spice/data/scripts/sample_nested_subsets.py

#!/usr/bin/env python3
"""Create nested FPS-based structure subsets from SPICE XYZ datasets.

Uses MACE's fine_tuning_select utility with FPS for diverse subset selection.
Smaller subsets are nested within larger ones (strict prefixes).

Usage:
    python sample_nested_subsets.py --input data/train_large_neut_no_bad_clean.xyz --percentages 50 20 10 5 1
    python sample_nested_subsets.py --input data/test_large_neut_all.xyz --percentages 50 20 10 5 1
"""

from __future__ import annotations

import argparse
import logging
import subprocess
import sys
from pathlib import Path

import numpy as np
from ase.io import read


def setup_logging() -> None:
    """Configure logging to stdout."""
    logging.basicConfig(
        level=logging.INFO,
        format="%(asctime)s | %(levelname)s | %(message)s",
        stream=sys.stdout,
    )


def count_structures(filepath: Path) -> int:
    """Count the number of structures in an XYZ file efficiently."""
    logging.info(f"Counting structures in {filepath.name}...")
    count = 0
    with open(filepath, "r") as f:
        while True:
            line = f.readline()
            if not line:
                break
            try:
                natoms = int(line.strip())
                f.readline()  # Skip comment
                for _ in range(natoms):
                    f.readline()  # Skip atom lines
                count += 1
            except (ValueError, StopIteration):
                break
    return count


def run_mace_fps_selection(
    input_path: Path,
    output_path: Path,
    num_samples: int,
    model: str = "/home/s5f/ev333.s5f/work/mace-omat-0-medium.model",
    device: str = "cpu",
    seed: int = 42,
) -> None:
    """
    Run MACE's fine_tuning_select tool with FPS sampling.
    
    Args:
        input_path: Path to input XYZ file
        output_path: Path to output XYZ file
        num_samples: Number of samples to select
        model: MACE model to use for descriptor computation
        device: Device to use (cpu or cuda)
        seed: Random seed
    """
    cmd = [
        "python", "-m", "mace.cli.fine_tuning_select",
        "--configs_pt", str(input_path),
        "--output", str(output_path),
        "--num_samples", str(num_samples),
        "--subselect", "fps",
        "--model", model,
        "--device", device,
        "--seed", str(seed),
        "--filtering_type", "none",
        "--disallow_random_padding",
    ]
    
    logging.info(f"Running FPS selection for {num_samples} samples...")
    logging.debug(f"Command: {' '.join(cmd)}")
    
    result = subprocess.run(cmd, capture_output=True, text=True)
    
    if result.returncode != 0:
        logging.error(f"FPS selection failed: {result.stderr}")
        raise RuntimeError(f"MACE fine_tuning_select failed with code {result.returncode}")
    
    logging.info(f"FPS selection completed successfully")


def create_nested_subsets_from_parent(
    parent_file: Path,
    output_dir: Path,
    base_name: str,
    subset_sizes: dict[float, int],
) -> None:
    """
    Create nested subsets by reading from the largest parent file.
    
    Args:
        parent_file: Path to the largest subset file
        output_dir: Directory for output files
        base_name: Base name for output files
        subset_sizes: Dict mapping percentages to counts (excluding the largest)
    """
    logging.info(f"Loading parent file: {parent_file}")
    parent_atoms = read(str(parent_file), index=":")
    logging.info(f"Loaded {len(parent_atoms)} structures from parent")
    
    # Create smaller nested subsets
    for pct in sorted(subset_sizes.keys(), reverse=True):
        size = subset_sizes[pct]
        output_path = output_dir / f"{base_name}{pct}pct_{size}.xyz"
        
        logging.info(f"Creating {pct}% subset ({size} structures)...")
        subset_atoms = parent_atoms[:size]
        
        from ase.io import write
        write(str(output_path), subset_atoms, format="extxyz")
        logging.info(f"Wrote {len(subset_atoms)} structures to {output_path}")


def parse_args() -> argparse.Namespace:
    parser = argparse.ArgumentParser(
        description=__doc__,
        formatter_class=argparse.RawDescriptionHelpFormatter,
    )
    parser.add_argument(
        "--input",
        type=str,
        required=True,
        help="Path to input XYZ file",
    )
    parser.add_argument(
        "--percentages",
        nargs="+",
        type=float,
        required=True,
        help="Subset percentages (e.g., 50 20 10 5 1 for 50%%, 20%%, etc.)",
    )
    parser.add_argument(
        "--output-dir",
        type=str,
        default=None,
        help="Output directory (defaults to same as input)",
    )
    parser.add_argument(
        "--prefix",
        type=str,
        default=None,
        help="Output file prefix (defaults to input filename + _subset_)",
    )
    parser.add_argument(
        "--model",
        type=str,
        default="/home/s5f/ev333.s5f/work/mace-omat-0-medium.model",
        help="MACE model for descriptor computation (default: /home/s5f/ev333.s5f/work/mace-omat-0-medium.model)",
    )
    parser.add_argument(
        "--device",
        type=str,
        default="cpu",
        choices=["cpu", "cuda"],
        help="Device to use (default: cpu)",
    )
    parser.add_argument(
        "--seed",
        type=int,
        default=42,
        help="Random seed for reproducibility (default: 42)",
    )
    return parser.parse_args()


def main() -> None:
    args = parse_args()
    setup_logging()
    
    input_path = Path(args.input).expanduser().resolve()
    if not input_path.is_file():
        raise FileNotFoundError(f"Input file not found: {input_path}")
    
    # Validate and sort percentages
    percentages = sorted([p for p in args.percentages if p > 0], reverse=True)
    if not percentages:
        raise ValueError("At least one positive percentage must be provided")
    
    if any(p > 100 for p in percentages):
        raise ValueError("Percentages must be <= 100")
    
    # Count total structures
    total_structures = count_structures(input_path)
    logging.info(f"Total structures in dataset: {total_structures}")
    
    # Calculate subset sizes
    subset_sizes = {}
    for pct in percentages:
        size = int(np.round(total_structures * pct / 100))
        if size == 0:
            logging.warning(f"Percentage {pct}% results in 0 structures, skipping")
            continue
        subset_sizes[pct] = size
    
    if not subset_sizes:
        raise ValueError("No valid subset sizes after conversion")
    
    # Log planned subsets
    logging.info("\nPlanned subsets:")
    for pct in sorted(subset_sizes.keys(), reverse=True):
        size = subset_sizes[pct]
        logging.info(f"  {pct}% = {size} structures")
    
    # Setup output
    output_dir = Path(args.output_dir).expanduser().resolve() if args.output_dir else input_path.parent
    output_dir.mkdir(parents=True, exist_ok=True)
    prefix = args.prefix or f"{input_path.stem}_subset_"
    
    # Get largest subset size and create it using MACE FPS
    largest_pct = max(subset_sizes.keys())
    largest_size = subset_sizes[largest_pct]
    
    logging.info(f"\n{'='*60}")
    logging.info(f"Creating largest subset ({largest_pct}% = {largest_size} structures) using MACE FPS")
    logging.info(f"{'='*60}\n")
    
    largest_output = output_dir / f"{prefix}{largest_pct}pct_{largest_size}.xyz"
    
    run_mace_fps_selection(
        input_path=input_path,
        output_path=largest_output,
        num_samples=largest_size,
        model=args.model,
        device=args.device,
        seed=args.seed,
    )
    
    # Create smaller nested subsets from the largest one
    if len(subset_sizes) > 1:
        logging.info(f"\n{'='*60}")
        logging.info("Creating nested smaller subsets from largest subset")
        logging.info(f"{'='*60}\n")
        
        smaller_sizes = {pct: size for pct, size in subset_sizes.items() if pct < largest_pct}
        create_nested_subsets_from_parent(
            parent_file=largest_output,
            output_dir=output_dir,
            base_name=prefix,
            subset_sizes=smaller_sizes,
        )
    
    logging.info("\n" + "="*60)
    logging.info("All nested subsets created successfully!")
    logging.info("="*60)


if __name__ == "__main__":
    main()