# HG changeset patch
# User Iannis <ulalume3@yahoo.com>
# Date 1488140910 -7200
# Node ID 6d6512752932f06ae9fb7c3d73650443a2d9a1b5
# Parent  d01c4cf7ea677666448a39b20c3280bfd77854ad
Licel2scc calibration measurement.

diff -r d01c4cf7ea67 -r 6d6512752932 atmospheric_lidar/scripts/licel2scc_depol.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/atmospheric_lidar/scripts/licel2scc_depol.py	Sun Feb 26 22:28:30 2017 +0200
@@ -0,0 +1,134 @@
+""" 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 ..licel_depol import LicelCalibrationMeasurement
+
+
+def create_custom_class(custom_netcdf_parameter_path, use_id_as_name=False, temperature=25., pressure=1020.):
+    """ 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).
+
+    Returns
+    -------
+    CustomLidarMeasurement:
+       A custom sub-class of LicelLidarMeasurement
+    """
+
+    custom_netcdf_parameters = read_settings_file(custom_netcdf_parameter_path)
+
+    class CustomLidarMeasurement(LicelCalibrationMeasurement):
+        extra_netcdf_parameters = custom_netcdf_parameters
+
+        def __init__(self, filelist=None):
+            super(CustomLidarMeasurement, self).__init__(filelist, use_id_as_name)
+
+        def get_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 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("plus45_string", nargs='?', help="Search string for plus 45 degree files (default '*.*')", default="*.*")
+    parser.add_argument("minus45_string", nargs='?', help="Search string for minus 45 degree files (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")
+    # 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
+                        )
+
+    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)
+
+    # Get a list of files to convert
+    plus45_files = glob.glob(args.plus45_string)
+    minus45_files = glob.glob(args.minus45_string)
+
+    if len(plus45_files)==0 or len(minus45_files)==0:
+        logger.error("No files found when searching for %s and %s." % (plus45_files, minus45_files))
+        sys.exit(1)
+
+    # Read the files
+    logger.info("Reading {0} files from {1}".format(len(plus45_files), args.plus45_string))
+    logger.info("Reading {0} files from {1}".format(len(minus45_files), args.minus45_string))
+
+    CustomLidarMeasurement = create_custom_class(args.parameter_file, args.id_as_name, args.temperature,
+                                                     args.pressure)
+
+    measurement = CustomLidarMeasurement(plus45_files, minus45_files)
+
+    try:
+        measurement = measurement.subset_by_scc_channels()
+    except ValueError as err:
+        logging.error(err)
+        sys.exit(1)
+
+    # Save the netcdf
+    logger.info("Saving netcdf")
+    measurement.set_measurement_id(args.measurement_id, args.measurement_number)
+    measurement.save_as_netcdf()
+    logger.info("Created file %s" % measurement.scc_filename)