428615e74edc5106af1c472f7fa07b3d2338acf9,scanpy/datasets/__init__.py,,visium_sge,#Any#,302

Before Change

    // setting filenames, tarfilenames, backup_urls
    // tarfilenames and backup_urls will be used for downloading data base
    files = dict(
        counts=settings.datasetdir / f"{sample_id}_filtered_feature_bc_matrix.h5",
        tissue_positions_file=settings.datasetdir / "spatial/tissue_positions_list.csv",
        scalefactors_json_file=settings.datasetdir / "spatial/scalefactors_json.json",
        hires_image=settings.datasetdir / "spatial/tissue_hires_image.png",
        lowres_image=settings.datasetdir / "spatial/tissue_lowres_image.png",
    )

    tarfiles = dict(
        tissue_positions_file=settings.datasetdir / f"{sample_id}_spatial.tar",
        scalefactors_json_file=settings.datasetdir / f"{sample_id}_spatial.tar",
        hires_image=settings.datasetdir / f"{sample_id}_spatial.tar",
        lowres_image=settings.datasetdir / f"{sample_id}_spatial.tar",
    )

    url_prefix = (
        f"http://cf.10xgenomics.com/samples/spatial-exp/1.0.0/{sample_id}/{sample_id}"
    )
    backup_urls = dict(
        counts=f"{url_prefix}_filtered_feature_bc_matrix.h5",
        tissue_positions_file=f"{url_prefix}_spatial.tar.gz",
        scalefactors_json_file=f"{url_prefix}_spatial.tar.gz",
        hires_image=f"{url_prefix}_spatial.tar.gz",
        lowres_image=f"{url_prefix}_spatial.tar.gz",
    )

    // download and untar files if necessary
    for f in tqdm(files, desc="Files"):
        if f in tarfiles:
            _utils.check_presence_download_untar(
                filename=files[f], tarfilename=tarfiles[f], backup_url=backup_urls[f]

After Change

    Annotated data matrix.
    
    _download_visium_dataset(sample_id)
    return read_visium(settings.datasetdir / sample_id)

Instances