File size: 2,027 Bytes
0226c36 1bc9257 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 | """Download, verify and open one small HESRT sample (public; no login needed)."""
from __future__ import annotations
import argparse
import json
from pathlib import Path
import anndata as ad
from PIL import Image
from hesrt_io import RELEASE_TAG, download_sample, load_catalog
def main() -> None:
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument("--gsm", default="GSM8915497", help="Default: 3.2 MB pancreas package")
parser.add_argument("--revision", default=RELEASE_TAG)
parser.add_argument("--output", type=Path, default=Path("hesrt_demo"))
parser.add_argument("--cache-dir", default=None)
args = parser.parse_args()
catalog, revision = load_catalog(args.revision, args.cache_dir)
selected = catalog.loc[catalog.gsm_id.eq(args.gsm)]
if len(selected) != 1:
parser.error(f"Expected one GSM, found {len(selected)}")
row = selected.iloc[0]
folder = download_sample(row, args.output, revision, args.cache_dir)
data = ad.read_h5ad(folder / "spatial.h5ad", backed="r")
try:
coordinate_source = row.coordinate_location
if coordinate_source == "obsm/spatial":
coordinates = data.obsm["spatial"]
elif coordinate_source == "obs/x,obs/y":
coordinates = data.obs[["x", "y"]].to_numpy()
else:
raise ValueError(f"Inspect provenance for coordinate layout {coordinate_source!r}")
with Image.open(folder / "wsi.tif") as image:
print(json.dumps({"gsm_id": args.gsm, "revision": revision,
"folder": str(folder), "shape": list(data.shape),
"coordinate_source": coordinate_source, "coordinate_shape": list(coordinates.shape),
"image_format": image.format, "image_size": list(image.size),
"archive_and_all_members_verified": True}, indent=2))
finally:
data.file.close()
print("Inspect alignment_qc.png and provenance.json before spatial modeling.")
if __name__ == "__main__":
main()
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