src/submission.py

"""
Submission script for 2-stage fMRI encoding with Flow Matching.

Generates predictions for friends-s7 (in-distribution) and ood (out-of-distribution)
test sets. Outputs are saved as .npy and .zip files matching the Algonauts 2025
challenge format.

Usage:
    python -m src.submission --checkpoint-dir output/two_stage_encoding
"""

import argparse
import warnings
from pathlib import Path

import numpy as np
import torch
from omegaconf import OmegaConf

from .data import Algonauts2025Dataset, load_sharded_features, episode_filter
from .stage1.medarc_architecture import MultiSubjectConvLinearEncoder

from .loaders import load_all_features, make_test_loader, DEFAULT_DATA_DIR, SUBJECTS
from .builder import build_models
from .loops import run_inference
from .evaluate import validate_submission
from .submission_utils import load_fmri_num_samples, print_summary, save_predictions

def main() -> None:
    parser = argparse.ArgumentParser(description="Generate submission predictions")
    parser.add_argument(
        "--checkpoint-dir",
        type=str,
        required=True,
        help=(
            "Path to trained model output directory "
            "(contains config.yaml, stage1_best.pt, stage2_epoch_*.pt)"
        ),
    )
    parser.add_argument(
        "--test-set",
        type=str,
        default="all",
        choices=["friends-s7", "ood", "all"],
        help="Which test set(s) to generate predictions for",
    )
    parser.add_argument(
        "--stage2-ckpt",
        type=str,
        default=None,
        help="Stage 2 checkpoint filename (default: latest)",
    )
    parser.add_argument(
        "--n-timesteps",
        type=int,
        default=None,
        help="Override number of ODE steps for stage 2",
    )
    parser.add_argument("--device", type=str, default="cuda")
    parser.add_argument("--datasets-root", type=str, default=None)
    parser.add_argument(
        "--output-dir",
        type=str,
        default=None,
        help="Output directory (default: <checkpoint-dir>/submission)",
    )
    args = parser.parse_args()

    ckpt_dir = Path(args.checkpoint_dir)
    cfg = OmegaConf.load(ckpt_dir / "config.yaml")

    datasets_root = Path(args.datasets_root or cfg.get("datasets_root") or DEFAULT_DATA_DIR)
    device = torch.device(args.device)
    subjects = list(cfg.get("subjects", list(DEFAULT_SUBJECTS)))
    n_timesteps = int(args.n_timesteps or cfg.stage2.get("n_timesteps", 25))

    out_dir = Path(args.output_dir) if args.output_dir else ckpt_dir / "submission"
    out_dir.mkdir(parents=True, exist_ok=True)

    np_version = tuple(int(x) for x in np.__version__.split(".")[:2])
    if np_version[0] >= 2:
        warnings.warn(
            (
                f"NumPy {np.__version__} detected. Codabench requires NumPy < 2.0. "
                "Submissions saved with NumPy 2.x can fail formatting checks."
            ),
            stacklevel=1,
        )

    print(f"Checkpoint dir: {ckpt_dir}")
    print(f"Output dir: {out_dir}")
    print(f"Device: {device}")
    print(f"Subjects: {subjects}")
    print(f"Stage 2 ODE timesteps: {n_timesteps}")

    print("Loading features...")
    all_features = load_all_features(cfg, datasets_root)

    print("Building models...")
    stage1_model, stage2_models = build_models(cfg, ckpt_dir, all_features, subjects, device, args.stage2_ckpt)

    test_sets = ["friends-s7", "ood"] if args.test_set == "all" else [args.test_set]

    for test_set_name in test_sets:
        print(f"\n{'=' * 60}")
        print(f"Generating predictions for: {test_set_name}")
        print(f"{'=' * 60}")

        fmri_num_samples = load_fmri_num_samples(datasets_root, test_set_name)
        test_loader = make_test_loader(cfg, all_features, fmri_num_samples, test_set_name)

        predictions = run_inference(
            stage1_model=stage1_model,
            stage2_models=stage2_models,
            test_loader=test_loader,
            fmri_num_samples=fmri_num_samples,
            subjects=subjects,
            device=device,
            n_timesteps=n_timesteps,
        )

        validate_submission(predictions, test_set_name, fmri_num_samples)
        print_summary(predictions)
        save_predictions(predictions, test_set_name, out_dir)

    print("\nDone!")

if __name__ == "__main__":
    main()