Mercurial > public > atmospheric_lidar / changeset

--- a/atmospheric_lidar/__init__.py	Thu Feb 16 12:23:32 2017 +0200
+++ b/atmospheric_lidar/__init__.py	Thu Feb 16 16:35:42 2017 +0200
@@ -1,1 +1,1 @@
-__version__ = '0.2.0'
\ No newline at end of file
+__version__ = '0.2.1'
\ No newline at end of file

--- a/atmospheric_lidar/generic.py	Thu Feb 16 12:23:32 2017 +0200
+++ b/atmospheric_lidar/generic.py	Thu Feb 16 16:35:42 2017 +0200
@@ -1,13 +1,13 @@
 # General imports
 import datetime
 from operator import itemgetter
+import logging
 
-# Science imports
-import numpy as np
 import matplotlib as mpl
-from matplotlib.ticker import ScalarFormatter
+import netCDF4 as netcdf
+import numpy as np
 from matplotlib import pyplot as plt
-import netCDF4 as netcdf
+from matplotlib.ticker import ScalarFormatter
 
 netcdf_format = 'NETCDF3_CLASSIC'  # choose one of 'NETCDF3_CLASSIC', 'NETCDF3_64BIT', 'NETCDF4_CLASSIC' and 'NETCDF4'
 
@@ -143,8 +143,15 @@
         """
         Subset the measurement based on the channels provided in the extra_netecdf_parameter file.
         """
-        extra_channels = self.extra_netcdf_parameters.channel_parameters.keys()
-        return self.subset_by_channels(extra_channels)
+        scc_channels = self.extra_netcdf_parameters.channel_parameters.keys()
+        common_channels = list(set(scc_channels).intersection(self.channels.keys()))
+
+        if not common_channels:
+            logging.debug("Config channels: %s." % ','.join(scc_channels))
+            logging.debug("Licel channels: %s." % ','.join(self.channels.keys()))
+            raise ValueError('No common channels between licel and configuration files.')
+
+        return self.subset_by_channels(common_channels)
 
     def subset_by_time(self, start_time, stop_time):
 
@@ -324,8 +331,8 @@
         else:
             raise ValueError('Channel parameters should define either "chanel_id" or "channel_string_ID".')
 
-        temp_v = f.createVariable(channel_var, variable_type, ('channels', ))
-        for channel, n in enumerate(channels):
+        temp_v = f.createVariable(channel_var, variable_type, ('channels',))
+        for n, channel in enumerate(channels):
             temp_v[n] = params.channel_parameters[channel][channel_var]
 
         # Write the values of fixed channel parameters
@@ -489,13 +496,13 @@
     def _nearest_dt(self, dtime):
         margin = datetime.timedelta(seconds=300)
         if ((dtime + margin) < self.start_time) | ((dtime - margin) > self.stop_time):
-            print "Requested date not covered in this file"
-            raise
+            logging.error("Requested date not covered in this file")
+            raise ValueError("Requested date not covered in this file")
         dt = abs(self.time - np.array(dtime))
         dtmin = min(dt)
 
         if dtmin > datetime.timedelta(seconds=60):
-            print "Nearest profile more than 60 seconds away. dt = %s." % dtmin
+            logging.warning("Nearest profile more than 60 seconds away. dt = %s." % dtmin)
         ind_t = np.where(dt == dtmin)
         ind_a = ind_t[0]
         if len(ind_a) > 1:

--- a/atmospheric_lidar/licel.py	Thu Feb 16 12:23:32 2017 +0200
+++ b/atmospheric_lidar/licel.py	Thu Feb 16 16:35:42 2017 +0200
@@ -1,8 +1,11 @@
+import datetime
+import logging
+
 import numpy as np
-import datetime
+
+import musa_2009_netcdf_parameters
+import musa_netcdf_parameters
 from generic import BaseLidarMeasurement, LidarChannel
-import musa_netcdf_parameters
-import musa_2009_netcdf_parameters
 
 licel_file_header_format = ['Filename',
                             'StartDate StartTime EndDate EndTime Altitude Longtitude Latitude ZenithAngle',
@@ -11,11 +14,10 @@
 licel_file_channel_format = 'Active AnalogPhoton LaserUsed DataPoints 1 HV BinW Wavelength d1 d2 d3 d4 ADCbits NShots Discriminator ID'
 
 
-
 class LicelFile:
     def __init__(self, filename, use_id_as_name=False):
         self.filename = filename
-        self.use_id_as_name=use_id_as_name
+        self.use_id_as_name = use_id_as_name
         self.start_time = None
         self.stop_time = None
         self.import_file(filename)
@@ -46,8 +48,9 @@
                 b = np.fromfile(f, 'b', 1)
 
                 if (a[0] != 13) | (b[0] != 10):
-                    print "Warning: No end of line found after record. File could be corrupt"
-                channel = LicelFileChannel(current_channel_info, raw_data, self.duration(), use_id_as_name=self.use_id_as_name)
+                    logging.warning("No end of line found after record. File could be corrupt: %s" % filename)
+                channel = LicelFileChannel(current_channel_info, raw_data, self.duration(),
+                                           use_id_as_name=self.use_id_as_name)
 
                 channel_name = channel.channel_name
 
@@ -198,7 +201,7 @@
 
     def import_file(self, filename):
         if filename in self.files:
-            print "File has been imported already:" + filename
+            logging.warning("File has been imported already: %s" % filename)
         else:
             current_file = LicelFile(filename, use_id_as_name=self.use_id_as_name)
             self.raw_info[current_file.filename] = current_file.raw_info
@@ -269,9 +272,9 @@
     list2 = f2.split()
 
     if len(list1) != len(list2):
-        print "Warning: Combining lists of different lengths."
-        print "List 1: %s" % list1
-        print "List 2: %s" % list2
+        logging.debug("Channel parameter list has different length from licel specifications.")
+        logging.debug("List 1: %s" % list1)
+        logging.debug("List 2: %s" % list2)
     combined = zip(list2, list1)
     combined = dict(combined)
     return combined

--- a/atmospheric_lidar/scripts/licel2scc.py	Thu Feb 16 12:23:32 2017 +0200
+++ b/atmospheric_lidar/scripts/licel2scc.py	Thu Feb 16 16:35:42 2017 +0200
@@ -1,10 +1,13 @@
 """ Command line tool to convert Licel binary files to SCC NetCDF format.
 """
+import argparse
+import glob
+import importlib
+import logging
 import os
 import sys
-import glob
-import argparse
-import importlib
+
+import coloredlogs
 
 from ..licel import LicelLidarMeasurement
 
@@ -71,7 +74,8 @@
     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("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")
@@ -85,25 +89,42 @@
     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 processing information.", 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
     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)
+        logger.info("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)
-        measurement = measurement.subset_by_scc_channels()
-        
+        try:
+            measurement = measurement.subset_by_scc_channels()
+        except ValueError as err:
+            logging.error(err)
+            sys.exit(1)
         # Save the netcdf
-        print "Saving netcdf."
+        logger.info("Saving netcdf")
         measurement.set_measurement_id(args.measurement_id, args.measurement_number)
         measurement.save_as_netcdf()
-        print "Created file ", measurement.scc_filename
+        logger.info("Created file %s" % measurement.scc_filename)
     else:
-        print "No files found when searching for ", search_str
+        logger.error("No files found when searching for %s." % search_str)
+        sys.exit(1)
\ No newline at end of file

--- a/setup.py	Thu Feb 16 12:23:32 2017 +0200
+++ b/setup.py	Thu Feb 16 16:35:42 2017 +0200
@@ -7,7 +7,7 @@
 
 # Read the long description from the readme file
 with open("readme.rst", "rb") as f:
-    long_descr = f.read().decode("utf-8")
+    long_description = f.read().decode("utf-8")
 
 
 # Read the version parameters from the __init__.py file. In this way
@@ -33,8 +33,8 @@
 setup(name='atmospheric_lidar_reader',
       packages=['atmospheric_lidar', 'atmospheric_lidar.scripts'],
       version=find_version("atmospheric_lidar", "__init__.py"),
-      description='Classes for reading raw atmospheric lidar data.',
-      long_description=long_descr,
+      description='Package for reading raw atmospheric lidar data.',
+      long_description=long_description,
       url='https://bitbucket.org/iannis_b/atmospheric-lidar/',
       author='Ioannis Binietoglou',
       author_email='ioannis@inoe.ro',
@@ -53,6 +53,7 @@
           "sphinx",
           "pytest",
           "netcdf4",
+          "coloredlogs",
       ],
       entry_points={
           'console_scripts': ['licel2scc = atmospheric_lidar.scripts.licel2scc:main'],