Mercurial > public > atmospheric_lidar / changeset

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/atmospheric_lidar/scripts/licel2scc.py	Thu Feb 16 09:22:05 2017 +0200
@@ -0,0 +1,108 @@
+""" Command line tool to convert Licel binary files to SCC NetCDF format.
+"""
+import os
+import sys
+import glob
+import argparse
+import importlib
+
+from ..licel import LicelLidarMeasurement
+
+
+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(LicelLidarMeasurement):
+        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):
+        raise IOError("The provided settings path does not correspond to a file.")
+
+    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("directory", nargs='?', help="Directory containing licel files (default '.')", default='.')
+    parser.add_argument("search_string", nargs='?', help="Search string for files in directory (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")
+    args = parser.parse_args()
+
+    # Get a list of files to convert
+    search_str = os.path.join(args.directory, args.search_string)
+    files = glob.glob(search_str)
+
+    print(args.parameter_file)
+    if files:
+        # Read the files
+        print "Reading {0} files from {1}".format(len(files), args.directory)
+        CustomLidarMeasurement = create_custom_class(args.parameter_file, args.id_as_name, args.temperature,
+                                                     args.pressure)
+        measurement = CustomLidarMeasurement(files)
+
+        # Save the netcdf
+        print "Saving netcdf."
+        measurement.set_measurement_id(args.measurement_id, args.measurement_number)
+        measurement.save_as_netcdf()
+        print "Created file ", measurement.scc_filename
+    else:
+        print "No files found when searching for ", search_str

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/example_scripts/convert_ipral.py	Thu Feb 16 09:22:05 2017 +0200
@@ -0,0 +1,74 @@
+""" Sample script to convert licel files to SCC netcdf format.
+
+The script assumes the following things:
+
+1. You have already installed the atmospheric_lidar module (e.g. using pip).
+2. You have create a class in a file "ipral" describing your system (described the readme file).
+   If you want to use it for a different system you need to change the script to use your own class
+
+Run the script using: python convert_ipral.py <your options>
+
+Examples
+--------
+# This will read all files starting with "l" from "my_dir".
+# It will guess the measurement ID based on the date of the files, and will assume measurement number 00.
+# For example, the new measurment id could be 20120101mb00
+python convert_ipral.py my_dir l*.
+
+# This will use the measurement id you defined.
+python convert_ipral.py my_dir l*. -m 20120204mb32  # It will create the file 20120204mb32.nc
+
+Help string
+-----------
+# To get this, run: python convert_ipral.py -h
+usage: convert_ipral.py [-h] [-m MEASUREMENT_ID] [-n MEASUREMENT_NUMBER]
+                        [directory] [searchstring]
+
+positional arguments:
+  directory             Directory with licel files.
+  searchstring          Processing system id.
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -m MEASUREMENT_ID, --measurement_id MEASUREMENT_ID
+                        The new measurement id
+  -n MEASUREMENT_NUMBER, --measurement_number MEASUREMENT_NUMBER
+                        The measurement number for the date, if no id is
+                        provided
+
+"""
+
+import glob
+import os
+import argparse
+
+from atmospheric_lidar import ipral
+
+
+if __name__ == "__main__":
+
+    # Define the command line arguments.
+    parser = argparse.ArgumentParser()
+    parser.add_argument("directory", nargs='?', help="Directory with licel files.", default='.')
+    parser.add_argument("searchstring", nargs='?', help="Processing system id.", default="*.*")
+    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, if no id is provided", default="00")
+    args = parser.parse_args()
+
+
+    # Get a list of files to convert
+    search_str = os.path.join(args.directory, args.searchstring)
+    files = glob.glob(search_str)
+
+    if files:
+        # Read the files
+        print "Reading {0} files from {1}".format(len(files), args.directory)
+        measurement = ipral.IpralLidarMeasurement(files)
+
+        #Save the netcdf
+        print "Saving netcdf."
+        measurement.set_measurement_id(args.measurement_id, args.measurement_number)
+        measurement.save_as_netcdf()
+        print "Created file ", measurement.scc_filename
+    else:
+        print "No files found when searching for ", search_str
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/example_scripts/convert_lilas.py	Thu Feb 16 09:22:05 2017 +0200
@@ -0,0 +1,74 @@
+""" Sample script to convert licel files to SCC netcdf format.
+
+The script assumes the following things:
+
+1. You have already installed the atmospheric_lidar module (e.g. using pip).
+2. You have create a class in a file "lilas" describing your system (described the readme file).
+   If you want to use it for a different system you need to change the script to use your own class
+
+Run the script using: python convert_lilas.py <your options>
+
+Examples
+--------
+# This will read all files starting with "l" from "my_dir".
+# It will guess the measurement ID based on the date of the files, and will assume measurement number 00.
+# For example, the new measurment id could be 20120101mb00
+python convert_lilas.py my_dir l*.
+
+# This will use the measurement id you defined.
+python convert_lilas.py my_dir l*. -m 20120204mb32  # It will create the file 20120204mb32.nc
+
+Help string
+-----------
+# To get this, run: python convert_lilas.py -h
+usage: convert_lilas.py [-h] [-m MEASUREMENT_ID] [-n MEASUREMENT_NUMBER]
+                        [directory] [searchstring]
+
+positional arguments:
+  directory             Directory with licel files.
+  searchstring          Processing system id.
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -m MEASUREMENT_ID, --measurement_id MEASUREMENT_ID
+                        The new measurement id
+  -n MEASUREMENT_NUMBER, --measurement_number MEASUREMENT_NUMBER
+                        The measurement number for the date, if no id is
+                        provided
+
+"""
+
+import glob
+import os
+import argparse
+
+from atmospheric_lidar import lilas
+
+
+if __name__ == "__main__":
+
+    # Define the command line arguments.
+    parser = argparse.ArgumentParser()
+    parser.add_argument("directory", nargs='?', help="Directory with licel files.", default='.')
+    parser.add_argument("searchstring", nargs='?', help="Processing system id.", default="*.*")
+    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, if no id is provided", default="00")
+    args = parser.parse_args()
+
+
+    # Get a list of files to convert
+    search_str = os.path.join(args.directory, args.searchstring)
+    files = glob.glob(search_str)
+
+    if files:
+        # Read the files
+        print "Reading {0} files from {1}".format(len(files), args.directory)
+        measurement = lilas.LilasLidarMeasurement(files)
+
+        #Save the netcdf
+        print "Saving netcdf."
+        measurement.set_measurement_id(args.measurement_id, args.measurement_number)
+        measurement.save_as_netcdf()
+        print "Created file ", measurement.scc_filename
+    else:
+        print "No files found when searching for ", search_str
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