Merge pull request #91 from scverse/fix/visium_no_dataset_id

Fixed visium() to support file counts without dataset_id

src/spatialdata_io/readers/_utils/_utils.py

@@ -29,7 +29,6 @@ def _read_counts(
 ) -> tuple[AnnData, str]:
  path = Path(path)
  if counts_file.endswith(".h5"):
- print(counts_file)
  adata: AnnData = _read_10x_h5(path / counts_file, **kwargs)
  with File(path / counts_file, mode="r") as f:
  attrs = dict(f.attrs)
@@ -50,9 +49,8 @@ def _read_counts(
  adata.uns["spatial"][library_id]["metadata"][key] = metadata
 
  return adata, library_id
-
  if library_id is None:
- raise ValueError("Please explicitly specify library id.")
+ raise ValueError("Please explicitly specify `library id`.")
 
  if counts_file.endswith((".csv", ".txt")):
  adata = read_text(path / counts_file, **kwargs)

src/spatialdata_io/readers/visium.py

@@ -42,7 +42,7 @@ def visium(
 
  This function reads the following files:
 
- - ``{vx.COUNTS_FILE!r}``: Counts and metadata file.
+ - ``(<dataset_id>_)`{vx.COUNTS_FILE!r}```: Counts and metadata file.
  - ``{vx.IMAGE_HIRES_FILE!r}``: High resolution image.
  - ``{vx.IMAGE_LOWRES_FILE!r}``: Low resolution image.
  - ``{vx.SCALEFACTORS_FILE!r}``: Scalefactors file.
@@ -59,8 +59,8 @@ def visium(
  path
  Path to the directory containing the data.
  dataset_id
- Dataset identifier. If not given will be determined automatically
- from the ``{vx.COUNTS_FILE!r}`` file.
+ Dataset identifier to name the constructed `SpatialData` elements. The reader will try to infer it from the
+ ``{vx.COUNTS_FILE!r}`` file name. If the file name does not contain the dataset id, it will try to infer it from the metadata, it needs to be provided.
  counts_file
  Name of the counts file. Use only if counts is not in `h5` format.
  fullres_image_file
@@ -81,39 +81,53 @@ def visium(
  path = Path(path)
  imread_kwargs = dict(imread_kwargs)
  image_models_kwargs = dict(image_models_kwargs)
- # get library_id
+ # try to infer library_id from the counts file
+ library_id = None
  try:
  patt = re.compile(f".*{VisiumKeys.COUNTS_FILE}")
  first_file = [i for i in os.listdir(path) if patt.match(i)][0]
 
  if f"_{VisiumKeys.COUNTS_FILE}" in first_file:
  library_id = first_file.replace(f"_{VisiumKeys.COUNTS_FILE}", "")
+ counts_file = f"{library_id}_{VisiumKeys.COUNTS_FILE}"
+ elif VisiumKeys.COUNTS_FILE == first_file:
+ library_id = None
+ counts_file = VisiumKeys.COUNTS_FILE
  else:
  raise ValueError(
- f"Cannot determine the library_id. Expecting a file with format <library_id>_{VisiumKeys.COUNTS_FILE}. Has "
- f"the files been renamed?"
+ f"Cannot determine the library_id. Expecting a file with format (<library_id>_){VisiumKeys.COUNTS_FILE}"
+ f". If the files have been renamed you may need to specify their file names (not their paths), with "
+ f"some of the following arguments: `counts_file`, `fullres_image_file`, `tissue_positions_file`, "
+ f"`scalefactors_file` arguments."
  )
- counts_file = f"{library_id}_{VisiumKeys.COUNTS_FILE}"
  except IndexError as e:
- logger.error(
- f"{e}. \nError is due to the fact that the library id could not be found, this is the case when the `counts_file` is `.mtx`.",
- )
- if dataset_id is None:
- raise ValueError("Cannot determine the `library_id`. Please provide `dataset_id`.")
- library_id = dataset_id
  if counts_file is None:
- raise ValueError("Cannot determine the library_id. Please provide `counts_file`.")
+ logger.error(
+ f"{e}. \nError is due to the fact that the library id could not be found, if the counts file is `.mtx` (or else), Please provide a `counts_file`.",
+ )
+ raise e
+ assert counts_file is not None
+
+ if library_id is None and dataset_id is None:
+ raise ValueError("Cannot determine the `library_id`. Please provide `dataset_id`.")
 
  if dataset_id is not None:
- if dataset_id != library_id:
+ if dataset_id != library_id and library_id is not None:
  logger.warning(
  f"`dataset_id: {dataset_id}` does not match `library_id: {library_id}`. `dataset_id: {dataset_id}` "
  f"will be used to build SpatialData."
  )
+ library_id = dataset_id
  else:
  dataset_id = library_id
+ assert dataset_id is not None
 
- adata, dataset_id = _read_counts(path, counts_file=counts_file, library_id=dataset_id, **kwargs)
+ # Yhe second element of the returned tuple is the full library as contained in the metadata of
+ # VisiumKeys.COUNTS_FILE. For instance for the spatialdata-sandbox/visium dataset it is:
+ # spaceranger100_count_30458_ST8059048_mm10-3_0_0_premrna
+ # We discard this value and use the one inferred from the filename of VisiumKeys.COUNTS_FILE, or the one provided by
+ # the user in dataset_id
+ adata, _ = _read_counts(path, counts_file=counts_file, library_id=library_id, **kwargs)
 
  if (path / "spatial" / VisiumKeys.SPOTS_FILE_1).exists() or (
  tissue_positions_file is not None and str(VisiumKeys.SPOTS_FILE_1) in str(tissue_positions_file)
@@ -142,6 +156,7 @@ def visium(
  adata.obs = pd.merge(adata.obs, coords, how="left", left_index=True, right_index=True)
  coords = adata.obs[[VisiumKeys.SPOTS_X, VisiumKeys.SPOTS_Y]].values
  adata.obsm["spatial"] = coords
+ adata.obs = pd.DataFrame(adata.obs)
  adata.obs.drop(columns=[VisiumKeys.SPOTS_X, VisiumKeys.SPOTS_Y], inplace=True)
  adata.obs["spot_id"] = np.arange(len(adata))
  adata.var_names_make_unique()
@@ -187,7 +202,7 @@ def visium(
 
  ImagePIL.MAX_IMAGE_PIXELS = imread_kwargs.pop("MAX_IMAGE_PIXELS")
  full_image = imread(fullres_image_file, **imread_kwargs).squeeze().transpose(2, 0, 1)
- full_image = DataArray(full_image, dims=("c", "y", "x"), name=dataset_id)
+ full_image = DataArray(full_image, dims=("c", "y", "x"))
  images[dataset_id + "_full_image"] = Image2DModel.parse(
  full_image,
  scale_factors=[2, 2, 2, 2],
@@ -199,13 +214,13 @@ def visium(
 
  if (path / VisiumKeys.IMAGE_HIRES_FILE).exists():
  image_hires = imread(path / VisiumKeys.IMAGE_HIRES_FILE, **imread_kwargs).squeeze().transpose(2, 0, 1)
- image_hires = DataArray(image_hires, dims=("c", "y", "x"), name=dataset_id)
+ image_hires = DataArray(image_hires, dims=("c", "y", "x"))
  images[dataset_id + "_hires_image"] = Image2DModel.parse(
  image_hires, transformations={"downscaled_hires": Identity()}
  )
  if (path / VisiumKeys.IMAGE_LOWRES_FILE).exists():
  image_lowres = imread(path / VisiumKeys.IMAGE_LOWRES_FILE, **imread_kwargs).squeeze().transpose(2, 0, 1)
- image_lowres = DataArray(image_lowres, dims=("c", "y", "x"), name=dataset_id)
+ image_lowres = DataArray(image_lowres, dims=("c", "y", "x"))
  images[dataset_id + "_lowres_image"] = Image2DModel.parse(
  image_lowres, transformations={"downscaled_lowres": Identity()}
  )