lemnatec-dataset-downloader

#!/usr/bin/env python

import argparse
from dsf.data import lemnatec


def options():
    parser = argparse.ArgumentParser(description='Retrieve data from a LemnaTec database.',
                                     formatter_class=argparse.ArgumentDefaultsHelpFormatter)
    parser.add_argument("-e", "--exp", help="Experiment name/Measurement label.", required=True)
    parser.add_argument("-d", "--db", help="Database name.", required=True)
    parser.add_argument("-c", "--config", help="JSON config file.", required=True)
    parser.add_argument("-o", "--outdir", help="Output directory for results.", required=True)
    args = parser.parse_args()

    return args


def main():
    # Read user options
    args = options()

    # Read the database connetion configuration file
    config = lemnatec.load_config(filename=args.config, database=args.db, experiment=args.exp)

    # Open an SFTP connection to the database server
    sftp = lemnatec.open_sftp_connection(config=config)

    # Open a database connection to the PostgreSQL server
    db = lemnatec.open_database_connection(config=config)

    # Initialize the dataset directory if it does not exist
    lemnatec.init_dataset(dataset_dir=args.outdir, config=config)

    # Load the dataset metadata
    meta = lemnatec.load_dataset(dataset_dir=args.outdir)

    # Query the database for snapshot metadata and update the local metadata
    meta = lemnatec.query_snapshots(db=db, metadata=meta, experiment=config.experiment, config=config)

    # Query the database for image metadata and update the local metadata
    meta = lemnatec.query_images(db=db, metadata=meta, experiment=config.experiment, config=config)

    # Update the local metadata file
    lemnatec.save_dataset(dataset_dir=args.outdir, metadata=meta)

    # Transfer the image data to the local directory
    lemnatec.transfer_images(metadata=meta, sftp=sftp, dataset_dir=args.outdir, config=config)

    # Close the SFTP connection
    sftp.close()

    # Close the database connection
    db.close()


if __name__ == "__main__":
    main()