Mercurial > public > atmospheric_lidar / changeset

--- a/atmospheric_lidar/scripts/licel2scc.py	Tue Sep 25 13:30:45 2018 +0300
+++ b/atmospheric_lidar/scripts/licel2scc.py	Wed Oct 10 14:01:42 2018 +0300
@@ -97,80 +97,6 @@
     return settings
 
 
-def get_cloud_free_files(LidarMeasurementClass, files, settings):
-    """ Find cloud free periods in the given files.
-
-    Depending on the provided settings, it could create plots of cloud mask and
-    selected cloud-free periods.
-
-    Parameters
-    ----------
-    LidarMeasurementClass : class
-       Class used to read the files.
-    files : list
-       A list of raw licel file paths.
-    settings : dict
-       A dictionary of cloud masking settings.
-
-    Returns
-    -------
-    file_list : list of lists
-       A list of lists containing paths to cloud-free files.
-    """
-    logger.warning("Starting cloud mask procedure. This is an experimental feature.")
-
-    try:
-        from cloudmask import cloudmask  # Import here until we setup a proper installation procedure
-    except ImportError:
-        logger.error("Cloud mask module could not be loaded. Please install manually.")
-        sys.exit(1)
-
-    measurement = LidarMeasurementClass(files)
-    channel = measurement.channels[settings['channel']]
-    cloud_mask = cloudmask.CloudMaskRaw(channel)
-
-    idxs = cloud_mask.cloud_free_periods(settings['cloudfree_period_min'],
-                                         settings['file_duration_max'],
-                                         settings['max_cloud_height'])
-
-    logger.debug('Cloud free indices: {0}'.format(idxs))
-
-    if len(idxs) == 0:  # If no cloud-free period found
-        logger.info('No cloud free period found. Nothing converted.')
-        sys.exit(1)
-
-    logger.info("{0} cloud free period(s) found.".format(len(idxs)))
-
-    if settings['plot']:
-        # Plot cloud free periods
-        cloudfree_filename = "cloudfree_{0}_{1}_{2}.png".format(channel.wavelength,
-                                                             channel.start_time.strftime('%Y%m%d_%H%M%S'),
-                                                             channel.stop_time.strftime('%Y%m%d_%H%M%S'))
-        cloudfree_path = os.path.join(settings['plot_directory'], cloudfree_filename)
-        fig, _ = cloud_mask.plot_cloudfree(idxs)
-
-        plt.savefig(cloudfree_path)
-        plt.close()
-
-        # Plot cloud mask
-        cloudmask_filename = "cloudmask_{0}_{1}_{2}.png".format(channel.wavelength,
-                                                                channel.start_time.strftime('%Y%m%d_%H%M%S'),
-                                                                channel.stop_time.strftime('%Y%m%d_%H%M%S'))
-        cloudmask_path = os.path.join(settings['plot_directory'], cloudmask_filename)
-
-        fig, _ = cloud_mask.plot_mask()
-
-        plt.savefig(cloudmask_path)
-        plt.close()
-
-    file_list = []
-    for idx_min, idx_max in idxs:
-        current_files = measurement.files[idx_min:idx_max]
-        file_list.append(current_files)
-
-    return file_list
-
-
 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:
@@ -216,7 +142,7 @@
     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="Location of licel files. Use relative path and filename wildcards. (default './*.*')",
+                        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",
@@ -232,14 +158,12 @@
                         help="The pressure (in hPa) at lidar level, required if using US Standard atmosphere",
                         default="1020")
     parser.add_argument('-D', '--dark_measurements',
-                        help="Location of files containing dark measurements. Use relative path and filename wildcars, see 'files' parameter for example.",
+                        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",
                         )
-    parser.add_argument('--cloudmask_settings', help="Experimental feature to automatically cloud mask measurements",
-                        default="")
 
     # Verbosity settings from http://stackoverflow.com/a/20663028
     parser.add_argument('-d', '--debug', help="Print dubuging information.", action="store_const",
@@ -276,13 +200,4 @@
     CustomLidarMeasurement = create_custom_class(args.parameter_file, args.id_as_name, args.temperature,
                                                  args.pressure, args.licel_timezone)
 
-    if args.cloudmask_settings:
-        cloudmask_settings = read_cloudmask_settings_file(args.cloudmask_settings)
-
-        file_lists = get_cloud_free_files(CustomLidarMeasurement, files, cloudmask_settings)
-
-        for n, files in enumerate(file_lists):
-            measurement_id, measurement_no = get_corrected_measurement_id(args, n)
-            convert_to_scc(CustomLidarMeasurement, files, args.dark_files, measurement_id, measurement_no)
-    else:
-        convert_to_scc(CustomLidarMeasurement, files, args.dark_files, args.measurement_id, args.measurement_number)
+    convert_to_scc(CustomLidarMeasurement, files, args.dark_files, args.measurement_id, args.measurement_number)