Source code for fibsem.main

import os

import fibsem.autoscript
import fibsem.logfile
import fibsem.milling
import fibsem.sample
import fibsem.send_email
import fibsem.user_input

config_default = os.path.join(os.path.abspath(os.path.dirname(__file__)),
                              '..', 'config_default.yml')


def run_milling(host='10.0.0.1', config=config_default):
    settings = fibsem.user_input.load_config(config)
    log_filename = fibsem.logfile._log_file_begins(settings)
    microscope = fibsem.autoscript.initialize(ip_address=host)
    samples = fibsem.sample.add_samples(microscope, settings)
    fibsem.milling.mill_all_samples(samples, microscope, settings)
    fibsem.send_email.send_email(
        settings['email'],
        'Your fibsem job has been completed successfully.',
        attachment_filename=log_filename
    )


if __name__ == '__main__':
    args = fibsem.user_input.configure_parser()
    run_milling(host=args.host, config=args.config)