ValueError with calculate_image_features() in tutorial_visium_hne.ipynb

[estellad]

Hi there,

Thank you for the tutorial! I was just running through the example data, and encountered this error at:

# calculate features for different scales (higher value means more context)
for scale in [1.0, 2.0]:
    feature_name = f"features_summary_scale{scale}"
    sq.im.calculate_image_features(
        adata2,
        img2.compute(),
        features="summary",
        key_added=feature_name,
        n_jobs=4,
        scale=scale,
    )

/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/anndata/_core/anndata.py:1113: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
if not is_categorical_dtype(df_full[k]):
/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/anndata/_core/anndata.py:1113: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
if not is_categorical_dtype(df_full[k]):
/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/anndata/_core/anndata.py:1113: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
if not is_categorical_dtype(df_full[k]):
/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/anndata/_core/anndata.py:1113: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
if not is_categorical_dtype(df_full[k]):

100%|██████████| 2688/2688 [00:14<00:00, 179.80/s]

�/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/anndata/_core/anndata.py:1113: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
if not is_categorical_dtype(df_full[k]):
/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/anndata/_core/anndata.py:1113: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
if not is_categorical_dtype(df_full[k]):
/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/anndata/_core/anndata.py:1113: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
if not is_categorical_dtype(df_full[k]):

{
"name": "ValueError",
"message": "applied function returned data with unexpected number of dimensions. Received 4 dimension(s) but expected 0 dimensions with names: ()",
"stack": "---------------------------------------------------------------------------
_RemoteTraceback Traceback (most recent call last)
_RemoteTraceback:
"""
Traceback (most recent call last):
File "/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/joblib/externals/loky/process_executor.py", line 463, in _process_worker
r = call_item()
File "/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/joblib/externals/loky/process_executor.py", line 291, in call
return self.fn(*self.args, **self.kwargs)
File "/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/joblib/parallel.py", line 589, in call
return [func(*args, **kwargs)
File "/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/joblib/parallel.py", line 589, in
return [func(*args, **kwargs)
File "/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/squidpy/im/_feature.py", line 119, in _calculate_image_features_helper
for crop in img.generate_spot_crops(
File "/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/squidpy/im/_container.py", line 830, in generate_spot_crops
crop = self.crop_center(y=y, x=x, radius=radius, library_id=obs_library_ids[i], **kwargs)
File "/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/squidpy/im/_container.py", line 661, in crop_center
return self.crop_corner( # type: ignore[no-any-return]
File "/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/squidpy/im/_container.py", line 568, in crop_corner
self._post_process(
File "/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/squidpy/im/_container.py", line 602, in _post_process
data = data.map(_rescale).assign_coords({"z": library_ids})
File "/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/xarray/core/dataset.py", line 6818, in map
variables = {
File "/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/xarray/core/dataset.py", line 6819, in
k: maybe_wrap_array(v, func(v, *args, **kwargs))
File "/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/squidpy/im/_container.py", line 597, in _rescale
return xr.DataArray(scaling_fn(arr).astype(dtype), dims=arr.dims)
File "/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/skimage/_shared/utils.py", line 328, in fixed_func
return func(*args, **kwargs)
File "/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/skimage/transform/_warps.py", line 289, in rescale
return resize(image, output_shape, order=order, mode=mode, cval=cval,
File "/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/skimage/transform/_warps.py", line 188, in resize
_clip_warp_output(image, out, mode, cval, clip)
File "/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/skimage/transform/_warps.py", line 692, in _clip_warp_output
np.clip(output_image, min_val, max_val, out=output_image)
File "<array_function internals>", line 180, in clip
File "/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/numpy/core/fromnumeric.py", line 2152, in clip
return _wrapfunc(a, 'clip', a_min, a_max, out=out, **kwargs)
File "/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/numpy/core/fromnumeric.py", line 57, in _wrapfunc
return bound(*args, **kwds)
File "/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/numpy/core/_methods.py", line 159, in _clip
return _clip_dep_invoke_with_casting(
File "/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/numpy/core/_methods.py", line 113, in _clip_dep_invoke_with_casting
return ufunc(*args, out=out, **kwargs)
File "/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/xarray/core/arithmetic.py", line 86, in array_ufunc
return apply_ufunc(
File "/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/xarray/core/computation.py", line 1197, in apply_ufunc
return apply_dataarray_vfunc(
File "/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/xarray/core/computation.py", line 304, in apply_dataarray_vfunc
result_var = func(*data_vars)
File "/opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/xarray/core/computation.py", line 786, in apply_variable_ufunc
raise ValueError(
ValueError: applied function returned data with unexpected number of dimensions. Received 4 dimension(s) but expected 0 dimensions with names: ()
"""

The above exception was the direct cause of the following exception:

ValueError Traceback (most recent call last)
/Users/estelladong/Downloads/tutorial_visium_hne.ipynb Cell 13 line 4
2 for scale in [1.0, 2.0]:
3 feature_name = f"features_summary_scale{scale}"
----> 4 sq.im.calculate_image_features(
5 adata2,
6 img2.compute(),
7 features="summary",
8 key_added=feature_name,
9 n_jobs=4,
10 scale=scale,
11 )

File /opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/squidpy/im/_feature.py:91, in calculate_image_features(adata, img, layer, library_id, features, features_kwargs, key_added, copy, n_jobs, backend, show_progress_bar, **kwargs)
88 n_jobs = _get_n_cores(n_jobs)
89 start = logg.info(f"Calculating features {list(features)} using {n_jobs} core(s)")
---> 91 res = parallelize(
92 _calculate_image_features_helper,
93 collection=adata.obs_names,
94 extractor=pd.concat,
95 n_jobs=n_jobs,
96 backend=backend,
97 show_progress_bar=show_progress_bar,
98 )(adata, img, layer=layer, library_id=library_id, features=features, features_kwargs=features_kwargs, **kwargs)
100 if copy:
101 logg.info("Finish", time=start)

File /opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/squidpy/_utils.py:168, in parallelize..wrapper(*args, **kwargs)
165 else:
166 pbar, queue, thread = None, None, None
--> 168 res = jl.Parallel(n_jobs=n_jobs, backend=backend)(
169 jl.delayed(runner if use_runner else callback)(
170 *((i, cs) if use_ixs else (cs,)),
171 *args,
172 **kwargs,
173 queue=queue,
174 )
175 for i, cs in enumerate(collections)
176 )
178 if thread is not None:
179 thread.join()

File /opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/joblib/parallel.py:1952, in Parallel.call(self, iterable)
1946 # The first item from the output is blank, but it makes the interpreter
1947 # progress until it enters the Try/Except block of the generator and
1948 # reach the first yield statement. This starts the aynchronous
1949 # dispatch of the tasks to the workers.
1950 next(output)
-> 1952 return output if self.return_generator else list(output)

File /opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/joblib/parallel.py:1595, in Parallel._get_outputs(self, iterator, pre_dispatch)
1592 yield
1594 with self._backend.retrieval_context():
-> 1595 yield from self._retrieve()
1597 except GeneratorExit:
1598 # The generator has been garbage collected before being fully
1599 # consumed. This aborts the remaining tasks if possible and warn
1600 # the user if necessary.
1601 self._exception = True

File /opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/joblib/parallel.py:1699, in Parallel._retrieve(self)
1692 while self._wait_retrieval():
1693
1694 # If the callback thread of a worker has signaled that its task
1695 # triggered an exception, or if the retrieval loop has raised an
1696 # exception (e.g. GeneratorExit), exit the loop and surface the
1697 # worker traceback.
1698 if self._aborting:
-> 1699 self._raise_error_fast()
1700 break
1702 # If the next job is not ready for retrieval yet, we just wait for
1703 # async callbacks to progress.

File /opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/joblib/parallel.py:1734, in Parallel._raise_error_fast(self)
1730 # If this error job exists, immediatly raise the error by
1731 # calling get_result. This job might not exists if abort has been
1732 # called directly or if the generator is gc'ed.
1733 if error_job is not None:
-> 1734 error_job.get_result(self.timeout)

File /opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/joblib/parallel.py:736, in BatchCompletionCallBack.get_result(self, timeout)
730 backend = self.parallel._backend
732 if backend.supports_retrieve_callback:
733 # We assume that the result has already been retrieved by the
734 # callback thread, and is stored internally. It's just waiting to
735 # be returned.
--> 736 return self._return_or_raise()
738 # For other backends, the main thread needs to run the retrieval step.
739 try:

File /opt/homebrew/Caskroom/mambaforge/base/lib/python3.10/site-packages/joblib/parallel.py:754, in BatchCompletionCallBack._return_or_raise(self)
752 try:
753 if self.status == TASK_ERROR:
--> 754 raise self._result
755 return self._result
756 finally:

ValueError: applied function returned data with unexpected number of dimensions. Received 4 dimension(s) but expected 0 dimensions with names: ()"
}

Could you please let us know the environment.yml you used? Thank you!

Sincerely,
Estella