Atmospheric Lidar Package: atmospheric_lidar/diva.py@b5bbfee2a898 (annotated)

atmospheric_lidar/diva.py@b5bbfee2a898 (annotated)

atmospheric_lidar/diva.py

Fri, 15 Dec 2017 13:33:10 +0200

author: Iannis <ulalume3@yahoo.com>
date: Fri, 15 Dec 2017 13:33:10 +0200
changeset 113: b5bbfee2a898
parent 112: 07bb7a219314
child 114: d11a94f03753
permissions: -rw-r--r--

* Ancillary variable group

* Example of analog and photon-counting channel parameters.

 """ This is a class for experimenting with the new DIVA / EARLINET NetCDF file format.
 In the long run, this should be places as a method in BaseLidarMeasurement class. For now it is kept
 separately not to interfere with normal development.
 """
 import netCDF4 as netcdf
 import pyyaml
 import datetime
 import os
 from .generic import BaseLidarMeasurement
 class DivaOutput(BaseLidarMeasurement):
     def save_as_diva(self, output_path, parameter_file):
         """ Save the current data in the 'draft' DIVA format. """
         with open(parameter_file, 'r') as f:
             parameters = pyyaml.load(f)
         global_parameters = parameters['global_parameters']  # Shortcut
         channels = parameters['channels']
         iso_date = datetime.datetime.utcnow().isoformat()
         python_file_name = os.path.basename(__file__)
         with netcdf.Dataset(output_path, 'w', format="NETCDF4") as f:
             # Global attributes
             f.title = global_parameters['title']
             f.source = global_parameters['source']
             f.institution = global_parameters['institution']
             f.references = global_parameters['references']
             f.location = global_parameters['location']
             f.data_version = global_parameters['data_version']
             f.conversion_date = iso_date
             f.comment = global_parameters['comment']
             f.Conventions = global_parameters['Conventions']
             f.history = global_parameters['history'].format(date=iso_date, file=python_file_name)
             f.featureType = "timeSeriesProfile"
             # Top level dimensions
             f.createDimension('name_strlen', size=40)
             f.createDimension('nv', size=2)
             # Top level variables
             latitude = f.createVariable('latitude', datatype='f4')
             latitude.standard_name = 'latitude'
             latitude.long_name = 'system latitude'
             latitude.units = 'degrees_north'
             longitude = f.createVariable('longitude', datatype='f4')
             longitude.standard_name = 'longitude'
             longitude.long_name = 'system longitude'
             longitude.units = 'degrees_east'
             laser_angle = f.createVariable('laser_zenith_angle', datatype='f4')
             laser_angle.standard_name = 'sensor_zenith_angle'
             laser_angle.long_name = 'zenith angle of emitted laser'
             laser_angle.units = 'degree'
             laser_azimuth = f.createVariable('laser_azimuth_angle', datatype='f4')
             laser_azimuth.standard_name = 'sensor_azimuth_angle'
             laser_azimuth.long_name = 'azimuth angle of emitted laser'
             laser_azimuth.units = 'degree'
             laser_azimuth.comment = 'Based on North. Optional'
             altitude = f.createVariable('altitude', datatype='f4')
             altitude.standard_name = 'altitude'
             altitude.long_name = 'system altitude'
             altitude.units = 'm'
             # Optional ancillary group
             ancillary = f.createGroup('ancillary')
             ancillary.featureType = "timeSeries"
             ancillary.createDimension('time', size=None)
             time = ancillary.createVariable('time', datatype='f8', dimensions=('time',))
             time.long_name = 'time'
             time.units = 'seconds since 1970-01-01 00:00'
             time.standard_name = 'time'
             temperature = ancillary.createVariable('air_temperature', datatype='f8', dimensions=('time',))
             temperature.long_name = 'air temperature at instrument level'
             temperature.units = 'K'
             temperature.standard_name = 'air_temperature'
             pressure = ancillary.createVariable('air_pressure', datatype='f8', dimensions=('time',))
             pressure.long_name = 'air pressure at instrument level'
             pressure.units = 'hPa'
             pressure.standard_name = 'air_pressure'
             # Create a separate group for each channel
             for channel_name, channel_parameters in channels.iteritems():
                 group_name = "channel_{0}".format(channel_name)  # Give channels groups a standard name
                 g = f.createGroup(group_name)
                 g.long_name = channel_parameters['long_name']
                 g.detector_manufacturer = channel_parameters['long_name']    # Optional
                 g.detector_model = channel_parameters['detector_model']
                 g.daq_manufacturer = channel_parameters['daq_manufacturer']
                 g.daq_model = channel_parameters['daq_model']
                 # Dimensions
                 g.createDimension('profile', size=None)  # Infinite dimension
                 g.createDimension('range', len(self.range))
                 # Variables
                 name = g.createVariable('channel_id', dimensions=('name_strlen',))
                 name.cf_role = 'timeseries_id'
                 name.long_name = 'channel identification'
                 laser_rep_rate = g.createVariable('laser_repetition_rate')
                 laser_rep_rate.long_name = 'nominal laser repetition rate'
                 laser_rep_rate.units = 'Hz'
                 emission_energy = g.createVariable('emission_energy', datatype='f8', dimensions=('profile',))
                 emission_energy.long_name = 'emission energy per pulse'
                 emission_energy.units = 'mJ'
                 emission_energy.standard_name = 'radiation_wavelength'
                 emission_energy.comment = "could be scalar, if value is nominal."
                 emission_pol = g.createVariable('emission_polarization', datatype='b')
                 emission_pol.long_name = 'nominal emission poalrization'
                 emission_pol.flag_values = '0b 1b 2b'
                 emission_pol.flag_meanings = 'linear circular none'
                 fov = g.createVariable('fov', datatype='f4')
                 fov.long_name = 'channel field of view full angle'
                 fov.units = 'mrad'
                 fov.comment = 'simulated'
                 detector_type = g.createVariable('detector_type', datatype='b')
                 detector_type.long_name = 'detector type'
                 detector_type.flag_values = '0b 1b'
                 detector_type.flag_meanings = 'PMT APD'
                 detection_mode = g.createVariable('detection_mode', datatype='b')
                 detection_mode.long_name = 'detection mode'
                 detection_mode.flag_values = '0b 1b'
                 detection_mode.flag_meanings = 'analog photon_counting'
                 detection_cw = g.createVariable('detection_wavelength', datatype='f8')
                 detection_cw.long_name = 'center wavelength of detection filters'
                 detection_cw.units = 'nm'
                 detection_cw.standard_name = 'sensor_band_central_radiation_wavelength'
                 detection_fwhm = g.createVariable('detection_fwhm', datatype='f8')
                 detection_fwhm.long_name = 'FWHM of detection filters'
                 detection_fwhm.units = 'nm'
                 detection_pol = g.createVariable('detection_polarization', datatype='b')
                 detection_pol.long_name = 'nominal detection poalrization'
                 detection_pol.flag_values = '0b 1b 2b'
                 detection_pol.flag_meanings = 'linear circular none'
                 polarizer_angle = g.createVariable('polarizer_angle', datatype='f4', dimensions=('profile', ), zlib=True)
                 polarizer_angle.long_name = 'polarizer angle in respect to laser plane of polarization'
                 polarizer_angle.units = 'degree'
                 polarizer_angle.comments = 'Optional'
                 dead_time_model = g.createVariable('dead_time_model', datatype='b')
                 dead_time_model.long_name = 'optimal dead time model of detection system'
                 dead_time_model.flag_values = '0b 1b 2b'
                 dead_time_model.flag_meanings = 'paralyzable non_paralyzable other'
                 dead_time = g.createVariable('dead_time', datatype='f8')
                 dead_time.long_name = 'dead time value'
                 dead_time.units = 'ns'
                 dead_time.comment = "Manufacturer. Source of the value."
                 bin_length = g.createVariable('bin_length', datatype='f4')
                 bin_length.long_name = "time duration of each bin"
                 bin_length.units = 'ns'
                 detector_voltage = g.createVariable('detector_voltage', datatype='f4', dimensions=('profile',), zlib=True)
                 detector_voltage.long_name = 'detector voltage'
                 detector_voltage.units = 'V'
                 detector_voltage.coordinates = "time"
                 discriminator = g.createVariable('discriminator', datatype='f8', dimensions=('profiles',))
                 discriminator.long_name = 'discriminator level'
                 discriminator.units = ''
                 adc_range = g.createVariable('adc_range', datatype='f4', dimensions=('profile',),
                                                     zlib=True)
                 adc_range.long_name = 'analog-to-digital converter range'
                 adc_range.units = 'mV'
                 adc_range.coordinates = "time"
                 adc_bits = g.createVariable('adc_bits', datatype='i4', dimensions=('profile',),
                                              zlib=True)
                 adc_bits.long_name = 'analog-to-digital converter bits'
                 adc_bits.coordinates = "time"
                 pulses = g.createVariable('pulses', datatype='i4', dimensions=('profile',),
                                           zlib=True)
                 pulses.long_name = 'accumulated laser pulses per record'
                 pulses.coordinates = "time"
                 nd_filter = g.createVariable('nd_filter_od', datatype='f8', dimensions=('profile',))
                 nd_filter.long_name = "neutral density filter optical depth "
                 nd_filter.coordinates = "time"
                 emission_delay = g.createVariable('emission_delay', datatype='f4')
                 emission_delay.long_name = "pulse emission difference from channel trigger"
                 emission_delay.units = 'ns'
                 emission_delay.comments = 'Positive values for pre-trigger systems. Negative for trigger delay.'
                 time = g.createVariable('time', datatype='f8', dimensions=('profile',),
                                         zlib=True)
                 time.long_name = 'profile start time '
                 time.units = "seconds since 1970-01-01 00:00:00"
                 time.standard_name = "time"
                 time.bounds = "time_bnds"
                 g.createVariable('time_bnds', datatype='f8', dimensions=('profile', 'nv'), zlib=True)
                 bin_time = g.createVariable('bin_time', datatype='f4', dimensions=('range',),
                                              zlib=True)  # Use name 'bin_range' to avoid conflict with built-in range
                 bin_time.long_name = 'bin start time since trigger'
                 bin_time.units = "ns"
                 signal = g.createVariable('signal', datatype='i4', dimensions=('profile', 'range'),
                                           zlib=True)
                 signal.long_name = 'signal'
                 signal.units = channel_parameters['signal_units']
                 signal.coordinates = "time"
                 signal.ancillary_variables = "signal_stddev"
                 # If measured
                 signal_stddev = g.createVariable('signal', datatype='i4', dimensions=('profile', 'range'),
                                           zlib=True)
                 signal_stddev.long_name = 'signal standard deviation'
                 signal_stddev.units = channel_parameters['signal_units']
                 signal_stddev.coordinates = "time"
                 # Assign variables
                 # TBD

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atmospheric_lidar/diva.py@b5bbfee2a898 (annotated)

atmospheric_lidar/diva.py