| """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() |
|
|
