| import argparse |
| import glob |
| import logging |
| import os |
|
|
| import ocpmodels |
|
|
| """ |
| This script provides users with an automated way to download, preprocess (where |
| applicable), and organize data to readily be used by the existing config files. |
| """ |
|
|
| DOWNLOAD_LINKS = { |
| "s2ef": { |
| "200k": "https://dl.fbaipublicfiles.com/opencatalystproject/data/s2ef_train_200K.tar", |
| "2M": "https://dl.fbaipublicfiles.com/opencatalystproject/data/s2ef_train_2M.tar", |
| "20M": "https://dl.fbaipublicfiles.com/opencatalystproject/data/s2ef_train_20M.tar", |
| "all": "https://dl.fbaipublicfiles.com/opencatalystproject/data/s2ef_train_all.tar", |
| "val_id": "https://dl.fbaipublicfiles.com/opencatalystproject/data/s2ef_val_id.tar", |
| "val_ood_ads": "https://dl.fbaipublicfiles.com/opencatalystproject/data/s2ef_val_ood_ads.tar", |
| "val_ood_cat": "https://dl.fbaipublicfiles.com/opencatalystproject/data/s2ef_val_ood_cat.tar", |
| "val_ood_both": "https://dl.fbaipublicfiles.com/opencatalystproject/data/s2ef_val_ood_both.tar", |
| "test": "https://dl.fbaipublicfiles.com/opencatalystproject/data/s2ef_test_lmdbs.tar.gz", |
| "rattled": "https://dl.fbaipublicfiles.com/opencatalystproject/data/s2ef_rattled.tar", |
| "md": "https://dl.fbaipublicfiles.com/opencatalystproject/data/s2ef_md.tar", |
| }, |
| "is2re": "https://dl.fbaipublicfiles.com/opencatalystproject/data/is2res_train_val_test_lmdbs.tar.gz", |
| } |
|
|
| S2EF_COUNTS = { |
| "s2ef": { |
| "200k": 200000, |
| "2M": 2000000, |
| "20M": 20000000, |
| "all": 133934018, |
| "val_id": 999866, |
| "val_ood_ads": 999838, |
| "val_ood_cat": 999809, |
| "val_ood_both": 999944, |
| "rattled": 16677031, |
| "md": 38315405, |
| }, |
| } |
|
|
|
|
| def get_data(datadir, task, split, del_intmd_files): |
| os.makedirs(datadir, exist_ok=True) |
|
|
| if task == "s2ef" and split is None: |
| raise NotImplementedError("S2EF requires a split to be defined.") |
|
|
| if task == "s2ef": |
| assert ( |
| split in DOWNLOAD_LINKS[task] |
| ), f'S2EF "{split}" split not defined, please specify one of the following: {list(DOWNLOAD_LINKS["s2ef"].keys())}' |
| download_link = DOWNLOAD_LINKS[task][split] |
|
|
| elif task == "is2re": |
| download_link = DOWNLOAD_LINKS[task] |
|
|
| os.system(f"wget {download_link} -P {datadir}") |
| filename = os.path.join(datadir, os.path.basename(download_link)) |
| logging.info("Extracting contents...") |
| os.system(f"tar -xvf {filename} -C {datadir}") |
| dirname = os.path.join( |
| datadir, |
| os.path.basename(filename).split(".")[0], |
| ) |
| if task == "s2ef" and split != "test": |
| compressed_dir = os.path.join(dirname, os.path.basename(dirname)) |
| if split in ["200k", "2M", "20M", "all", "rattled", "md"]: |
| output_path = os.path.join(datadir, task, split, "train") |
| else: |
| output_path = os.path.join(datadir, task, "all", split) |
| uncompressed_dir = uncompress_data(compressed_dir) |
| preprocess_data(uncompressed_dir, output_path) |
|
|
| verify_count(output_path, task, split) |
| if task == "s2ef" and split == "test": |
| os.system(f"mv {dirname}/test_data/s2ef/all/test_* {datadir}/s2ef/all") |
| elif task == "is2re": |
| os.system(f"mv {dirname}/data/is2re {datadir}") |
|
|
| if del_intmd_files: |
| cleanup(filename, dirname) |
|
|
|
|
| def uncompress_data(compressed_dir): |
| import uncompress |
|
|
| parser = uncompress.get_parser() |
| args, _ = parser.parse_known_args() |
| args.ipdir = compressed_dir |
| args.opdir = os.path.dirname(compressed_dir) + "_uncompressed" |
| uncompress.main(args) |
| return args.opdir |
|
|
|
|
| def preprocess_data(uncompressed_dir, output_path): |
| import preprocess_ef as preprocess |
|
|
| parser = preprocess.get_parser() |
| args, _ = parser.parse_known_args() |
| args.data_path = uncompressed_dir |
| args.out_path = output_path |
| preprocess.main(args) |
|
|
|
|
| def verify_count(output_path, task, split): |
| paths = glob.glob(os.path.join(output_path, "*.txt")) |
| count = 0 |
| for path in paths: |
| lines = open(path, "r").read().splitlines() |
| count += len(lines) |
| assert ( |
| count == S2EF_COUNTS[task][split] |
| ), f"S2EF {split} count incorrect, verify preprocessing has completed successfully." |
|
|
|
|
| def cleanup(filename, dirname): |
| import shutil |
|
|
| if os.path.exists(filename): |
| os.remove(filename) |
| if os.path.exists(dirname): |
| shutil.rmtree(dirname) |
| if os.path.exists(dirname + "_uncompressed"): |
| shutil.rmtree(dirname + "_uncompressed") |
|
|
|
|
| if __name__ == "__main__": |
| parser = argparse.ArgumentParser() |
| parser.add_argument("--task", type=str, help="Task to download") |
| parser.add_argument( |
| "--split", type=str, help="Corresponding data split to download" |
| ) |
| parser.add_argument( |
| "--keep", |
| action="store_true", |
| help="Keep intermediate directories and files upon data retrieval/processing", |
| ) |
| |
| parser.add_argument( |
| "--get-edges", |
| action="store_true", |
| help="Store edge indices in LMDB, ~10x storage requirement. Default: compute edge indices on-the-fly.", |
| ) |
| parser.add_argument( |
| "--num-workers", |
| type=int, |
| default=1, |
| help="No. of feature-extracting processes or no. of dataset chunks", |
| ) |
| parser.add_argument( |
| "--ref-energy", action="store_true", help="Subtract reference energies" |
| ) |
| parser.add_argument( |
| "--data-path", |
| type=str, |
| default=os.path.join(os.path.dirname(ocpmodels.__path__[0]), "data"), |
| help="Specify path to save dataset. Defaults to 'ocpmodels/data'", |
| ) |
|
|
| args, _ = parser.parse_known_args() |
| get_data( |
| datadir=args.data_path, |
| task=args.task, |
| split=args.split, |
| del_intmd_files=not args.keep, |
| ) |
|
|
