ValueError with calculate_image_features() in tutorial_visium_hne.ipynb

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]

{ "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

scverse / squidpy_notebooks

ValueError with calculate_image_features() in tutorial_visium_hne.ipynb #123