Mercurial > public > atmospheric_lidar / file revision

""" Command line tool to convert Licel binary files to SCC NetCDF format.
"""
import argparse
import glob
import importlib
import logging
import os
import sys

from matplotlib import pyplot as plt
import yaml

from ..licel import LicelLidarMeasurement
from ..__init__ import __version__

logger = logging.getLogger(__name__)


def create_custom_class(custom_netcdf_parameter_path, use_id_as_name=False, temperature=25., pressure=1020.,
                        licel_timezone='UTC'):
    """ This funtion creates a custom LicelLidarMeasurement subclass,
    based on the input provided by the users.

    Parameters
    ----------
    custom_netcdf_parameter_path : str
       The path to the custom channels parameters.
    use_id_as_name : bool
       Defines if channels names are descriptive or transient digitizer IDs.
    temperature : float
       The ground temperature in degrees C (default 25.0).
    pressure : float
       The ground pressure in hPa (default: 1020.0).
    licel_timezone : str
       String describing the timezone according to the tz database.

    Returns
    -------
    CustomLidarMeasurement:
       A custom sub-class of LicelLidarMeasurement
    """
    logger.debug('Reading parameter files: %s' % custom_netcdf_parameter_path)
    custom_netcdf_parameters = read_settings_file(custom_netcdf_parameter_path)

    class CustomLidarMeasurement(LicelLidarMeasurement):
        extra_netcdf_parameters = custom_netcdf_parameters

        def __init__(self, file_list=None):
            super(CustomLidarMeasurement, self).__init__(file_list, use_id_as_name=use_id_as_name,
                                                         licel_timezone=licel_timezone)

        def set_PT(self):
            ''' Sets the pressure and temperature at station level. This is used if molecular_calc parameter is
            set to 0 (i.e. use US Standard atmosphere).

            The results are stored in the info dictionary.
            '''

            self.info['Temperature'] = temperature
            self.info['Pressure'] = pressure

    return CustomLidarMeasurement


def read_settings_file(settings_path):
    """ Read the settings file.

    The file should contain python code."""
    if not os.path.isfile(settings_path):
        logging.error("The provided settings path does not correspond to a file.")
        sys.exit(1)

    dirname, basename = os.path.split(settings_path)
    sys.path.append(dirname)

    module_name, _ = os.path.splitext(basename)
    settings = importlib.import_module(module_name)
    return settings


def read_cloudmask_settings_file(settings_file_path):
    """ Read the configuration file.

    The file should be in YAML syntax."""

    if not os.path.isfile(settings_file_path):
        logging.error("Wrong path for cloudmask settings file (%s)" % settings_file_path)
        sys.exit(1)

    with open(settings_file_path) as yaml_file:
        try:
            settings = yaml.load(yaml_file)
            logging.debug("Read cloudmask settings file(%s)" % settings_file_path)
        except:
            logging.error("Could not parse YAML file (%s)" % settings_file_path)
            sys.exit(1)

    return settings


def get_corrected_measurement_id(args, n):
    """ Correct the provided measurement id, in case of multiple cloud-free periods. """
    if args.measurement_id is not None:
        order = int(args.measurement_id[-2:])
        new_no = order + n
        measurement_id = args.measurement_id[:-2] + str(new_no)
        measurement_no = args.measurement_number  # The same
    else:
        measurement_no = str(int(args.measurement_number) + n).zfill(2)
        measurement_id = None

    return measurement_id, measurement_no


def convert_to_scc(CustomLidarMeasurement, files, dark_pattern, measurement_id, measurement_number):
    """ Convert files to SCC. """
    measurement = CustomLidarMeasurement(files)
    # Get a list of files containing dark measurements
    if dark_pattern != "":
        dark_files = glob.glob(dark_pattern)

        if dark_files:
            logger.debug("Using %s as dark measurements files!" % ', '.join(dark_files))
            measurement.dark_measurement = CustomLidarMeasurement(dark_files)
        else:
            logger.warning(
                'No dark measurement files found when searching for %s. Will not use any dark measurements.' % dark_pattern)
    try:
        measurement = measurement.subset_by_scc_channels()
    except ValueError as err:
        logger.error(err)
        sys.exit(1)

    # Save the netcdf
    logger.info("Saving netcdf")
    measurement.set_measurement_id(measurement_id, measurement_number)
    measurement.save_as_SCC_netcdf()
    logger.info("Created file %s" % measurement.scc_filename)


def main():
    # Define the command line argument
    parser = argparse.ArgumentParser(description="A program to convert Licel binary files to the SCC NetCDF format.")
    parser.add_argument("parameter_file", help="The path to a parameter file linking licel and SCC channels.")
    parser.add_argument("files",
                        help="Search pattern of Licel files. Use filename wildcards. (default './*.*')",
                        default="./*.*")
    parser.add_argument("-i", '--id_as_name',
                        help="Use transient digitizer ids as channel names, instead of descriptive names",
                        action="store_true")
    parser.add_argument("-m", "--measurement_id", help="The new measurement id", default=None)
    parser.add_argument("-n", "--measurement_number",
                        help="The measurement number for the date from 00 to 99. Used if no id is provided",
                        default="00")
    parser.add_argument("-t", "--temperature", type=float,
                        help="The temperature (in C) at lidar level, required if using US Standard atmosphere",
                        default="25")
    parser.add_argument("-p", "--pressure", type=float,
                        help="The pressure (in hPa) at lidar level, required if using US Standard atmosphere",
                        default="1020")
    parser.add_argument('-D', '--dark_measurements',
                        help="Search pattern of files containing dark measurements. Use filename wildcars, see 'files' parameter for example.",
                        default="", dest="dark_files"
                        )
    parser.add_argument('--licel_timezone', help="String describing the timezone according to the tz database.",
                        default="UTC", dest="licel_timezone",
                        )

    # Verbosity settings from http://stackoverflow.com/a/20663028
    parser.add_argument('-d', '--debug', help="Print dubuging information.", action="store_const",
                        dest="loglevel", const=logging.DEBUG, default=logging.INFO,
                        )
    parser.add_argument('-s', '--silent', help="Show only warning and error messages.", action="store_const",
                        dest="loglevel", const=logging.WARNING
                        )
    parser.add_argument('--version', help="Show current version.", action='store_true')

    args = parser.parse_args()

    # Get the logger with the appropriate level
    logging.basicConfig(format='%(levelname)s: %(message)s', level=args.loglevel)
    logger = logging.getLogger(__name__)

    # coloredlogs.install(fmt='%(levelname)s: %(message)s', level=args.loglevel)

    # Check for version
    if args.version:
        print("Version: %s" % __version__)
        sys.exit(0)

    # Get a list of files to convert
    files = glob.glob(args.files)

    # If not files found, exit
    if len(files) == 0:
        logger.error("No files found when searching for %s." % args.files)
        sys.exit(1)

    # If everything OK, proceed
    logger.info("Found {0} files matching {1}".format(len(files), os.path.abspath(args.files)))
    CustomLidarMeasurement = create_custom_class(args.parameter_file, args.id_as_name, args.temperature,
                                                 args.pressure, args.licel_timezone)

    convert_to_scc(CustomLidarMeasurement, files, args.dark_files, args.measurement_id, args.measurement_number)