"""Loader for the Splatter cube dataset. Single file, no install: drop it next to your code, or from huggingface_hub import hf_hub_download exec(open(hf_hub_download("btraven/splatter-cube-pbmc3k", "loader.py", repo_type="dataset")).read()) Works against the Hub or a local copy of the dataset directory: catalog() # every simulation, as a DataFrame load(de_prob=0.02, de_fac_loc=1.3, n_groups=8, seed=42) # -> AnnData for ad in load_many(de_prob=0.01): ... # all seeds / cluster counts Requires pandas and anndata; huggingface_hub only when reading from the Hub. """ from __future__ import annotations import os from functools import lru_cache REPO = "btraven/splatter-cube-pbmc3k" # substituted per cube by package_hf.R # The CSV keeps splatter's own parameter names, which contain dots and camel # case. Callers get python-friendly keywords instead. ALIASES = { "de_prob": "de.prob", "de_fac_loc": "de.facLoc", "bcv_common": "bcv.common", "dropout_mid": "dropout.mid", "dropout_type": "dropout.type", "lib_loc": "lib.loc", "n_groups": "nGroups", "point": "point", "seed": "seed", "sparsity": "sparsity", } def _fetch(relpath: str, source: str | None = None) -> str: """Local path for a file in the dataset, downloading from the Hub if needed.""" if source is not None: p = os.path.join(os.path.expanduser(source), relpath) if not os.path.exists(p): raise FileNotFoundError(f"{p} (is {source} a copy of the dataset?)") return p from huggingface_hub import hf_hub_download return hf_hub_download(REPO, relpath, repo_type="dataset") @lru_cache(maxsize=8) def catalog(source: str | None = None): """Every simulation: parameters, realised sparsity, clustering scores.""" import pandas as pd return pd.read_csv(_fetch("metrics.csv", source)) def _select(source=None, **query): import numpy as np df = catalog(source) for key, want in query.items(): if key not in ALIASES: raise TypeError( f"unknown parameter {key!r}; choose from {sorted(ALIASES)}") col = df[ALIASES[key]] # float levels are written to CSV at full precision, so compare # approximately rather than trusting 1.3 == 1.3000000000000003 hit = np.isclose(col, want) if np.issubdtype(col.dtype, np.floating) \ else col == want if not hit.any(): raise ValueError( f"no simulation with {key}={want!r}; " f"available: {sorted(col.unique().tolist())}") df = df[hit] return df def _read(row, source): import anndata ad = anndata.read_h5ad(_fetch(row["file"], source)) ad.uns["cube"] = row.to_dict() # the parameters travel with the data return ad def load(source: str | None = None, **query): """The single simulation matching `query`, as an AnnData. Ground truth is in `.obs["Group"]`; the generating parameters are in `.uns["cube"]`. Raises if the query is ambiguous, so a silently arbitrary pick is never returned. """ hits = _select(source, **query) if len(hits) > 1: varies = [c for c in ALIASES.values() if hits[c].nunique() > 1] raise ValueError( f"{len(hits)} simulations match; narrow by {varies or ['seed']}") return _read(hits.iloc[0], source) def load_many(source: str | None = None, **query): """Every simulation matching `query`, lazily, in catalog order.""" for _, row in _select(source, **query).iterrows(): yield _read(row, source) import sys # Only when actually run as `python loader.py` -- the README's exec(open(...).read()) # idiom inherits __name__ == "__main__" from its caller and would trip this. if __name__ == "__main__" and os.path.basename(sys.argv[0]) == "loader.py": src = (sys.argv[1] if len(sys.argv) > 1 else os.path.dirname(os.path.abspath(sys.argv[0]))) cat = catalog(src) assert len(cat) == 180, len(cat) assert cat["ari_kmeans"].between(0, 1.01).all() ad = load(src, de_prob=0.02, de_fac_loc=1.3, n_groups=8, seed=42) assert ad.shape == (2000, 16085), ad.shape assert ad.obs["Group"].nunique() == 8 assert ad.uns["cube"]["de.prob"] == 0.02 assert ad.X.min() >= 0 assert len(list(load_many(src, de_prob=0.01, n_groups=4))) == 12 for bad, err in [(dict(de_prob=0.5), ValueError), (dict(nonsense=1), TypeError), (dict(de_prob=0.02), ValueError)]: # ambiguous try: load(src, **bad) except err: pass else: raise AssertionError(f"{bad} should have raised {err.__name__}") print(f"ok: {len(cat)} sims, loaded {ad.shape[0]}x{ad.shape[1]}, " f"{ad.obs['Group'].nunique()} groups")