Source code for coseda.export

import os
import datetime
import subprocess



def hkl2mtz(input_hkl, output_dir, cellfile_path):
    """
    Convert a .hkl file to .mtz using get_hkl.
    All outputs (MTZ, logs) will be written into a new export_<timestamp> folder under output_dir.

    Parameters:
        input_hkl (str): Path to the input CrystFEL .hkl file (absolute or relative).
        output_dir (str): Directory under which to create export_<timestamp> folder.
        cellfile_path (str): Path to the cell file (.cell or .inp) for get_hkl (absolute or relative).
    """
    # Create a timestamped export directory
    timestamp = datetime.datetime.now().strftime("%Y%m%d_%H%M%S")
    export_dir = os.path.join(output_dir, f"export_{timestamp}")
    os.makedirs(export_dir, exist_ok=True)

    # Derive output MTZ filename from input_hkl
    base_name = os.path.splitext(os.path.basename(input_hkl))[0]
    output_mtz = f"{base_name}.mtz"

    # Construct full paths
    input_hkl_path = input_hkl if os.path.isabs(input_hkl) else os.path.join(output_dir, input_hkl)
    output_mtz_path = os.path.join(export_dir, output_mtz)
    cellfile_full = cellfile_path if os.path.isabs(cellfile_path) else os.path.join(output_dir, cellfile_path)

    # Ensure the input HKL exists
    if not os.path.exists(input_hkl_path):
        raise FileNotFoundError(f"Input HKL file not found: {input_hkl_path}")

    # Prepare log files
    stdout_log = os.path.join(export_dir, "hkl2mtz_stdout.log")
    stderr_log = os.path.join(export_dir, "hkl2mtz_stderr.log")

    # Build the get_hkl command
    hkl2mtz_cmd = [
        'get_hkl',
        '-i', input_hkl_path,
        '-o', output_mtz_path,
        '-p', cellfile_full,
        '--output-format=mtz'
    ]

    # Run the command
    with open(stdout_log, "w") as stdout_f, open(stderr_log, "w") as stderr_f:
        subprocess.run(hkl2mtz_cmd, stdout=stdout_f, stderr=stderr_f, check=True)

    return export_dir, output_mtz_path, stdout_log, stderr_log