| """Step 4: leakage audit + count tables -> audit_report.md. Exit code 1 if any leakage check fails. |
| |
| python -m fsbench.audit --bench data/bench |
| """ |
| import argparse |
| import sys |
| from pathlib import Path |
|
|
| import pandas as pd |
|
|
| from .common import CLASSES |
|
|
| USED = ["train", "val", "cal", "test", "test_ood", "test_openset"] |
|
|
|
|
| def _md(df): |
| df = df.reset_index() |
| head = "| " + " | ".join(map(str, df.columns)) + " |" |
| sep = "|" + "---|" * len(df.columns) |
| return "\n".join([head, sep] + ["| " + " | ".join(map(str, r)) + " |" for r in df.itertuples(index=False)]) |
|
|
|
|
| def main(argv=None): |
| ap = argparse.ArgumentParser() |
| ap.add_argument("--bench", required=True) |
| a = ap.parse_args(argv) |
| bench = Path(a.bench) |
| s = pd.read_csv(bench / "splits.csv", dtype=str, keep_default_na=False) |
| u = s[s.split.isin(USED)] |
| pairs = pd.read_csv(bench / "near_duplicates.csv", dtype=str, keep_default_na=False) |
| split_of = dict(zip(s.image_id, s.split)) |
|
|
| checks = [] |
|
|
| def check(name, bad): |
| checks.append((name, len(bad) == 0, len(bad))) |
| return bad |
|
|
| |
| u = u.assign(leak_key=u.split.where(~u.split.str.startswith("test"), "held_out")) |
| split_of = {i: (k if k != "held_out" else "held_out") for i, k in zip(u.image_id, u.leak_key)} |
| check("leakage group in >1 split", u.groupby("group_id").leak_key.nunique().loc[lambda x: x > 1]) |
| check("identical file (SHA-256) in >1 split", u[u.sha256 != ""].groupby("sha256").leak_key.nunique().loc[lambda x: x > 1]) |
| pp = u[u.patient_id != ""].groupby(["source", "patient_id"]).leak_key.nunique() |
| check("patient in >1 split", pp[pp > 1]) |
| xp = pairs[[x in split_of and y in split_of and split_of[x] != split_of[y] |
| for x, y in zip(pairs.image_id_a, pairs.image_id_b)]] |
| check("near-duplicate pair across splits", xp) |
| fam = u.assign(side=u.split.str.startswith("test")).groupby("family").side.nunique() |
| check("acquisition family on both dev and test side", fam[fam > 1]) |
| dev_src, test_src = set(u.source[u.split.isin(["train", "val", "cal"])]), set(u.source[u.split.str.startswith("test")]) |
| check("source on both dev and test side", sorted(dev_src & test_src)) |
| check("cal image without cal_A/cal_B", u[(u.split == "cal") & (u.cal_subset == "")]) |
|
|
| classes = [c for c in [*CLASSES, "OPENSET"] if c in set(u.label)] |
| by_split = pd.crosstab(u.split, u.label).reindex(index=USED, columns=classes, fill_value=0) |
| by_split["total"] = by_split.sum(axis=1) |
| by_src = pd.crosstab([u.source, u.split], u.label).reindex(columns=classes, fill_value=0) |
| ncls = (by_src.groupby(level=0).sum() > 0).sum(axis=1).value_counts().sort_index() |
| cal = pd.crosstab(u.cal_subset[u.split == "cal"], u.label[u.split == "cal"]).reindex(columns=classes, fill_value=0) |
| unused = s[s.split == "unused"].unused_reason.value_counts().rename("images") |
| dr = u[u.dr_grade != ""] |
| dr_tab = pd.crosstab(dr.split, dr.dr_grade) if len(dr) else pd.DataFrame() |
|
|
| lines = ["# FundusShift — audit report", "", |
| f"Inventory rows: {len(s)} | used in protocol: {len(u)} | unused: {len(s) - len(u)} | " |
| f"sources used: {u.source.nunique()}", "", "## Leakage checks", "", |
| "| check | result | violations |", "|---|---|---|"] |
| lines += [f"| {n} | {'PASS' if ok else 'FAIL'} | {k} |" for n, ok, k in checks] |
| lines += ["", "## Images per split and class", "", _md(by_split), |
| "", "## Calibration halves", "", _md(cal), |
| "", "## Mapped classes per source (count of sources)", "", _md(ncls.rename("sources").rename_axis("n_classes")), |
| "", "## Source x split x class", "", _md(by_src), |
| "", "## Unused images by reason", "", _md(unused.rename_axis("reason"))] |
| if len(dr_tab): |
| lines += ["", "## Secondary task: ICDR DR grade per split", "", _md(dr_tab)] |
| (bench / "audit_report.md").write_text("\n".join(lines) + "\n") |
|
|
| for n, ok, k in checks: |
| print(f"{'PASS' if ok else 'FAIL'} {n} ({k})") |
| print(f"\n{by_split.to_string()}\n\nreport -> {bench / 'audit_report.md'}") |
| sys.exit(0 if all(ok for _, ok, _ in checks) else 1) |
|
|
|
|
| if __name__ == "__main__": |
| main() |
|
|
