Bug in v0.1.5 visium_hd reader

t-a-m-i commented 1 month ago

Hi, I get an error when trying to read in a Visium HD dataset with the visium_hd reader of v0.1.5. The same code works perfectly fine with v0.1.4.

from spatialdata_io import visium_hd
sdata = visium_hd(
    path_read,
    load_all_images=True,
    fullres_image_file=fullres_image_file,
    dataset_id=dataset_id
)

Throws:

FileNotFoundError: [Errno 2] Unable to synchronously open file (unable to open file: name = '/files/03-SpaceRanger-Results/P31904_402/outs/P31904_402_feature_slice.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

"P31904_402_feature_slice.h5" indeed does not exist, it should simply be "feature_slice.h5" in "outs" of the "P31904_402" folder.

Here is the full traceback:

FileNotFoundError Traceback (most recent call last)
Cell In[4], line 2
1 from spatialdata_io import visium_hd
----> 2 sdata = visium_hd(
3 path_read,
4 load_all_images=True,
5 annotate_table_by_labels=True,
6 fullres_image_file=fullres_image_file,
7 dataset_id=dataset_id
8 )

File ~/anaconda3/envs/sd_pr_test/lib/python3.12/site-packages/spatialdata_io/readers/visium_hd.py:115, in visium_hd(path, dataset_id, filtered_counts_file, bin_size, bins_as_squares, annotate_table_by_labels, fullres_image_file, load_all_images, imread_kwargs, image_models_kwargs, anndata_kwargs)
104 def load_image(path: Path, suffix: str, scale_factors: list[int] | None = None) -> None:
105 _load_image(
106 path=path,
107 images=images,
(...)
112 scale_factors=scale_factors,
113 )
--> 115 metadata, hd_layout = _parse_metadata(path, filename_prefix)
116 transform_matrices = _get_transform_matrices(metadata, hd_layout)
117 file_format = hd_layout[VisiumHDKeys.FILE_FORMAT]

File ~/anaconda3/envs/sd_pr_test/lib/python3.12/site-packages/spatialdata_io/readers/visium_hd.py:471, in _parse_metadata(path, filename_prefix)
470 def _parse_metadata(path: Path, filename_prefix: str) -> tuple[dict[str, Any], dict[str, Any]]:
--> 471 with h5py.File(path / f"{filename_prefix}{VisiumHDKeys.FEATURE_SLICE_FILE.value}", "r") as f5:
472 metadata = json.loads(dict(f5.attrs)[VisiumHDKeys.METADATA_JSON])
473 hd_layout = json.loads(metadata[VisiumHDKeys.HD_LAYOUT_JSON])

File ~/anaconda3/envs/sd_pr_test/lib/python3.12/site-packages/h5py/_hl/files.py:562, in File.init(self, name, mode, driver, libver, userblock_size, swmr, rdcc_nslots, rdcc_nbytes, rdcc_w0, track_order, fs_strategy, fs_persist, fs_threshold, fs_page_size, page_buf_size, min_meta_keep, min_raw_keep, locking, alignment_threshold, alignment_interval, meta_block_size, **kwds)
553 fapl = make_fapl(driver, libver, rdcc_nslots, rdcc_nbytes, rdcc_w0,
554 locking, page_buf_size, min_meta_keep, min_raw_keep,
555 alignment_threshold=alignment_threshold,
556 alignment_interval=alignment_interval,
557 meta_block_size=meta_block_size,
558 **kwds)
559 fcpl = make_fcpl(track_order=track_order, fs_strategy=fs_strategy,
560 fs_persist=fs_persist, fs_threshold=fs_threshold,
561 fs_page_size=fs_page_size)
--> 562 fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
564 if isinstance(libver, tuple):
565 self._libver = libver

File ~/anaconda3/envs/sd_pr_test/lib/python3.12/site-packages/h5py/_hl/files.py:235, in make_fid(name, mode, userblock_size, fapl, fcpl, swmr)
233 if swmr and swmr_support:
234 flags |= h5f.ACC_SWMR_READ
--> 235 fid = h5f.open(name, flags, fapl=fapl)
236 elif mode == 'r+':
237 fid = h5f.open(name, h5f.ACC_RDWR, fapl=fapl)

File h5py/_objects.pyx:54, in h5py._objects.with_phil.wrapper()

File h5py/_objects.pyx:55, in h5py._objects.with_phil.wrapper()

File h5py/h5f.pyx:102, in h5py.h5f.open()

LucaMarconato commented 1 month ago

Thanks for reporting. Tagging @melonora, the bug seems due to https://github.com/scverse/spatialdata-io/pull/204 and https://github.com/scverse/spatialdata-io/pull/206.

LucaMarconato commented 1 month ago

scverse / spatialdata-io

Bug in v0.1.5 visium_hd reader #216