"""Convert the obj/ + pcd/ + metadata.csv layout into WebDataset tar shards (train/, test/). Each sample key is the sample id, with members: {id}.vertices.npy (V, 3) float32 {id}.faces.npy (F, 3) int32 {id}.pcd.npy (8192, 3) float32 {id}.json {"id", "genus", "components", "sample_code"} """ import io, json, tarfile from multiprocessing import Pool from pathlib import Path import numpy as np import pandas as pd ROOT = Path(__file__).resolve().parents[1] PER_SHARD = 600 # ~1 GB per shard SEED = 0 meta = pd.read_csv(ROOT / "metadata.csv").set_index("id") obj_path = {p.stem: p for p in (ROOT / "obj").glob("*/*.npz")} pcd_path = {p.stem: p for p in (ROOT / "pcd").glob("*/*.npy")} def npy_bytes(a: np.ndarray) -> bytes: buf = io.BytesIO() np.save(buf, a) return buf.getvalue() def add(tar: tarfile.TarFile, name: str, data: bytes): info = tarfile.TarInfo(name) info.size = len(data) tar.addfile(info, io.BytesIO(data)) def write_shard(args): out, ids = args tmp = out.with_suffix(".tar.tmp") with tarfile.open(tmp, "w", format=tarfile.USTAR_FORMAT) as tar: for i in ids: z = np.load(obj_path[i]) row = meta.loc[i] add(tar, f"{i}.vertices.npy", npy_bytes(z["vertices"].astype(np.float32))) # (V, 3) add(tar, f"{i}.faces.npy", npy_bytes(z["faces"].astype(np.int32))) # (F, 3) add(tar, f"{i}.pcd.npy", npy_bytes(np.load(pcd_path[i]).astype(np.float32))) # (8192, 3) add(tar, f"{i}.json", json.dumps({ "id": i, "genus": int(row.genus), "components": int(row.components), "sample_code": json.loads(row.sample_code), }).encode()) tmp.rename(out) return out.name if __name__ == "__main__": jobs = [] for split in ["train", "test"]: ids = np.array((ROOT / "splits/full" / f"{split}.txt").read_text().split()) ids = ids[np.random.default_rng(SEED).permutation(len(ids))] # shuffle so shards are i.i.d. (ROOT / split).mkdir(exist_ok=True) for s, k in enumerate(range(0, len(ids), PER_SHARD)): out = ROOT / split / f"{split}-{s:05d}.tar" if not out.exists(): jobs.append((out, ids[k:k + PER_SHARD].tolist())) with Pool(8) as pool: for name in pool.imap_unordered(write_shard, jobs): print(name, flush=True)