobs)
88 start = logg.info(f"Calculating features `{list(features)}` using `{n_jobs}` core(s)")
---> 90 res = parallelize(
91 _calculate_image_features_helper,
92 collection=adata.obs_names,
93 extractor=pd.concat,
94 n_jobs=n_jobs,
95 backend=backend,
96 show_progress_bar=show_progress_bar,
97 )(adata, img, layer=layer, library_id=library_id, features=features, features_kwargs=features_kwargs, **kwargs)
99 if copy:
100 logg.info("Finish", time=start)
File /path/to/squidpy_env/lib/python3.9/site-packages/squidpy/_utils.py:174, in parallelize.<locals>.wrapper(*args, **kwargs)
171 else:
172 pbar, queue, thread = None, None, None
--> 174 res = jl.Parallel(n_jobs=n_jobs, backend=backend)(
175 jl.delayed(runner if use_runner else callback)(
176 *((i, cs) if use_ixs else (cs,)),
177 *args,
178 **kwargs,
179 queue=queue,
180 )
181 for i, cs in enumerate(collections)
182 )
184 if thread is not None:
185 thread.join()
File /path/to/squidpy_env/lib/python3.9/site-packages/joblib/parallel.py:1918, in Parallel.__call__(self, iterable)
1916 output = self._get_sequential_output(iterable)
1917 next(output)
-> 1918 return output if self.return_generator else list(output)
1920 # Let's create an ID that uniquely identifies the current call. If the
1921 # call is interrupted early and that the same instance is immediately
1922 # re-used, this id will be used to prevent workers that were
1923 # concurrently finalizing a task from the previous call to run the
1924 # callback.
1925 with self._lock:
File /path/to/squidpy_env/lib/python3.9/site-packages/joblib/parallel.py:1847, in Parallel._get_sequential_output(self, iterable)
1845 self.n_dispatched_batches += 1
1846 self.n_dispatched_tasks += 1
-> 1847 res = func(*args, **kwargs)
1848 self.n_completed_tasks += 1
1849 self.print_progress()
File /path/to/squidpy_env/lib/python3.9/site-packages/squidpy/im/_feature.py:118, in _calculate_image_features_helper(obs_ids, adata, img, layer, library_id, features, features_kwargs, queue, **kwargs)
106 def _calculate_image_features_helper(
107 obs_ids: Sequence[str],
108 adata: AnnData,
(...)
115 **kwargs: Any,
116 ) -> pd.DataFrame:
117 features_list = []
--> 118 for crop in img.generate_spot_crops(
119 adata, obs_names=obs_ids, library_id=library_id, return_obs=False, as_array=False, **kwargs
120 ):
121 if TYPE_CHECKING:
122 assert isinstance(crop, ImageContainer)
File /path/to/squidpy_env/lib/python3.9/site-packages/squidpy/im/_container.py:839, in ImageContainer.generate_spot_crops(self, adata, spatial_key, library_id, spot_diameter_key, spot_scale, obs_names, as_array, squeeze, return_obs, **kwargs)
837 y = int(y - self.data.attrs[Key.img.coords].y0)
838 x = int(x - self.data.attrs[Key.img.coords].x0)
--> 839 crop = self.crop_center(y=y, x=x, radius=radius, library_id=obs_library_ids[i], **kwargs)
840 crop.data.attrs[Key.img.obs] = obs
841 crop = crop._maybe_as_array(as_array, squeeze=squeeze, lazy=False)
File /path/to/squidpy_env/lib/python3.9/site-packages/squidpy/im/_container.py:660, in ImageContainer.crop_center(self, y, x, radius, **kwargs)
658 y, x = self._convert_to_pixel_space((y, x))
659 _assert_in_range(y, 0, self.shape[0], name="height")
--> 660 _assert_in_range(x, 0, self.shape[1], name="width")
662 if not isinstance(radius, Iterable):
663 radius = (radius, radius)
File /path/to/squidpy_env/lib/python3.9/site-packages/squidpy/gr/_utils.py:189, in _assert_in_range(value, minn, maxx, name)
187 def _assert_in_range(value: float, minn: float, maxx: float, *, name: str) -> None:
188 if not (minn <= value <= maxx):
--> 189 raise ValueError(f"Expected `{name}` to be in interval `[{minn}, {maxx}]`, found `{value}`.")
ValueError: Expected `width` to be in interval `[0, 1985]`, found `2026`.Version
squidpy==1.6.5
Also occurs when squidpy==1.6.1