#!/usr/bin/env python3 """Run excluded-domain builders and conversion into a private output tree.""" from __future__ import annotations import argparse import json import os import subprocess import sys from pathlib import Path PROCESSING = Path(__file__).resolve().parents[1] RELEASE = PROCESSING.parent DOMAINS = ("covla", "cuhk_x_har", "mimic_death", "mimic_disch", "pixelrec", "sp500") IMAGE_DOMAINS = {"mimic_death", "mimic_disch", "pixelrec", "sp500"} def run_stage(script: str, *arguments: object) -> None: """Use the current interpreter and keep bytecode out of the release.""" group = script.split("/", 1)[0] if group in DOMAINS: modality = "image-timeseries" if group in IMAGE_DOMAINS else "video-timeseries" path = RELEASE / "sample" / modality / script else: path = PROCESSING / script subprocess.run( [sys.executable, "-B", str(path), *map(str, arguments)], check=True, ) def require_path(parser: argparse.ArgumentParser, path: Path | None, option: str) -> Path: if path is None or not path.exists(): parser.error(f"{option} must identify an existing local input") return path.resolve() def build_prompts( args: argparse.Namespace, parser: argparse.ArgumentParser, output: Path, ) -> Path: if args.input_jsonl: return require_path(parser, args.input_jsonl, "--input-jsonl") prompts = output / "intermediate" if args.domain in {"mimic_death", "mimic_disch"}: hosp = require_path(parser, args.mimic_hosp_dir, "--mimic-hosp-dir") notes = require_path(parser, args.mimic_note_dir, "--mimic-note-dir") metadata = require_path(parser, args.cxr_metadata_csv, "--cxr-metadata-csv") images = require_path(parser, args.cxr_jpg_root, "--cxr-jpg-root") prompts.mkdir() buckets = args.chartevents_root if buckets is None: events = require_path(parser, args.chartevents, "--chartevents") buckets = prompts / "chartevents_bucketed" run_stage("mimic_death/bucket_chartevents.py", "--input", events, "--output-root", buckets, "--chunksize", args.chunksize) else: buckets = require_path(parser, buckets, "--chartevents-root") raw = prompts / "patients.jsonl" common = ["--mimic-hosp-dir", hosp, "--mimic-note-dir", notes, "--cxr-metadata-csv", metadata, "--cxr-jpg-root", images, "--chartevents-root", buckets, "--out-jsonl", raw, "--qc-csv", prompts / "patient_qc.csv", "--seed", args.seed] if args.domain == "mimic_death": icu = require_path(parser, args.mimic_icu_dir, "--mimic-icu-dir") run_stage("mimic_death/build_json_QA_death.py", *common, "--mimic-icu-dir", icu, "--n-death", args.n_positive, "--n-alive", args.n_negative, "--require-image-file-exists") prompt_script = "mimic_death/json_prompt_death.py" else: run_stage("mimic_disch/build_json_QA.py", *common, "--max-pos", args.n_positive, "--max-neg", args.n_negative) prompt_script = "mimic_disch/json_prompt.py" all_prompts = prompts / "all.jsonl" run_stage(prompt_script, "--in-jsonl", raw, "--out-jsonl", all_prompts) run_stage("mimic_death/split_dataset.py", all_prompts, "--out-dir", prompts, "--seed", args.seed + (args.domain == "mimic_disch")) (prompts / "all_train.jsonl").rename(prompts / "train.jsonl") (prompts / "all_test.jsonl").rename(prompts / "test.jsonl") elif args.domain == "covla": source = require_path(parser, args.source_root, "--source-root") for name in ("states", "front_car", "metadata.jsonl"): require_path(parser, source / name, f"--source-root/{name}") prompts.mkdir() brakes = prompts / "brake_reasons" run_stage("covla/extract_brake_reasons.py", "--root", source, "--output-dir", brakes) enriched = prompts / "enriched.jsonl" run_stage( "covla/enrich_segments.py", "--root", source, "--input", brakes / "all_brake_reasons.jsonl", "--output", enriched, "--sample-output", prompts / "enriched_inspection.jsonl", ) all_prompts = prompts / "all.jsonl" run_stage( "covla/build_prompts.py", "--root", source, "--input", enriched, "--output", all_prompts, "--sample-output", prompts / "inspection.jsonl", ) run_stage( "covla/split_dataset.py", "--root", source, "--input", all_prompts, "--train-output", prompts / "train.jsonl", "--test-output", prompts / "test.jsonl", "--stats-output", prompts / "split_stats.json", "--seed", args.seed, ) elif args.domain == "cuhk_x_har": source = require_path(parser, args.source_root, "--source-root") skeleton = require_path(parser, args.skeleton_root or source / "Skeleton", "--skeleton-root") prompts.mkdir() if args.aligned_jsonl: aligned = require_path(parser, args.aligned_jsonl, "--aligned-jsonl") else: imu = require_path(parser, args.imu_root or source / "IMU", "--imu-root") local_imu = prompts / "IMU" local_skeleton = prompts / "Skeleton" run_stage("cuhk_x_har/xlsx_to_csv.py", "--input-root", imu, "--output-root", local_imu) run_stage("cuhk_x_har/images_to_video.py", skeleton, "--output-root", local_skeleton, "--fps", args.fps, "--split-mode", args.skeleton_crop) aligned = prompts / "imu_skeleton_aligned.jsonl" run_stage("cuhk_x_har/imu_skeleton_to_jsonl.py", "--imu-root", local_imu, "--skeleton-root", local_skeleton, "--output", aligned) run_stage( "cuhk_x_har/prepare.py", "--root", source, "--input", aligned, "--skeleton-root", skeleton, "--train-output", prompts / "train.jsonl", "--test-output", prompts / "test.jsonl", "--train-sample-output", prompts / "train_inspection.jsonl", "--test-sample-output", prompts / "test_inspection.jsonl", "--seed", args.seed, ) elif args.domain == "pixelrec": interactions = require_path(parser, args.interactions, "--interactions") item_info = require_path(parser, args.item_info, "--item-info") images = require_path(parser, args.image_root, "--image-root") prompts.mkdir() run_stage( "pixelrec/prepare.py", "--interactions", interactions, "--item-info", item_info, "--image-root", images, "--output", prompts / f"{args.split}.jsonl", "--limit", args.limit or 0, ) elif args.domain == "sp500": prices = require_path(parser, args.time_series_dir, "--time-series-dir") news = require_path(parser, args.news_dir, "--news-dir") images = require_path(parser, args.image_root, "--image-root") prompts.mkdir() run_stage( "sp500/prepare.py", "--time-series-dir", prices, "--news-dir", news, "--image-dir", images, "--out-jsonl", prompts / f"{args.split}.jsonl", "--max-files", args.limit or -1, "--fut-len", args.horizon, "--news-timezone", args.news_timezone, ) return prompts / f"{args.split}.jsonl" def main(domain: str) -> None: if domain not in DOMAINS: raise ValueError(f"Unsupported excluded domain: {domain}") parser = argparse.ArgumentParser(description=__doc__) parser.set_defaults(domain=domain, input_jsonl=None) parser.add_argument("--output-dir", type=Path, required=True, help="New private workspace outside MMTA-v1.0; a domain child is created.") if domain != "sp500": parser.add_argument("--input-jsonl", type=Path, help="Optional existing task prompts to convert.") parser.add_argument("--source-root", type=Path, help="Local source root or base for relative media.") parser.add_argument("--path-map", action="append", default=[], metavar="OLD=NEW") parser.add_argument("--split", choices=("train", "test"), default="test") parser.add_argument("--limit", type=int, help="Maximum converted records; default processes all.") if domain in {"covla", "cuhk_x_har", "mimic_death", "mimic_disch"}: parser.add_argument("--seed", type=int, default=42) if domain in {"covla", "cuhk_x_har"}: parser.add_argument("--num-workers", type=int, default=1) if domain == "cuhk_x_har": parser.add_argument("--aligned-jsonl", type=Path, help="Optional existing aligned IMU/skeleton input.") parser.add_argument("--imu-root", type=Path, help="Defaults to /IMU.") parser.add_argument("--skeleton-root", type=Path, help="Skeleton action directory tree.") parser.add_argument("--fps", type=int, default=20) parser.add_argument("--skeleton-crop", choices=("left-half", "auto", "none"), default="left-half") if domain in {"mimic_death", "mimic_disch"}: parser.add_argument("--mimic-hosp-dir", type=Path) parser.add_argument("--mimic-icu-dir", type=Path) parser.add_argument("--mimic-note-dir", type=Path) parser.add_argument("--cxr-metadata-csv", type=Path) parser.add_argument("--cxr-jpg-root", type=Path) events = parser.add_mutually_exclusive_group() events.add_argument("--chartevents", type=Path, help="Raw chartevents.csv or chartevents.csv.gz.") events.add_argument("--chartevents-root", type=Path, help="Existing subject/admission buckets.") parser.add_argument("--chunksize", type=int, default=1000000) parser.add_argument("--n-positive", type=int, default=20 if domain == "mimic_death" else 50) parser.add_argument("--n-negative", type=int, default=130 if domain == "mimic_death" else 100) if domain == "pixelrec": parser.add_argument("--interactions", type=Path) parser.add_argument("--item-info", type=Path) parser.add_argument("--image-root", type=Path) if domain == "sp500": parser.add_argument("--time-series-dir", type=Path) parser.add_argument("--news-dir", type=Path) parser.add_argument("--image-root", "--image-dir", type=Path) parser.add_argument("--horizon", type=int, default=12) parser.add_argument("--news-timezone", default="America/New_York") args = parser.parse_args() if args.limit is not None and args.limit < 1: parser.error("--limit must be positive") if getattr(args, "num_workers", 1) < 1: parser.error("--num-workers must be positive") if getattr(args, "fps", 1) < 1 or getattr(args, "chunksize", 1) < 1: parser.error("--fps and --chunksize must be positive") if domain in {"mimic_death", "mimic_disch"} and (args.n_positive < 0 or args.n_negative < 0): parser.error("--n-positive and --n-negative must be nonnegative") if any("=" not in item for item in args.path_map): parser.error("--path-map must have the form OLD=NEW") output = args.output_dir.expanduser().resolve() / domain if output.is_relative_to(RELEASE): parser.error("Restricted output must be outside MMTA-v1.0") if output.exists(): parser.error(f"Output already exists: {output}; choose a new workspace") output.mkdir(parents=True) input_jsonl = build_prompts(args, parser, output) output_jsonl = output / f"{domain}.omnits.jsonl" arguments: list[object] = [ "--in-jsonl", input_jsonl, "--out-jsonl", output_jsonl, "--csv-dir", output / "timeseries", "--dataset-name", f"{domain}_{args.split}", ] if args.source_root: arguments.extend(("--source-root", args.source_root.resolve())) for item in args.path_map: arguments.extend(("--path-map", item)) if args.limit: arguments.extend(("--limit", args.limit)) if domain in IMAGE_DOMAINS: task = "prediction" if domain in {"pixelrec", "sp500"} else "classification" arguments.extend(("--default-task", task)) run_stage("common/convert_images.py", *arguments) else: arguments.extend(("--clip-dir", output / "video_clips", "--num-workers", args.num_workers)) run_stage("common/convert_videos.py", *arguments) # Keep converted assets and relative references local to this private tree. temporary = output_jsonl.with_suffix(".tmp") count = 0 with output_jsonl.open(encoding="utf-8") as source, temporary.open("w", encoding="utf-8") as target: for line in source: record = json.loads(line) if "id" not in record: record["id"] = f"{domain}_{args.split}_{Path(record['timeseries_path']).stem}" record.pop("video_id", None) record.setdefault("task", "classification") record.update(domain=domain, split=args.split, variant="original") for field in ("timeseries_path", "video_path", "image_path"): if field not in record: continue values = record[field] if isinstance(record[field], list) else [record[field]] paths = [os.path.relpath(Path(value).resolve(), output).replace(os.sep, "/") for value in values] record[field] = paths if isinstance(record[field], list) else paths[0] target.write(json.dumps(record, ensure_ascii=False, allow_nan=False) + "\n") count += 1 if not count: raise RuntimeError("No local tasks were generated") temporary.replace(output_jsonl) print(json.dumps({"domain": domain, "split": args.split, "records": count, "output": str(output_jsonl), "path_base": str(output), "scope": "private_local_reconstruction"}, indent=2))